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# -*- mode: org -*-
Archived entries from file /usr/home/alex/projects/blog/notes/books.org
* TODO Beowulf
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-25 Thu 23:16
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/books.org
:ARCHIVE_OLPATH: Litterature
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: TODO
:END:
* KILL Learn you a haskell for great good :haskell:
CLOSED: [2021-03-02 Tue 17:25]
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 16:55
:ARCHIVE_FILE: ~/projects/blog/books.org
:ARCHIVE_OLPATH: CS
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: cs
:END:
Just began functors and applicative
http://learnyouahaskell.com/functors-applicative-functors-and-monoids#functors-redux
* KILL Real World Haskell :haskell:
CLOSED: [2021-03-02 Tue 17:26]
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 16:55
:ARCHIVE_FILE: ~/projects/blog/books.org
:ARCHIVE_OLPATH: CS
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: cs
:END:
Chap 03
Trop vieux
cite:RWH
* KILL Haskell: The Craft of Functional Programming :haskell:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 16:55
:ARCHIVE_FILE: ~/projects/blog/books.org
:ARCHIVE_OLPATH: CS
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: cs
:END:
* HOLD Practical Common Lisp :lisp:
:PROPERTIES:
:author: Seibel
:year: 2005
:ARCHIVE_TIME: 2021-09-06 Mon 10:47
:ARCHIVE_FILE: /usr/home/alex/code/blog/books.org
:ARCHIVE_OLPATH: Computer science
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: HOLD
:ARCHIVE_ITAGS: cs
:END:
* KILL Differential topology
CLOSED: [2021-08-24 Tue 16:25]
:PROPERTIES:
:url: http://www.uib.no/People/nmabd/dt/080627dt.pdf
:ARCHIVE_TIME: 2021-09-06 Mon 10:48
:ARCHIVE_FILE: /usr/home/alex/code/blog/books.org
:ARCHIVE_OLPATH: Math
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: math
:END:
* KILL Math MPSI
CLOSED: [2021-09-06 Mon 10:48]
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:48
:ARCHIVE_FILE: /usr/home/alex/code/blog/books.org
:ARCHIVE_OLPATH: Math
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: math
:END:
Lu jusqu'à l'anneau des entiers relatifs
* KILL Les maths en tête (MP) : analyse, algèbre
CLOSED: [2021-08-24 Tue 16:24]
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:48
:ARCHIVE_FILE: /usr/home/alex/code/blog/books.org
:ARCHIVE_OLPATH: Math
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: math
:END:
* KILL Hall, J. (2016): Guyton and hall textbook of medical physiology :physiology:
CLOSED: [2021-08-07 Sat 14:48]
:PROPERTIES:
:Custom_ID: hall16_guyton_hall
:ARCHIVE_TIME: 2021-09-06 Mon 10:48
:ARCHIVE_FILE: /usr/home/alex/code/blog/books.org
:ARCHIVE_OLPATH: Medecine
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: KILL
:END:
** DONE Chap 61 en cours
** DONE Chap 34
* KILL Herring, W. (2020): Learning radiology : recognizing the basics :radiology:
CLOSED: [2021-08-07 Sat 14:48]
:PROPERTIES:
:Custom_ID: herring20_learn
:ARCHIVE_TIME: 2021-09-06 Mon 10:48
:ARCHIVE_FILE: /usr/home/alex/code/blog/books.org
:ARCHIVE_OLPATH: Medecine
:ARCHIVE_CATEGORY: books
:ARCHIVE_TODO: KILL
:END:
** DONE Chap 3
# -*- mode: org -*-
Archived entries from file /home/alex/code/blog/notes/haskell.org
* DONE Simplifier
DEADLINE: <2021-09-08 Wed> SCHEDULED: <2021-09-07 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-09 Thu 12:20
:ARCHIVE_FILE: ~/code/blog/notes/haskell.org
:ARCHIVE_OLPATH: GHC/20261
:ARCHIVE_CATEGORY: ghc
:ARCHIVE_TODO: DONE
:END:
On fait les tests avec stack:
#+begin_src fish
set PATH $PATH ~/softwares/ghc-9.0.1/bin/
stack build --system-ghc --resolver "ghc-9.0.1"
#+end_src
Et
#+begin_src fish
stack build --system-ghc --resolver "ghc-8.10.7"
#+end_src
Résultats
Long version (4k lines of code)
- 8.10.7
!!! Renamer/typechecker [Parse]: finished in 820.76 milliseconds, allocated 512.257 megabytes
- 9.0.1 is bad
!!! Renamer/typechecker [Parse]: finished in 13214.27 milliseconds, allocated 26776.972 megabytes
Mid version (1.7k)
- 8.10.7
!! Renamer/typechecker [Parse]: finished in 380.19 milliseconds, allocated 197.154 megabytes
- 9.0.1
!!! Renamer/typechecker [Parse]: finished in 1271.98 milliseconds, allocated 2834.054 megabytes
| | Long (ms) | Medium (ms) |
| 8.10.7 | 820.76 | 380.19 |
| 9.0.1 | 13214.27 | 1271.98 |
| Factor | 16.10 | 3.34 |
Attention, Parser.hs n'était pas la bonne version, il faut utiliser celle de stack...
#+begin_src
fd Parse.hs .stack-work
#+end_src
* STARTED Lire https://www.aosabook.org/en/ghc.html
DEADLINE: <2021-09-11 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-14 Tue 10:58
:ARCHIVE_FILE: ~/code/blog/notes/haskell.org
:ARCHIVE_OLPATH: Contributing/GHC
:ARCHIVE_CATEGORY: ghc
:ARCHIVE_TODO: STARTED
:END:
* DONE Haskell love
DEADLINE: <2021-09-10 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-30 Thu 17:46
:ARCHIVE_FILE: ~/code/blog/notes/haskell.org
:ARCHIVE_OLPATH: Conference
:ARCHIVE_CATEGORY: haskell
:ARCHIVE_TODO: DONE
:END:
- [X] All You Wanted to Know About Type Classes (Alejandro Serrano Mena)
Paterson condition (see Flexible Constraints) for defining constraints
- [X] Exceptions and concurrency ( Ivan Gromakovskii )
+ Use safe-exceptions (good documentation)
+ With threads, use async library: if the children raise an exception, it will wait forever otherwise.
Use concurrently
- [X] Competitive Programming in Haskell (Brent Yorgey)
Manque le début
- [X] Sound design with Haskell (Anton Kholomiov)
Manque la fin
* Conference
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-30 Thu 17:46
:ARCHIVE_FILE: ~/code/blog/notes/haskell.org
:ARCHIVE_CATEGORY: haskell
:END:
# -*- mode: org -*-
Archived entries from file /home/alex/code/blog/notes/internat.org
* Comment faire de la génétique ?
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-19 Sun 19:42
:ARCHIVE_FILE: ~/code/blog/notes/internat.org
:ARCHIVE_CATEGORY: internat
:END:
** Option 1 : génétique médicale
Assez de places pour les internes mais pas le choix des villes
Les internes de biologie médicale sont avantagé car ils peuvent signer des examens
** Option 2 : généraliste + formations supplémentaire
Compliqué car "pas dans le cursus"
Il y a une demande des généticiens pour que les généralistes prennent le relais mais pas de formation reconnue pour le moment.
Ce sont des formations informelles (vidéos etc) et cela semble plutôt fonctionner au bouche-à-oreille
1. Faire une FST mais compliqué, même pour les internes de génétique ! 4 possibilités
- bio-informatique : le plus "faisable". Au pire, juste assister aux cours afin de le noter sur le CV !
- foetopathologie : :(
- génétique moléculaire
2. DU/DIU: difficile pour généraliste donc insister plusieurs fois (réseau++)
- dysmorphologie (Rennes)
- séquencage haut débit (Dijon) : difficile d'y rentrer
- cytogénétique:
- médecine personnalisée (Montpellier +/- Dijon) : insister
- autres: https://interne-genetique.org/formation-complementaire/du-diu/
3. Année recherche : avant la fin de l'internat (certaines villes proposent la possibilité après).
Ne pas faire en parallèle de l'internat.
Plus ou moins difficile selon les villes.
Plusieurs bourses possibles.
Il faut trouver un stage en même temps que le financement
Au final, inutile car le suivi des maladies génétiques ne nécessite pas autant de formation
** Option 3 : biologie médicale
*** Dr Denommé-Pichon.
Formation faite par Dr Denommé-Pichon. Plus de chances d'avoir un poste de PH à la sortie (conseillé par son tuteur à l'époque)
Inconvénient : 2 premières années "laboratoire" puis 2 ans de spé en génétique possible.
Pour faire des consultations, il faut "forcer" pour faire des consultations pendant l'internat
(ex: consultations d'hémostase en hémato). Et faire des gardes aux urgences
*** Discussion avec Tristan Celse (interne de bio spécialisé en génétique, ancien président du syndicat des internes de bio)
Avantages :
- Grenoble possible
- Très bonne équipe
- Possibilité d'être seul sur sa région donc liberté+++
- Internat comprenant la recherche. Il a réussi à faire son master et
sa thèse en 6 mois, et à faire le stage du master dans son cursus
(!)
- Agrément pour examens (gros avantage par rapport aux génét médicaux selon lui, et ça ne changera pas)
- Possibilté de faire de la bioinformatique : plateforme Auragen (NGS) entre Lyon et Grenoble (Le chef de clinique chapeaute)
- Consultation possible en génétique
- FST permettant de faire de la consultation (accessible) et plus utile qu'en génétique médicale...
Inconvénients :
- perte des compétences cliniques (3 internes sur 4 ont arrêté dans
sa promo...). Gardes aux urgences en théorie possible mais peu
utile
- 1 an et demi assez ennuyeux
Pour généraliste + génétique: formation en théorie possible mais pas besoin en
pratique. On fait un travail de généraliste car le diagnostic est
déjà posé...
Marseille: déconseille pour l'internat
*** Visite du laboratoire de bio à Grenoble par Sébastien Vérizan et Lydie Andre (internes de pharmacie)
Discussion avec Aurélien (intere de bio médical)
Avantages
+ Bonne ambiance, bons chefs
+ Intellectuellement plutôt intéressant : possibilité de prescrire des examens complémentaires pour caractériser. Hémostase : dianostic posé par les cliniciens
+ Staff pluridisciplinaire
+ Spécialisation en génétique au bout de 2 ans de tronc commun
+ Horaires, 2 internes par gardes et peu mouvementée (à Grenoble)
+ Discussion avec les clinicien
+ 1 seul stage en périph (à Chamberry, cytogénétique mais à mixer avec le reste)
Inconvéients
- répétitif
- plus de clinique. Les consultations sont du suivi bio et possible seulement en hémostase.
Reprendre des gardes aux urgences semble possible mais ne doit pas empiéter sur les gardes de bio
Contact pris avec Tristan (génétique biologique avec
** Alternative: médecine générale + recherch
*** Entretien avec Marie Ecollan (amie de Miva, ACC en médecine générale)
Med gé = stimulant, plusieurs possibilités d'exercice, aménagement pour qualité de vie+++
Beaucoup d'inconnu dans les consultations (rarement "le" diagnostic)
Filière universitaire: toute jeune, on commence seulement à avoir des encadrants formés
Recherche clinique ou qualitative (sociologie) possible. Orienté épidémio/santé publique
Compliqué de sortir du champ de la MG. Notamment en génétique, semble inutile de se former en plus
En pratique, on participe à des réunions pour gérer les essais, qui sont chapeautés par des PU
Marie ne continue pas la partie universitaire mais bascule en CDD sur des postes d'assistant
À faire: contacter
*** Entretien avec Dr Olivier Hanriot
A fait peu de recherche surtout de l'enseignement
Format: 50% de cabinet, 50% enseignement-recherche (la part est à préciser au début du contrat)
Possibilité de faire un clinicat (x2 donc 4 ans) et de ne pas continuer en recherche.
Possibilité de continuer les cours en tant que vacataire à côté de son activité de MG
Sinon, faire une thèse de sciences
Plus de candidats que de postes en maître de conf (ex: 1 MCU et 2 PU à Nancy...
mais à Nancy, plus de postes de cilnicat que de candidat)
Sujets de recherche variés avec différents labos mais à valider par le chef du DMG( département de médecine générale)
Donc peut-être compliqué de faire de la génétique
Par contre, plusieurs modes d'exercices comme MG
- EHPAD, PMI, médecine poly...
=> besoin de médecins dans les petits hôpitaux qui payent les DU (géria++)
** En résumé
Petite communauté où il faut insister et se faire connaître+++
** Contacts
- Dr Lambert : en attente
- Dr Denommé-Pichon : excellent contact, visite du labo prévue 2 septembre cet été. Membre des comités pour FST et contriube à la filière
- Geoffroy DELPLANCQ : futur assistant à Paris à la rentrée, a donné des infos sur l'internat de génétique à Besançon
Recontacter si je choisis la génétiques
- Julien Thevenon à Grenoble : *à contacter* rapidement de la part du Dr Denommé-Pichon si je choisis la bio
- Charles Philippe (bio), Laurence Faivre (clinique) = chefs du labo de Dijon
** Villes
*** Génétique
**** Besançon
(infos par Geoffroy Delplanc)
Ville peu animée. UN des plus petits CHU de France. Tout l'internat s'y fait au CHU
. Chefs sympathiques mais peu encadrant. Charge de travail légère.
Ancien chef de clinique ne faisait pas le travail mais décédé donc devrait s'améliorer
Avantage: "on voit de tout"
Labo : publications possible avec le chef++
Clinique : chefs sympathiques. Consultations de maladies rares. Autonomie rapidement
Pas de gardes
Inter-CHU: 3 max, utile pour compléter la formation
DU: facile à avoir, sauf bioinfo. À choisir selon la sur-spé
Formation: 1 semaine à Paris
Master: "celui que tout le monde fait" (européen ?) = À paris avec cours condensables sur 2 mois + 6 mois de stage, possible à l'étranger. Salaire d'interne. Possibilité de "se la couler douce"
Besançon: avec le nouveau chef de service, devrait être intéressant
Peu de clinique ?
**** Dijon
Journées chargées (9-19h) mais bon encadrement
***** Visite du labo de Dijon
Quotidien: beaucoup de biblio (4-5h pour les résultats de génétique)
À Dijon, "machine à publier" (en théorie, 1 article par semaine est possible...).
Très axés recherche (contrairement à Nancy) mais gros horaires (soirs et week-end)
RCP: discussion clinicien-bio(-technicien (??)) pour valider ou non les résultats et décider de la prise en charge
Pas de patient vu mais dossier à bien éplucher, assez complexes
À Montpellier, Lyon et Dijon, la formation est bonne en génétique et des
retours que j'ai eus des internes, il a été assez facile d'avoir la
génétique en deuxième partie d'internat. Pour les autres villes
(Marseille, Nice, Saint-Etienne, Besançon), je ne sais pas.
**** Nice: entretien avec dr Plutino
CS
- anomalie dev +/- DPN (1 medecin)
- oncogénigique digestif + cardio (1 médecin)
- neurogénétique (1 médecin: adulte et enfant)
- conseil (Dr Plutino + 1 autre médecin)
Recherche
- Unité INSERM assignée. Possibilité de faire de spetits projets + master 2
- Centre de référence des maladise mitchondriales
Stages
- Cf CS et labo
- Libre: pédiatrie, lutte anti-cancer
- Inter-CHU recommandé (Lyon en cytogénétique
DU locaux : maladie mitho (en decembre de cette année (! pas tous les ans)
Pratique:
- charge de travail :
- 7h-17 au labo (+ travail perso)
- 8-18h en CS + courrier
- gardes : urgences en 1ere année, puis étage
Bioinformatique:
- pas de bioinformaticien mais 2 ingénieurs s'y connaissent et 1 a publié
À noter: arrivée d'un dermato-généticien (épidermolyse bulleuse)
Bio:
- exome
- mitochondr
- amyotrophie spinale, deletion chromosome Y
3 site: génétique =
- Archer (proche gynéco)
- hopital pédiatrique
- Paster (urgence)
- gériatrie
Encadrement: possibilité de faire "ce qu'on veut" mais encadré néanmoins
1 autre interne en novembre en CHU
Conclusion: écho contradictoire entre le dernier interne qui a fait un droit au remord vers la bio et la présentation par la PH
**** Marseille
Contradictoire: Geoffrey déconseille, le chef de clinique de Dijon conseille plutôt
Peu de clinique ?
*** Biologie
- Montpellier:
- (dr ADP) bonne formation en génétique, assez facile d'avoir la génétique en 2eme partie
- (mail de Grgoire Pasquier). 9-18h, 1 garde par semaine. Encadrement variable selon les services
Pas eu de retour de l'interne de génétique (Luke Mansard)
- Lyon:
- (Dr ADP) bonne formation
- (mail d'Alexis Daudé): bon terrains de stages, formateurs (sauf quelques-un mais connus), très bon encadrement (mais moins d'autonomie !)
. 8h30-17h30. Bone ambian
Pas eu le contact de sa co-interne en génétique
- Dijon: bonne formation, facile d'avoir la génétique (Dr ADP)
- Marseille, Nice, Saint-Etienne, Besançon ?
*** MG
Meilleurs stages = autour de Nîmes
Pas mal : Bagnols, Alès, Mende
Urg = Alès et Mende > Montpellier
Internat de Narbonne = beaucoup de places (même pour les vieux)
Bonne ambiance mais "mur" entre Montpellier et Nîmes
** Logiciel de NGS
- Diagho (suite de Regovar) : version open-source, payée par la région.
- Auragen : version privée (?), développée par Lyon/Grenoble
** DU/DIU
:PROPERTIES:
:COLUMNS: %25ITEM %TYPE %STAGE %COÛT
:END:
*** Cytogénétique classique et moléculaire
:PROPERTIES:
:type: DIU
:stage: oui
:coût: 394€
:END:
*** Cytogénétique médicale
:PROPERTIES:
:type: DIU
:stage: non
:coût: 700€
:END:
*** Déficience intellectuelle
:PROPERTIES:
:type: DIU
:stage: non
:coût: 1200€
:END:
Non génétique
*** [#A] Diagnostic de précision et médecine personnalisée
:PROPERTIES:
:type: DIU
:stage: non
:coût: 684€
:END:
** FST
* Logement
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-29 Wed 10:26
:ARCHIVE_FILE: ~/code/blog/notes/internat.org
:ARCHIVE_CATEGORY: internat
:END:
** VISIT [#A] T3 60m^2
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**** https://www.leboncoin.fr/locations/1999480156.htm
25min de route
Agence
**** https://www.leboncoin.fr/locations/2005761486.htm
500€
**** https://www.leboncoin.fr/locations/2030666696.htm
500€
**** https://www.leboncoin.fr/locations/2034564752.htm
680€
10min
**** https://www.leboncoin.fr/locations/2009492357.htm
21min
**** https://www.leboncoin.fr/locations/2035112020.htm
**** https://www.leboncoin.fr/locations/2010787699.htm
**** https://www.leboncoin.fr/locations/2016017935.htm
* DONE Récupérer diplôme FASM3
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-13 Wed 23:18
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/internat.org
:ARCHIVE_OLPATH: Démarches
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Changement sécu
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-13 Wed 23:18
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/internat.org
:ARCHIVE_OLPATH: Démarches
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
En ligne
* DONE CVEC
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-13 Wed 23:18
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/internat.org
:ARCHIVE_OLPATH: Démarches
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
BFC1 CQZBNM 20
Faite le <2021-09-29 Wed>
* DONE Souscription SIGF
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-13 Wed 23:18
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/internat.org
:ARCHIVE_OLPATH: Démarches
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Souscription association internes Besançon
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-13 Wed 23:19
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/internat.org
:ARCHIVE_OLPATH: Démarches
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
# -*- mode: org -*-
Archived entries from file /home/alex/code/blog/notes/japanese.org
* Expressions
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-08 Fri 22:41
:ARCHIVE_FILE: ~/code/blog/notes/japanese.org
:ARCHIVE_CATEGORY: japanese
:END:
@@html:<ruby>長時間<rt>ちょうじかん</rt></ruby>の<ruby>飛行<rt>ひこう</rt></ruby>@@ : un long trajet en avion
@@html:それなりの<ruby>価値<rt>かち</rt></ruby>があります@@ : cela vaut le coup
@@html:ゆっくり<ruby>時間<rt>じかん</rt></ruby>を<ruby>取<rt>と</rt></ruby>る@@ : prendre son temps
* Grammaire
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-08 Fri 22:41
:ARCHIVE_FILE: ~/code/blog/notes/japanese.org
:ARCHIVE_CATEGORY: japanese
:END:
〜する @@html:<ruby>習慣<rt>しゅうかん</rt></ruby>@@がある: avoir l'habitude de 〜
@@html:〜と〜の<ruby>間<rt>あいだ</rt></ruby>@@ : entre 2 〜
# -*- mode: org -*-
Archived entries from file /usr/home/alex/projects/blog/notes/mam.org
* DONE Voltaire
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-03 Wed 11:41
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE Histoire de la guerre de 1741
https://classiques-garnier.com/histoire-de-la-guerre-de-1741.html
** DONE Essai sur les mœurs et l’esprit des nations. Tome II
https://classiques-garnier.com/essai-sur-les-moeurs-et-l-esprit-des-nations-tome-ii.html
** DONE Essai sur les mœurs et l’esprit des nations. Tome I
https://classiques-garnier.com/essai-sur-les-moeurs-et-l-esprit-des-nations-tome-i.html
** DONE Dialogues et anecdotes philosophiques
https://classiques-garnier.com/dialogues-et-anecdotes-philosophiques.html
** DONE Lettres philosophiques
https://classiques-garnier.com/lettres-philosophiques-2.html
** DONE Contes en vers et en prose. Tome I
https://classiques-garnier.com/contes-en-vers-et-en-prose-tome-i.html
** DONE Contes en vers et en prose. Tome II
https://classiques-garnier.com/contes-en-vers-et-en-prose-tome-ii.html
** DONE Lettres choisies
https://classiques-garnier.com/lettres-choisies-1.html
** DONE Le Siècle de Louis XIV. Tome I
https://classiques-garnier.com/le-siecle-de-louis-xiv-tome-i.html
** DONE Le Siècle de Louis XIV. Tome II
https://classiques-garnier.com/le-siecle-de-louis-xiv-tome-ii-chapitres-xxvi-xxxix.html
** DONE La Henriade suivie du Poème de Fontenoy (1745)
https://classiques-garnier.com/la-henriade-suivie-du-poeme-de-fontenoy-1745.html
** DONE Histoire de Charles XII roi de Suède
https://classiques-garnier.com/histoire-de-charles-xii-roi-de-suede.html
** DONE Précis du siècle de Louis XV
https://classiques-garnier.com/precis-du-siecle-de-louis-xv.html
** DONE Histoire du Parlement de Paris
https://classiques-garnier.com/histoire-du-parlement-de-paris.html
** DONE La Pucelle d’Orléans
https://classiques-garnier.com/la-pucelle-d-orleans-poeme-divise-en-vingt-et-un-chants.html
** DONE Le Sottisier suivi de Remarques sur le Discours sur l’inégalité des conditions et sur le Contrat social de Rousseau
https://classiques-garnier.com/le-sottisier-suivi-de-remarques-sur-le-discours-sur-l-inegalite-des-conditions-et-sur-le-contrat-social-de-rousseau.html
** DONE Théâtre contenant tous ses chefs-d’œuvre dramatiques. Tome I
https://classiques-garnier.com/voltaire-theatre-contenant-tous-ses-chefs-d-oeuvre-dramatiques-tome-i.html
** DONE Théâtre. Tome II
https://classiques-garnier.com/voltaire-theatre-tome-ii.html
** DONE Épîtres, satires, contes, épigrammes suivis de fragments de La Pucelle d’Orléans
https://classiques-garnier.com/epitres-satires-contes-epigrammes-suivis-de-fragments-de-la-pucelle-d-orleans.html
** DONE Dictionnaire philosophique
https://classiques-garnier.com/dictionnaire-philosophique-la-raison-par-alphabet.html
* DONE Abbé Prévost
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-03 Wed 14:51
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE Histoire du chevalier des Grieux et de Manon Lescaut
https://classiques-garnier.com/histoire-du-chevalier-des-grieux-et-de-manon-lescaut-texte-de-1753-suivi-des-variantes-de-1731.html
** DONE Contes singuliers tirés du Pour et Contre
https://classiques-garnier.com/contes-singuliers-tires-du-pour-et-contre-1.html
* DONE Request post pour referenc
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-04 Thu 17:59
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)/Script/Haskell/Accélere upload ?
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
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La Henriade: suivie du Poème de Fontenoy
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In La Henriade, Voltaire offers a poetic and captivating account of the wars of religion, from Saint-Barthélemy to the conquest of Paris by Henri IV. Alternating the narratives of battles with political analysis, philosophical reflection and the vision of history, it addresses the major debates that will animate the thought of the Enlightenment, such as the place of religion in society, tolerance, the figure of the sovereign or the progress of the arts. A decade after the death of Louis XIV, he laid the foundation stone of the myth of the "Great Century", sketching the emblems of the Nation, as they would be constituted in modern France. A remarkable illustration of poetry at the beginning of the 18th century, La Henriade was an immense success from its publication and has become, over the years, a key crossroads in literary and philosophical life. <br />(Jean-Marie Roulin)<br /><br /><hr /><br />"Dans La Henriade, Voltaire offre un récit poétique et captivant des guerres de religion, depuis la Saint-Barthélemy jusqu’à la conquête de Paris par Henri IV. Alternant les récits de batailles et l’analyse politique, la réflexion philosophique et la vision de l’Histoire, il aborde les grands débats qui animeront la pensée des Lumières, comme la place de la religion dans la société, la tolérance, la figure du souverain ou le progrès des arts. Une décennie après la mort de Louis XIV, il y pose la première pierre du mythe du « Grand Siècle », esquissant les emblèmes de la Nation, tels qu’ils se constitueront dans la France moderne. Illustration remarquable de la poésie au début du XVIIIe siècle, La Henriade a connu dès sa parution un immense succès et est devenue au fil de ses multiples rééditions un carrefour capital de la vie littéraire et philosophique. Cet ouvrage collectif analyse le parcours éditorial de ce poème, en étudie la poétique et la conception de la fiction, notamment dans le rapport à l’Histoire, et explore la trace qu’il a laissée dans la mémoire critique et la tradition scolaire."<br />(Jean-Marie Roulin)
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** DONE Python
*** DONE Fusion pdf
*** DONE Télécharger automatiquement
*** DONE Renommer automatiquement pdf
*** DONE Lister toutes les oeuvres avec liens
*** DONE Automatiser création torrent
* DONE Alexandre Dumas
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-04 Thu 21:47
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE La Reine Margot
https://classiques-garnier.com/la-reine-margot-drame-1.html
** DONE Vingt ans après
https://classiques-garnier.com/vingt-ans-apres.html
** DONE Le Comte de Monte-Cristo. Tome I
https://classiques-garnier.com/le-comte-de-monte-cristo-tome-i.html
** DONE Le Comte de Monte-Cristo. Tome II
https://classiques-garnier.com/le-comte-de-monte-cristo-tome-ii.html
** DONE Les Trois Mousquetaires
https://classiques-garnier.com/les-trois-mousquetaires.html
* DONE Arthur Rimbaud
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-04 Thu 21:57
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE Œuvres
https://classiques-garnier.com/rimbaud-arthur-oeuvres.html
* DONE Charles Perrault
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-06 Sat 12:14
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE Contes
https://classiques-garnier.com/contes-2.html
* DONE Christine de Pizan
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-06 Sat 15:56
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE Le Livre des epistres du debat sus le Rommant de la Rose
https://classiques-garnier.com/le-livre-des-epistres-du-debat-sus-le-rommant-de-la-rose-1.html
* DONE Eugène Labiche
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-07 Sun 12:02
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE Théâtre. Tome I
https://classiques-garnier.com/labiche-eugene-theatre-tome-i.html
** DONE Théâtre. Tome II
https://classiques-garnier.com/labiche-eugene-theatre-tome-ii.html
** DONE Théâtre. Tome III
https://classiques-garnier.com/labiche-eugene-theatre-tome-iii.html
* DONE Emmanuel de Las Cases
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-07 Sun 14:44
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE Mémorial de Sainte-Hélène. Tome I
https://classiques-garnier.com/memorial-de-sainte-helene-tome-i.html
** DONE Mémorial de Sainte-Hélène. Tome II
https://classiques-garnier.com/memorial-de-sainte-helene-tome-ii.html
* DONE Charles Baudelaire
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-13 Sat 19:28
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Classiques Jaunes (638)
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE Curiosités esthétiques suivies de L’Art romantique
https://classiques-garnier.com/curiosites-esthetiques-suivies-de-l-art-romantique.html
** DONE Les Fleurs du Mal
https://classiques-garnier.com/les-fleurs-du-mal.html
** DONE Petits Poèmes en prose
https://classiques-garnier.com/petits-poemes-en-prose-le-spleen-de-paris.html
* DONE [#C] E-books Wiley
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-14 Wed 15:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
PDF accessible directement ! ( médecine++, bio, dentaire)
https://olabout-wiley-com.bases-doc.univ-lorraine.fr/WileyCDA/Section/id-829486.html
Remplacer dans l'url pdf par book pour avoir la description
** DONE [#C] Life science
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118430699][Atlas of Developmental Field Anomalies of the Human Skeleton: A Paleopathology Perspective]]
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118430309][Bergman's Comprehensive Encyclopedia of Human Anatomic Variation]]
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118685150][Sports Rehabilitation and Injury Prevention]]
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118284551][Ultrastructure Atlas Of Human Tissues]]
*** DONE Genetics
**** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9783527636778][Alternative pre-mRNA Splicing - Theory and Protocols]]
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118412602][Cytogenetic Abnormalities: Chromosomal, FISH and Microarray-Based Clinical Reporting]]
**** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9780470893159][Management of Genetic Syndromes, Third Edition]]
Pas accès à la dernière édition
**** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118300312][MicroRNAs in Medicie]]
*** DONE Microbiology
**** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118301234][A Concise Manual of Pathogenic Microbiology]]
trop vieux
**** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444354690][Atlas of Human Infectious Diseases]]
Trop vieux
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119021872][Commercial Methods in Clinical Microbiology]]
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118597361][Essentials of Travel Medicine]]
**** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118101773][Fundamental Medical Mycology]]
trop vieux
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118644843][Human Emerging and Re-emerging Infections]]
**** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118393321][Immunity to Parasitic Infection]]
trop vieux
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118663721][Vaccines and Autoimmunity]]
*** DONE Neuroscience
**** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118971758][Handbook of Olfaction and Gustation, Third Edition]]
** DONE [#C] Medecine
*** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118744185][Food Allergy: Adverse Reaction to Foods and Food Additives]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444346688][Inflammation and Allergy Drug Design]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118609125][Mount Sinai Expert Guides: Allergy & Clinical Immunology]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444329711][Clinical Pain Management - A Practical Guide]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444314380][Evidence-based Chronic Pain Management]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119950462][How to Survive in Anaesthesia 4e]]
*** DONE [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118618189][Atlas of Clinical Vascular Medicine]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444318456][Cardiovascular Disease - Nutritional and Metabolic Bases]]
*** DONE [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118821350][ECGs for Beginners]]
*** DONE [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119066446][ECGs from Basics to Essentials]]
*** DONE [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118480007][Pocket Guide to Echocardiography]]
*** DONE [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118938164][Clinical Dermatology 5e]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118655566][Cosmetic Dermatology - Products and Procedures 2e]]
Duplicate
*** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118655412][Plastic and Reconstructive Surgery - Approachesand Techniques]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444319545][Acute Medical Emergencies - The Practical Approach]]
*** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119241225][Advanced Paediatric Life Support - A Practical Approach to Emergencies 6e with Wiley E-Text]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119959809][Cardiovascular Problems in Emergency Medicine - A Discussion-based Review]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444397994][Visual Diagnosis in Emergency and Critical Care Medicine]]
*** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118387658][International Textbook of Diabetes Mellitus 4e Two-Volume set]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119951827][Diagnostic Tests Toolkit]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118482117][Evidence-Based Emergency Care - Diagnostic Testing and Clinical Decision Rules 2e]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118655153][Esophageal Cancer and Barrett's Esophagus 3e]]
*** DONE [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119959762][Essentials of Gastroenterology]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118307816][Pancreatic Cancer, Cystic Neoplasms and Endocrine Tumors - Diagnosis and Management]]
*** KILL [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118512104][Yamada's Atlas of Gastroenterology 5e]]
Duplicate
*** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118728130][Clinical Communication in Medicine]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118143797][Hospital Images: A Clinical Atlas]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444341300][Getting Started in Health Research]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118715598][Guidelines for Reporting Health Research - A Users Manual]]
*** DONE [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118105955][Medical Toxicology of Drug Abuse: Synthesized Chemicals and Psychoactive Plants]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118472361][Understanding Medical Education - Evidence, Theory and Practice]]
*** KILL [#B] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118281796][Evidence-Based Geriatric Medicine - A Practical Clinical Guide]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118430965][Substance Use and Older People]]
*** DONE [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118355244][Inflammatory Diseases of Blood Vessels]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118398258][Textbook of Hemophilia]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444322972][Clinical Electrophysiology - A Handbook for Neurologists]]
*** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118936979][The Treatment of Epilepsy 4e]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444398519][Endometriosis - Science and Practice]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118538555][Practical Pediatric and Adolescent Gynecology]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118310311][Cancer as a Metabolic Disease: On the Origin, Management, and Prevention of Cancer]]
*** DONE [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119013143][UICC Manual of Clinical Oncology 9e]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118702871][Clinical Orthoptics 3e]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118712368][Diagnosis and Management of Ocular Motility Disorders]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118819494][Neonatal Formulary - Drug Use in Pregnancy and the First Year of Life 7e]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118340851][Clinical Handbook of Adolescent Addiction]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9780470669600][Principles and Practice of Geriatric Psychiatry 3e]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118381953][Rutter's Child and Adolescent Psychiatry 6e]]
*** KILL [#A] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118500484][Anatomy in Diagnostic Imaging 3e]]
dupe
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118633953][Magnetic Resonance Imaging: Physical Principles and Sequence Design]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118405444][Interpreting Lung Function Tests - A Step-by-Step Guide]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9780470710425][Occupational and Environmental Lung Diseases]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118692318][Encyclopaedia of Sports Medicine: Sports Nutrition]]
*** KILL [#B] [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444315233][Orthopaedics and Fractures 4e]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118777305][Jones' Clinical Paediatric Surgery]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444325287][Manual Of Perioperative Care In Adult Cardiac Surgery, 5e]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444397949][AST Handbook of Transplant Infections]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118651292][Atlas of Male Genitourethral Surgery - The Illustrated Guide]]
*** KILL [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118814789][Pediatric Incontinence - Evaluation and Clinical Management]]
** KILL Denistry
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119053231][Anesthesia Complications in the Dental Office]]
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118993729][Atlas of Operative Oral and Maxillofacial Surgery]]
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119140474][Dental Implant Complications: Etiology, Prevention, and Treatment, Second Edition]]
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119019916][Horizontal Alveolar Ridge Augmentation in Implant Dentistry: A Surgical Manual]]
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118987742][Lasers in Dentistry: Guide for Clinical Practice]]
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118925263][Recognizing and Correcting Developing Malocclusions: A Problem-Oriented Approach to Orthodontics]]
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781119082835][Vertical Alveolar Ridge Augmentation in Implant Dentistry: A Surgical Manual]]
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118704707][Case Studies in Palliative and End-of-Life Care]]
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781444341928][Examination of the Newborn - An Evidence Based Guide]]
*** [[http://onlinelibrary.wiley.com.bases-doc.univ-lorraine.fr/doi/pdf/10.1002/9781118783009][Tinnitus - A Multidisciplinary Approach 2e]]
* KILL Lippincott
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-14 Wed 15:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: KILL
:END:
* KILL Katzung
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-14 Wed 15:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: KILL
:END:
* KILL Learning Radiology
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-14 Wed 15:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: KILL
:END:
* KILL Cecil-goldman ?
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-14 Wed 15:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: KILL
:END:
* DONE Oeuvres de zola complètes
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-14 Wed 15:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
PDF directement accessible (!!!) avec
https://www-numeriquepremium-com.bases-doc.univ-lorraine.fr/flexpaper/common/docserver/fulltext/books/nouveau-monde/9782847360158/978-2847360158.pdf
où 9782847360158 est l'identifiant du livre, qui est contenu dans l'URL ...
Le second identifiant est le même mais avec un tiret
** DONE 1
** DONE 2
** DONE 3
** DONE 4
** DONE 5
** DONE 6
** DONE 7
** DONE 8
** DONE 9
** DONE 10
** DONE 11
** DONE 12
** DONE 13
** DONE 14
** DONE 15
** DONE 16
** DONE 17
** DONE 18
** DONE 19
** DONE 20
** DONE 21
** DONE Ajouter type de pdf
* DONE Liste des livres sur askhistorians
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-10 Mon 19:29
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/mam.org
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** DONE Parser la liste de livres
*** DONE v1 avec python sur goodreads
*** DONE v2 avec haskell sur reddit
Utiliser l'API de reddit
Doc ici
https://github.com/reddit-archive/reddit/wiki/OAuth2-Quick-Start-Example
Example
1) Retrouver l'access token
curl -X POST -d 'grant_type=password&username=clumsyKnife&password=TODO --user 'CLIENTID:CLIENTSECRET' https://www.reddit.com/api/v1/access_token
1) Valable 1h par défaut. On utilise le token
curl -H "Authorization: bearer 16127239-LAbyvE6sz_oHQKGPmnfxCmb-wZtl6Q" -A "ChangeMeClient/0.1 by YourUsername" https://oauth.reddit.com/api/v1/me
*** DONE Example simple
**** DONE titre + description
**** DONE category
*** DONE Vérifier page par page sur 3 exemple
**** DONE general (11 livres)
**** DONE Biographies
**** DONE Historiagraphy
*** DONE Liste des pages
Toutes les URL sans #, et sans "documentaries"
*** DONE API MaM
*** KILL Récupérer l'auteur pour avoir moins de résultats
**** DONE Parser wiki
Très manuel
**** KILL Requêtes google books avec l'isbn
ISBN dans l'URL amazon, après dp
https://www.amazon.com/Human-Past-History-Development-Societies/dp/050029335X
*** KILL Réécrire le parser pour tenir compte des 2 syntaxes
Nouvelle syntaxe dans /general : le titre est en italique
Mais on reste sur l'ancienne syntaxe ailleurs...
Nouvelle stratégie :
on récupérer le premier lien pour chaque item, qui contient le titre
A priori, pas besoin d'aller chercher sur le site distant
**** DONE Récupérer les liens dans chaque items
**** DONE Gérer les listes récursives
**** DONE Gérer les liens sans listes
**** KILL Gérer les items sans listes, just avec italiques
Ex: africa
**** KILL Extraire title depuis lien markdown
À voir si cela suffit
**** KILL Extraire nfo depuis amazon
***** KILL Gérer les autres liens
Liste : gutenberg, worlcat, archive.org
*** KILL À la main
**** KILL [[/usr/home/alex/projects/askhistorians/data/ageofexploration.md][ageofexploration.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/americas.md][americas.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/australia.md][australia.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/biographies.md][biographies.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/coldwar.md][coldwar.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/culturalhistory.md][culturalhistory.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/eastasia.md][eastasia.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/europe.md][europe.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/general.md][general.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/historiography.md][historiography.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/holocaust.md][holocaust.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/innerasia.md][innerasia.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/latinamerica.md][latinamerica.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/middleeast.md][middleeast.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/southasia.md][southasia.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/wwi.md][wwi.md]]
**** KILL [[/usr/home/alex/projects/askhistorians/data/wwii.md][wwii.md]]
*** DONE Utiliser la liste sur goodreadrs
**** KILL Récupérer liste complète à partir du RSS
Tout à l'air deeedans
***** DONE Titre
***** DONE Auteur
***** DONE Couverture
***** DONE Review
***** DONE Catégories !
***** KILL Seulement 100 résultats ...
**** DONE Récupérer données depuis HTML
Tout sauf les categories...
Le plus simple est de récupérer chaque bookshelf et de parser le HTML
**** DONE Corriger les accents
**** DONE Gérer exceptions
**** DONE Récupérer catégories
** DONE Résultats sur Mam
Rerchere automatique et fait à la main
*** DONE Parser liste des auteurs
*** DONE Récupérer toute la liste
*** DONE Filtrer résultats
**** DONE Calculer la distance de levensein sur le titre
**** DONE Comparaison manuelle
*** DONE Fusionner cover, review dans mam-curated
** DONE Post final
*** DONE Formatter depuis CSV
*** DONE Stats : 271/939
*** DONE Grouper par catégories
**** DONE Arbre des catégories
**** DONE Grouper
* DONE Article + notes
:PROPERTIES:
:ARCHIVE_TIME: 2021-07-22 Thu 19:46
:ARCHIVE_FILE: ~/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn/Version ebook
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
<div id="article" class="traitement-ouvcol typeart-article">
-> <div id=panel-plan>
On ne peut pas utiliser /section pour 1. vu les sous-sections
* DONE Supprimer les numéro de paragraphes
:PROPERTIES:
:ARCHIVE_TIME: 2021-07-22 Thu 19:47
:ARCHIVE_FILE: ~/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn/Version ebook
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
<a class="no-para" href="#pa9">9</a>
* DONE Récupérer les images pour pandoc
:PROPERTIES:
:ARCHIVE_TIME: 2021-07-22 Thu 19:47
:ARCHIVE_FILE: ~/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn/Version ebook
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
<img src="load.php/*.jpg>
ok pour 1 chapitre
* DONE Ajouter un header avec le titre
:PROPERTIES:
:ARCHIVE_TIME: 2021-07-22 Thu 19:47
:ARCHIVE_FILE: ~/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn/Version ebook
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
<!DOCTYPE html>
<html>
<head>
<title> Croisades et Orient latin : XIe-XIVe siècle</title>
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* DONE Ajouter un titre de chapitre avec h1
:PROPERTIES:
:ARCHIVE_TIME: 2021-07-22 Thu 19:47
:ARCHIVE_FILE: ~/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn/Version ebook
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
* DONE Corriger les headings
:PROPERTIES:
:ARCHIVE_TIME: 2021-07-22 Thu 19:47
:ARCHIVE_FILE: ~/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn/Version ebook
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
2 types pour l'instant:
Sections -> h2
<section class="section section1" id="s1n4">
Subsections -> h3
<section class="section section2" id="s2n4">
* DONE Page de titre séparée + infos
:PROPERTIES:
:ARCHIVE_TIME: 2021-07-22 Thu 19:47
:ARCHIVE_FILE: ~/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn/Version ebook
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
Auteur, année etc
* DONE Corriger footer
:PROPERTIES:
:ARCHIVE_TIME: 2021-07-22 Thu 19:47
:ARCHIVE_FILE: ~/projects/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn/Version ebook
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
* DONE Vérifier à la main [207/593]
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 11:21
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/mam.org
:ARCHIVE_OLPATH: Askhistorians
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
** KILL A Call to Arms: Propaganda, Public Opinion, and Newspapers in the Great War (Troy R. E. Paddock)
** KILL A Dark and Bloody Ground: The H\252rtgen Forest and the Roer River Dams, 1944-1945 (Edward G. Miller)
** KILL A Fatherly Eye: Indian Agents, Government Power, and Aboriginal Resistance in Ontario, 1918-1939 (Robin Jarvis Brownlie)
** KILL A Forest of Kings: The Untold Story of the Ancient Maya (Linda Schele)
** KILL A Guide to Western Historical Scripts from Antiquity to 1600 (Michelle P. Brown)
** KILL A History of Florence, 1200 - 1575 (John M. Najemy)
** KILL A History of Greek Fire and Gunpowder (James Riddick Partington)
** KILL A History of Modern France (Jeremy D. Popkin)
** DONE A History of Western Music (J. Peter Burkholder)
** DONE A History of the Archaic Greek World: ca. 1200-479 BCE (Jonathan Hall)
** KILL A Month and a Day: A Detention Diary (Ken Saro-Wiwa)
** KILL A Nation Under Our Feet: Black Political Struggles in the Rural South from Slavery to the Great Migration (Steven Hahn)
** KILL A New History of Jazz (Alyn Shipton)
** KILL A Quiet Revolution: The First Palestinian Intifada and Nonviolent Resistance (Mary Elizabeth King)
** KILL A Shopkeeper's Millennium: Society and Revivals in Rochester, New York, 1815-1837 (Paul E. Johnson)
** KILL A Social History of Truth: Civility and Science in Seventeenth-Century England (Steven Shapin)
** KILL A Social History of Women in Ireland: 1870-1970 (Rosemary Cullen Owens)
** KILL A Terrible Beauty: British Artists in the First World War (Paul Gough)
** KILL A Tragedy Revealed: The Story of Italians from Istria, Dalmatia, and Venezia Giulia, 1943-1956 (Arrigo Petacco)
** KILL A War Imagined: The First World War and English Culture (Samuel Hynes)
** KILL A Year in Pyongyang (Andrew Holloway)
** DONE Absolute War: Soviet Russia in the Second World War (Christopher Bellamy)
** KILL Across the Red River: Rwanda, Burundi, and the Heart of Darkness (Christian Jennings)
** KILL Addicts Who Survived: An Oral History of Narcotic Use in America, 1923-1965 (David T. Courtwright)
** KILL Africa Since Independence: A Comparative History (Paul Nugent)
** KILL Africa and Africans in the Making of the Atlantic World, 1400-1800 (John K. Thornton)
** KILL Against Wind and Tide: The African American Struggle Against the Colonization Movement (Ousmane K. Power-Greene)
** KILL Alamein 1933-1962 (Paolo Caccia Dominioni)
** KILL Alaska's Skyboys: Cowboy Pilots and the Myth of the Last Frontier (Katherine Johnson Ringsmuth)
** KILL Ale, Beer, and Brewsters in England: Women's Work in a Changing World, 1300-1600 (Judith M. Bennett)
** KILL Alfred Deakin; A Biography (2 volume set) (J.A. La Nauze)
** KILL Aloha Betrayed: Native Hawaiian Resistance to American Colonialism (Noenoe K. Silva)
** KILL Ambivalent Conquests: Maya and Spaniard in Yucatan, 1517-1570 (Inga Clendinnen)
** KILL America Divided: The Civil War of the 1960s (Maurice Isserman)
** KILL America's Geisha Ally: Reimagining the Japanese Enemy (Naoko Shibusawa)
** KILL America's Longest War: The United States and Vietnam, 1950-1975 (George C. Herring)
** KILL American Babylon: Race and the Struggle for Postwar Oakland (Robert O. Self)
** KILL American Crucible: Race and Nation in the Twentieth Century (Gary Gerstle)
** KILL American Slavery: 1619-1877 (Peter Kolchin)
** KILL Americanos: Latin America's Struggle for Independence (John Charles Chasteen)
** KILL An Environmental History of the Middle Ages: The Crucible of Nature (John Aberth)
** KILL Ancient Egyptian Materials and Technology (Paul T. Nicholson)j
** KILL Ancient Greece: A History in Eleven Cities (Paul Anthony Cartledge)
** KILL Ancient India: From the Origins to the XIII Century Ad (Marilia Albanese)
** KILL Ancient Israel: What Do We Know and How Do We Know It? (Lester L. Grabbe)
** KILL Ancient Mexico & Central America: Archaeology and Culture History (Susan Toby Evans)
** KILL Ancient Turkey (Antonio Sagona)
** KILL Ancient West Mexico: Art and Archaeology of the Unknown Past (Richard F. Townsend)
** KILL And Be One People: Alfred Deakin's Federal Story (Alfred Deakin)
** KILL Andean Archaeology (Helaine Silverman)
** KILL Anecdotal Sculpture of Ancient West Mexico. [By] Hasso von Winning, Olga Hammer. (Natural History Museum County)
** DONE Antecedents to Modern Rwanda: The Nyiginya Kingdom (Jan Vansina)
** KILL Archaeology of The Southwest (Linda S. Cordell)
** KILL Archaic Greece: The Age of Experiment (Anthony Snodgrass)
** KILL Armour of the English Knight 1400-1450 (Tobias Capwell)
** KILL Ars Sacra: Christian Art and Architecture of the Western World from the Very Beginning Up Until Today (Rolf Toman)
** KILL As We Saw Them: The First Japanese Embassy to the United States (Masao Miyoshi)
** KILL Atlantic Canada: A History (Margaret Conrad)
** KILL Atlantic Crossings: Social Politics in a Progressive Age (Revised) (Daniel T. Rodgers)
** KILL Australia's Democracy: A Short History (John Hirst)
** DONE Australians: Origins to Eureka (Australians, #1) (Thomas Keneally)
** KILL Avoiding Armageddon: From the Great War to the Fall of France, 1918-40 (Jeremy Black)
** KILL Aztec Thought and Culture: A Study of the Ancient Nahuatl Mind (Miguel Le\243n-Portilla)
** KILL Aztec Warfare: Imperial Expansion and Political Control (Ross Hassig)
** KILL Bachelors and Bunnies: The Sexual Politics of Playboy (Carrie Pitzulo)
** KILL Baptism Of Fire: The Second Battle of Ypres and the Forging of Canada, April 1915 (Nathan Greenfield)
** DONE Barbarossa: Hitler's Invasion of Russia 1941 (David M. Glantz)
** DONE Batavia's Graveyard: The True Story of the Mad Heretic Who Led History's Bloodiest Mutiny (Mike Dash)
** KILL Beautiful Death: Jewish Poetry and Martyrdom in Medieval France (Susan L. Einbinder)
** KILL Becoming Zimbabwe. A History From The Pre Colonial Period To 2008 (Brian Raftopoulos)
** KILL Beneath the United States: A History of U.S. Policy Toward Latin America (Lars Schoultz)
** KILL Between Worlds: Early Exchanges Between Maori And Europeans, 1773 1815 (Anne Salmond)
** KILL Bhutan - Dragon Kingdom in Crisis (Nari Rustomji)
** KILL Bhutan: The Kingdom at the Centre of the World (Omair Ahmad)
** KILL Biblical History and Israel\8217s Past: The Changing Study of the Bible and History (Megan Bishop Moore)
** DONE Big Chief Elizabeth: The Adventures and Fate of the First English Colonists in America (Giles Milton)
** KILL Black Garden: Armenia and Azerbaijan Through Peace and War (Thomas de Waal)
** KILL Black Kettle And Full Moon: Daily Life In A Vanished Australia (Geoffrey Blainey)
** KILL Black Majority: Negroes in Colonial South Carolina from 1670 through the Stono Rebellion (Peter H. Wood)
** KILL Border Lines: The Partition of Judaeo-Christianity (Daniel Boyarin)
** KILL Born to Die: Disease and New World Conquest, 1492-1650 (Noble David Cook)
** KILL Breaking the Maya Code (Michael D. Coe)
** KILL Britain on the Brink: The Cold War S Most Dangerous Weekend, 27-28 October 1962 (Jim Wilson)
** KILL British Propaganda During the First World War, 1914-18 (Michael S. Sanders)
** KILL Broken Waves: A History of the Fiji Islands in the Twentieth Century (Brij V. Lal)
** KILL Buddhism in China: A Historical Survey (Kenneth K.S. Ch'en)
** KILL Byzantium in the Seventh Century: The Transformation of a Culture (John F. Haldon)
** KILL Byzantium: Revised Edition (Rowena Loverance)
** DONE Byzantium: The Apogee (John Julius Norwich)
** DONE Byzantium: The Decline and Fall (John Julius Norwich)
** DONE Byzantium: The Early Centuries (John Julius Norwich)
** KILL Cabinets and the Bomb (Peter Hennessy)
** KILL Canada and Arctic North America: An Environmental History (Graeme Wynn)
** KILL Capital and Labour in the British Columbia Forest Industry, 1934-74 (Gordon Hak)
** KILL Carthage: A History (Serge Lancel)
** KILL Challenging the Regional Stereotype Essa (E.R. Forbes)
** KILL Changes in the Land: Indians, Colonists, and the Ecology of New England (William Cronon)
** KILL Charm Offensive (William Thacker)
** KILL Chen Village: Revolution to Globalization (Anita Chan)
** KILL Cherokee Women: Gender and Culture Change, 1700-1835 (Theda Perdue)
** KILL China's Rise in Historical Perspective (Brantly Womack)
** KILL Chinese Ceramics: From the Paleolithic Period through the Qing Dynasty (Li Zhiyan)
** KILL Chinese Village, Socialist State (Edward Friedman)
** KILL Christian Materiality: An Essay on Religion in Late Medieval Europe (Caroline Walker Bynum)
** KILL Chronicle of the Maya Kings and Queens: Deciphering the Dynasties of the Ancient Maya (Simon Martin)
** KILL Church, State, And Christian Society At The Time Of The Investiture Contest (Gerd Tellenbach)
** KILL Churchill: Blood, Toil, Tears, and Sweat (John Lukacs)
** KILL Cities of Ladies: Beguine Communities in the Medieval Low Countries, 1200-1565 (Walter Simons)
** KILL Citizen Docker: Making a New Deal on the Vancouver Waterfront, 1919-1939 (Andrew Parnaby)
** KILL Civilization and Monsters: Spirits of Modernity in Meiji Japan (Gerald Figal)
** KILL Cloth in West African History (Colleen E. Kriger)
** KILL Cocaine: From Medical Marvel to Modern Menace in the United States, 1884-1920 (Joseph F. Spillane)
** KILL Cold War Civil Rights: Race and the Image of American Democracy (Mary L. Dudziak)
** KILL Cold War Triumphalism: The Misuse of History After the Fall of Communism (Ellen Schrecker)
** KILL Cold War and the Color Line: American Race Relations in the Global Arena (Revised) (Thomas Borstelmann)
** KILL Commercial Agreements and Social Dynamics in Medieval Genoa (Quentin Van Doosselaere)
** KILL Companion to the History of Modern Science (Geoffrey N. Cantor)
** DONE Company K (The Library of Alabama Classics) (William March)
** KILL Confucian China and Its Modern Fate: A Trilogy (Joseph Richmond Levenson)
** KILL Contesting the French Revolution (Paul Hanson)
** KILL Creating G.I. Jane: Sexuality and Power in the Women's Army Corps During World War II (Leisa D. Meyer)
** DONE Crucible of War: The Seven Years' War and the Fate of Empire in British North America, 1754 - 1766 (Fred Anderson)
** KILL Cuba: A New History (Richard Gott)
** KILL Cuba: Between Reform and Revolution (Louis A. P\233rez Jr.)
** DONE Cult of the Nation in France: Inventing Nationalism, 1680-1800 (David A. Bell)
** KILL Culture and Conquest in Mongol Eurasia (Thomas T. Allsen)
** KILL Cultures of Commemoration: The Politics of War, Memory, and History in the Mariana Islands (Keith Camacho)
** KILL Daily Life of the Aztecs: People of the Sun and Earth (Dav\237d Carrasco)
** KILL Daily Lives of Civilians in Wartime Asia: From the Taiping Rebellion to the Vietnam War (Stewart Lone)
** KILL Damned Nation: Hell in America from the Revolution to Reconstruction (Kathryn Gin Lum)
** KILL Daring to Be Bad: Radical Feminism in America, 1967-1975 (Alice Echols)
** KILL Dark Paradise: A History of Opiate Addiction in America (David T. Courtwright)
** KILL Death So Noble: Memory, Meaning, and the First World War (Jonathan F. Vance)
** KILL Debating the Civil Rights Movement, 1945 1968 (Steven F. Lawson)
** KILL Deceptions and Doublecross: How the NHL Conquered Hockey (Morey Holzman)
** KILL Defeat Is the Only Bad News: Rwanda under Musinga, 1896\8211\&1931 (Alison Liebhafsky Des Forges)
** KILL Defining Chu: Image and Reality in Ancient China (Constance A. Cook)
** KILL Dictionary of Scientific Biography (16 volume set) (Scribner)
** KILL Dictionary of the History of Science (William Bynum)
** DONE Did God Have a Wife? Archaeology and Folk Religion in Ancient Israel (William G. Dever)
** KILL Discovering Women's History: A Practical Guide to Researching the Lives of Women since 1800 (Deirdre Beddoe)
** KILL Disunion!: The Coming of the American Civil War, 1789-1859 (Elizabeth R. Varon)
** KILL Divided by God: America's Church-State Problem--and What We Should Do About It (Noah Feldman)
** KILL Do Glaciers Listen?: Local Knowledge, Colonial Encounters, and Social Imagination (Julie Cruikshank)
** KILL Documentary Culture and the Laity in the Early Middle Ages (Warren Brown)
** KILL Downwind: A People's History of the Nuclear West (Sarah Alisabeth Fox)
** KILL Dreaming of What Might Be: The Knights of Labor in Ontario, 1880 1900 (Gregory S. Kealey)
** KILL Drink, Power, and Cultural Change: A Social History of Alcohol in Ghana, C. 1800 to Recent Times (Emmanuel Kwaku Akyeampong)
** DONE Dunkirk - The Men They Left Behind (Sean Longden)
** KILL Early Japanese Railways 1853-1914: Engineering Triumphs That Transformed Meiji-era Japan (Dan Free)
** DONE Ecological Imperialism: The Biological Expansion of Europe, 900-1900 (Studies in Environment and History) (Alfred W. Crosby)
** KILL El Dorado In West Africa: The Gold Mining Frontier, African Labor, And Colonial Capitalism In The Gold Coast, 1875 1900 (Raymond E. Dumett)
** KILL Emperor Worship and Roman Religion (Ittai Gradel)
** DONE Empire of Blue Water: Captain Morgan's Great Pirate Army, the Epic Battle for the Americas, and the Catastrophe That Ended the Outlaws' Bloody Reign (Stephan Talty)
** KILL Encounters on the Passage: Inuit Meet the Explorers (Dorothy Harley Eber)
** KILL Energy In World History (Vaclav Smil)
** KILL Engineering the Revolution: Arms and Enlightenment in France, 1763-1815 (Ken Alder)
** KILL English in Singapore: Modernity and Management (Asian Englishes Today Series) (Lisa Lim)
** KILL Exploring the World of the Celts (Simon James)
** KILL Faith and the Founders of the American Republic (Mark David Hall)
** KILL Family, Fields, and Ancestors: Constancy and Change in China's Social and Economic History, 1550-1949 (Lloyd E. Eastman)
** DONE Famine in North Korea: Markets, Aid, and Reform (Stephan Haggard)
** KILL Federation Fathers (L.F. Crisp)
** KILL Fighting Different Wars: Experience, Memory, and the First World War in Britain (Janet S.K. Watson)
** KILL Final Passages: The Intercolonial Slave Trade of British America, 1619-1807 (Gregory E. O'Malley)
** KILL Fire-Eater. the Memoirs of a VC (A.O. Pollard)
** KILL Fog of War: The Second World War and the Civil Rights Movement (Kevin M. Kruse)
** KILL Forgotten Victory - The First World War: Myths and Reality (Gary Sheffield)
** KILL Fragile Lives: Violence, Power, and Solidarity in Eighteenth-Century Paris (Arlette Farge)
** KILL France and the Dreyfus Affair: A Documentary History (Michael Burns)
** KILL French Society in Revolution, 1789-1799 (David Andress)
** KILL From Memory to Written Record: England 1066 - 1307 (M.T. Clanchy)
** KILL From Slave Trade to 'Legitimate' Commerce: The Commercial Transition in Nineteenth-Century West Africa (Robin Law)
** KILL Frontier Contact Between Choson Korea and Tokugawa Japan (James B. Lewis)
** DONE Frontsoldaten: The German Soldier in World War II (Stephen G. Fritz)
** KILL Galileo, Courtier: The Practice of Science in the Culture of Absolutism (Mario Biagioli)
** KILL Genghis Khan and Mongol Rule (George Lane)
** KILL Genoa and the Genoese, 958-1528 (Steven A. Epstein)
** KILL German History 1770-1866 (James J. Sheehan)
** KILL Ghosts have warm hands: A memoir of the Great War, 1916-1919 (CEF classics) (Will R. Bird)
** KILL Grand Expectations: The United States, 1945-1974 (James T. Patterson)
** KILL Greece in the Bronze Age (Emily Vermeule)
** KILL Greece in the Making, 1200-479 B.C. (Robin Osborne)
** KILL Greek History: The Basics (Robin Osborne)
** KILL Greek Literature and the Roman Empire: The Politics of Imitation (Tim Whitmarsh)
** KILL Greek Thought, Arabic Culture: The Graeco-Arabic Translation Movement in Baghdad and Early Abbasid Society (Dimitri Gutas)
** KILL Griff nach der Weltmacht: Die Kriegszielpolitik des kaiserlichen Deutschland 1914/1918 (Fritz Fischer)
** KILL Guardians of Islam: Religious Authority and Muslim Communities of Late Medieval Spain (Kathryn A. Miller)
** KILL Half Slave and Half Free: The Roots of Civil War (Bruce Levine)
** KILL Hep-Cats, Narcs, and Pipe Dreams: A History of America's Romance With Illegal Drugs (Jill Jonnes)
** KILL Hirohito and War: Imperial Tradition and Military Decision Making in Pre-War Japan (Peter Michael Wetzler)
** KILL History in the Vernacular (Raziuddin Aquil)
** KILL Hitler's Army: Soldiers, Nazis, and War in the Third Reich (Omer Bartov)
** DONE Hitler's Forgotten Ally: Ion Antonescu and his Regime, Romania, 1940 -1944 (Dennis Deletant)
** DONE Hitler's Italian Allies: Royal Armed Forces, Fascist Regime, and the War of 1940-1943 (MacGregor Knox)
** KILL Hitler's Legions: The German Army Order of Battle, World War II (Samuel W. Mitcham Jr.)
** KILL Hitler's Second Army: The Waffen SS (Edmund L. Blandford)
** KILL Holy Feast and Holy Fast: The Religious Significance of Food to Medieval Women (Caroline Walker Bynum)
** KILL Homeward Bound: American Families in the Cold War Era (Elaine Tyler May)
** KILL Hong Kong and the Cold War: Anglo-American Relations 1949-1957: Anglo-American Relations 1949-1957 (Chi-kwan Mark)
** KILL How History's Greatest Pirates Pillaged, Plundered, and Got Away With It: The Stories, Techniques, and Tactics of the Most Feared Sea Rovers from 1500-1800 (Benerson Little)
** KILL How We Advertised America: The First Telling Of The Amazing Story Of The Committee On Public Information That Carried The Gospel Of Americanism To Every Corner Of The Globe (1920) (George Creel)
** DONE How We Forgot the Cold War: A Historical Journey across America (Jon Wiener)
** KILL How to Write the History of the New World: Histories, Epistemologies, and Identities in the Eighteenth-Century Atlantic World (Jorge Ca\241izares Esguerra)
** KILL Huia Histories of M\257ori: Ng\257 T\257huhu K\333rero (Huia Publishers)
** KILL I Die With My Country: Perspectives on the Paraguayan War, 1864-1870 (Hendrik Kraay)
** DONE I've Got the Light of Freedom: The Organizing Tradition and the Mississippi Freedom Struggle, With a New Preface (Charles M. Payne)
** TODO Imperial China 900-1800 (Frederick W. Mote)
** TODO Imperial Spain, 1469 - 1716 (J.H. Elliott)
** TODO In Parenthesis (David Jones)
** TODO In Pursuit of Equity: Women, Men, and the Quest for Economic Citizenship in 20th-Century America (Alice Kessler-Harris)
** TODO In the Realm of 8 Deer: The Archaeology of the Mixtec Codices (Bruce E. Byland)
** TODO Introduction to Folklore: Traditional Studies in Europe and Elsewhere (Ronald M. James)
** TODO Introduction to Manuscript Studies (Raymond Clemens)
** TODO Irresistible Empire: America's Advance Through Twentieth-Century Europe (Victoria de Grazia)
** TODO Ishiwara Kanji and Japan's Confrontation with the West (Mark R. Peattie)
** TODO Ivan's War: The Red Army, 1939-45 (Catherine Merridale)
** TODO James Henry Hammond and the Old South: A Design for Mastery (Drew Gilpin Gaust)
** TODO Japan Prepares for Total War: The Search for Economic Security, 1919 1941 (Michael A. Barnhart)
** TODO Japan's Quest for Autonomy: National Security and Foreign Policy, 1930-1938 (James Buckley Crowley)
** TODO Japan's Total Empire: Manchuria and the Culture of Wartime Imperialism (Louise Young)
** TODO Japanese Destroyer Captain: Pearl Harbor, Guadalcanal, Midway - The Great Naval Battles As Seen Through Japanese Eyes (Tameichi Hara)
** TODO Jean-Marie Tjibaou, Kanak Witness to the World: An Intellectual Biography (Eric Waddell)
** TODO Kiev 1941 (David Stahel)
** TODO King Hammurabi of Babylon: A Biography (Marc Van De Mieroop)
** TODO Kingdoms of the Savanna (Jan Vansina)
** TODO Know Your Enemy: The Rise and Fall of America's Soviet Experts (David C. Engerman)
** TODO Kursk: The Greatest Battle (Lloyd Clark)
** TODO Labor's War at Home: The CIO in World War II (Labor in Crisis) (Nelson Lichtenstein)
** TODO Landscape Traveled by Coyote and Crane: The World of the Schitsu'umsh (Rodney Frey)
** TODO Late Ancient Christianity: A People's History Of Christianity, Vol. 2 (Virginia Burrus)
** TODO Latin Palaeography: Antiquity and the Middle Ages (Bernhard Bischoff)
** TODO Learning Latin the Ancient Way: Latin Textbooks from the Ancient World (Eleanor Dickey)
** TODO Lexicon Abbreviaturarum: Dizionario Di Abbreviature Latine Ed Italiane (Manuali Hoepli) (Adriano Cappelli)
** TODO Life in Biblical Israel (Philip J. King)
** TODO Local Knowledge and Microidentities in the Imperial Greek World (Tim Whitmarsh)
** TODO Local People: The Struggle for Civil Rights in Mississippi (John Dittmer)
** TODO Lords of the Rinks: The Emergence of the National Hockey League, 1875-1936 (John Chi-Kit Wong)
** TODO Louis Riel and the Creation of Modern Canada: Mythic Discourse and the Postcolonial State (Jennifer Reid)
** TODO Lourdes: Body and Spirit in the Secular Age (Ruth Harris)
** TODO Loyalty and Liberty: American Countersubversion from World War 1 to the McCarthy Era (Alex Goodall)
** TODO Luther and Erasmus: Free Will and Salvation (Library of Christian Classics) (Erasmus)
** TODO Mad as Hell: The Crisis of the 1970s and the Rise of the Populist Right (Dominic Sandbrook)
** TODO Mak\250k: A New History of Aboriginal-White Relations (John Sutton Lutz)
** TODO Making Peoples: A History of the New Zealanders: From Polynesian Settlement to the End of the Nineteenth Century (James Belich)
** TODO Making Revolution: The Communist Movement in Eastern and Central China, 1937-1945 (Yung-fa Chen)
** TODO Making a New Deal: Industrial Workers in Chicago, 1919-1939 (Lizabeth Cohen)
** TODO Managing Sino-American Crises: Case Studies and Analysis (Michael D. Swaine)
** TODO Manliness and Civilization: A Cultural History of Gender and Race in the United States, 1880-1917 (Gail Bederman)
** TODO Many Are the Crimes: McCarthyism in America (Ellen Schrecker)
** TODO March of the Twenty-Six (R.F. Delderfield)
** TODO Marking the Hours: English People and Their Prayers, 1240-1570 (Eamon Duffy)
** TODO Mass and Elite in Democratic Athens: Rhetoric, Ideology, and the Power of the People (Josiah Ober)
** TODO Masters of Small Worlds: Yeoman Households, Gender Relations, and the Political Culture of the Antebellum South Carolina Low Country (Stephanie McCurry)
** TODO Maya Conquistador (Matthew Restall)
** TODO Maya Cosmos: Three Thousand Years on the Shaman's Path (David A. Freidel)
** TODO Maya Society Under Colonial Rule: The Collective Enterprise of Survival (Nancy M. Farriss)
** TODO Mayflower Bastard: A Stranger Among the Pilgrims (Dave Lindsay)
** TODO Medieval Canon Law (James A. Brundage)
** TODO Medieval Studies: An Introduction (James M. Powell)
** TODO Mediterranean Anarchy, Interstate War, and the Rise of Rome (Arthur M. Eckstein)
** TODO Memories of War: Micronesians in the Pacific War (Suzanne Falgout)
** TODO Mesoamerican Archaeology: Theory And Practice (Rosemary A. Joyce)
** TODO Mexicans in Revolution, 1910-1946: An Introduction (William H. Beezley)
** TODO Minamata: Pollution and the Struggle for Democracy in Postwar Japan (Timothy S. George)
** TODO Minimalism: Origins (Edward Strickland)
** TODO More with Less: Work Reorganization in the Canadian Mining Industry (Bob Russell)
** TODO Mothers and Children: Jewish Family Life in Medieval Europe (Elisheva Baumgarten)
** TODO Mr Bligh's Bad Language: Passion, Power and Theatre on the Bounty (Greg Dening)
** TODO Muhammad and the Believers: At the Origins of Islam (Fred M. Donner)
** TODO Muslim Societies in Africa: A Historical Anthropology (Roman Loimeier)
** TODO Muslim Societies in African History (David Robinson)
** TODO Mussolini Unleashed, 1939-1941: Politics and Strategy in Fascist Italy's Last War (MacGregor Knox)
** TODO Nan'y\333: The Rise and Fall of the Japanese in Micronesia, 1885-1945 (Mark R. Peattie)
** TODO Napoleon's Cavalry And Its Leaders (David R. Johnson)
** TODO Napoleon's Great Adversary: The Archduke Charles and the Austrian Army, 1792-1814 (Gunther E. Rothenberg)
** TODO Natives and Exotics: World War II and Environment in the Southern Pacific (Judith A. Bennett)
** TODO Nature's Metropolis: Chicago and the Great West (William Cronon)
** TODO New Day in Babylon: The Black Power Movement and American Culture, 1965-1975 (William L. Van DeBurg)
** TODO New Guinea: Crossing Boundaries And History (Clive Moore)
** TODO No Constitutional Right to Be Ladies: Women and the Obligations of Citizenship (Linda K. Kerber)
** TODO No Place of Grace: Antimodernism and the Transformation of American Culture, 1880\8211\&1920 (T.J. Jackson Lears)
** TODO No Right Turn: Conservative Politics in a Liberal America (David T. Courtwright)
** TODO Northwest Europe in the Early Middle Ages, C.Ad 600-1150: A Comparative Archaeology (Christopher Loveluck)
** TODO Ockham Explained: From Razor to Rebellion (Rondo Keele)
** TODO Of Revelation and Revolution, Volume 1: Christianity, Colonialism, and Consciousness in South Africa (Jean Comaroff)
** TODO Olmec Archaeology Early Mesoamerica (Christopher A. Pool)
** TODO On the Job: Confronting the Labour Process in Canada (Craig Heron)
** TODO On the Road of the Winds: An Archaeological History of the Pacific Islands before European Contact (Patrick Vinton Kirch)
** TODO Once Were Pacific: Maori Connections to Oceania (Alice Te Punga Somerville)
** TODO Opera: A History in Documents (Piero Weiss)
** TODO Origins of Modern Europe, 1660-1789 (James Llewelyn White)
** TODO Osman's Dream: The Story of the Ottoman Empire 1300-1923 (Caroline Finkel)
** TODO Over Here: The First World War and American Society (David M. Kennedy)
** TODO Oxford History of Western Music: 6-Volume Set (Richard Taruskin)
** TODO Pacific Worlds (Matt K. Matsuda)
** TODO Paradise Reforged: A History of the New Zealanders from the 1880s to the Year 2000 (James Belich)
** TODO Peoples of the Northwest Coast: Their Archaeology and Prehistory (Kenneth M. Ames)
** TODO Personal Politics: The Roots of Women's Liberation in the Civil Rights Movement & the New Left (Sara M. Evans)
** TODO Petra and the Lost Kingdom of the Nabataeans (Jane Taylor)
** TODO Pirate Hunting: The Fight Against Pirates, Privateers, and Sea Raiders from Antiquity to the Present (Benerson Little)
** TODO Pitied But Not Entitled: Single Mothers and the History of Welfare, 1890-1935 (Linda Gordon)
** TODO Playboy and the Making of the Good Life in Modern America (Elizabeth Fraterrigo)
** TODO Policing Sexuality (Jessica R Pliley)
** TODO Politics and Policy in Traditional Korea (James B. Palais)
** TODO Politics, Economics and Society in Argentina in the Revolutionary Period (Tulio Halperin-Donghi)
** TODO Popular Politics and the English Reformation (Ethan H. Shagan)
** TODO Possessing Nature: Museums, Collecting, and Scientific Culture in Early Modern Italy (Paula Findlen)
** TODO Power and Culture: The Japanese-American War, 1941-1945 (Akira Iriye)
** TODO Propaganda Technique in World War I (Harold D. Lasswell)
** TODO Propaganda and Censorship During Canada's Great War (Jeffrey A. Keshen)
** TODO Provincializing Europe: Postcolonial Thought and Historical Difference - New Edition (Dipesh Chakrabarty)
** TODO Race and Reunion: The Civil War in American Memory (David W. Blight)
** TODO Racial Crossings: Race, Intermarriage, and the Victorian British Empire (Oxford Historical Monographs) (Damon Ieremia Salesa)
** TODO Railroaded: The Transcontinentals and the Making of Modern America (Richard White)
** TODO Re-Imagining Rwanda: Conflict, Survival and Disinformation in the Late Twentieth Century (Johan Pottier)
** TODO Rearranging the Landscape of the Gods: The Politics of a Pilgrimage Site in Japan, 1573-1912 (Sarah Thal)
** TODO Reasoning Otherwise: Leftists and the People's Enlightenment in Canada, 1890-1920 (Ian McKay)
** TODO Red Hills and Cotton (Ben Robertson)
** TODO Reform and Revolution in China: The 1911 Revolution in Hunan and Hubei (Joseph W. Esherick)
** TODO Replenishing the Earth: The Settler Revolution and the Rise of the Angloworld (James Belich)
** TODO Resistance and Integration: Peronism and the Argentine Working Class, 1946-1976 (Daniel James)
** TODO Rethinking Japanese History (Yoshihiko Amino)
** TODO Rethinking the Holocaust (Yehuda Bauer)
** TODO Retribution: The Battle for Japan, 1944-45 (Max Hastings)
** TODO Rhetorical Conquests: Cortes, Gomara, and Renaissance Imperialism (Glen Carman)
** TODO Rites of Spring: The Great War and the Birth of the Modern Age (Modris Eksteins)
** TODO Ruling Race: A History of American Slaveholders (James Oakes)
** TODO Sagittarius Rising (Cecil Lewis)
** TODO Sainthood in the Later Middle Ages (Andr\233 Vauchez)
** TODO Samurai Invasion: Japan's Korean War 1592 -1598 (Stephen Turnbull)
** TODO Saracens: Islam in the Medieval European Imagination (John Tolan)
** TODO Scribes and Scholars: A Guide to the Transmission of Greek and Latin Literature (L.D. Reynolds)
** TODO Secrets of Crewe House; The Story of a Famous Campaign (Campbell Stuart)
** TODO Seeing Islam as Others Saw It: A Survey and Evaluation of Christian, Jewish, and Zoroastrian Writings on Early Islam (Robert G. Hoyland)
** TODO Selling the Congo: A History of European Pro-Empire Propaganda and the Making of Belgian Imperialism (Matthew G. Stanard)
** TODO Separate but Equal: Cistercian Lay Brothers 1120-1350 (James France)
** TODO Skyscrapers Hide the Heavens: A History of Indian-White Relations in Canada (J.R. Miller)
** TODO Slavery and Freedom: An Interpretation of the Old South (James Oakes)
** TODO Slavery and the Evolution of Cherokee Society: 1540-1866 (Theda Perdue)
** TODO Slaves on Horses: The Evolution of the Islamic Polity (Patricia Crone)
** TODO Soldiers of the Dragon: Chinese Armies 1500 BC\8211AD 1840 (Chris (C.J.) Peers)
** TODO Soul by Soul: Life Inside the Antebellum Slave Market (Walter Johnson)
** TODO Sovereignty and Authenticity: Manchukuo and the East Asian Modern (Prasenjit Duara)
** TODO Soviet Military Deception in the Second World War (David M. Glantz)
** TODO Spain's Men of the Sea: Daily Life on the Indies Fleets in the Sixteenth Century (Pablo E. P\233rez-Malla\237na)
** TODO Stalin and the Cold War in Europe: The Emergence and Development of East-West Conflict, 1939-1953 (Gerhard Wettig)
** TODO Stalingrad to Kursk: Triumph of the Red Army (Geoffrey Jukes)
** TODO Strange Parallels: Southeast Asia in Global Context, c. 800-1830. Volume 1, Integration on the Mainland (Victor B. Lieberman)
** TODO Strange Parallels: Southeast Asia in Global Context, c. 800-1830. Volume 2, Mainland Mirrors: Europe, Japan, China, South Asia, and the Islands (Victor B. Lieberman)
** TODO Strangers in Their Own Land: A Century of Colonial Rule in the Caroline and Marshall Islands (Francis X. Hezel)
** TODO Strangers in the Land: Patterns of American Nativism, 1860-1925 (John Higham)
** TODO Sun Yat-sen (Marie-Claire Berg\232re)
** TODO Survivors of a Kind: Memoirs of the Western Front (Brian Bond)
** TODO Swords around a Throne: Napoleon's Grande Armee (John R. Elting)
** TODO Taiwan China: A Most Ticklish Standoff (Adam W. Clarke)
** TODO Taken by Storm, 1938: A Social and Meteorological History of the Great New England Hurricane (Lourdes B. Aviles)
** TODO Taming Manhattan: Environmental Battles in the Antebellum City (Catherine McNeur)
** TODO Tangata Whenua: An Illustrated History (Judith Atholl Anderson Harris)
** TODO Tar\237acuri's Legacy: The Prehispanic Tarascan State (Helen Perlstein Pollard)
** TODO That Infernal Little Cuban Republic: The United States and the Cuban Revolution (Lars Schoultz)
** TODO That Noble Dream: The \Objectivity Question\ and the American Historical Profession (Peter Novick)
** TODO The Abortive Revolution: China Under Nationalist Rule, 1927-1937 (Harvard East Asian Monographs) (Lloyd E. Eastman)
** TODO The Age of Battles: The Quest for Decisive Warfare from Breitenfeld to Waterloo (Russell F. Weigley)
** TODO The Age of Reconnaissance (John H. Parry)
** TODO The Arab Conquest of Spain: 710 - 797 (Roger Collins)
** TODO The Archaeology Of Islam In Sub Saharan Africa (Timothy Insoll)
** TODO The Archaeology of China: From the Late Paleolithic to the Early Bronze Age (Li Liu)
** TODO The Art of Ancient Egypt (Gay Robins)
** TODO The Art of Art History: A Critical Anthology (Donald Preziosi)
** TODO The Athenian Democracy in the Age of Demosthenes: Structure, Principles, and Ideology (Mogens Herman Hansen)
** TODO The Autumn of the Middle Ages (Johan Huizinga)
** TODO The Battle Against Anarchist Terrorism: An International History, 1878-1934 (Richard Bach Jensen)
** TODO The Bayonets of the Republic: Motivation and Tactics in the Army of Revolutionary France, 1791-1794 (John A. Lynn)
** TODO The Beginnings of Western Science: The European Scientific Tradition in Philosophical, Religious, and Institutional Context, 600 B.C. to A.D. 1450 (David C. Lindberg)
** TODO The Birth of the Modern World, 1780-1914: Global Connections and Comparisons (C.A. Bayly)
** TODO The Birth of the Palestinian Refugee Problem Revisited (Benny Morris)
** TODO The Black Death 1346-1353: The Complete History (Ole J\248rgen Benedictow)
** TODO The Body and Society: Men, Women and Sexual Renunciation in Early Christianity (Peter R.L. Brown)
** TODO The Bonds of Womanhood: \Woman's Sphere\ in New England, 1780-1835 (Nancy F. Cott)
** TODO The Book Of The Year: Middle American Calendrical Systems (Munro S. Edmonson)
** TODO The Broken Spears: The Aztec Account of the Conquest of Mexico (Miguel Le\243n-Portilla)
** TODO The Byzantines (Averil Cameron)
** TODO The Cambridge Companion to the Talmud and Rabbinic Literature (Charlotte E. Fonrobert)
** TODO The Cambridge History of the Byzantine Empire, c. 500 to 1492 (Jonathan Shepard)
** TODO The Chaco Meridian: Centers of Political Power in the Ancient Southwest (Stephen H. Lekson)
** TODO The Changing Shape of Church History (Justo L. Gonz\225lez)
** TODO The Cherokee Cases (Jill Norgren)
** TODO The Children's Civil War (James Marten)
** TODO The Chile Reader: History, Culture, Politics (Elizabeth Quay Hutchison)
** TODO The Church in the Later Middle Ages (The I.B.Tauris History of the Christian Church) (Norman P. Tanner)
** TODO The Church in the Shadow of the Mosque: Christians and Muslims in the World of Islam (Sidney H. Griffith)
** TODO The Cities of the Ancient Andes (Adriana Von Hagen)
** TODO The Cloud People: Divergent Evolution of the Zapotec and Mixtec Civilizations (Kent V. Flannery)
** TODO The Code of Kings: The Language of Seven Sacred Maya Temples and Tombs (Linda Schele)
** TODO The Cold War In East Asia 1945-1991 (Tsuyoshi Hasegawa)
** TODO The Coming of the Third Reich (The History of the Third Reich, #1) (Richard J. Evans)
** TODO The Complete Pyramids: Solving the Ancient Mysteries (Mark Lehner)
** TODO The Concise Oxford Companion to the Theatre (Phyllis Hartnoll)
** TODO The Confederate Battle Flag: America's Most Embattled Emblem (John M. Coski)
** TODO The Confucian Transformation of Korea: A Study of Society and Ideology (Martina Deuchler)
** TODO The Conquest All Over Again: Nahuas and Zapotecs Thinking, Writing, and Painting Spanish Colonialism (Susan Schroeder)
** TODO The Conquest of Ainu Lands: Ecology and Culture in Japanese Expansion,1590-1800 (Brett L. Walker)
** TODO The Conquest of Michoacan: The Spanish Domination of the Tarascan Kingdom in Western Mexico, 1521-1530 (J. Benedict Warren)
** TODO The Conquest of the Last Maya Kingdom (Grant Jones)
** TODO The Constitutional Origins of the American Revolution (Jack P. Greene)
** TODO The Creation of the American Republic, 1776-1787 (Gordon S. Wood)
** TODO The Culture of the Babylonian Talmud (Jeffrey L. Rubenstein)
** TODO The Culture of the Cold War (Stephen J. Whitfield)
** TODO The Culture of the Horse: Status, Discipline, and Identity in the Early Modern World (Karen L. Raber)
** TODO The Death of William Gooch: A History's Anthropology (Greg Dening)
** TODO The Decline and Fall of the British Aristocracy (David Cannadine)
** TODO The Diligent: A Voyage Through the Worlds of the Slave Trade (Robert W. Harms)
** TODO The Early Abbasid Caliphate: A Political History (Hugh Kennedy)
** TODO The Early Islamic Conquests (Fred M. Donner)
** TODO The Ecology Of The Ancient Greek World (Robert Sallares)
** TODO The Economic Aspects Of The History Of The Civilization Of Japan (Yoseburo Takekoshi)
** TODO The Ecuador Reader: History, Culture, Politics (Latin America Readers) (Carlos De La Torre)
** TODO The Eichmann Trial (Deborah E. Lipstadt)
** TODO The Elizabethan Puritan Movement (Patrick Collinson)
** TODO The Elusive Republic: Political Economy in Jeffersonian America (Drew R. McCoy)
** TODO The Empire Within: Postcolonial Thought and Political Activism in Sixties Montreal (Sean Mills)
** TODO The End of the Bronze Age: Changes in Warfare and the Catastrophe ca. 1200 B.C. (Robert Drews)
** TODO The Failure of Union: Central America, 1824-1960 (Thomas L. Karnes)
** TODO The Fall of France: The Nazi Invasion of 1940 (Julian T. Jackson)
** TODO The Fall of Rome and the End of Civilization (Bryan Ward-Perkins)
** TODO The First Decade of the Australian Commonwealth a Chronicle of Contemporary Politics (Henry Gyles Turner)
** TODO The First Jesuits (John W. O'Malley)
** TODO The First Taint of Civilization: A History of the Caroline and Marshall Islands in Pre-Colonial Days, 1521-1885 (Francis X. Hezel)
** TODO The First World War and British Military History (Brian Bond)
** TODO The Formation of a Persecuting Society: Power and Deviance in Western Europe, 950 - 1250 (R.I. Moore)
** TODO The Fourteen Dalai Lamas: A Sacred Legacy of Reincarnation (Glenn H. Mullin)
** TODO The French Enlightenment and the Jews: The Origins of Modern Anti-Semitism (Arthur Hertzberg)
** TODO The French Nobility in the Eighteenth Century: From Feudalism to Enlightenment (Guy Chaussinand-Nogaret)
** TODO The French Revolution: Recent Debates and New Controversies (Gary Kates)
** TODO The Fur Trade in Canada: An Introduction to Canadian Economic History (Harold A. Innis)
** TODO The Gender of Breadwinners: Women, Men and Change in Two Industrial Towns, 1880-1950 (Joy Parr)
** TODO The Ghost of Freedom: A History of the Caucasus (Charles King)
** TODO The Gilded Stage: A Social History of Opera (Daniel Snowman)
** TODO The Great Lakes of Africa: Two Thousand Years of History (Jean-Pierre Chr\233tien)
** TODO The Great War of Words: British, American and Canadian Propaganda and Fiction, 1914-1933 (Peter Buitenhuis)
** TODO The Great War: Myth and Memory (Dan Todman)
** TODO The Greek World 479-323 BC (Simon Hornblower)
** TODO The Greek World After Alexander: 323-30 BC (Graham Shipley)
** TODO The Green Archipelago: Forestry in Pre-Industrial Japan (Conrad D. Totman)
** TODO The Guatemala Reader: History, Culture, Politics (Greg Grandin)
** TODO The Historian's Craft: Reflections on the Nature and Uses of History and the Techniques and Methods of Those Who Write It. (Marc Bloch)
** TODO The Historical Demography of Pre-Modern Japan (Akira Hayami)
** TODO The History Of Islam In Africa (Nehemia Levtzion)
** TODO The History of Science from Augustine to Galileo (Alistair Cameron Crombie)
** TODO The Holocaust: The Jewish Tragedy (Martin Gilbert)
** TODO The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World (David W. Anthony)
** TODO The Human Past: World Prehistory and the Development of Human Societies (Christopher Scarre)
** TODO The Imjin War: Japan's Sixteenth-Century Invasion of Korea and Attempt to Conquer China (Samuel Hawley)
** TODO The Impending Crisis: America Before the Civil War, 1848-1861 (David Morris Potter)
** TODO The Imperial Cult in the Latin West: Studies in the Ruler Cult of the Western Provinces of the Roman Empire, Volume 2, Part 1 (Religions in the Graeco-Roman World) (Duncan Fishwick)
** TODO The Incorporation of America: Culture and Society in the Gilded Age (Alan Trachtenberg)
** TODO The Institute Of Pacific Relations: Asian Scholars And American Politics (John N. Thomas)
** TODO The Island at the Centre of the World (Russell Shorto)
** TODO The Italian Navy In World War Ii (James J. Sadkovich)
** TODO The Japanese Discovery of Europe, 1720-1830: Revised Edition (Donald Keene)
** TODO The Japanese Wartime Empire, 1931-1945 (Peter Duus)
** TODO The Jews Under Roman Rule: From Pompey To Diocletian: A Study In Political Relations (E. Mary Smallwood)
** TODO The Kanak Awakening: The Rise of Nationalism in New Caledonia (David A. Chappell)
** TODO The Kongolese Saint Anthony: Dona Beatriz Kimpa Vita and the Antonian Movement, 1684-1706 (John K. Thornton)
** TODO The Land beyond the Mists: Essays on Identity and Authority in Precolonial Congo and Rwanda (David Newbury)
** TODO The Last Days of Hitler: Thet Legends, the Evidence, the Truth (Anton Joachimsthaler)
** TODO The Last Expedition: Stanley's Mad Journey Through the Congo (Daniel Liebowitz)
** TODO The Last Great Frenchman: A Life Of General De Gaulle (Charles Williams)
** TODO The Last Soldiers of the King: Life in Wartime Italy, 1943-1945 (Eugenio Corti)
** TODO The Life and Struggles of Our Mother Walatta Petros: A Seventeenth-Century African Biography of an Ethiopian Woman (Galawdewos)
** TODO The Lord's First Night: The Myth of the Droit de Cuissage (Alain Boureau)
** TODO The Lost History of 1914: Reconsidering the Year the Great War Began (Jack Beatty)
** TODO The Love of Learning and the Desire for God: A Study of Monastic Culture (Jean Leclercq)
** TODO The Making of Modern Colombia: A Nation in Spite of Itself (David Bushnell)
** TODO The Making of the Georgian Nation (Ronald Grigor Suny)
** TODO The Maritime Rights Movement, 1919-1927: A Study in Canadian Regionalism (Ernest R. Forbes)
** TODO The Market Revolution: Jacksonian America, 1815-1846 (Charles Grier Sellers)
** TODO The Marketplace of Revolution: How Consumer Politics Shaped American Independence (T.H. Breen)
** TODO The Maya (Ancient Peoples & Places) (Michael D. Coe)
** TODO The Medieval Super-Companies: A Study of the Peruzzi Company of Florence (Edwin S. Hunt)
** TODO The Mediterranean and the Mediterranean World in the Age of Philip II, Volume I (Fernand Braudel)
** TODO The Mediterranean and the Mediterranean World in the Age of Philip II, Volume II (Fernand Braudel)
** TODO The Memory of Bones: Body, Being, and Experience Among the Classic Maya (Stephen Houston)
** TODO The Middle Ground: Indians, Empires, and Republics in the Great Lakes Region, 1650 - 1815 (Richard White)
** TODO The Movement and the Sixties (Terry H. Anderson)
** TODO The Nahuas After the Conquest: A Social and Cultural History of the Indians of Central Mexico, Sixteenth Through Eighteenth Centuries (James Lockhart)
** TODO The New Knighthood: A History of the Order of the Temple (Malcolm Barber)
** TODO The North Korean Economy: Between Crisis and Catastrophe (Nicholas Eberstadt)
** TODO The Old Religion in a New World: The History of North American Christianity (Mark A. Noll)
** TODO The Order Of Genocide: Race, Power, And War In Rwanda (Scott Straus)
** TODO The Origins of World War I (Richard F. Hamilton)
** TODO The Origins of the Boxer Uprising (Joseph W. Esherick)
** TODO The Origins of the Choson Dynasty (John B. Duncan)
** TODO The Origins of the First World War: Diplomatic and Military Documents (Annika Mombauer)
** TODO The Ornament of the World: How Muslims, Jews, and Christians Created a Culture of Tolerance in Medieval Spain (Mar\237a Rosa Menocal)
** TODO The Oxford Handbook of Cuneiform Culture (Karen Radner)
** TODO The Oxford Handbook of Latin American History (Jos\233 C. Moya)
** TODO The Pacific Theater: Island Representations Of World War II (Lamont Lindstrom)
** TODO The Pacific War, 1931-1945 : A Critical Perspective on Japan's Role in World War II (The Pantheon Asia Library) (Saburo Ienaga)
** TODO The Palaeography of Gothic Manuscript Books: From the Twelfth to the Early Sixteenth Century (Albert Derolez)
** TODO The Paraguay Reader: History, Culture, Politics (Peter Lambert)
** TODO The Partings Of The Ways: Between Christianity And Judaism And Their Significance For The Character Of Christianity (James D.G. Dunn)
** TODO The People of the Parish: Community Life in a Late Medieval English Diocese (Katherine L. French)
** TODO The People of the Sea: Environment, Identity, and History in Oceania (Paul D'Arcy)
** TODO The People's Armies: The Armees Revolutionnaires, Instrument of the Terror in the Departments, April 1793 to Floreal Year II (Richard Cobb)
** TODO The Phoenicians and the West: Politics, Colonies and Trade (Maria Eugenia Aubet)
** TODO The Politics of Rage: George Wallace, the Origins of the New Conservatism, and the Transformation of American Politics (Dan T. Carter)
** TODO The Prophet and the Age of the Caliphates: The Islamic Near East from the 6th to the 11th Century (Hugh Kennedy)
** TODO The Rebel League: The Short and Unruly Life of the World Hockey Association (Ed Willes)
** TODO The Red Machine: the Soviet Quest to Dominate Canada's Game (Lawrence Martin)
** TODO The Reformation and the English People (J.J. Scarisbrick)
** TODO The Regenerators: Social Criticism in Late Victorian English Canada (Ramsay Cook)
** TODO The Reign of Philip the Fair (Joseph R. Strayer)
** TODO The Republic of Pirates: Being the True and Surprising Story of the Caribbean Pirates and the Man Who Brought Them Down (Colin Woodard)
** TODO The Rise and Fall of Arab Presidents for Life (Roger Owen)
** TODO The Rise of African Slavery in the Americas (David Eltis)
** TODO The Rise of American Democracy: Jefferson to Lincoln (Sean Wilentz)
** TODO The Rise of Modern Warfare from the Age of Mercenaries through Napoleon (Hannsjoachim Wolfgang Koch)
** TODO The Road to Stalingrad: Stalin`s War with Germany (John Erickson)
** TODO The Roar and the Silence: A History of Virginia City and the Comstock Lode (Ronald M. James)
** TODO The Roots of Rural Capitalism: Western Massachusetts, 1780-1860 (Christopher Clark)
** TODO The Russian Revolution 1917-1932 (Sheila Fitzpatrick)
** TODO The Secret Lives of the Dalai Lama: Holder of the White Lotus (Alexander Norman)
** TODO The Secret War on the United States in 1915: A Tale of Sabotage, Labor Unrest, and Border Troubles (Heribert von Feilitzsch)
** TODO The Sephardic Frontier: The \reconquista\ and the Jewish Community in Medieval Iberia (Jonathan Ray)
** TODO The Seventies: The Great Shift In American Culture, Society, And Politics (Bruce J. Schulman)
** TODO The Sixteenth Century: 1485-1603 (Short Oxford History of the British Isles) (Patrick Collinson)
** TODO The Slave Community: Plantation Life in the Antebellum South (John W. Blassingame)
** TODO The South in Modern America: A Region at Odds (Dewey W. Grantham)
** TODO The Sun in the Church: Cathedrals as Solar Observatories (J.L. Heilbron)
** TODO The Swadeshi Movement In Bengal, 1903 1908 (Sumit Sarkar)
** TODO The Third Reich: Politics and Propaganda (David Welch)
** TODO The Tomb in Ancient Egypt: Royal and Private Sepulchres from the Early Dynastic Period to the Romans (Aidan Dodson)
** TODO The Trail of the Stanley Cup, Volume 1 (Charles L. Coleman)
** TODO The Twilight of Ancient Egypt: First Millennium B.C.E. (Karol Mysliwiec)
** TODO The Two Italies: Economic Relations Between The Norman Kingdom Of Sicily And The Northern Communes (David Abulafia)
** TODO The Typhoon Of War: Micronesian Experiences Of The Pacific War (Lin Poyer)
** TODO The Unquiet Western Front: Britain's Role in Literature and History (Brian Bond)
** TODO The Unredeemed Captive: A Family Story from Early America (John Putnam Demos)
** TODO The Venture of Islam, Vol 1: The Classical Age of Islam (Marshall G.S. Hodgson)
** TODO The Venture of Islam, Vol 2: The Expansion of Islam in the Middle Periods (Marshall G.S. Hodgson)
** TODO The Venture of Islam, Vol 3: The Gunpowder Empires and Modern Times (Marshall G.S. Hodgson)
** TODO The Village of Cannibals: Rage and Murder in France, 1870 (Alain Corbin)
** TODO The Witch-Hunt in Early Modern Europe (Brian P. Levack)
** TODO The Wolf: How One German Raider Terrorized the Allies in the Most Epic Voyage of WWI (Richard Guilliatt)
** TODO The World of Late Antiquity 150-750 (Peter R.L. Brown)
** TODO The Worlds of Christopher Columbus (William D. Phillips)
** TODO The Writing of Canadian History: Aspects of English-Canadian Historical Writing Since 1900 (Carl Berger)
** TODO The Wrong Hands: Popular Weapons Manuals and Their Historic Challenges to a Democratic Society (Ann Larabee)
** TODO The Zionist Idea: A Historical Analysis and Reader (Arthur Hertzberg)
** TODO Theology and the Scientific Imagination from the Middle Ages to the Seventeenth Century (Amos Funkenstein)
** TODO Things Fall Apart (The African Trilogy, #1) (Chinua Achebe)
** TODO Thinking with Demons: The Idea of Witchcraft in Early Modern Europe (Stuart Clark)
** TODO Third Axis, Fourth Ally: Romanian Armed Forces in the European War, 1941-1945 (Mark Axworthy)
** TODO Through The Jade Gate To Rome: A Study Of The Silk Routes During The Later Han Dynasty 1st To 2nd Centuries CE (John E. Hill)
** TODO Thundering Zeus: The Making of Hellenistic Bactria (Frank L. Holt)
** TODO Time Longer Than Rope: A Century of African American Activism, 1850-1950 (Charles M. Payne)
** TODO Toronto Workers Respond to Industrial Capitalism, 1867-1892 (Gregory S. Kealey)
** TODO Toward Defining the Prairies: Region, Culture, and History (Robert Wardhaugh)
** TODO Transformations in Slavery: A History of Slavery in Africa (Paul E. Lovejoy)
** TODO Transforming Labour: Women and Work in Post-War Canada (Joan Sangster)
** TODO Trojans and their neighbours (Trevor Bryce)
** TODO Troy Between Greece and Rome: Local Tradition and Imperial Power (Andrew Erskine)
** TODO Turkey: A Modern History (Erik-Jan Z\252rcher)
** TODO Two Worlds: First Meetings Between Maori and Europeans, 1642-1772 (Anne Salmond)
** TODO Unbecoming Citizens: Culture, Nationhood, and the Flight of Refugees from Bhutan (Michael James Hutt)
** TODO Uncertain Empire: American History and the Idea of the Cold War (Joel Isaac)
** TODO Unquiet Souls: Fourteenth-Century Saints and Their Religious Milieu (Richard Kieckefer)
** TODO Up South: Civil Rights and Black Power in Philadelphia (Matthew J. Countryman)
** TODO Us Taiwan Strait Policy: The Origins of Strategic Ambiguity (Dean P. Chen)
** TODO V Was for Victory: Politics and American Culture During World War II (John Morton Blum)
** TODO Venice: A Maritime Republic (Frederic C. Lane)
** TODO Venice: A New History (Thomas F. Madden)
** TODO Wanderings in West Africa (Richard Francis Burton)
** TODO War Without Fronts: The USA in Vietnam (Bernd Greiner)
** TODO War Without Garlands: Operation Barbarossa 1941-42 (Robert Kershaw)
** TODO War and Genocide: A Concise History of the Holocaust (Doris L. Bergen)
** TODO Wartime Women: Sex Roles, Family Relations, And The Status Of Women During World War Ii (Karen Anderson)
** TODO Way of Death: Merchant Capitalism and the Angolan Slave Trade, 1730-1830 (Joseph C. Miller)
** TODO Wealth of the Solomons: A History of a Pacific Archepelago, 1800-1978 (Judith A. Bennett)
** TODO What Is History? (Edward Hallett Carr)
** TODO Who Killed Canadian History? (J.L. Granatstein)
** TODO Who Owns Antiquity?: Museums and the Battle Over Our Ancient Heritage (James Cuno)
** TODO Who Owns History?: Rethinking the Past in a Changing World (Eric Foner)
** TODO Why Stalin's Soldiers Fought: The Red Army's Military Effectiveness in World War II (Roger R. Reese)
** TODO Witness to Transformation: Refugee Insights into North Korea (Marcus Noland)
** TODO Women's Letters: America from the Revolutionary War to the Present (Lisa Grunwald)
** TODO Working in Steel: The Early Years in Canada, 1883-1935 (Craig Heron)
** TODO Working-Class War: American Combat Soldiers and Vietnam (Christian G. Appy)
** TODO World Eras: West African Kingdoms 500-1590 (Pierre-Damien Mvuyekure)
** TODO Yugoslavia as History: Twice There Was a Country (John R. Lampe)
** TODO Yugoslavia: Death of a Nation (Laura Silber)
* KILL [#C] Dalloz (droit)
:PROPERTIES:
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:ARCHIVE_FILE: ~/code/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: KILL
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https://www-dalloz-bibliotheque-fr.bases-doc.univ-lorraine.fr/
Voir pour requête (sinon trop manuel...)
https://imanalytic.dalloz-bibliotheque.fr.bases-doc.univ-lorraine.fr/services/logevent.php?fct=Print¶m=%7B%22shopname%22%3A%22dallozbndpro%22%2C%22code%22%3A%22004294%22%2C%22number%22%3A%22222%22%2C%22pvgpuserid%22%3A%2233751%22%2C%22referer%22%3A%22https%3A//dallozbndpro-pvgpsla6-dalloz-bibliotheque-fr.bases-doc.univ-lorraine.fr/fr/pvPageH5B.asp%3Fpuc%3D004294%26nu%3D222%26pa%3D1%22%2C%22page%22%3A%224%7C5%7C6%7C7%7C296%7C299%22%7D
Parameters : (changer le nombre de pages)
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Dans firefox, erreur 404...
* KILL [#A] Collection U as PDF [53/101]
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-09 Thu 12:05
:ARCHIVE_FILE: ~/code/blog/notes/mam.org
:ARCHIVE_OLPATH: Upload/Cairn/Histoire
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:ARCHIVE_TODO: KILL
:END:
101 ouvrages
https://www-cairn-info.bases-doc.univ-lorraine.fr/liste-des-ouvrages.php?searchTermAccess=all&editeur=&collection=ARCO_U&discipline=3&orderby=titre&offset=100
** DONE [[https://www.cairn.info/citoyennete-republique-et-democratie-en-france--9782200294045.htm][Citoyenneté, République et Démocratie en France]]
** DONE [[https://www.cairn.info/croisades-et-orient-latin--9782200264987.htm][Croisades et Orient latin : XIe-XIVe siècle]]
** DONE [[https://www.cairn.info/droit-de-conquete-et-droits-des-indiens--9782200293055.htm][Droit de conquête et droits des Indiens]]
** DONE [[https://www.cairn.info/eglise-et-societe-en-occident--9782200355876.htm][Église et société en Occident]]
** DONE [[https://www.cairn.info/eglise-et-societe-en-occident-xiiie-xve-siecles--9782200267636.htm][Église et société en Occident]]
** DONE [[https://www.cairn.info/famille-et-societe-dans-le-monde-grec-et-en-italie--9782200625627.htm][Famille et société dans le monde grec et en Italie]]
** DONE [[https://www.cairn.info/film-et-histoire--9782200345570.htm][Film et histoire]]
** DONE [[https://www.cairn.info/geohistoire-de-la%20mondialisation--9782200602949.htm][Géohistoire de la mondialisation]]
** DONE [[https://www.cairn.info/histoire-culturelle-de-la-france-au-xixe-siecle--9782200353278.htm][Histoire culturelle de la France au XIXe siècle]]
** DONE [[https://www.cairn.info/histoire-de-l-art--9782200622350.htm][Histoire de l'art]]
** DONE [[https://www.cairn.info/histoire-de-l-autriche--9782200355906.htm][Histoire de l'Autriche]]
** DONE [[https://www.cairn.info/histoire-de-l-espagne-contemporaine--9782200614607.htm][Histoire de l'Espagne contemporaine]]
** DONE [[https://www.cairn.info/histoire-de-l-europe-de-l-est--9782200248994.htm][Histoire de l'Europe de l'Est]]
** DONE [[https://www.cairn.info/histoire-de-l-italie-depuis-1943-a-nos-jours--9782200262150.htm][Histoire de l'Italie depuis 1943 à nos jours]]
** DONE [[https://www.cairn.info/histoire-de-l-oceanie--9782200601300.htm][Histoire de l'Océanie]]
** DONE [[https://www.cairn.info/histoire-de-la-globalisation-financiere--9782200355388.htm][Histoire de la globalisation financière]]
** DONE [[https://www.cairn.info/histoire-de-la-presse-en-france--9782200613327.htm][Histoire de la presse en France]]
** DONE [[https://www.cairn.info/histoire-de-la-republique-populaire-de-chine--9782200614881.htm][Histoire de la République Populaire de Chine]]
** DONE [[https://www.cairn.info/histoire-des-bibliotheques--9782200616250.htm][Histoire des bibliothèques]]
** DONE [[https://www.cairn.info/histoire-des-etats-unis--9782200618094.htm][Histoire des États-Unis]]
** DONE [[https://www.cairn.info/histoire-des-pays-d-islam--9782200618421.htm][Histoire des pays d'Islam]]
** DONE [[https://www.cairn.info/histoire-des-sciences-epoque-moderne--9782200345211.htm][Histoire des sciences à l'époque moderne]]
** DONE [[https://www.cairn.info/histoire-du-christianisme-en-france--9782200290665.htm][Histoire du christianisme en France]]
** DONE [[https://www.cairn.info/histoire-du-livre-en-occident--9782200277512.htm][Histoire du livre en Occident]]
** DONE [[https://www.cairn.info/histoire-economique-de-l-afrique-tropicale--9782200602642.htm][Histoire économique de l'Afrique tropicale]]
** DONE [[https://www.cairn.info/histoire-politique-de-la-v-e-republique--9782200346935.htm][Histoire politique de la Ve République]]
** DONE [[https://www.cairn.info/histoire-romaine--9782200622909.htm][Histoire romaine]]
** DONE [[https://www.cairn.info/hommes-et-femmes-d-egypte-ive-siecle-av-n-e--9782200346454.htm][Hommes et femmes d’Égypte (IV]]
** DONE [[https://www.cairn.info/imperialisme-et-democratie-a-athenes--9782200269289.htm][Impérialisme et démocratie à Athènes]]
** DONE [[https://www.cairn.info/l-afrique-du-20-e-siecle-a-nos-jours--9782200285074.htm][L'Afrique du 20e siècle à nos jours]]
** DONE [[https://www.cairn.info/l-allemagne-de-1870-a-nos-jours--9782200285050.htm][L'Allemagne de 1870 à nos jours]]
** DONE [[https://www.cairn.info/l-amerique-iberique--9782200625641.htm][L'Amérique ibérique]]
** DONE [[https://www.cairn.info/l-anatolie-hellenistique--9782200268329.htm][L'Anatolie hellénistique]]
** DONE [[https://www.cairn.info/l-aristocratie-medievale--9782200262938.htm][L'aristocratie médiévale]]
** DONE [[https://www.cairn.info/l-armee-romaine--9782200276539.htm][L'armée romaine]]
** DONE [[https://www.cairn.info/education-physique-de-1945-a-nos-jours--9782200600686.htm][L'éducation physique de 1945 à nos jours]]
** DONE [[https://www.cairn.info/l-egypte-grecque-et-romaine--9782200262884.htm][L'Égypte grecque et romaine]]
** DONE [[https://www.cairn.info/l-empire-austro-hongrois--9782200248888.htm][L'Empire austro-hongrois]]
** DONE [[https://www.cairn.info/l-europe--9782200601386.htm][L'Europe]]
** TODO [[https://www.cairn.info/l-europe-au-19-e-siecle--9782200622565.htm][L'Europe au 19]]
** DONE [[https://www.cairn.info/l-europe-centrale-et-orientale--9782200602635.htm][L'Europe centrale et orientale]]
** DONE [[https://www.cairn.info/l-heritage-ambigu-de-la-colonisation--9782200281335.htm][L'héritage ambigu de la colonisation]]
** DONE [[https://www.cairn.info/l-histoire-immediate--9782200277390.htm][L'histoire immédiate]]
** DONE [[https://www.cairn.info/la-construction-de-l-europe--9782200353056.htm][La construction de l’Europe]]
** DONE [[https://www.cairn.info/la-culture-materielle-de-la-france--9782200286569.htm][La culture matérielle de la France]]
** DONE [[https://www.cairn.info/la-famille-en-france-a-l-epoque-moderne--9782200244170.htm][La famille en France à l'époque moderne]]
** DONE [[https://www.cairn.info/la-france-a-l-epoque-moderne--9782200626181.htm][La France à l'époque moderne]]
** DONE [[https://www.cairn.info/la-france-au-xix-e-siecle--9782200622596.htm][La France au XIX]]
** TODO [[https://www.cairn.info/la-france-et-l-europe-de-napoleon--9782200265335.htm][La France et l'Europe de Napoléon]]
** DONE [[https://www.cairn.info/la-grande-bretagne-et-le-monde--9782200244576.htm][La Grande-Bretagne et le monde]]
** TODO [[https://www.cairn.info/la-guerre-dans-le-monde-grec--9782200600297.htm][La guerre dans le monde grec]]
** TODO [[https://www.cairn.info/la-peninsule-iberique-aux-epoques-romaines--9782200268336.htm][La péninsule Ibérique aux époques romaines]]
** TODO [[https://www.cairn.info/la-republique-romaine-et-son-empire--9782200622053.htm][La République romaine et son empire]]
** DONE [[https://www.cairn.info/la-revolution-francaise--9782200627690.htm][La Révolution française]]
** DONE [[https://www.cairn.info/La-revolution-francaise-et-l-histoire-du-monde--9782200257699.htm][La Révolution française et l'histoire du monde]]
** TODO [[https://www.cairn.info/la-societe-du-haut-moyen-age--9782200265779.htm][La société du haut Moyen Âge]]
** TODO [[https://www.cairn.info/la-societe-francaise-de-1945-a-nos-jours--9782200613082.htm][La société française de 1945 à nos jours]]
** DONE [[https://www.cairn.info/le-christianisme-antique--9782200626914.htm][Le christianisme antique]]
** TODO [[https://www.cairn.info/le-christianisme-occidental-au-moyen-age--9782200251871.htm][Le christianisme occidental au Moyen Âge]]
** TODO [[https://www.cairn.info/le-maghreb-par-les-textes--9782200627294.htm][Le Maghreb par les textes]]
** TODO [[https://www.cairn.info/le-monde-grec-a-l-epoque-classique--9782200614713.htm][Le monde grec à l’époque classique]]
** TODO [[https://www.cairn.info/monde-hellenistique--9782200618179.htm][Le monde hellénistique]]
** DONE [[https://www.cairn.info/le-reich-allemand--9782200262334.htm][Le Reich allemand]]
** TODO [[https://www.cairn.info/saint-empire-1500-1800--9782200617639.htm][Le Saint-Empire]]
** TODO [[https://www.cairn.info/le-second-empire--9782200246075.htm][Le Second Empire]]
** TODO [[https://www.cairn.info/le-xx-e-siecle--9782200271534.htm][Le XX]]
** TODO [[https://www.cairn.info/les-accords-d-evian--9782200249076.htm][Les accords d'Evian (1962)]]
** TODO [[https://www.cairn.info/les-annees-1970--9782200623289.htm][Les années 1970]]
** TODO [[https://www.cairn.info/les-decolonisations-au-xxe-siecle--9782200249458.htm][Les décolonisations au XX]]
** TODO [[https://www.cairn.info/les-etats-unis-et-le-monde-au-19e-siecle--9782200266929.htm][Les États-Unis et le monde au 19e siècle]]
** TODO [[https://www.cairn.info/les-femmes-dans-la-france-moderne--9782200601584.htm][Les femmes dans la France moderne]]
** TODO [[https://www.cairn.info/les-femmes-actrices-histoire-de-france--9782200246549.htm][Les femmes, actrices de l’histoire France, de 1789 à nos jours]]
** DONE [[https://www.cairn.info/les-mondes-mediterraneens-au-moyen-age--9782200620288.htm][Les mondes méditerranéens au Moyen Âge]]
** TODO [[https://www.cairn.info/les-ouvriers-en-france--9782200277420.htm][Les ouvriers en France]]
** TODO [[https://www.cairn.info/les-perses-vus-par-les-grecs--9782200270353.htm][Les Perses vus par les Grecs]]
** TODO [[https://www.cairn.info/les-provinces-unies-a-l-epoque-moderne--9782200614515.htm][Les Provinces-Unies à l'époque moderne]]
** TODO [[https://www.cairn.info/les-relations-internationales-dans-l-europe-modern--9782200623005.htm][Les relations internationales dans l'Europe moderne]]
** TODO [[https://www.cairn.info/les-relations-internationales-depuis-1945--9782200622558.htm][Les relations internationales depuis 1945]]
** TODO [[https://www.cairn.info/les-societes-en-guerre--9782200265649.htm][Les sociétés en guerre]]
** TODO [[https://www.cairn.info/les-villes-portuaires-maritimes-dans-la-france--9782200278205.htm][Les villes portuaires maritimes dans la France moderne]]
** TODO [[https://www.cairn.info/l-affaire-dreyfus--9782200244163.htm][L’affaire Dreyfus]]
** TODO [[https://www.cairn.info/l-alimentation-en-europe-a-l-epoque-moderne--9782200244071.htm][L’alimentation en Europe à l’époque moderne]]
** TODO [[https://www.cairn.info/l-empire-colonial-francais-de-richelieu-a-napoleon--9782200354909.htm][L’empire colonial français de Richelieu à Napoléon]]
** TODO [[https://www.cairn.info/l-enseignement-de-l-histoire-en-france--9782200262754.htm][L’enseignement de l’Histoire en France]]
** TODO [[https://www.cairn.info/l-italie-fasciste--9782200614584.htm][L’Italie fasciste]]
** TODO [[https://www.cairn.info/manuel-d-archeologie--9782200266769.htm][Manuel d'archéologie]]
** TODO [[https://www.cairn.info/manuel-d-archeologie-medievale-et-moderne--9782200281397.htm][Manuel d'archéologie médiévale et moderne]]
** TODO [[https://www.cairn.info/manuel-d-histoire-globale--9782200278995.htm][Manuel d’histoire globale]]
** TODO [[https://www.cairn.info/naissance-de-litalie-contemporaine--9782200267926.htm][Naissance de l'Italie contemporaine]]
** TODO [[https://www.cairn.info/paysans-et-seigneurs-au-moyen-age--9782200618162.htm][Paysans et seigneurs au Moyen-Age]]
** TODO [[https://www.cairn.info/petite-histoire-de-la-france--9782200285128.htm][Petite histoire de la France]]
** TODO [[https://www.cairn.info/pouvoir-et-religion-en-europe--9782200623463.htm][Pouvoir et religion en Europe]]
** TODO [[https://www.cairn.info/pouvoir-royal-et-institutions-dans-la-france-moder--9782200613075.htm][Pouvoir royal et institutions dans la France moderne]]
** TODO [[https://www.cairn.info/precis-d-histoire-europeenne--9782200601188.htm][Précis d'histoire européenne]]
** TODO [[https://www.cairn.info/revoltes-et-repressions-dans-la-france-moderne--9782200274900.htm][Révoltes et répressions dans la France moderne]]
** TODO [[https://www.cairn.info/rome-et-le-monde-provincial--9782200249526.htm][Rome et le monde provincial]]
** TODO [[https://www.cairn.info/rome-paysage-urbain-et-ideologie--9782200263843.htm][Rome. Paysage urbain et idéologie]]
** TODO [[https://www.cairn.info/royaute-et-ideologie-au-moyen-age--9782200249212.htm][Royauté et idéologie au Moyen Âge]]
** TODO [[https://www.cairn.info/sparte--9782200618148.htm][Sparte]]
** TODO [[https://www.cairn.info/un-siecle-d-histoire-culturelle-en-france--9782200286637.htm][Un siècle d'histoire culturelle en France]]
** TODO [[https://www.cairn.info/une-histoire-culturelle-des-etats-unis--9782200278588.htm][Une histoire culturelle des États-Unis]]
* DONE Ajout Biblio
DEADLINE: <2021-09-16 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-16 Thu 12:01
:ARCHIVE_FILE: ~/code/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Uploader canada
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
panel-bibliographie mais pas de découpe text
* TODO Regénérer autres epub
DEADLINE: <2021-09-17 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-25 Sat 08:17
:ARCHIVE_FILE: ~/code/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Corriger layout biblio
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
* DONE Ajouter présentation
* DONE Corriger span class pour siècle
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-25 Sat 08:17
:ARCHIVE_FILE: ~/code/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn/Version ebook
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
Cf 1 siècle d'histoire culturelle en France
* DONE Version ebook
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-25 Sat 08:17
:ARCHIVE_FILE: ~/code/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
* DONE Passer tout en Text
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-25 Sat 08:17
:ARCHIVE_FILE: ~/code/blog/notes/mam.org
:ARCHIVE_OLPATH: Script/Cairn
:ARCHIVE_CATEGORY: mam
:ARCHIVE_TODO: DONE
:END:
# -*- mode: org -*-
Archived entries from file /usr/home/alex/code/blog/notes/music.org
* DONE Vol. 01 Sacred Cantatas
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-05 Sun 11:37
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/music.org
:ARCHIVE_OLPATH: Bach 2000
:ARCHIVE_CATEGORY: music
:ARCHIVE_TODO: DONE
:END:
** DONE CD 01
** DONE CD 02
** DONE CD 03
** DONE CD 04
** DONE CD 05
** DONE CD 06
** DONE CD 07
** DONE CD 08
** DONE CD 09
** DONE CD 10
** DONE CD 11
** DONE CD 12
** DONE CD 13
** DONE CD 14
** DONE CD 15
#+TITLE: Papers
* Math :math:
** TOREAD Reinhart, A. (): Statistics done wrong :stats:
:PROPERTIES:
:Custom_ID: statisticsdonewrong
:END:
L
** TOREAD Knill, O. (2018): Some fundamental theorems in mathematics :math:
:PROPERTIES:
:Custom_ID: knill18:some_fundam_theor_mathem
:END:
** TOREAD Greenland, S., Senn, S. J., Rothman, K. J., Carlin, J. B., Poole, C., Goodman, S. N., & Altman, D. G. (2016): Statistical tests, p values, confidence intervals, and power: a guide to misinterpretations :math:stats:
:PROPERTIES:
:Custom_ID: greenland-2016-p-values
:END:
** TOREAD Fong, B., & Spivak, D. I. (2018): Seven sketches in compositionality: an invitation to applied category theory :book:math:
:PROPERTIES:
:Custom_ID: fong18_seven_sketc_compos
:END:
* CS
** Inpainting :maths:
** TOREAD Amsterdam, V. U. (2018): Machine learning course :course:
:PROPERTIES:
:Custom_ID: machinelearningVUUniv2018
:END:
** TOREAD Steffen, J. H. (2008): Optimal boarding method for airline passengers
:PROPERTIES:
:Custom_ID: steffen08_optim_board_method_airlin_passen
:END:
* Physics :physics:
** TOREAD Maldacena, J. (2015): The symmetry and simplicity of the laws of physics and the higgs boson
:PROPERTIES:
:Custom_ID: maldacena2015symmetry
:END:
* Medecine :medecine:
** TOREAD Rudnicka, A. R. (2005): 2. essential medical statistics (2nd edn). betty r. kirkwood and jonathan a. c. sterne, blackwell science, oxford, 2003. no. of pages: 512. price: £22.95. isbn 0-86542-871-9
:PROPERTIES:
:Custom_ID: rudnicka05
:END:
Seems to answer my questions about stats in med school
** DONE Fang, Y., Zhang, H., Xie, J., Lin, M., Ying, L., Pang, P., & Ji, W. (2020): Sensitivity of chest ct for covid-19: comparison to rt-pcr :infectious::covid19:
** TOREAD Thomas, D. L. (2019): Global elimination of chronic hepatitis :infectious:
:PROPERTIES:
:Custom_ID: thomas19_global_elimin_chron_hepat
:END:
** TOREAD Grenfell, B. T., Bjørnstad, O. N., & Finkenstädt, B. F. (2002): DYNAMICS OF MEASLES EPIDEMICS: SCALING NOISE, DETERMINISM, AND PREDICTABILITY WITH THE TSIR MODEL :infectious:modeling
:PROPERTIES:
:Custom_ID: Grenfell_2002
:END:
Technique++ : modélisation stochastique
** TOREAD Jaulhac, B., Saunier, A., Caumes, E., ouiller, K., Gehanno, J., Rabaud, C., Perrot, S., … (2019): Lyme borreliosis and other tick-borne diseases. guidelines from the french scientific societies (ii). biological diagnosis, treatment, persistent symptoms after documented or suspected lyme borreliosis :infectious:
:PROPERTIES:
:Custom_ID: jaulhac19_lyme_borrel_other_tick_borne_diseas
:END:
Dernières recos sur Lyme
** TOREAD Figoni, J., Chirouze, C., Hansmann, Y., Lemogne, C., Hentgen, V., Saunier, A., Bouiller, K., … (2019): Lyme borreliosis and other tick-borne diseases. guidelines from the french scientific societies (i): prevention, epidemiology, diagnosis :infectious:
:PROPERTIES:
:Custom_ID: figoni19_lyme_borrel_other_tick_borne_diseas
:END:
Dernières recos sur Lyme
** TOREAD Khuong, T. M., Wang, Q., Manion, J., Oyston, L. J., Lau, M., Towler, H., Lin, Y. Q., … (2019): Nerve injury drives a heightened state of vigilance and neuropathic sensitization in drosophila :animals
* :PROPERTIES:
* :Custom_ID: khuong19_nerve_injur_drives_heigh_state
* :END:
** TOREAD Goupil, B., Fr\'ed\'eric Balusson, Naudet, F., Esvan, M., Bastian, B., Chapron, A., & Frouard, P. (2019): Association between gifts from pharmaceutical companies to french general practitioners and their drug prescribing patterns in 2016: retrospective study using the french transparency in healthcare and national health data system databases medecine:
:PROPERTIES:
:Custom_ID: goupil19_assoc_between_gifts_from_pharm
:END:
** DONE Doremalen, N. v., Bushmaker, T., Morris, D. H., Holbrook, M. G., Gamble, A., Williamson, B. N., Tamin, A., … (2020): Aerosol and surface stability of sars-cov-2 as compared with sars-cov-1 :infectious:covid19:
:PROPERTIES:
:Custom_ID: doremalen20_aeros_surfac_stabil_sars_cov
:END:
Viability : plastic + stainless steel = 72h, cardboard = 48h
* Other
** SKIMMED Hausfather, Z., Drake, H. F., Abbott, T., & Schmidt, G. A. (2019): Evaluating the performance of past climate model projections :climate:
:PROPERTIES:
:Custom_ID: hausfather19_evaluat_perfor_past_climat_model_projec
:END:
Comparaison de modèles de climat contre des observations pour la température
moyenne : même des vieux modèles des années 70 sont précis.
** TOREAD Keehn, R. J. J., Iversen, J. R., Schulz, I., & Patel, A. D. (2019): Spontaneity and diversity of movement to music are not uniquely human animals:
:PROPERTIES:
:Custom_ID: keehn19_spont_diver_movem_to_music
:END:
** SKIMMED Mueller, P. A., & Oppenheimer, D. M. (2014): The pen is mightier than the keyboard
:PROPERTIES:
:Custom_ID: mueller14_pen_is_might_than_keyboar
:END:
Notes papier + études > notes sans étude, PC avec étude et PC sans études
Mais ça ne montre pas que les notes PC sont moins bonnes ?
Par contre, les notes sous PC sont plus copiés-collées donc moins de réflexion
** TOREAD Steffen, J. H., & Hotchkiss, J. (2012): Experimental test of airplane boarding methods
:PROPERTIES:
:Custom_ID: steffen12_exper_test_airpl_board_method
:END:
** SKIMMED Dunson, D. B. (2002): Changes with age in the level and duration of fertility in the menstrual cycle :gyneco:
:PROPERTIES:
:Custom_ID: dunson02_chang_with_age_level_durat
:END:
Donne une idée de la baisse de la fertilité après 35 ans (-50% ??). Mais ils
mentionnent un grand intervalle interquatile... Sur la figure : ~50% -> ~30%
** SKIMMED Gnoth, C. (2003): Time to pregnancy: results of the german prospective study and impact on the management of infertility :gyneco:
:PROPERTIES:
:Custom_ID: gnoth03_time_to_pregn
:END:
Donne une idée du temps pour concevoir : 92% au bout de 12 cycles pour tous les
couples de l'étude.
:PROPERTIES:
:Custom_ID: fang20_sensit_chest_ct_covid
:END:
Sensitivity of RT-PCR on swab = 71% vs 98 for chest CT-scan (51 patients)
# -*- mode: org -*-
Archived entries from file /home/alex/projects/journal/revisions.org
* Anglais
:PROPERTIES:
:ARCHIVE_TIME: 2019-02-06 Wed 21:42
:ARCHIVE_FILE: ~/projects/journal/revisions.org
:ARCHIVE_CATEGORY: revisions
:END:
** DONE Trouver case report avan 31/10
DEADLINE: <2018-10-31 Wed>
** DONE Oral à partir du 22/01 (être prêt pour 22/01)
DEADLINE: <2019-01-22 Tue>
Archived entries from file /home/alex/projects/journal/revisions.org
* P2
:PROPERTIES:
:ARCHIVE_TIME: 2019-02-06 Wed 21:42
:ARCHIVE_FILE: ~/projects/journal/revisions.org
:ARCHIVE_CATEGORY: revisions
:END:
** CANCELLED Roneos P2
*** TODO Pneumo 1
*** TODO Pneumo 2
*** TODO Cardio 1
*** TODO Cardio 2
** LU Lecture accélérée de l'ECG
** CANCELLED Physiologie Humaine
** LU Nutrition FGSM2-3
** TODO Sémiologie
*** TODO Chapitres
Survolé cardio et digestif
*** TODO Check-up
Apprentissage en cours
* Archive
** DONE Superfiches endocrino
DEADLINE: <2019-02-11 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-22 Wed 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Endocrino
:ARCHIVE_CATEGORY: endocrino
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: A1 semestre1
:END:
** DONE Arche : tout transférer sur Arche
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-27 Mon 11:15
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Stage chirurgie orthopédique
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:END:
*** TODO 3/9 : Chabot (AM)
*** TODO 4/09 : Chabot (matin, AM)
*** TODO 5/9 : Chabot (AM)
*** DONE 6/9 : Sadoul (matin)
*** TODO 7/9 [/]
**** TODO Chabot (matin),
**** DONE Sadoul (AM)
*** TODO 10/9
**** REFUS Julière (matin)
**** TODO Chaouat (AM)
*** DONE 11/9 : Whal (matin)
*** DONE 12/09 : Gierd (matin), Chabot (AM)
*** DONE 13/9 : Chaouat (matin)
*** TODO 17/09 : matin (à publier)
*** TODO Zuhly : récupérer cours
** Stage chirurgie orthopédique
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-27 Mon 11:16
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_CATEGORY: revisions
:END:
*** DONE Lecture : préparer stage
**** DONE Biblio traumato :ATTACH:
:PROPERTIES:
:Attachments: bible-traumatologie-adulte.pdf
:ID: cfe45470-13c0-49e0-8c69-4c479640149b
:END:
https://www.saintluc.be/professionnels/services/orthopedie/bible-traumatologie-adulte.pdf
Classification de garden,
**** DONE Traitements antalgiques (Medline douleur)
**** DONE Autres
GALOIS - Fractures extrémité supérieure fémur
*** DONE Examen clinique locomoteur
CLOSED: [2019-05-27 Mon 11:15]
** CANCELLED Lire mikbook
:PROPERTIES:
:ARCHIVE_TIME: 2019-06-10 Mon 22:08
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: ORL
:ARCHIVE_CATEGORY: orl
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: A1 semestre2
:END:
** DONE Lire fiches collège
CLOSED: [2019-06-16 Sun 12:01] DEADLINE: <2019-06-13 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2019-07-01 Mon 16:49
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: ORL
:ARCHIVE_CATEGORY: orl
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: A1 semestre2
:END:
:LOGBOOK:
CLOCK: [2019-06-16 Sun 10:43]--[2019-06-16 Sun 11:15] => 0:32
CLOCK: [2019-06-15 Sat 22:15]--[2019-06-15 Sat 23:05] => 0:50
CLOCK: [2019-06-15 Sat 21:01]--[2019-06-15 Sat 21:11] => 0:10
CLOCK: [2019-06-15 Sat 12:06]--[2019-06-15 Sat 12:26] => 0:20
CLOCK: [2019-06-13 Thu 14:51]--[2019-06-13 Thu 15:10] => 0:19
CLOCK: [2019-06-13 Thu 13:13]--[2019-06-13 Thu 13:19] => 0:06
CLOCK: [2019-06-13 Thu 11:09]--[2019-06-13 Thu 11:25] => 0:16
CLOCK: [2019-06-09 Sun 18:49]--[2019-06-09 Sun 19:01] => 0:12
CLOCK: [2019-06-09 Sun 18:03]--[2019-06-09 Sun 18:20] => 0:17
CLOCK: [2019-06-08 Sat 12:32]--[2019-06-08 Sat 12:42] => 0:10
CLOCK: [2019-04-29 Mon 21:34]--[2019-04-29 Mon 22:17] => 0:43
CLOCK: [2019-04-29 Mon 10:39]--[2019-04-29 Mon 11:28] => 0:49
CLOCK: [2019-04-28 Sun 23:24]--[2019-04-28 Sun 23:32] => 0:08
:END:
-> tumeurs (en cours)
** CANCELLED Ficher référentiel
:PROPERTIES:
:ARCHIVE_TIME: 2019-07-01 Mon 16:49
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: ORL
:ARCHIVE_CATEGORY: orl
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: A1 semestre2
:END:
** CANCELLED Ficher référentiel
CLOSED: [2019-05-20 Mon 22:33]
:PROPERTIES:
:ARCHIVE_TIME: 2019-07-01 Mon 16:50
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Chirurgie maxillo-faciale
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: A1 semestre2
:END:
** DONE Résumé collège
:PROPERTIES:
:ARCHIVE_TIME: 2019-07-01 Mon 16:50
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Chirurgie maxillo-faciale
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: A1 semestre2
:END:
** DONE Mémoire généraliste
CLOSED: [2019-07-02 Tue 12:00] DEADLINE: <2019-06-23 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2019-07-02 Tue 12:00
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Stages
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:END:
*** DONE 1ere version envoyée
CLOSED: [2019-06-26 Wed 13:46]
* CANCELLED CC Masson cardio [24/24] + QI [/85]
CLOSED: [2019-05-31 Fri 14:06]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Cardiologie
:ARCHIVE_CATEGORY: cardiologie
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 cardio
:END:
:LOGBOOK:
CLOCK: [2019-05-03 Fri 10:36]--[2019-05-03 Fri 11:10] => 0:34
CLOCK: [2019-04-30 Tue 18:43]--[2019-04-30 Tue 19:05] => 0:22
CLOCK: [2019-04-30 Tue 18:07]--[2019-04-30 Tue 18:19] => 0:12
CLOCK: [2019-04-30 Tue 14:35]--[2019-04-30 Tue 14:55] => 0:20
CLOCK: [2019-04-30 Tue 13:00]--[2019-04-30 Tue 14:19] => 1:19
CLOCK: [2019-04-30 Tue 11:18]--[2019-04-30 Tue 11:41] => 0:23
CLOCK: [2019-04-23 Tue 22:15]--[2019-04-23 Tue 22:32] => 0:17
CLOCK: [2019-04-23 Tue 21:36]--[2019-04-23 Tue 21:51] => 0:15
CLOCK: [2019-04-22 Mon 23:30]--[2019-04-22 Mon 23:53] => 0:23
CLOCK: [2019-04-22 Mon 22:47]--[2019-04-22 Mon 23:14] => 0:27
CLOCK: [2019-04-22 Mon 22:15]--[2019-04-22 Mon 22:28] => 0:13
CLOCK: [2019-04-16 Tue 21:33]--[2019-04-16 Tue 21:40] => 0:07
CLOCK: [2019-04-16 Tue 18:22]--[2019-04-16 Tue 18:42] => 0:20
CLOCK: [2019-04-16 Tue 17:26]--[2019-04-16 Tue 18:05] => 0:39
CLOCK: [2019-04-16 Tue 16:26]--[2019-04-16 Tue 16:46] => 0:20
:END:
* CANCELLED Lire ECNi
CLOSED: [2019-06-01 Sat 23:16] DEADLINE: <2019-05-30 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Cardiologie
:ARCHIVE_CATEGORY: cardiologie
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 cardio
:END:
:LOGBOOK:
CLOCK: [2019-06-01 Sat 12:35]--[2019-06-01 Sat 13:02] => 0:27
:END:
* DONE Conférence cardio
CLOSED: [2019-06-01 Sat 23:14] DEADLINE: <2019-05-31 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Cardiologie
:ARCHIVE_CATEGORY: cardiologie
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 cardio
:END:
:LOGBOOK:
CLOCK: [2019-06-01 Sat 22:33]--[2019-06-01 Sat 23:14] => 0:41
CLOCK: [2019-06-01 Sat 21:14]--[2019-06-01 Sat 21:59] => 0:45
:END:
* DONE Annales
CLOSED: [2019-06-02 Sun 12:11]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Cardiologie
:ARCHIVE_CATEGORY: cardiologie
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 cardio
:END:
:LOGBOOK:
CLOCK: [2019-06-02 Sun 10:03]--[2019-06-02 Sun 12:10] => 2:07
CLOCK: [2019-06-01 Sat 16:49]--[2019-06-01 Sat 19:35] => 2:46
CLOCK: [2019-06-01 Sat 14:48]--[2019-06-01 Sat 16:21] => 1:33
CLOCK: [2019-06-01 Sat 14:16]--[2019-06-01 Sat 14:34] => 0:18
CLOCK: [2019-06-01 Sat 13:02]--[2019-06-01 Sat 13:12] => 0:10
CLOCK: [2019-06-01 Sat 09:22]--[2019-06-01 Sat 09:58] => 0:36
CLOCK: [2019-05-31 Fri 22:01]--[2019-06-01 Sat 00:12] => 2:11
CLOCK: [2019-05-31 Fri 18:34]--[2019-05-31 Fri 18:43] => 0:09
CLOCK: [2019-05-31 Fri 17:03]--[2019-05-31 Fri 18:05] => 1:02
CLOCK: [2019-05-31 Fri 14:40]--[2019-05-31 Fri 15:00] => 0:20
CLOCK: [2019-05-31 Fri 14:07]--[2019-05-31 Fri 14:30] => 0:23
CLOCK: [2019-05-20 Mon 18:04]--[2019-05-20 Mon 19:56] => 1:52
CLOCK: [2019-05-20 Mon 11:16]--[2019-05-20 Mon 12:32] => 1:16
CLOCK: [2019-05-19 Sun 23:20]--[2019-05-20 Mon 00:05] => 0:45
CLOCK: [2019-05-19 Sun 21:48]--[2019-05-19 Sun 23:00] => 1:12
CLOCK: [2019-05-19 Sun 19:20]--[2019-05-19 Sun 19:44] => 0:24
CLOCK: [2019-05-19 Sun 17:23]--[2019-05-19 Sun 18:07] => 0:44
CLOCK: [2019-05-19 Sun 15:23]--[2019-05-19 Sun 16:36] => 1:13
CLOCK: [2019-05-19 Sun 11:51]--[2019-05-19 Sun 13:01] => 1:10
CLOCK: [2019-05-18 Sat 23:12]--[2019-05-18 Sat 23:57] => 0:45
CLOCK: [2019-05-18 Sat 21:41]--[2019-05-18 Sat 22:00] => 0:19
CLOCK: [2019-05-18 Sat 19:09]--[2019-05-18 Sat 20:11] => 1:02
CLOCK: [2019-05-18 Sat 15:03]--[2019-05-18 Sat 15:52] => 0:49
CLOCK: [2019-05-18 Sat 11:25]--[2019-05-18 Sat 13:22] => 1:57
CLOCK: [2019-05-18 Sat 00:09]--[2019-05-18 Sat 00:37] => 0:28
CLOCK: [2019-05-17 Fri 22:53]--[2019-05-17 Fri 23:23] => 0:30
CLOCK: [2019-05-17 Fri 18:58]--[2019-05-17 Fri 19:25] => 0:27
CLOCK: [2019-05-17 Fri 15:02]--[2019-05-17 Fri 16:46] => 1:44
CLOCK: [2019-05-17 Fri 14:11]--[2019-05-17 Fri 14:49] => 0:38
CLOCK: [2019-05-17 Fri 12:39]--[2019-05-17 Fri 13:00] => 0:21
CLOCK: [2019-05-16 Thu 16:50]--[2019-05-16 Thu 19:20] => 2:30
CLOCK: [2019-05-16 Thu 15:53]--[2019-05-16 Thu 16:05] => 0:12
CLOCK: [2019-05-16 Thu 15:18]--[2019-05-16 Thu 15:41] => 0:23
:END:
** DONE 2015-2016
CLOSED: [2019-05-20 Mon 19:56] DEADLINE: <2019-05-17 Fri> SCHEDULED: <2019-05-16 Thu>
*** DONE Janvier 2015
CLOSED: [2019-05-17 Fri 23:01]
*** DONE Octobre 2015
CLOSED: [2019-05-18 Sat 23:12]
*** DONE Janvier 2016
CLOSED: [2019-05-19 Sun 22:08]
:LOGBOOK:
- State "DONE" from "TODO" [2019-05-19 Sun 22:08]
:END:
*** DONE Juin 2016
CLOSED: [2019-05-20 Mon 19:56]
** DONE 2017-2018
CLOSED: [2019-06-01 Sat 19:36] SCHEDULED: <2019-05-30 Thu> DEADLINE: <2019-05-31 Fri>
*** CANCELLED Janvier 2017
CLOSED: [2019-07-04 Thu 10:07]
*** CANCELLED Juin 2017
CLOSED: [2019-05-31 Fri 14:08]
*** DONE Janvier 2018
CLOSED: [2019-06-01 Sat 19:35]
*** DONE Juin 2018
CLOSED: [2019-06-01 Sat 19:35]
** DONE 2019
CLOSED: [2019-06-02 Sun 12:11]
* DONE CC Masson endocrino [31/31]
CLOSED: [2019-05-03 Fri 00:01]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Endocrino
:ARCHIVE_CATEGORY: endocrino
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 endocrino
:END:
:LOGBOOK:
CLOCK: [2019-05-02 Thu 23:39]--[2019-05-03 Fri 00:01] => 0:22
CLOCK: [2019-05-02 Thu 22:42]--[2019-05-02 Thu 23:28] => 0:46
CLOCK: [2019-05-02 Thu 18:59]--[2019-05-02 Thu 20:02] => 1:03
CLOCK: [2019-05-02 Thu 18:00]--[2019-05-02 Thu 18:16] => 0:16
CLOCK: [2019-05-02 Thu 17:40]--[2019-05-02 Thu 17:51] => 0:11
CLOCK: [2019-05-02 Thu 16:41]--[2019-05-02 Thu 16:59] => 0:18
CLOCK: [2019-05-02 Thu 15:02]--[2019-05-02 Thu 16:41] => 1:39
CLOCK: [2019-05-02 Thu 14:34]--[2019-05-02 Thu 14:42] => 0:08
CLOCK: [2019-04-28 Sun 22:22]--[2019-04-28 Sun 23:07] => 0:45
CLOCK: [2019-04-28 Sun 20:52]--[2019-04-28 Sun 21:11] => 0:19
CLOCK: [2019-04-28 Sun 19:50]--[2019-04-28 Sun 19:54] => 0:04
CLOCK: [2019-04-28 Sun 18:22]--[2019-04-28 Sun 18:50] => 0:28
CLOCK: [2019-04-28 Sun 16:29]--[2019-04-28 Sun 17:45] => 1:16
CLOCK: [2019-04-28 Sun 13:48]--[2019-04-28 Sun 14:03] => 0:15
CLOCK: [2019-04-28 Sun 12:49]--[2019-04-28 Sun 13:03] => 0:14
:END:
* CANCELLED Lire ECNi
CLOSED: [2019-06-02 Sun 18:13] DEADLINE: <2019-06-01 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Endocrino
:ARCHIVE_CATEGORY: endocrino
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 endocrino
:END:
* CANCELLED Conférence
CLOSED: [2019-06-06 Thu 10:29] DEADLINE: <2019-06-02 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Endocrino
:ARCHIVE_CATEGORY: endocrino
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 endocrino
:END:
* DONE Annales
CLOSED: [2019-06-06 Thu 10:29]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Endocrino
:ARCHIVE_CATEGORY: endocrino
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 endocrino
:END:
:LOGBOOK:
CLOCK: [2019-06-02 Sun 18:14]--[2019-06-02 Sun 19:04] => 0:50
CLOCK: [2019-06-02 Sun 16:19]--[2019-06-02 Sun 16:59] => 0:40
CLOCK: [2019-05-26 Sun 23:50]--[2019-05-27 Mon 00:52] => 1:02
CLOCK: [2019-05-26 Sun 22:47]--[2019-05-26 Sun 23:15] => 0:28
CLOCK: [2019-05-26 Sun 19:30]--[2019-05-26 Sun 19:40] => 0:10
CLOCK: [2019-05-26 Sun 18:50]--[2019-05-26 Sun 19:10] => 0:20
CLOCK: [2019-05-26 Sun 15:56]--[2019-05-26 Sun 17:27] => 1:31
CLOCK: [2019-05-26 Sun 14:17]--[2019-05-26 Sun 14:44] => 0:27
CLOCK: [2019-05-26 Sun 11:52]--[2019-05-26 Sun 12:28] => 0:36
CLOCK: [2019-05-25 Sat 23:53]--[2019-05-26 Sun 01:10] => 1:17
CLOCK: [2019-05-25 Sat 22:44]--[2019-05-25 Sat 23:32] => 0:48
CLOCK: [2019-05-25 Sat 19:39]--[2019-05-25 Sat 20:37] => 0:58
CLOCK: [2019-05-25 Sat 16:36]--[2019-05-25 Sat 18:12] => 1:36
CLOCK: [2019-05-25 Sat 13:47]--[2019-05-25 Sat 14:30] => 0:43
CLOCK: [2019-05-25 Sat 10:42]--[2019-05-25 Sat 11:43] => 1:01
CLOCK: [2019-05-25 Sat 00:40]--[2019-05-25 Sat 00:41] => 0:01
:END:
** DONE 2015-2016
CLOSED: [2019-05-27 Mon 10:49] DEADLINE: <2019-05-25 Sat> SCHEDULED: <2019-05-24 Fri>
*** DONE Janvier 2015
CLOSED: [2019-05-25 Sat 20:57]
*** DONE Juin 2015
CLOSED: [2019-05-26 Sun 18:42]
*** DONE Janvier 2016
CLOSED: [2019-05-26 Sun 18:42]
*** DONE Juin 2016
CLOSED: [2019-05-27 Mon 00:00]
** DONE 2017-2018
CLOSED: [2019-06-06 Thu 10:29] DEADLINE: <2019-06-02 Sun>
*** DONE Janvier 2017
CLOSED: [2019-06-02 Sun 19:04]
*** CANCELLED Juin 2017
CLOSED: [2019-06-02 Sun 16:06]
*** CANCELLED Janvier 2018
CLOSED: [2019-07-02 Tue 14:30]
*** CANCELLED Juin 2018
CLOSED: [2019-07-02 Tue 14:30]
** CANCELLED 2019
CLOSED: [2019-06-06 Thu 10:29] DEADLINE: <2019-06-03 Mon>
* DONE CC [31/31] et QI [75/101] du collège
CLOSED: [2019-05-09 Thu 11:52] DEADLINE: <2019-05-08 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
:LOGBOOK:
- State "DONE" from "TODO" [2019-05-09 Thu 11:52]
CLOCK: [2019-05-09 Thu 11:23]--[2019-05-09 Thu 11:52] => 0:29
CLOCK: [2019-04-19 Fri 10:41]--[2019-04-19 Fri 11:42] => 1:01
CLOCK: [2019-04-18 Thu 22:51]--[2019-04-18 Thu 22:59] => 0:08
CLOCK: [2019-04-18 Thu 21:34]--[2019-04-18 Thu 21:49] => 0:15
CLOCK: [2019-04-18 Thu 21:12]--[2019-04-18 Thu 21:15] => 0:03
CLOCK: [2019-04-18 Thu 16:24]--[2019-04-18 Thu 16:49] => 0:25
CLOCK: [2019-04-18 Thu 15:01]--[2019-04-18 Thu 15:44] => 0:43
CLOCK: [2019-04-18 Thu 14:16]--[2019-04-18 Thu 14:40] => 0:24
CLOCK: [2019-04-18 Thu 11:50]--[2019-04-18 Thu 12:20] => 0:30
CLOCK: [2019-04-18 Thu 10:49]--[2019-04-18 Thu 11:00] => 0:11
CLOCK: [2019-04-17 Wed 22:44]--[2019-04-17 Wed 23:15] => 0:31
CLOCK: [2019-04-17 Wed 14:47]--[2019-04-17 Wed 15:47] => 1:00
CLOCK: [2019-04-17 Wed 11:36]--[2019-04-17 Wed 12:22] => 0:46
CLOCK: [2019-04-17 Wed 11:14]--[2019-04-17 Wed 11:21] => 0:07
CLOCK: [2019-04-16 Tue 22:41]--[2019-04-16 Tue 23:25] => 0:44
:END:
* DONE Conférence [2/2]
CLOSED: [2019-05-11 Sat 14:47] SCHEDULED: <2019-05-08 Wed> DEADLINE: <2019-05-08 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
:LOGBOOK:
- State "DONE" from "TODO" [2019-05-11 Sat 14:47]
CLOCK: [2019-05-11 Sat 13:40]--[2019-05-11 Sat 14:10] => 0:30
CLOCK: [2019-05-11 Sat 12:11]--[2019-05-11 Sat 13:28] => 1:17
CLOCK: [2019-05-11 Sat 10:15]--[2019-05-11 Sat 10:48] => 0:33
CLOCK: [2019-05-11 Sat 09:44]--[2019-05-11 Sat 10:02] => 0:18
CLOCK: [2019-05-10 Fri 20:30]--[2019-05-10 Fri 20:33] => 0:03
CLOCK: [2019-05-10 Fri 16:43]--[2019-05-10 Fri 17:12] => 0:29
CLOCK: [2019-05-10 Fri 14:24]--[2019-05-10 Fri 15:00] => 0:36
:END:
* CANCELLED Annales
CLOSED: [2019-05-20 Mon 22:34]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
:LOGBOOK:
CLOCK: [2019-05-11 Sat 22:27]--[2019-05-11 Sat 23:22] => 0:55
CLOCK: [2019-05-11 Sat 18:18]--[2019-05-11 Sat 18:55] => 0:37
CLOCK: [2019-05-11 Sat 17:41]--[2019-05-11 Sat 17:58] => 0:17
CLOCK: [2019-05-10 Fri 12:00]--[2019-05-10 Fri 12:20] => 0:20
CLOCK: [2019-05-10 Fri 09:47]--[2019-05-10 Fri 11:12] => 1:25
CLOCK: [2019-05-09 Thu 21:52]--[2019-05-09 Thu 23:52] => 2:00
CLOCK: [2019-05-09 Thu 18:26]--[2019-05-09 Thu 19:10] => 0:44
CLOCK: [2019-05-09 Thu 14:21]--[2019-05-09 Thu 16:24] => 2:03
CLOCK: [2019-05-09 Thu 12:22]--[2019-05-09 Thu 12:59] => 0:37
CLOCK: [2019-05-08 Wed 21:45]--[2019-05-08 Wed 23:39] => 1:54
CLOCK: [2019-05-08 Wed 19:38]--[2019-05-08 Wed 20:21] => 0:43
CLOCK: [2019-05-08 Wed 18:34]--[2019-05-08 Wed 19:30] => 0:56
CLOCK: [2019-05-08 Wed 16:31]--[2019-05-08 Wed 16:52] => 0:21
:END:
** CANCELLED 2015 [/2]
** CANCELLED 2016 [1/2]
** DONE 2017 [2/2]
CLOSED: [2019-05-11 Sat 17:41]
:LOGBOOK:
- State "DONE" from "TODO" [2019-05-11 Sat 17:41]
:END:
Aout en cours
** DONE 2018 [2/2]
CLOSED: [2019-05-09 Thu 16:24]
:LOGBOOK:
- State "DONE" from "TODO" [2019-05-09 Thu 16:24]
:END:
* CANCELLED ECNI tout en un
CLOSED: [2019-07-04 Thu 10:07]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
* CANCELLED 2015 [/2]
CLOSED: [2019-07-04 Thu 10:07]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro/College
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
* CANCELLED 2016 [/2]
CLOSED: [2019-07-04 Thu 10:07]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro/College
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
* CANCELLED 2017 [/2]
CLOSED: [2019-07-04 Thu 10:07]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro/College
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
* CANCELLED 2018 [/2]
CLOSED: [2019-07-04 Thu 10:07]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro/College
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
* CANCELLED Annales x3
CLOSED: [2019-05-20 Mon 22:33]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Maladies infectieuses
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions D1 malinf
:END:
:LOGBOOK:
CLOCK: [2019-07-04 Thu 12:18]--[2019-07-04 Thu 13:07] => 0:49
:END:
Annale 2 ok
* Néphrologie :A1:semestre2:nephro:
:PROPERTIES:
:CATEGORY: nephro
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_CATEGORY: nephro
:ARCHIVE_ITAGS: revisions
:END:
:LOGBOOK:
CLOCK: [2019-06-22 Sat 16:17]--[2019-06-22 Sat 16:50] => 0:33
:END:
** DONE Lire fiches collège
:LOGBOOK:
CLOCK: [2019-04-27 Sat 17:35]--[2019-04-27 Sat 18:24] => 0:49
CLOCK: [2019-04-27 Sat 16:15]--[2019-04-27 Sat 16:40] => 0:25
CLOCK: [2019-04-27 Sat 14:27]--[2019-04-27 Sat 15:07] => 0:40
CLOCK: [2019-04-27 Sat 11:04]--[2019-04-27 Sat 11:23] => 0:19
CLOCK: [2019-04-27 Sat 10:04]--[2019-04-27 Sat 10:40] => 0:36
CLOCK: [2019-04-26 Fri 22:54]--[2019-04-26 Fri 23:04] => 0:10
CLOCK: [2019-04-26 Fri 22:18]--[2019-04-26 Fri 22:38] => 0:20
CLOCK: [2019-04-26 Fri 17:33]--[2019-04-26 Fri 17:42] => 0:09
CLOCK: [2019-04-26 Fri 14:41]--[2019-04-26 Fri 15:11] => 0:30
CLOCK: [2019-04-26 Fri 13:17]--[2019-04-26 Fri 13:54] => 0:37
CLOCK: [2019-04-26 Fri 11:31]--[2019-04-26 Fri 11:46] => 0:15
CLOCK: [2019-04-26 Fri 10:02]--[2019-04-26 Fri 11:02] => 1:00
CLOCK: [2019-04-25 Thu 22:58]--[2019-04-25 Thu 23:25] => 0:27
CLOCK: [2019-04-25 Thu 22:08]--[2019-04-25 Thu 22:31] => 0:23
CLOCK: [2019-04-24 Wed 22:59]--[2019-04-24 Wed 23:05] => 0:06
CLOCK: [2019-04-24 Wed 21:39]--[2019-04-24 Wed 22:00] => 0:21
CLOCK: [2019-04-24 Wed 18:47]--[2019-04-24 Wed 19:16] => 0:29
CLOCK: [2019-04-24 Wed 16:44]--[2019-04-24 Wed 17:47] => 1:03
CLOCK: [2019-04-24 Wed 14:52]--[2019-04-24 Wed 15:55] => 1:03
CLOCK: [2019-04-24 Wed 11:45]--[2019-04-24 Wed 12:46] => 1:01
CLOCK: [2019-04-23 Tue 22:48]--[2019-04-23 Tue 23:46] => 0:58
:END:
** CANCELLED Ficher collège
** CANCELLED Conférence
** CANCELLED Annales
CLOSED: [2019-05-20 Mon 22:34]
** CANCELLED Lire fiches colleges
CLOSED: [2019-06-27 Thu 10:07] DEADLINE: <2019-06-16 Sun>
** DONE Lire ECNi tout en un
CLOSED: [2019-06-27 Thu 10:07] DEADLINE: <2019-06-16 Sun>
:LOGBOOK:
CLOCK: [2019-06-26 Wed 22:14]--[2019-06-26 Wed 22:40] => 0:26
CLOCK: [2019-06-26 Wed 19:45]--[2019-06-26 Wed 20:10] => 0:25
CLOCK: [2019-06-26 Wed 16:54]--[2019-06-26 Wed 17:41] => 0:47
CLOCK: [2019-06-26 Wed 15:24]--[2019-06-26 Wed 16:12] => 0:48
CLOCK: [2019-06-26 Wed 13:56]--[2019-06-26 Wed 14:10] => 0:14
CLOCK: [2019-06-26 Wed 11:10]--[2019-06-26 Wed 11:50] => 0:40
CLOCK: [2019-06-26 Wed 10:15]--[2019-06-26 Wed 10:50] => 0:35
CLOCK: [2019-06-25 Tue 21:45]--[2019-06-25 Tue 23:18] => 1:33
CLOCK: [2019-06-24 Mon 21:45]--[2019-06-24 Mon 22:48] => 1:03
CLOCK: [2019-06-23 Sun 21:54]--[2019-06-23 Sun 22:18] => 0:24
CLOCK: [2019-06-23 Sun 14:28]--[2019-06-23 Sun 15:00] => 0:32
CLOCK: [2019-06-23 Sun 15:42]--[2019-06-23 Sun 16:20] => 0:38
:END:
-> sd néphrotique exclus
* CANCELLED CC Masson ophtalmo CC [4/] QI [0/]
CLOSED: [2019-07-02 Tue 14:30]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Ophtalmologie
:ARCHIVE_CATEGORY: ophtalmo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 ophtalmo
:END:
* DONE Lire ECNi
CLOSED: [2019-05-28 Tue 00:00] DEADLINE: <2019-05-27 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Ophtalmologie
:ARCHIVE_CATEGORY: ophtalmo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 ophtalmo
:END:
:LOGBOOK:
CLOCK: [2019-05-27 Mon 22:52]--[2019-05-27 Mon 23:44] => 0:52
CLOCK: [2019-05-27 Mon 14:36]--[2019-05-27 Mon 15:18] => 0:42
CLOCK: [2019-05-27 Mon 13:52]--[2019-05-27 Mon 14:20] => 0:28
CLOCK: [2019-05-27 Mon 11:16]--[2019-05-27 Mon 12:17] => 1:01
:END:
* DONE Conférence
CLOSED: [2019-05-27 Mon 22:49] DEADLINE: <2019-05-27 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Ophtalmologie
:ARCHIVE_CATEGORY: ophtalmo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 ophtalmo
:END:
:LOGBOOK:
CLOCK: [2019-05-28 Tue 11:23]--[2019-05-28 Tue 11:24] => 0:01
CLOCK: [2019-05-27 Mon 22:24]--[2019-05-27 Mon 22:49] => 0:25
CLOCK: [2019-05-27 Mon 21:42]--[2019-05-27 Mon 22:00] => 0:18
CLOCK: [2019-05-27 Mon 21:12]--[2019-05-27 Mon 21:22] => 0:10
CLOCK: [2019-05-27 Mon 18:29]--[2019-05-27 Mon 18:41] => 0:12
CLOCK: [2019-05-27 Mon 16:48]--[2019-05-27 Mon 17:43] => 0:55
:END:
* CANCELLED Annales
CLOSED: [2019-07-02 Tue 14:30]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Ophtalmologie
:ARCHIVE_CATEGORY: ophtalmo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 ophtalmo
:END:
:LOGBOOK:
CLOCK: [2019-05-28 Tue 23:26]--[2019-05-28 Tue 23:50] => 0:24
CLOCK: [2019-05-28 Tue 22:33]--[2019-05-28 Tue 22:50] => 0:17
CLOCK: [2019-05-28 Tue 22:01]--[2019-05-28 Tue 22:23] => 0:22
CLOCK: [2019-05-28 Tue 17:41]--[2019-05-28 Tue 18:15] => 0:34
CLOCK: [2019-05-28 Tue 16:46]--[2019-05-28 Tue 17:21] => 0:35
CLOCK: [2019-05-28 Tue 15:07]--[2019-05-28 Tue 15:47] => 0:40
CLOCK: [2019-05-28 Tue 11:24]--[2019-05-28 Tue 12:36] => 1:12
CLOCK: [2019-05-27 Mon 23:46]--[2019-05-28 Tue 00:18] => 0:32
CLOCK: [2019-05-21 Tue 22:02]--[2019-05-22 Wed 00:00] => 1:58
CLOCK: [2019-05-21 Tue 18:48]--[2019-05-21 Tue 19:29] => 0:41
CLOCK: [2019-05-21 Tue 17:38]--[2019-05-21 Tue 18:27] => 0:49
CLOCK: [2019-05-21 Tue 16:26]--[2019-05-21 Tue 17:25] => 0:59
CLOCK: [2019-05-21 Tue 14:23]--[2019-05-21 Tue 15:29] => 1:06
CLOCK: [2019-05-21 Tue 11:27]--[2019-05-21 Tue 13:00] => 1:33
CLOCK: [2019-05-20 Mon 23:06]--[2019-05-21 Tue 00:02] => 0:56
CLOCK: [2019-05-20 Mon 22:25]--[2019-05-20 Mon 22:48] => 0:23
:END:
** DONE 2015-2016
CLOSED: [2019-05-22 Wed 00:24] DEADLINE: <2019-05-21 Tue> SCHEDULED: <2019-05-20 Mon>
*** DONE Janvier 2015
CLOSED: [2019-05-21 Tue 14:25]
*** CANCELLED Mai 2015
CLOSED: [2019-05-21 Tue 14:26]
*** DONE Janvier 2016
CLOSED: [2019-05-21 Tue 21:52]
*** DONE Mai 2016
CLOSED: [2019-05-22 Wed 00:24]
** DONE 2017-2018
CLOSED: [2019-05-29 Wed 00:00] DEADLINE: <2019-05-27 Mon> SCHEDULED: <2019-05-27 Mon>
*** DONE Janvier 2017
CLOSED: [2019-05-28 Tue 12:56]
*** CANCELLED Juin 2017 non dispo ?
CLOSED: [2019-05-28 Tue 14:06]
** DONE 2019
CLOSED: [2019-06-06 Thu 10:28] DEADLINE: <2019-06-03 Mon> SCHEDULED: <2019-06-03 Mon>
* DONE Lire ECNi
CLOSED: [2019-05-31 Fri 14:06] DEADLINE: <2019-05-28 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
:LOGBOOK:
CLOCK: [2019-05-31 Fri 13:57]--[2019-05-31 Fri 14:05] => 0:08
CLOCK: [2019-05-29 Wed 22:27]--[2019-05-29 Wed 23:03] => 0:36
CLOCK: [2019-05-29 Wed 21:07]--[2019-05-29 Wed 21:50] => 0:43
CLOCK: [2019-05-29 Wed 18:54]--[2019-05-29 Wed 19:29] => 0:35
CLOCK: [2019-05-29 Wed 14:40]--[2019-05-29 Wed 15:44] => 1:04
CLOCK: [2019-05-29 Wed 12:55]--[2019-05-29 Wed 13:15] => 0:20
CLOCK: [2019-05-29 Wed 12:16]--[2019-05-29 Wed 12:34] => 0:18
:END:
* DONE Conférence
CLOSED: [2019-05-31 Fri 12:48] DEADLINE: <2019-05-29 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
:LOGBOOK:
CLOCK: [2019-05-31 Fri 12:12]--[2019-05-31 Fri 12:48] => 0:36
CLOCK: [2019-05-31 Fri 10:37]--[2019-05-31 Fri 11:17] => 0:40
:END:
* CANCELLED Annales
CLOSED: [2019-07-02 Tue 14:30]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
:LOGBOOK:
CLOCK: [2019-05-30 Thu 23:42]--[2019-05-31 Fri 00:14] => 0:32
CLOCK: [2019-05-30 Thu 21:48]--[2019-05-30 Thu 23:14] => 1:26
CLOCK: [2019-05-30 Thu 19:10]--[2019-05-30 Thu 19:31] => 0:21
CLOCK: [2019-05-30 Thu 16:09]--[2019-05-30 Thu 17:37] => 1:28
CLOCK: [2019-05-30 Thu 15:44]--[2019-05-30 Thu 15:58] => 0:14
CLOCK: [2019-05-30 Thu 13:05]--[2019-05-30 Thu 13:40] => 0:35
CLOCK: [2019-05-30 Thu 10:42]--[2019-05-30 Thu 12:20] => 1:38
CLOCK: [2019-05-29 Wed 23:04]--[2019-05-30 Thu 00:39] => 1:35
CLOCK: [2019-05-29 Wed 17:28]--[2019-05-29 Wed 17:53] => 0:25
CLOCK: [2019-05-29 Wed 16:56]--[2019-05-29 Wed 17:09] => 0:13
CLOCK: [2019-05-24 Fri 23:52]--[2019-05-25 Sat 00:26] => 0:34
CLOCK: [2019-05-24 Fri 23:26]--[2019-05-24 Fri 23:43] => 0:17
CLOCK: [2019-05-24 Fri 22:16]--[2019-05-24 Fri 22:59] => 0:43
CLOCK: [2019-05-24 Fri 19:09]--[2019-05-24 Fri 19:37] => 0:28
CLOCK: [2019-05-24 Fri 16:12]--[2019-05-24 Fri 18:05] => 1:53
CLOCK: [2019-05-24 Fri 15:08]--[2019-05-24 Fri 15:26] => 0:18
CLOCK: [2019-05-24 Fri 14:22]--[2019-05-24 Fri 14:42] => 0:20
CLOCK: [2019-05-24 Fri 11:09]--[2019-05-24 Fri 12:26] => 1:17
CLOCK: [2019-05-23 Thu 22:49]--[2019-05-24 Fri 00:22] => 1:33
CLOCK: [2019-05-23 Thu 22:00]--[2019-05-23 Thu 22:19] => 0:19
CLOCK: [2019-05-23 Thu 21:29]--[2019-05-23 Thu 21:59] => 0:30
CLOCK: [2019-05-23 Thu 17:02]--[2019-05-23 Thu 18:54] => 1:52
CLOCK: [2019-05-23 Thu 15:55]--[2019-05-23 Thu 16:15] => 0:20
CLOCK: [2019-05-23 Thu 14:19]--[2019-05-23 Thu 15:30] => 1:11
CLOCK: [2019-05-23 Thu 13:47]--[2019-05-23 Thu 13:59] => 0:12
CLOCK: [2019-05-23 Thu 11:53]--[2019-05-23 Thu 12:11] => 0:18
CLOCK: [2019-05-22 Wed 15:12]--[2019-05-22 Wed 15:43] => 0:31
CLOCK: [2019-05-22 Wed 14:38]--[2019-05-22 Wed 15:04] => 0:26
CLOCK: [2019-05-22 Wed 13:55]--[2019-05-22 Wed 14:11] => 0:16
CLOCK: [2019-05-22 Wed 11:05]--[2019-05-22 Wed 11:34] => 0:29
:END:
** DONE 2015-2016
CLOSED: [2019-05-25 Sat 00:25] DEADLINE: <2019-05-22 Wed> SCHEDULED: <2019-05-23 Thu>
*** DONE Janvier 2015
CLOSED: [2019-05-23 Thu 19:35]
*** DONE Mai 2015
CLOSED: [2019-05-24 Fri 14:21]
*** DONE Janvier 2016
CLOSED: [2019-05-24 Fri 18:05]
*** DONE Juin 2016
CLOSED: [2019-05-25 Sat 00:25]
** DONE 2017-2018
CLOSED: [2019-05-31 Fri 00:14] DEADLINE: <2019-05-29 Wed>
*** DONE Janvier 2017
CLOSED: [2019-05-30 Thu 13:06]
*** CANCELLED Juin 2017
CLOSED: [2019-05-29 Wed 15:52]
*** DONE Janvier 2018
CLOSED: [2019-05-30 Thu 17:37]
*** DONE Juin 2018
CLOSED: [2019-05-31 Fri 00:14]
** DONE 2019
CLOSED: [2019-06-02 Sun 16:05] DEADLINE: <2019-05-29 Wed>
:LOGBOOK:
CLOCK: [2019-06-02 Sun 14:49]--[2019-06-02 Sun 16:05] => 1:16
CLOCK: [2019-06-02 Sun 13:23]--[2019-06-02 Sun 14:00] => 0:37
:END:
* CANCELLED UECN Concours blanc pneumo
CLOSED: [2019-06-08 Sat 12:06]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
:LOGBOOK:
CLOCK: [2019-04-25 Thu 21:43]--[2019-04-25 Thu 22:00] => 0:17
CLOCK: [2019-04-25 Thu 18:00]--[2019-04-25 Thu 18:19] => 0:19
CLOCK: [2019-04-25 Thu 15:58]--[2019-04-25 Thu 17:20] => 1:22
CLOCK: [2019-04-25 Thu 11:09]--[2019-04-25 Thu 11:30] => 0:21
CLOCK: [2019-04-25 Thu 10:11]--[2019-04-25 Thu 10:57] => 0:46
CLOCK: [2019-04-24 Wed 23:21]--[2019-04-24 Wed 23:33] => 0:12
:END:
** DONE Concours 1: dossier [6/6] QI [1/1]
** CANCELLED Concours 2: dossier [5/6] QI [0/1]
CLOSED: [2019-07-02 Tue 14:30]
** CANCELLED Concours 3: dossier [0/6] QI [0/1]
CLOSED: [2019-07-02 Tue 14:30]
* CANCELLED Conférence ECN-asso
CLOSED: [2019-06-08 Sat 12:06]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
QI en freestyle..
* DONE Conférence
CLOSED: [2019-05-08 Wed 14:50] SCHEDULED: <2019-05-06 Mon> DEADLINE: <2019-05-06 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
:LOGBOOK:
- State "DONE" from "TODO" [2019-05-08 Wed 14:50]
CLOCK: [2019-05-08 Wed 13:58]--[2019-05-08 Wed 14:50] => 0:52
CLOCK: [2019-05-08 Wed 13:32]--[2019-05-08 Wed 13:41] => 0:09
:END:
* CANCELLED Annales [1/4]
CLOSED: [2019-05-20 Mon 22:34]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
:LOGBOOK:
CLOCK: [2019-05-13 Mon 18:01]--[2019-05-13 Mon 18:53] => 0:52
CLOCK: [2019-05-07 Tue 22:27]--[2019-05-07 Tue 22:53] => 0:26
CLOCK: [2019-05-07 Tue 21:08]--[2019-05-07 Tue 22:16] => 1:08
CLOCK: [2019-05-07 Tue 17:11]--[2019-05-07 Tue 18:00] => 1:05
CLOCK: [2019-05-07 Tue 16:10]--[2019-05-07 Tue 16:40] => 0:30
CLOCK: [2019-05-07 Tue 13:20]--[2019-05-07 Tue 13:32] => 0:12
CLOCK: [2019-05-07 Tue 10:40]--[2019-05-07 Tue 11:20] => 0:40
CLOCK: [2019-05-06 Mon 15:41]--[2019-05-06 Mon 16:17] => 0:36
CLOCK: [2019-05-06 Mon 14:47]--[2019-05-06 Mon 15:36] => 0:49
CLOCK: [2019-05-06 Mon 10:20]--[2019-05-06 Mon 11:10] => 0:50
:END:
** CANCELLED 2015 [1/2]
mai
** CANCELLED 2016 [/2]
** CANCELLED 2017 [1/2]
aout
:LOGBOOK:
CLOCK: [2019-05-13 Mon 20:50]--[2019-05-13 Mon 21:21] => 0:31
CLOCK: [2019-05-13 Mon 19:22]--[2019-05-13 Mon 20:23] => 1:01
:END:
** DONE 2018 [2/2]
CLOSED: [2019-05-07 Tue 22:53]
:LOGBOOK:
- State "DONE" from "TODO" [2019-05-07 Tue 22:53]
:END:
* DONE CC "Dossier ECNI" [30/30]
CLOSED: [2019-05-06 Mon 23:58] DEADLINE: <2019-05-05 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
:LOGBOOK:
- State "DONE" from "TODO" [2019-05-06 Mon 23:58]
CLOCK: [2019-05-06 Mon 23:05]--[2019-05-06 Mon 23:58] => 0:53
CLOCK: [2019-05-06 Mon 19:56]--[2019-05-06 Mon 20:11] => 0:15
CLOCK: [2019-05-06 Mon 18:24]--[2019-05-06 Mon 19:21] => 0:57
CLOCK: [2019-05-05 Sun 21:04]--[2019-05-05 Sun 21:41] => 0:37
CLOCK: [2019-05-05 Sun 18:40]--[2019-05-05 Sun 19:09] => 0:29
CLOCK: [2019-04-15 Mon 15:33]--[2019-04-15 Mon 16:16] => 0:43
CLOCK: [2019-04-15 Mon 14:17]--[2019-04-15 Mon 14:53] => 0:36
CLOCK: [2019-04-15 Mon 11:47]--[2019-04-15 Mon 12:22] => 0:35
CLOCK: [2019-04-15 Mon 11:12]--[2019-04-15 Mon 11:25] => 0:13
CLOCK: [2019-04-14 Sun 22:03]--[2019-04-14 Sun 22:36] => 0:33
CLOCK: [2019-04-14 Sun 20:48]--[2019-04-14 Sun 21:10] => 0:22
CLOCK: [2019-04-14 Sun 14:42]--[2019-04-14 Sun 15:39] => 0:57
CLOCK: [2019-04-14 Sun 14:04]--[2019-04-14 Sun 14:34] => 0:30
CLOCK: [2019-04-14 Sun 12:19]--[2019-04-14 Sun 12:33] => 0:14
CLOCK: [2019-04-14 Sun 11:26]--[2019-04-14 Sun 11:51] => 0:25
CLOCK: [2019-04-14 Sun 10:49]--[2019-04-14 Sun 11:09] => 0:20
:END:
* CANCELLED Lire ECNi tout en un
CLOSED: [2019-07-02 Tue 14:30]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Psychiatrie
:ARCHIVE_CATEGORY: psy
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions psy
:END:
* CANCELLED Annales
CLOSED: [2019-05-20 Mon 22:34]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Urologie
:ARCHIVE_CATEGORY: uro
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions uro
:END:
* CANCELLED Lire fiches colleges
CLOSED: [2019-06-27 Thu 10:10] DEADLINE: <2019-06-15 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Urologie
:ARCHIVE_CATEGORY: uro
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions uro
:END:
:LOGBOOK:
CLOCK: [2019-06-16 Sun 14:54]--[2019-06-16 Sun 15:57] => 1:03
:END:
Jusque dysfonction érectile incluse
* TODO Lire ECNI tout en un
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Urologie
:ARCHIVE_CATEGORY: uro
:ARCHIVE_TODO: TODO
:ARCHIVE_ITAGS: revisions uro
:END:
:LOGBOOK:
CLOCK: [2019-06-23 Sun 10:42]--[2019-06-23 Sun 11:10] => 0:28
CLOCK: [2019-06-22 Sat 23:33]--[2019-06-23 Sun 00:10'u=> 0:37
CLOCK: [2019-06-22 Sat 19:28]--[2019-06-22 Sat 20:07] => 0:39
CLOCK: [2019-06-22 Sat 11:58]--[2019-06-22 Sat 12:15] => 0:17
CLOCK: [2019-06-20 Thu 22:07]--[2019-06-20 Thu 22:21] => 0:14
CLOCK: [2019-06-20 Thu 16:51]--[2019-06-20 Thu 17:32] => 0:41
CLOCK: [2019-06-16 Sun 20:56]--[2019-06-16 Sun 21:42] => 0:46
CLOCK: [2019-06-16 Sun 17:48]--[2019-06-16 Sun 18:01] => 0:13
CLOCK: [2019-06-16 Sun 17:32]--[2019-06-16 Sun 17:44] => 0:12
:END:
- Génito scrotale
- Troubles miction
- Trouble érection
- HBP
- IU
- Lithiase
- Rétention urinaire
- Tumeur prostate
* Début stage <2019-02-14 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Partiels/Rattrapages
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_ITAGS: revisions
:END:
* Oral <2019-02-26 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Partiels/Rattrapages
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_ITAGS: revisions
:END:
* DONE <2018-11-07 Wed> Samu
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gardes
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* DONE <2018-12-09 Sun> CAP
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gardes
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* DONE <2019-07-05 Fri> Pont-à-Mousson
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:37
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gardes
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* Fin stage <2019-03-31 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:38
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Partiels/Rattrapages
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_ITAGS: revisions
:END:
* DONE <2018-11-17 Sat> Pont-à-Mousson
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:38
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gardes
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* DONE <2018-12-13 Thu> Chir ortho
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:39
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gardes
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* DONE Lire résumé médecine nucléaire
SCHEDULED: <2019-08-17 Sat> DEADLINE: <2019-08-18 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-18 Sun 12:46
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Stages
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE DFGSM3
** DONE Masson
* DONE Slides de révisions
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:15
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Chirurgie maxillo-faciale
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 maxillo
:END:
* DONE CC Masson [10/10] et QRM [80/80]
SCHEDULED: <2019-08-07 Wed> DEADLINE: <2019-08-10 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:15
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Chirurgie maxillo-faciale
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 maxillo
:END:
:LOGBOOK:
CLOCK: [2019-08-09 Fri 22:43]--[2019-08-09 Fri 22:53] => 0:10
CLOCK: [2019-08-09 Fri 20:04]--[2019-08-09 Fri 20:12] => 0:08
CLOCK: [2019-08-09 Fri 17:26]--[2019-08-09 Fri 18:39] => 1:13
CLOCK: [2019-08-09 Fri 14:44]--[2019-08-09 Fri 15:45] => 1:01
CLOCK: [2019-08-09 Fri 11:56]--[2019-08-09 Fri 13:04] => 1:08
CLOCK: [2019-08-08 Thu 18:55]--[2019-08-08 Thu 19:25] => 0:30
CLOCK: [2019-08-08 Thu 18:12]--[2019-08-08 Thu 18:30] => 0:18
CLOCK: [2019-08-08 Thu 15:00]--[2019-08-08 Thu 16:00] => 1:00
CLOCK: [2019-08-08 Thu 14:38]--[2019-08-08 Thu 14:45] => 0:07
CLOCK: [2019-08-08 Thu 11:45]--[2019-08-08 Thu 12:45] => 1:00
CLOCK: [2019-08-08 Thu 10:33]--[2019-08-08 Thu 10:45] => 0:12
CLOCK: [2019-08-07 Wed 23:00]--[2019-08-07 Wed 23:50] => 0:50
CLOCK: [2019-08-07 Wed 22:21]--[2019-08-07 Wed 22:35] => 0:14
CLOCK: [2019-08-07 Wed 18:59]--[2019-08-07 Wed 19:44] => 0:45
:END:
* DONE Lire ECNI
DEADLINE: <2019-08-25 Sun> SCHEDULED: <2019-08-23 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:15
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Chirurgie maxillo-faciale
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 maxillo
:END:
:LOGBOOK:
CLOCK: [2019-08-24 Sat 17:00]--[2019-08-24 Sat 17:45] => 5:53
CLOCK: [2019-08-23 Fri 21:28]--[2019-08-23 Fri 21:44] => 0:16
CLOCK: [2019-08-23 Fri 14:56]--[2019-08-23 Fri 15:15] => 0:19
:END:
* DONE Annales [0/5]
DEADLINE: <2019-08-24 Sat> SCHEDULED: <2019-08-19 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:16
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Chirurgie maxillo-faciale
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 maxillo
:END:
:LOGBOOK:
CLOCK: [2019-08-26 Mon 19:02]--[2019-08-26 Mon 19:36] => 0:34
CLOCK: [2019-08-25 Sun 19:57]--[2019-08-25 Sun 20:32] => 0:35
CLOCK: [2019-08-25 Sun 18:28]--[2019-08-25 Sun 18:58] => 0:30
CLOCK: [2019-08-25 Sun 11:57]--[2019-08-25 Sun 12:39] => 0:42
CLOCK: [2019-08-25 Sun 10:56]--[2019-08-25 Sun 11:24] => 0:28
CLOCK: [2019-08-24 Sat 23:26]--[2019-08-24 Sat 23:56] => 0:30
CLOCK: [2019-08-24 Sat 22:59]--[2019-08-24 Sat 23:12] => 0:13
CLOCK: [2019-08-24 Sat 19:06]--[2019-08-24 Sat 19:40] => 0:34
CLOCK: [2019-08-24 Sat 17:59]--[2019-08-24 Sat 18:20] => 0:21
CLOCK: [2019-08-24 Sat 13:41]--[2019-08-24 Sat 14:11] => 0:30
CLOCK: [2019-08-24 Sat 12:28]--[2019-08-24 Sat 13:00] => 0:32
CLOCK: [2019-08-23 Fri 17:00]--[2019-08-23 Fri 17:20] => 0:20
CLOCK: [2019-08-23 Fri 15:49]--[2019-08-23 Fri 16:27] => 0:38
CLOCK: [2019-08-23 Fri 13:48]--[2019-08-23 Fri 14:33] => 0:45
CLOCK: [2019-08-21 Wed 21:14]--[2019-08-21 Wed 22:00] => 0:46
CLOCK: [2019-08-21 Wed 20:37]--[2019-08-21 Wed 21:06] => 0:29
CLOCK: [2019-08-20 Tue 21:16]--[2019-08-20 Tue 21:16] => 0:00
CLOCK: [2019-08-20 Tue 20:03]--[2019-08-20 Tue 20:26] => 0:23
CLOCK: [2019-08-19 Mon 19:14]--[2019-08-19 Mon 19:52] => 0:38
CLOCK: [2019-07-15 Mon 16:09]--[2019-07-15 Mon 16:37] => 0:28
:END:
** TODO 2015 Session [2/2] Passe [1/2]
** TODO 2016 Session [2/2] Passe [1/2]
** TODO 2017 Session [2/2] Passe [1/2]
** TODO 2018 Session [2/2] Passe [1/2]
** TODO 2019 Session [1/1] Passe [1/2]
* DONE DP ORL+maxillo [30/30]
DEADLINE: <2019-08-16 Fri> SCHEDULED: <2019-08-10 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:16
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Chirurgie maxillo-faciale
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 maxillo
:END:
:LOGBOOK:
CLOCK: [2019-08-17 Sat 21:46]--[2019-08-17 Sat 22:07] => 0:21
CLOCK: [2019-08-17 Sat 19:46]--[2019-08-17 Sat 20:00] => 0:14
CLOCK: [2019-08-17 Sat 18:21]--[2019-08-17 Sat 19:25] => 1:04
CLOCK: [2019-08-17 Sat 17:04]--[2019-08-17 Sat 17:42] => 0:38
CLOCK: [2019-08-17 Sat 12:00]--[2019-08-17 Sat 12:30] => 0:30
CLOCK: [2019-08-16 Fri 20:24]--[2019-08-16 Fri 20:50] => 0:26
CLOCK: [2019-08-16 Fri 19:19]--[2019-08-16 Fri 20:03] => 0:44
CLOCK: [2019-08-16 Fri 17:26]--[2019-08-16 Fri 18:17] => 0:51
CLOCK: [2019-08-16 Fri 16:28]--[2019-08-16 Fri 17:02] => 0:34
CLOCK: [2019-08-16 Fri 15:13]--[2019-08-16 Fri 16:02] => 0:49
CLOCK: [2019-08-16 Fri 13:54]--[2019-08-16 Fri 14:12] => 0:18
CLOCK: [2019-08-16 Fri 00:14]--[2019-08-16 Fri 00:28] => 0:14
CLOCK: [2019-08-15 Thu 23:21]--[2019-08-15 Thu 23:34] => 0:13
CLOCK: [2019-08-15 Thu 20:14]--[2019-08-15 Thu 20:25] => 0:11
CLOCK: [2019-08-15 Thu 19:08]--[2019-08-15 Thu 19:23] => 0:15
CLOCK: [2019-08-15 Thu 17:27]--[2019-08-15 Thu 18:20] => 0:53
CLOCK: [2019-08-15 Thu 15:58]--[2019-08-15 Thu 16:11] => 0:13
CLOCK: [2019-08-15 Thu 14:01]--[2019-08-15 Thu 14:26] => 0:25
CLOCK: [2019-08-14 Wed 16:21]--[2019-08-14 Wed 16:44] => 0:23
CLOCK: [2019-08-14 Wed 15:54]--[2019-08-14 Wed 16:17] => 0:23
CLOCK: [2019-08-14 Wed 15:06]--[2019-08-14 Wed 15:39] => 0:33
CLOCK: [2019-08-14 Wed 14:30]--[2019-08-14 Wed 15:00] => 0:30
CLOCK: [2019-08-14 Wed 12:02]--[2019-08-14 Wed 12:22] => 0:20
CLOCK: [2019-08-14 Wed 11:31]--[2019-08-14 Wed 11:56] => 0:25
CLOCK: [2019-08-14 Wed 10:59]--[2019-08-14 Wed 11:24] => 0:25
CLOCK: [2019-08-13 Tue 23:48]--[2019-08-14 Wed 00:21] => 0:33
CLOCK: [2019-08-13 Tue 22:45]--[2019-08-13 Tue 23:22] => 0:37
CLOCK: [2019-08-13 Tue 19:24]--[2019-08-13 Tue 20:20] => 0:56
CLOCK: [2019-08-13 Tue 15:58]--[2019-08-13 Tue 17:11] => 1:13
CLOCK: [2019-08-13 Tue 15:03]--[2019-08-13 Tue 15:43] => 0:40
CLOCK: [2019-08-13 Tue 11:54]--[2019-08-13 Tue 12:35] => 0:41
CLOCK: [2019-08-12 Mon 15:10]--[2019-08-12 Mon 16:12] => 1:02
CLOCK: [2019-08-11 Sun 00:08]--[2019-08-11 Sun 00:42] => 0:34
:END:
* DONE Lire ECNi tout en un
DEADLINE: <2019-08-16 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:16
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Chirurgie maxillo-faciale
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 maxillo
:END:
- Dev. buccodentaire
- Traumatisme maxiollo faciale
* CANCELLED Lire référentiel ?
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:16
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Chirurgie maxillo-faciale
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre2 maxillo
:END:
* DONE Lire ECNI
DEADLINE: <2019-08-25 Sun> SCHEDULED: <2019-08-23 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:16
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: ORL
:ARCHIVE_CATEGORY: orl
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 orl
:END:
:LOGBOOK:
CLOCK: [2019-08-25 Sun 22:18]--[2019-08-25 Sun 22:32] => 0:14
CLOCK: [2019-08-25 Sun 21:27]--[2019-08-25 Sun 21:42] => 0:15
CLOCK: [2019-08-25 Sun 17:04]--[2019-08-25 Sun 17:45] => 0:41
CLOCK: [2019-08-25 Sun 13:46]--[2019-08-25 Sun 14:11] => 0:25
:END:
-> otites (incluses)
* DONE DP Masson [20/31] QI [0/29]
DEADLINE: <2019-08-13 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:16
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: ORL
:ARCHIVE_CATEGORY: orl
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 orl
:END:
:LOGBOOK:
CLOCK: [2019-07-14 Sun 21:02]--[2019-07-14 Sun 21:41] => 0:39
CLOCK: [2019-07-14 Sun 18:51]--[2019-07-14 Sun 19:30] => 0:39
CLOCK: [2019-07-14 Sun 17:29]--[2019-07-14 Sun 18:17] => 0:48
CLOCK: [2019-07-13 Sat 23:59]--[2019-07-14 Sun 00:22] => 0:23
CLOCK: [2019-07-13 Sat 23:04]--[2019-07-13 Sat 23:28] => 0:24
CLOCK: [2019-07-13 Sat 16:53]--[2019-07-13 Sat 17:30] => 0:37
CLOCK: [2019-07-13 Sat 14:56]--[2019-07-13 Sat 15:40] => 0:44
CLOCK: [2019-07-13 Sat 11:55]--[2019-07-13 Sat 12:06] => 0:11
CLOCK: [2019-07-13 Sat 00:13]--[2019-07-13 Sat 00:41] => 0:28
CLOCK: [2019-07-11 Thu 19:25]--[2019-07-11 Thu 19:47] => 0:22
CLOCK: [2019-07-11 Thu 16:57]--[2019-07-11 Thu 18:26] => 1:29
CLOCK: [2019-07-11 Thu 15:57]--[2019-07-11 Thu 16:13] => 0:16
CLOCK: [2019-07-11 Thu 14:29]--[2019-07-11 Thu 14:46] => 0:17
CLOCK: [2019-07-09 Tue 20:01]--[2019-07-09 Tue 20:21] => 0:20
CLOCK: [2019-07-09 Tue 19:17]--[2019-07-09 Tue 19:34] => 0:17
CLOCK: [2019-07-09 Tue 16:57]--[2019-07-09 Tue 18:05] => 1:08
CLOCK: [2019-07-09 Tue 16:17]--[2019-07-09 Tue 16:44] => 0:27
CLOCK: [2019-07-09 Tue 15:58]--[2019-07-09 Tue 16:06] => 0:08
:END:
* DONE Conférence ORL-maxillo
DEADLINE: <2019-08-14 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:16
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: ORL
:ARCHIVE_CATEGORY: orl
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 orl
:END:
:LOGBOOK:
CLOCK: [2019-08-18 Sun 21:04]--[2019-08-18 Sun 21:36] => 0:32
CLOCK: [2019-08-18 Sun 17:16]--[2019-08-18 Sun 18:52] => 1:36
CLOCK: [2019-08-18 Sun 15:49]--[2019-08-18 Sun 16:28] => 0:39
- State "DONE" from "TODO" [2019-05-12 Sun 15:49]
:END:
* DONE Annales [0/5]
DEADLINE: <2019-08-24 Sat> SCHEDULED: <2019-08-19 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:16
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: ORL
:ARCHIVE_CATEGORY: orl
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre2 orl
:END:
:LOGBOOK:
CLOCK: [2019-08-26 Mon 18:08]--[2019-08-26 Mon 18:37] => 0:29
CLOCK: [2019-08-26 Mon 17:14]--[2019-08-26 Mon 17:48] => 0:34
CLOCK: [2019-08-25 Sun 21:46]--[2019-08-25 Sun 22:12] => 0:26
CLOCK: [2019-08-25 Sun 15:12]--[2019-08-25 Sun 16:25] => 1:13
CLOCK: [2019-08-25 Sun 14:20]--[2019-08-25 Sun 14:36] => 0:16
CLOCK: [2019-08-25 Sun 09:31]--[2019-08-25 Sun 10:39] => 1:08
CLOCK: [2019-08-24 Sat 23:57]--[2019-08-25 Sun 00:13] => 0:16
CLOCK: [2019-08-24 Sat 21:31]--[2019-08-24 Sat 22:52] => 1:21
CLOCK: [2019-08-24 Sat 20:00]--[2019-08-24 Sat 20:25] => 0:25
CLOCK: [2019-08-24 Sat 10:59]--[2019-08-24 Sat 12:10] => 1:11
CLOCK: [2019-08-23 Fri 21:53]--[2019-08-23 Fri 22:52] => 0:59
CLOCK: [2019-08-23 Fri 19:33]--[2019-08-23 Fri 21:28] => 1:55
CLOCK: [2019-08-23 Fri 18:42]--[2019-08-23 Fri 19:05] => 0:23
CLOCK: [2019-08-23 Fri 12:18]--[2019-08-23 Fri 12:48] => 0:30
CLOCK: [2019-08-23 Fri 10:32]--[2019-08-23 Fri 11:42] => 1:10
CLOCK: [2019-08-22 Thu 22:20]--[2019-08-22 Thu 22:44] => 0:24
CLOCK: [2019-08-22 Thu 17:57]--[2019-08-22 Thu 19:22] => 1:25
CLOCK: [2019-08-20 Tue 21:16]--[2019-08-20 Tue 22:09] => 0:53
:END:
** TODO 2015 Session [2/2] Passe [1/2]
** TODO 2016 Session [2/2] Passe [1/2]
** TODO 2017 Session [2/2] Passe [1/2]
** TODO 2018 Session [2/2] Passe [2/2]
Aout 2018 fait
** TODO 2019 Session [1/1] Passe [1/2]
* CANCELLED Reprendre fiches déjà faites
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:54
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
* DONE Ficher HGE
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:54
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
* DONE College
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:54
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hépato-Gastro
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 hge
:END:
** Addiction
:PROPERTIES:
:Fiche: X
:Lu: X
:QI: NA
:END:
** Hépatite
:PROPERTIES:
:Fiche: X
:Lu: X
:QI: Odd
:END:
** Parasitoses
:PROPERTIES:
:Fiche: X
:Lu: X
:QI: All
:END:
** Transplantation
:PROPERTIES:
:Fiche: X
:Lu: X
:QI: NA
:END:
** Patho fer
:PROPERTIES:
:Fiche: X
:Lu: X
:QI: NA
:END:
** Dénutrition
:PROPERTIES:
:Fiche: X
:Lu: X
:QI: NA
:END:
** Douleur abdo
:PROPERTIES:
:Fiche: X
:Lu: X
:QI: All
:END:
** RGO
:PROPERTIES:
:Fiche:
:Lu: X
:QI: All
:END:
** Ulcère
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Dysphagie
:PROPERTIES:
:Lu: X
:Fiche:
:QI: NA
:END:
** Vomissements
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** HMG
:PROPERTIES:
:Lu: X
:Fiche:
:QI: All
:END:
** Lithiases
:PROPERTIES:
:Lu: X
:Fiche:
:QI: All
:END:
** Ictère
:PROPERTIES:
:Lu: X
:QI: All
:END:
** Cirrhose
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Ascite
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Pancréatite chronique
:PROPERTIES:
:Lu: X
:QI: All
:Fiche: X
:END:
** Maladies inflammatoires chroniques
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Constipation
:PROPERTIES:
:Lu: X
:QI: All
:Fiche: X
:END:
:PROPERTIES:
:Lu: X
:END:
** Colopathie fonctionnelle
:PROPERTIES:
:Lu: X
:QI: All
:END:
** Diarrhée chronique
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Diarrhée aigüe
:PROPERTIES:
:Lu: X
:QI: All
:Fiche: X
:END:
** Diverticulose
:PROPERTIES:
:Lu: X
:Fiche: X
:ORDERED: t
:QI: All
:END:
** Hémorroides
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Hernie pariétale
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Tumeurs du colôn
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Tumeurs de l'estomac
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Tumeurs du foie
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Tumeurs du pancreas
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Sd occlusif
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Appendicite
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Péritonite
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
** Pancréatite aigue
:PROPERTIES:
:Lu: X
:Fiche: X
:QI: All
:END:
* DONE Passe 1 ECNI et collège
SCHEDULED: <2019-10-31 Thu> DEADLINE: <2019-11-10 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:54
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hémato
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions hémato A2 semestre1
:END:
* DONE DP Masson [2/2] et QRM [2/2]
SCHEDULED: <2019-11-23 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:54
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hémato
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions hémato A2 semestre1
:END:
** DONE DP 1-8 [8/8] et QRM 1-70 [70/70]
DEADLINE: <2019-11-23 Sat>
** DONE DP 9-17 [2/9] et QRM 71-139 [/69]
DEADLINE: <2019-11-24 Sun>
* DONE Cas cliniques profs
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:55
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hémato
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions hémato A2 semestre1
:END:
** DONE CC [2/2]
*** DONE 2019
*** DONE 2017
** DONE Révisions
* CANCELLED Abrégé des très bien classés :D1:
DEADLINE: <2019-12-09 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:55
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hémato
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions hémato A2 semestre1
:END:
* CANCELLED Révisions profs ?
DEADLINE: <2019-12-13 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:55
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hémato
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions hémato A2 semestre1
:END:
* CANCELLED Annales
DEADLINE: <2019-12-13 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:55
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hémato
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions hémato A2 semestre1
:END:
:LOGBOOK:
CLOCK: [2019-12-14 Sat 21:04]--[2019-12-14 Sat 22:00] => 0:56
CLOCK: [2019-12-14 Sat 19:07]--[2019-12-14 Sat 19:45] => 0:38
CLOCK: [2019-12-14 Sat 16:38]--[2019-12-14 Sat 18:25] => 1:47
CLOCK: [2019-12-14 Sat 13:30]--[2019-12-14 Sat 14:25] => 0:55
CLOCK: [2019-12-14 Sat 11:39]--[2019-12-14 Sat 12:33] => 0:54
CLOCK: [2019-12-14 Sat 10:26]--[2019-12-14 Sat 11:16] => 0:50
CLOCK: [2019-12-13 Fri 22:27]--[2019-12-13 Fri 23:58] => 1:31
:END:
** CANCELLED Décembre 2018 [1/2]
** CANCELLED Décembre 2017 [1/2]
** CANCELLED Avril 2017 [/2]
* DONE Passe 1 ECNI et collège
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:55
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Immunologie
:ARCHIVE_CATEGORY: immuno
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions immuno A2 semestre1
:END:
* DONE DP Masson [12/12] et QRM [46/46]
DEADLINE: <2019-11-29 Fri> SCHEDULED: <2019-11-28 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:55
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Immunologie
:ARCHIVE_CATEGORY: immuno
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions immuno A2 semestre1
:END:
* DONE Révisions profs
DEADLINE: <2019-12-12 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:55
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Immunologie
:ARCHIVE_CATEGORY: immuno
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions immuno A2 semestre1
:END:
:LOGBOOK:
CLOCK: [2019-12-13 Fri 21:47]--[2019-12-13 Fri 22:11] => 0:24
CLOCK: [2019-12-13 Fri 20:50]--[2019-12-13 Fri 21:37] => 0:47
CLOCK: [2019-12-13 Fri 17:46]--[2019-12-13 Fri 18:50] => 1:04
:END:
* DONE Relire fiches
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:55
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Maladies infectieuses
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions D1 malinf
:END:
Passe 1 : p14
* DONE Collège
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Ophtalmologie
:ARCHIVE_CATEGORY: ophtalmo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 ophtalmo
:END:
** DONE 1 Sémiologie [1/2]
** DONE 2 Réfraction [1/2]
** DONE 3 Suivi nourisson [1/2]
** DONE 4 Strabisme [/]
** DONE 5 Diplopie [/]
** DONE 6 Oeil rouge/douloureux [1/2]
** DONE 7 Altération de fonction visuelle [1/2]
** DONE 8 Anomalies de la vision brutales [1/2]
** DONE 9, 10 Prélèvement et greffe de cornée [1/2]
** DONE 11 Trauma oculaire [1/2]
** DONE 12 Brûlures oculaires [1/2]
** DONE 13 Cataracte [1/2]
** DONE 14 Glaucome chronique [1/2]
** DONE 15 DMLA [1/2]
** DONE 16 Occlusion artérielles rétiniennes [1/2]
** DONE 17 Occlusion veineuses rétiniennes [1/2]
** DONE 18 Patho paupières [1/2]
** DONE 19 SEP [1/2]
** DONE 20 Neuropathie optique ischémique antérieure[1/2]
** DONE 21 Rétinopathie diabétique[1/2]
** DONE 22 Orbitopathie dysthyroïdienne[1/2]
** DONE Rétinopathie hypertensive [1/2]
* DONE Superfiches ophtalmo
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Ophtalmologie
:ARCHIVE_CATEGORY: ophtalmo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 ophtalmo
:END:
* DONE Superfiches pneumologie
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
* DONE Ficher collège
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
* DONE Collège
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
* CANCELLED Ficher référentiel
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pneumologie
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 pneumo
:END:
* DONE Passe 1 ECNI et collège
DEADLINE: <2019-09-29 Sun> SCHEDULED: <2019-09-22 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Rhumato
:ARCHIVE_CATEGORY: rhumato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre1 rhumato
:END:
:LOGBOOK:
CLOCK: [2019-10-07 Mon 15:49]--[2019-10-07 Mon 16:49] => 1:00
CLOCK: [2019-10-07 Mon 14:10]--[2019-10-07 Mon 15:10] => 1:00
CLOCK: [2019-10-07 Mon 11:21]--[2019-10-07 Mon 12:55] => 1:34
CLOCK: [2019-10-07 Mon 10:27]--[2019-10-07 Mon 11:00] => 0:33
CLOCK: [2019-09-29 Sun 19:49]--[2019-09-29 Sun 20:30] => 0:41
CLOCK: [2019-09-29 Sun 16:49]--[2019-09-29 Sun 18:10] => 1:21
CLOCK: [2019-09-26 Thu 17:41]--[2019-09-26 Thu 18:06] => 0:25
CLOCK: [2019-09-26 Thu 16:13]--[2019-09-26 Thu 16:55] => 0:42
CLOCK: [2019-09-26 Thu 13:21]--[2019-09-26 Thu 14:30] => 1:09
CLOCK: [2019-09-26 Thu 11:03]--[2019-09-26 Thu 11:59] => 0:56
CLOCK: [2019-09-25 Wed 22:36]--[2019-09-25 Wed 23:33] => 0:57
CLOCK: [2019-09-25 Wed 21:33]--[2019-09-25 Wed 22:04] => 0:31
CLOCK: [2019-09-25 Wed 16:41]--[2019-09-25 Wed 17:39] => 0:58
CLOCK: [2019-09-25 Wed 14:09]--[2019-09-25 Wed 14:33] => 0:24
CLOCK: [2019-09-25 Wed 11:16]--[2019-09-25 Wed 12:26] => 1:10
CLOCK: [2019-09-24 Tue 13:37]--[2019-09-24 Tue 13:47] => 0:10
CLOCK: [2019-09-24 Tue 09:30]--[2019-09-24 Tue 10:45] => 13:38
CLOCK: [2019-09-23 Mon 21:43]--[2019-09-23 Mon 23:08] => 1:25
CLOCK: [2019-09-23 Mon 18:24]--[2019-09-23 Mon 19:13] => 0:49
CLOCK: [2019-09-23 Mon 14:47]--[2019-09-23 Mon 16:22] => 1:35
CLOCK: [2019-09-23 Mon 14:02]--[2019-09-23 Mon 14:36] => 0:34
CLOCK: [2019-09-23 Mon 10:09]--[2019-09-23 Mon 11:22] => 1:13
CLOCK: [2019-09-22 Sun 22:27]--[2019-09-22 Sun 23:17] => 0:50
CLOCK: [2019-09-22 Sun 18:32]--[2019-09-22 Sun 19:15] => 0:43
:END:
* DONE DP Masson [33/33]
DEADLINE: <2019-10-31 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Rhumato
:ARCHIVE_CATEGORY: rhumato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre1 rhumato
:END:
:LOGBOOK:
CLOCK: [2019-10-28 Mon 20:17]--[2019-10-28 Mon 21:30] => 1:13
CLOCK: [2019-10-28 Mon 18:24]--[2019-10-28 Mon 20:17] => 1:53
CLOCK: [2019-10-28 Mon 17:17]--[2019-10-28 Mon 18:24] => 1:07
CLOCK: [2019-10-28 Mon 15:14]--[2019-10-28 Mon 16:10] => 0:56
CLOCK: [2019-10-28 Mon 13:48]--[2019-10-28 Mon 14:55] => 1:07
CLOCK: [2019-10-28 Mon 11:00]--[2019-10-28 Mon 11:45] => 0:45
:END:
* DONE Cas cliniques profs
DEADLINE: <2019-12-07 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Rhumato
:ARCHIVE_CATEGORY: rhumato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre1 rhumato
:END:
:LOGBOOK:
CLOCK: [2019-12-09 Mon 14:43]--[2019-12-09 Mon 14:57] => 0:14
CLOCK: [2019-12-09 Mon 13:44]--[2019-12-09 Mon 14:32] => 0:48
CLOCK: [2019-12-09 Mon 12:22]--[2019-12-09 Mon 12:45] => 0:23
CLOCK: [2019-12-09 Mon 11:00]--[2019-12-09 Mon 12:00] => 1:00
:END:
* DONE Abrégé des très bien classés
DEADLINE: <2019-12-09 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Rhumato
:ARCHIVE_CATEGORY: rhumato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre1 rhumato
:END:
:LOGBOOK:
:END:
* CANCELLED Révisions profs ?
DEADLINE: <2019-12-12 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Rhumato
:ARCHIVE_CATEGORY: rhumato
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A2 semestre1 rhumato
:END:
* CANCELLED Annales
DEADLINE: <2019-12-13 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Rhumato
:ARCHIVE_CATEGORY: rhumato
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A2 semestre1 rhumato
:END:
:LOGBOOK:
CLOCK: [2019-12-15 Sun 14:27]--[2019-12-15 Sun 15:49] => 1:22
CLOCK: [2019-12-15 Sun 13:28]--[2019-12-15 Sun 13:58] => 0:30
CLOCK: [2019-12-15 Sun 10:58]--[2019-12-15 Sun 12:15] => 1:17
CLOCK: [2019-12-14 Sat 22:26]--[2019-12-14 Sat 22:47] => 0:21
:END:
** CANCELLED Décembre 2018 [1/2]
** CANCELLED Décembre 2017 [/2]
* CANCELLED Conférence
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Urologie
:ARCHIVE_CATEGORY: uro
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 uro
:END:
* CANCELLED Ficher référentiel
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Urologie
:ARCHIVE_CATEGORY: uro
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 uro
:END:
* DONE Collège
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Cardiologie
:ARCHIVE_CATEGORY: cardiologie
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions D1
:END:
** 218 Athérome
:PROPERTIES:
:QI: All
:Lu: X
:Fiche:
:SuperFiche: X
:END:
** 219 Facteurs de risques
:PROPERTIES:
:Lu: X
:Fiche:
:QI: Half
:SuperFiche: X
:END:
** 220 Dyslipidémie
:PROPERTIES:
:QI: NA
:Lu: X
:Fiche: X
:SuperFiche: X
:END:
** 334 SCA
:PROPERTIES:
:QI: Half
:Lu: X
:Fiche:
:SuperFiche: X
:END:
** 228 Douleur thoracique
:PROPERTIES:
:QI: Half
:Fiche:
:Lu: X
:SuperFiche: X
:END:
** 223 AOMI
:PROPERTIES:
:QI: Half
:Fiche:
:Lu: X
:SuperFiche: X
:END:
** 231 Rétrécissement aortique, insuf mitrale, insuf aortique
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** Surveillance porteurs de valve
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche: X
:QI: Odd
:SuperFiche: X
:END:
** 149 Endocardite infectieuses
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 236 Souffles de l'enfant
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 337 Malaises
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 238 Fibrillation atriale
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 234 Troubles de la conduction
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 229 ECG
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 253 Palpitations
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 232 Insuf cardiaque
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 222 HTAP
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 199 Dyspnée
:PROPERTIES:
:Lu: X
:Fiche:
:QI: Done : non
:SuperFiche: X
:END:
** 224 TVP et EP
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 221 HTA
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 225 Varices
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 233 Péricardite aigüe
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 327 Arrêt cardiocirculatoire
:PROPERTIES:
:Lu: X
:Fiche:
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 264 Diurétiques
:PROPERTIES:
:Lu: X
:Fiche:
:QI: Odd
:SuperFiche: X
:END:
** 326 Antithrombotiques
:PROPERTIES:
:Lu: X
:Fiche: X
:Fiche: X
:QI: Odd (jusque 41...)
:SuperFiche: X
:END:
:PROPERTIES:
:COLUMNS: %25ITEM %Lu %Fiche %QI
:QI_source: 1000 QI
:SuperFiche_ALL: X
:END:
* CANCELLED Simplifier fiches
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Cardiologie
:ARCHIVE_CATEGORY: cardiologie
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions D1
:END:
* DONE Passe 1 ECNI et collège
DEADLINE: <2019-09-09 Mon> SCHEDULED: <2019-09-02 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Dermato
:ARCHIVE_CATEGORY: dermato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre1 dermato
:END:
:LOGBOOK:
CLOCK: [2019-09-14 Sat 18:17]--[2019-09-14 Sat 19:13] => 0:56
CLOCK: [2019-09-14 Sat 16:59]--[2019-09-14 Sat 17:36] => 0:37
CLOCK: [2019-09-14 Sat 16:12]--[2019-09-14 Sat 16:37] => 0:25
CLOCK: [2019-09-14 Sat 14:48]--[2019-09-14 Sat 15:31] => 0:43
CLOCK: [2019-09-14 Sat 11:30]--[2019-09-14 Sat 12:30] => 1:00
CLOCK: [2019-09-13 Fri 22:48]--[2019-09-13 Fri 22:59] => 0:11
CLOCK: [2019-09-13 Fri 21:19]--[2019-09-13 Fri 21:55] => 0:36
CLOCK: [2019-09-13 Fri 18:55]--[2019-09-13 Fri 19:12] => 0:17
CLOCK: [2019-09-13 Fri 17:59]--[2019-09-13 Fri 18:38] => 0:39
CLOCK: [2019-09-13 Fri 13:11]--[2019-09-13 Fri 14:00] => 0:49
CLOCK: [2019-09-11 Wed 20:56]--[2019-09-11 Wed 21:17] => 0:21
CLOCK: [2019-09-11 Wed 17:47]--[2019-09-11 Wed 18:03] => 0:16
CLOCK: [2019-09-08 Sun 21:22]--[2019-09-08 Sun 22:14] => 0:52
CLOCK: [2019-09-08 Sun 18:06]--[2019-09-08 Sun 18:26] => 0:20
CLOCK: [2019-09-08 Sat 11:20]--[2019-09-08 Sun 11:40] => 0:20
CLOCK: [2019-09-07 Sat 14:00]--[2019-09-07 Sat 14:30] => 0:30
CLOCK: [2019-09-07 Sat 12:13]--[2019-09-07 Sat 13:06] => 0:53
CLOCK: [2019-09-05 Thu 22:20]--[2019-09-05 Thu 22:56] => 0:36
CLOCK: [2019-09-02 Mon 21:46]--[2019-09-02 Mon 22:10] => 0:24
:END:
* DONE DP Masson : QRM [71/71] DP [33/33]
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Dermato
:ARCHIVE_CATEGORY: dermato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre1 dermato
:END:
:LOGBOOK:
CLOCK: [2019-10-27 Sun 18:14]--[2019-10-27 Sun 20:05] => 1:51
CLOCK: [2019-10-27 Sun 16:36]--[2019-10-27 Sun 1 :12] => 0:36
CLOCK: [2019-10-27 Sun 15:35]--[2019-10-27 Sun 16:13] => 0:38
CLOCK: [2019-10-27 Sun 14:13]--[2019-10-27 Sun 15:10] => 0:57
:END:
* DONE Abrégé des très bien classés
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Dermato
:ARCHIVE_CATEGORY: dermato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre1 dermato
:END:
* CANCELLED Annales [2/2]
DEADLINE: <2019-12-12 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Dermato
:ARCHIVE_CATEGORY: dermato
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A2 semestre1 dermato
:END:
:LOGBOOK:
CLOCK: [2019-12-16 Mon 20:11]--[2019-12-16 Mon 20:53] => 0:42
CLOCK: [2019-12-12 Thu 15:28]--[2019-12-12 Thu 15:41] => 0:13
CLOCK: [2019-12-12 Thu 12:46]--[2019-12-12 Thu 14:05] => 1:19
CLOCK: [2019-12-12 Thu 00:06]--[2019-12-12 Thu 00:32] => 0:26
:END:
** CANCELLED décembre 2018 [1/2]
** CANCELLED décembre 2017 [1/2]
** CANCELLED avril 2017 [1/2]
** CANCELLED décembre 2016 [1/2]
** CANCELLED avril 2016
* CANCELLED Révisions profs ?
DEADLINE: <2019-12-12 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:56
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Dermato
:ARCHIVE_CATEGORY: dermato
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A2 semestre1 dermato
:END:
* CANCELLED Fiches nutrition
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Endocrino
:ARCHIVE_CATEGORY: endocrino
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A1 semestre1 endocrino
:END:
* DONE Collège
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Endocrino
:ARCHIVE_CATEGORY: endocrino
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 semestre1 endocrino
:END:
* DONE Passe 1 ECNI et collège
DEADLINE: <2019-10-16 Wed> SCHEDULED: <2019-10-13 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gériatrie
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions géria A2 semestre1
:END:
* DONE DP Masson [14/14] QI [228/228]
DEADLINE: <2019-11-15 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gériatrie
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions géria A2 semestre1
:END:
:LOGBOOK:
CLOCK: [2019-11-16 Sat 18:57]--[2019-11-16 Sat 23:12] => 4:15
CLOCK: [2019-11-16 Sat 16:04]--[2019-11-16 Sat 16:30] => 0:26
CLOCK: [2019-11-16 Sat 13:25]--[2019-11-16 Sat 14:19] => 0:54
CLOCK: [2019-11-16 Sat 11:15]--[2019-11-16 Sat 12:00] => 0:45
CLOCK: [2019-11-15 Fri 21:44]--[2019-11-15 Fri 23:30] => 1:46
CLOCK: [2019-11-15 Fri 17:07]--[2019-11-15 Fri 18:52] => 1:45
CLOCK: [2019-11-15 Fri 14:23]--[2019-11-15 Fri 16:00] => 1:37
CLOCK: [2019-11-15 Fri 11:15]--[2019-11-15 Fri 12:06] => 0:51
:END:
* CANCELLED Révisions profs ?
DEADLINE: <2019-12-12 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gériatrie
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions géria A2 semestre1
:END:
* DONE Cas cliniques profs
DEADLINE: <2019-12-12 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gériatrie
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions géria A2 semestre1
:END:
:LOGBOOK:
CLOCK: [2019-12-13 Fri 14:19]--[2019-12-13 Fri 15:06] => 0:47
:END:
* DONE Abrégé des très bien classés
DEADLINE: <2019-12-09 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gériatrie
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions géria A2 semestre1
:END:
* CANCELLED Annales
DEADLINE: <2019-12-12 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gériatrie
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions géria A2 semestre1
:END:
:LOGBOOK:
CLOCK: [2019-12-13 Fri 12:10]--[2019-12-13 Fri 12:55] => 0:45
CLOCK: [2019-12-13 Fri 11:21]--[2019-12-13 Fri 11:39] => 0:18
CLOCK: [2019-12-12 Thu 22:39]--[2019-12-12 Thu 23:52] => 1:13
CLOCK: [2019-12-12 Thu 22:17]--[2019-12-12 Thu 22:28] => 0:11
CLOCK: [2019-12-12 Thu 21:43]--[2019-12-12 Thu 21:55] => 0:08
CLOCK: [2019-12-12 Thu 17:14]--[2019-12-12 Thu 18:25] => 1:11
:END:
** CANCELLED décembre 2018 [1/2]
** CANCELLED décembre 2017 [1/2]
** CANCELLED avril 2017 [1/2]
** CANCELLED décembre 2016
** CANCELLED avril 2016
** CANCELLED avril 2015
** CANCELLED décembre 2014
** CANCELLED novembre 2014
** CANCELLED entraînement
* CANCELLED Cas cliniques profs
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Immunologie
:ARCHIVE_CATEGORY: immuno
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions immuno A2 semestre1
:END:
** CANCELLED Cours
** CANCELLED De révisions
* CANCELLED Annales
DEADLINE: <2019-12-12 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Immunologie
:ARCHIVE_CATEGORY: immuno
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions immuno A2 semestre1
:END:
:LOGBOOK:
CLOCK: [2019-12-15 Sun 17:31]--[2019-12-15 Sun 18:45] => 1:14
CLOCK: [2019-12-15 Sun 16:11]--[2019-12-15 Sun 16:36] => 0:25
:END:
** CANCELLED Décembre 2018 [1/2]
** CANCELLED Décembre 2017 [1/2]
:LOGBOOK:
CLOCK: [2019-12-15 Sun 19:14]--[2019-12-15 Sun 19:42] => 0:28
:END:
* CANCELLED Abrégé des très bien classés
DEADLINE: <2019-12-10 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-13 Mon 10:57
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Immunologie
:ARCHIVE_CATEGORY: immuno
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions immuno A2 semestre1
:END:
* TODO [#A] 150 problèmes d'ECG [94/150]
SCHEDULED: <2019-09-14 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Cardiologie
:ARCHIVE_CATEGORY: cardiologie
:ARCHIVE_TODO: TODO
:ARCHIVE_ITAGS: revisions D1
:END:
* DONE Dossier 1
DEADLINE: <2019-12-05 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Dermato/UE Ecn en concours blanc 2016
:ARCHIVE_CATEGORY: dermato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre1 dermato
:END:
* DONE DP [10/10] QI [40/40]
DEADLINE: <2019-12-06 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gériatrie/Ecn intensif DP et QI
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions géria A2 semestre1
:END:
* DONE Collège
DEADLINE: <2020-03-24 Tue> SCHEDULED: <2020-03-18 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Gynécologie
:ARCHIVE_CATEGORY: gynéco
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 gynéco
:END:
* DONE Dossier [10/10]
DEADLINE: <2019-12-09 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Hémato/Les dossiers ECNI
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions hémato A2 semestre1
:END:
:LOGBOOK:
CLOCK: [2019-12-10 Tue 23:19]--[2019-12-10 Tue 23:40] => 0:21
CLOCK: [2019-12-10 Tue 21:50]--[2019-12-10 Tue 22:55] => 1:05
CLOCK: [2019-12-10 Tue 17:46]--[2019-12-10 Tue 18:46] => 1:00
CLOCK: [2019-12-10 Tue 17:26]--[2019-12-10 Tue 17:35] => 0:09
CLOCK: [2019-12-10 Tue 16:03]--[2019-12-10 Tue 17:02] => 0:59
CLOCK: [2019-12-10 Tue 14:40]--[2019-12-10 Tue 15:23] => 0:43
CLOCK: [2019-12-10 Tue 14:08]--[2019-12-10 Tue 14:31] => 0:23
CLOCK: [2019-12-09 Mon 19:37]--[2019-12-09 Mon 20:03] => 0:26
CLOCK: [2019-12-09 Mon 17:49]--[2019-12-09 Mon 18:23] => 0:34
CLOCK: [2019-12-09 Mon 15:31]--[2019-12-09 Mon 16:22] => 0:51
:END:
* DONE Dossier 1
DEADLINE: <2019-12-10 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Immunologie/UE Ecn en concours blanc 2016
:ARCHIVE_CATEGORY: immuno
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions immuno A2 semestre1
:END:
:LOGBOOK:
CLOCK: [2019-12-11 Wed 23:45]--[2019-12-11 Wed 23:55] => -0:30
CLOCK: [2019-12-11 Wed 21:49]--[2019-12-11 Wed 23:15] => 1:21
CLOCK: [2019-12-11 Wed 21:30]--[2019-12-11 Wed 21:38] => 0:08
CLOCK: [2019-12-11 Wed 18:34]--[2019-12-11 Wed 19:14] => 0:40
CLOCK: [2019-12-11 Wed 17:35]--[2019-12-11 Wed 18:26] => 0:51
CLOCK: [2019-12-11 Wed 14:56]--[2019-12-11 Wed 15:48] => 0:52
CLOCK: [2019-12-11 Wed 14:26]--[2019-12-11 Wed 14:38] => 0:12
CLOCK: [2019-12-11 Wed 13:52]--[2019-12-11 Wed 14:09] => 0:17
CLOCK: [2019-12-11 Wed 12:41]--[2019-12-11 Wed 13:00] => 0:19
CLOCK: [2019-12-11 Wed 11:25]--[2019-12-11 Mon 12:05] => 0:40
:END:
* TODO [#B] Lire ECNI (cf LATE et tag retard) [2/23]
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Nephrologie
:ARCHIVE_CATEGORY: nephro
:ARCHIVE_TODO: TODO
:ARCHIVE_ITAGS: revisions A1 semestre2 nephro
:END:
:LOGBOOK:
CLOCK: [2019-08-18 Sun 22:55]--[2019-08-18 Sun 23:00] => 0:05
:END:
** TODO [[23 Principales complications de la grossesse]]
** TODO [[126 Personne agée malade]]
** TODO [[157 Infections urinaires]]
** TODO [[190 Lupus erythémateux systémique]]
** TODO [[197 Transplantation d'organes]]
** TODO [[217 Amylose]]
** TODO [[221 HTA]]
** TODO [[245 Diabète]]
** TODO [[254 Syndromes oedemateux]]
** TODO [[255 Élévation de la créatinine]]
** DONE [[256 Protéinurie et syndrome néphrotique]]
** TODO [[257 Hématurie]]
** TODO [[258 Néphropathies glomérulaires]]
** TODO [[259 Néphropathies interstitielles chroniques]]
** TODO [[260 Néphropathies vasculaires]]
** DONE [[261 Insuffisance rénale chronique]]
** TODO [[262 Lithiase urinaire]]
** TODO [[263 Polykystose rénale]]
** TODO [[264 Diurétiques]]
** TODO [[265 Hypocalcémie, dyskaliémie, hyponatrémie]]
** TODO [[266 Hypercalcémie]]
** TODO [[317 Myélome multiple]]
** TODO [[326 Médicaments les plus courants]]
* DONE 1ere passe
SCHEDULED: <2020-03-02 Mon> DEADLINE: <2020-03-05 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Orthopédie/ECNI intensif (non disponible en ligne)
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 ortho
:END:
** DONE DP [26/35]
** DONE QI [70/150]
* DONE DP [1-10] (doute sur dossiers entre 10 et 15...)
DEADLINE: <2020-03-17 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Pédiatrie/Les dossiers ECNI 2016
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 pedia
:END:
:LOGBOOK:
CLOCK: [2020-03-19 Thu 21:00]--[2020-03-19 Thu 21:53] => 0:53
CLOCK: [2020-03-19 Thu 17:45]--[2020-03-19 Thu 18:25] => 0:40
CLOCK: [2020-03-19 Thu 10:57]--[2020-03-19 Thu 12:29] => 1:32
CLOCK: [2020-03-18 Wed 23:50]--[2020-03-19 Thu 00:09] => 0:19
CLOCK: [2020-03-18 Wed 17:51]--[2020-03-18 Wed 18:21] => 0:30
CLOCK: [2020-03-18 Wed 19:11]--[2020-03-18 Wed 19:30] => 0:19
:END:
* DONE DP [12/12]
DEADLINE: <2019-12-09 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Rhumato/Les dossiers ECNI
:ARCHIVE_CATEGORY: rhumato
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre1 rhumato
:END:
:LOGBOOK:
CLOCK: [2019-12-08 Sun 23:08]--[2019-12-08 Sun 23:26] => 0:18
CLOCK: [2019-12-08 Sun 21:04]--[2019-12-08 Sun 22:18] => 1:14
CLOCK: [2019-12-08 Sun 18:01]--[2019-12-08 Sun 18:46] => 0:45
:END:
* DONE Cardio, pneumo, digestif [2/2]
DEADLINE: <2020-04-17 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Garde/Urgences/Examen clinique
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
:LOGBOOK:
CLOCK: [2020-04-17 Fri 15:47]--[2020-04-17 Fri 16:57] => 1:10
:END:
** DONE Sémiologie médicale
Digestif, pneumo
** DONE Vidéos
Digestif
* CANCELLED Neuro, locomoteur, autre
DEADLINE: <2020-04-19 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-20 Wed 11:31
:ARCHIVE_FILE: ~/projects/tasks/revisions.org
:ARCHIVE_OLPATH: Garde/Urgences/Examen clinique
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions
:END:
** CANCELLED Sémiologie médicale
neuro
** CANCELLED Vidéos
* CANCELLED QCM en orthopédie (en ligne)
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-18 Thu 18:01
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Orthopédie
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A2 semestre2 ortho
:END:
http://univ.scholarvox.com.bases-doc.univ-lorraine.fr/catalog/book/docid/88830153
* CANCELLED Pôle locomoteur (en ligne)
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-18 Thu 18:01
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Orthopédie
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: revisions A2 semestre2 ortho
:END:
https://www-elsevierelibrary-fr.bases-doc.univ-lorraine.fr/epubreader/ple-locomoteur-orthopdietraumatologie-rhumatologie
* DONE ECN asso
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-20 Sat 17:39
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Orthopédie
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 ortho
:END:
** DONE 09/04/202
** DONE Conf [2020-06-18 Thu]
DEADLINE: <2020-06-18 Thu>
:LOGBOOK:
CLOCK: [2020-06-19 Fri 22:52]--[2020-06-19 Fri 23:29] => 0:37
CLOCK: [2020-06-19 Fri 18:43]--[2020-06-19 Fri 19:02] => 0:19
CLOCK: [2020-06-19 Fri 17:21]--[2020-06-19 Fri 17:46] => 0:25
CLOCK: [2020-06-19 Fri 16:38]--[2020-06-19 Fri 17:12] => 0:34
CLOCK: [2020-06-19 Fri 14:16]--[2020-06-19 Fri 15:30] => 1:14
CLOCK: [2020-06-18 Thu 18:38]--[2020-06-18 Thu 19:08] => 0:30
CLOCK: [2020-06-18 Thu 18:01]--[2020-06-18 Thu 18:09] => 0:08
:END:
* DONE Relire fiches
DEADLINE: <2020-06-11 Thu> SCHEDULED: <2020-06-11 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-20 Sat 17:39
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Orthopédie
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 ortho
:END:
:LOGBOOK:
CLOCK: [2020-06-18 Thu 23:31]--[2020-06-18 Thu 23:57] => 0:26
CLOCK: [2020-06-18 Thu 17:28]--[2020-06-18 Thu 17:51] => 0:23
CLOCK: [2020-06-18 Thu 12:19]--[2020-06-18 Thu 13:00] => 0:41
:END:
ECNI ok
* DONE Relire fiches
DEADLINE: <2020-06-08 Mon> SCHEDULED: <2020-06-03 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-21 Sun 18:03
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Gynécologie
:ARCHIVE_CATEGORY: gynéco
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 gyneco
:END:
:LOGBOOK:
CLOCK: [2020-06-09 Tue 23:32]--[2020-06-09 Tue 23:55] => 0:23
CLOCK: [2020-06-09 Tue 15:13]--[2020-06-09 Tue 16:02] => 0:49
CLOCK: [2020-06-09 Tue 14:12]--[2020-06-09 Tue 14:40] => 0:28
CLOCK: [2020-06-09 Tue 12:49]--[2020-06-09 Tue 13:11] => 0:22
CLOCK: [2020-06-09 Tue 11:28]--[2020-06-09 Tue 11:57] => 0:29
CLOCK: [2020-06-09 Tue 00:00]--[2020-06-09 Tue 00:20] => 0:20
CLOCK: [2020-06-08 Mon 21:58]--[2020-06-08 Mon 22:16] => 0:18
CLOCK: [2020-06-08 Mon 21:14]--[2020-06-08 Mon 21:47] => 0:33
CLOCK: [2020-06-08 Mon 14:42]--[2020-06-08 Mon 14:57] => 0:15
CLOCK: [2020-06-08 Mon 12:38]--[2020-06-08 Mon 13:47] => 1:09
CLOCK: [2020-06-08 Mon 11:14]--[2020-06-08 Mon 11:34] => 0:20
:END:
Ok ecni tout en un
Compléter items du collège
* DONE Ecn asso
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-22 Mon 11:16
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Gynécologie
:ARCHIVE_CATEGORY: gynéco
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 gyneco
:END:
** DONE Conf [2020-06-15 Mon]
:LOGBOOK:
CLOCK: [2020-06-15 Mon 15:11]--[2020-06-15 Mon 16:20] => 1:09
:END:
*** DONE Faire conférence
DEADLINE: <2020-06-15 Mon>
*** DONE Relire conférence
DEADLINE: <2020-06-16 Tue>
DP1 ok
:LOGBOOK:
CLOCK: [2020-06-17 Wed 15:30]--[2020-06-17 Wed 15:48] => 0:18
CLOCK: [2020-06-17 Wed 14:16]--[2020-06-17 Wed 15:00] => 0:44
CLOCK: [2020-06-17 Wed 12:25]--[2020-06-17 Wed 13:17] => 0:52
CLOCK: [2020-06-17 Wed 09:43]--[2020-06-17 Wed 10:03] => 0:20
CLOCK: [2020-06-16 Tue 22:34]--[2020-06-16 Tue 23:04] => 0:30
:END:
* DONE Collège
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-22 Mon 12:25
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Pédiatrie
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 pedia
:END:
* DONE Collège QI DP
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-22 Mon 12:25
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Pédiatrie
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 pedia
:END:
* DONE Conf ecn asso <2020-06-04 Thu>
DEADLINE: <2020-06-04 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-22 Mon 12:25
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Pédiatrie
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 semestre2 pedia
:END:
:LOGBOOK:
CLOCK: [2020-06-07 Sun 19:09]--[2020-06-07 Sun 19:41] => 0:32
CLOCK: [2020-06-07 Sun 17:25]--[2020-06-07 Sun 17:56] => 0:31
CLOCK: [2020-06-07 Sun 16:00]--[2020-06-07 Sun 17:25] => 1:25
CLOCK: [2020-06-04 Thu 14:59]--[2020-06-04 Thu 15:19] => 0:20
:END:
** DONE Faire conf ecn asso
DEADLINE: <2020-06-05 Fri>
** DONE Reprendre corrigé conf
DEADLINE: <2020-06-05 Fri>
* DONE Article d'entraînement " Pregnancy induces persistent changes in vascular compliance in primiparous women"
:PROPERTIES:
:ARCHIVE_TIME: 2020-07-19 Sun 16:21
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Anglais
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions anglais
:END:
:LOGBOOK:
CLOCK: [2020-05-18 Mon 11:54]--[2020-05-18 Mon 12:46] => 0:52
CLOCK: [2020-05-11 Mon 21:27]--[2020-05-11 Mon 21:50] => 0:23
CLOCK: [2020-05-11 Mon 16:44]--[2020-05-11 Mon 17:09] => 0:25
:END:
** DONE Lire
** DONE QCM
* DONE Article d'examen
:PROPERTIES:
:ARCHIVE_TIME: 2020-07-19 Sun 16:21
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Anglais
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions anglais
:END:
** DONE Lire article
DEADLINE: <2020-05-20 Wed>
:LOGBOOK:
CLOCK: [2020-05-21 Thu 11:57]--[2020-05-21 Thu 12:32] => 0:35
:END:
** DONE Réfléchir aux limitations
DEADLINE: <2020-05-22 Fri>
:LOGBOOK:
CLOCK: [2020-05-24 Sun 21:26]--[2020-05-24 Sun 21:45] => 0:19
CLOCK: [2020-05-24 Sun 16:03]--[2020-05-24 Sun 16:18] => 0:15
CLOCK: [2020-05-24 Sun 15:22]--[2020-05-24 Sun 15:41] => 0:19
CLOCK: [2020-05-24 Sun 10:44]--[2020-05-24 Sun 12:26] => 1:42
:END:
* DONE Conf ecn asso
:PROPERTIES:
:ARCHIVE_TIME: 2020-09-03 Thu 22:20
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Neurologie
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Faire
** DONE Assister correction
** DONE Relire corrigé
* DONE 2019-12-16 :endocrino:
:PROPERTIES:
:ARCHIVE_TIME: 2020-09-19 Sat 12:28
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
[[file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_endoc_sujet_2019-12-16.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_endoc_sujet_2019-12-16.pdf]]
* DONE <2020-05-27 Wed> :endocrino:
:PROPERTIES:
:ARCHIVE_TIME: 2020-09-19 Sat 12:28
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
:LOGBOOK:
CLOCK: [2020-05-28 Thu 22:30]--[2020-05-28 Thu 23:35] => 1:05
CLOCK: [2020-05-28 Thu 12:47]--[2020-05-28 Thu 13:47] => 1:00
:END:
** DONE Sujet
DEADLINE: <2020-05-26 Tue>
:LOGBOOK:
CLOCK: [2020-05-26 Tue 22:55]--[2020-05-26 Tue 23:42] => 0:47
CLOCK: [2020-05-26 Tue 20:59]--[2020-05-26 Tue 21:42] => 0:43
CLOCK: [2020-05-26 Tue 19:42]--[2020-05-26 Tue 20:10] => 0:28
CLOCK: [2020-05-26 Tue 18:49]--[2020-05-26 Tue 19:13] => 0:24
:END:
** DONE Relire
DEADLINE: <2020-05-28 Thu>
:LOGBOOK:
CLOCK: [2020-05-28 Thu 17:05]--[2020-05-28 Thu 17:06] => 0:01
CLOCK: [2020-05-28 Thu 15:22]--[2020-05-28 Thu 16:00] => 0:38
CLOCK: [2020-05-27 Wed 12:45]--[2020-05-27 Wed 13:30] => 0:45
:END:
** DONE Copier diapo dès qu'elle sera disponible
DEADLINE: <2020-05-30 Sat>
:LOGBOOK:
CLOCK: [2020-05-29 Fri 11:35]--[2020-05-29 Fri 11:36] => 0:01
:END:
* DONE [2020-08-13 Thu] :pneumo:
:PROPERTIES:
:ARCHIVE_TIME: 2020-09-19 Sat 22:32
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
:LOGBOOK:
CLOCK: [2020-08-15 Sat 18:25]--[2020-08-15 Sat 20:01] => 1:36
:END:
* DONE <2020-09-14 Mon> :nephro:
:PROPERTIES:
:ARCHIVE_TIME: 2020-09-20 Sun 10:49
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Faire épreuve
** DONE Corrigé
DEADLINE: <2020-09-16 Wed>
* DONE <2020-07-15 Wed>
DEADLINE: <2020-09-16 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2020-10-11 Sun 10:06
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: ECNi interfacs
:ARCHIVE_CATEGORY: inter-fac
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Faire l'épreuve
DEADLINE: <2020-07-17 Fri> SCHEDULED: <2020-07-15 Wed>
*** DONE DP 1
*** DONE DP 2
*** DONE DP 3
*** DONE QI
*** DONE QI LCA
** DONE Regarder le corrigé
*** DONE QI
-> 14
*** DONE DP1
**** DONE Dermato
**** DONE médecine interne
*** DONE DP2
**** DONE Méd gé
**** DONE Juillet
*** DONE DP3
**** DONE ECNi blanche Paris 6 Juillet 2020 DP EM
**** DONE Médecine interne
*** DONE LCA
* Pilly, slides et DP
:PROPERTIES:
:ARCHIVE_TIME: 2020-10-11 Sun 10:53
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Maladies infectieuses
:ARCHIVE_CATEGORY: ???
:ARCHIVE_ITAGS: revisions D1 malinf
:END:
| *** TODO Item | Pilly | Slides | Livres uECN |
|--------------------------------+-------+--------------------------------+-------------|
| UE1-4 Sécurité | X | non | |
| UE2-26 Risques foetaux | X | Venard | |
| UE6-142 Surveillance | X | non | 1 QI |
| UE6-143 Vaccinations | X | | 1 QI |
| UE6-144 Fièvre aigüe | X | non | 1 QI |
| UE6-145 Infections naso-sinus | X | non | 1 DP |
| UE6-146 Angines | X | Jacquet | 1 QI |
| UE6-147 Otites | X | non | 1 DP |
| UE6-148 Méningites | X | {Lozniewski, Legof, Schvoerer} | |
| UE6-149, 150 Endocardites | X | Goehringer | 1 DP, 2 QI |
| UE6-151 Infections pulmonaires | X | Lozniewski | |
| UE6-152 Infections cutanéo-muq | X | | 1 DP |
| UE6-153 Infections ostéo-art | X | | |
| UE6-154 Septicémie | X | 1 QI | |
| UE6-155 Tuberculose | X | | 1DP |
| UE6-156 Tétanos | X | Non ? | |
| UE6-157 Infections urinaires | X | {Lozniewski, Henard} | 1 DP, 1 QI |
| UE6-158 IST | X | {Lozniewski, Jacquet} | |
| UE6-159 Coqueluche | X | Lozniewski | |
| UE6-161 Oreillons | X | Non | |
| UE6-160 Eruptives | X | {Jeulin, May} | |
| UE6-162 Grippe | X | Shroever | |
| UE6-163 Hépatites virales | X | | 1 DP |
| UE6-164 Herpès | X | Jeulin | 1 DP |
| UE6-165 VIH | X | {Venard, Jeulin, May, Boyer} | |
| UE6-166 Paludisme | X | Debourgogne | |
| UE6-167 Gale et pédiculose | X | | |
| UE6-168 Parasitoses digestives | X | | 1 DP, 1 QI |
| UE6-169 Zoonose | X | | 1 QI |
| UE6-170 Migrants | X | | |
| UE6-171 Voyage | X | | |
| UE6-172 Diarrhées infectieuses | X | 1 DP | |
| UE6-173 ATB | X | Pulcini | |
| UE6-174 Risques | X | non | |
| UE6-186 Fièvre prolongée | X | | |
| UE6-187 Fièvre chez ID | X | | |
| UE6-211 Purpuras | X | | |
| UE6-213 Sd mononucléosique | X | Jacquet | |
| UE6-214 Éosinophilie | lu | | |
| UE6-216 Adénopathie | lu | | |
| UE11-352 Péritonite | lu | | |
| UE11-363 Exposition | lu | | |
* KILL UE Ecn en concours blanc 2016 [3/3]
:PROPERTIES:
:ARCHIVE_TIME: 2020-10-31 Sat 13:38
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Dermato
:ARCHIVE_CATEGORY: dermato
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 dermato
:END:
** KILL Dossier 2
** KILL Dossier 3
** KILL Dossier 4
* Hémato :hémato:A2:
:PROPERTIES:
:CATEGORY: hémato
:ARCHIVE_TIME: 2020-11-08 Sun 10:32
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_ITAGS: revisions
:END:
** KILL Les dossiers ECNI
:PROPERTIES:
:CATEGORY: hémato
:END:
*** KILL Dossier 13-30
* TODO Les dossiers ECNI
:PROPERTIES:
:CATEGORY: hémato
:ARCHIVE_TIME: 2020-11-08 Sun 10:33
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Hémato
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_TODO: TODO
:ARCHIVE_ITAGS: revisions hémato A2
:END:
** KILL Dossier 13-30
* Anglais :anglais:
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:33
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_CATEGORY: ???
:ARCHIVE_ITAGS: revisions
:END:
* DONE Collège
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:33
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Cancérologie
:ARCHIVE_CATEGORY: cancero
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 cancero
:END:
* KILL Annales
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:33
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Cancérologie
:ARCHIVE_CATEGORY: cancero
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 cancero
:END:
:LOGBOOK:
CLOCK: [2020-06-18 Thu 15:18]--[2020-06-18 Thu 16:20] => 1:02
CLOCK: [2020-06-18 Thu 10:52]--[2020-06-18 Thu 11:20] => 0:28
CLOCK: [2020-06-17 Wed 22:25]--[2020-06-17 Wed 23:40] => 1:15
CLOCK: [2020-06-17 Wed 19:41]--[2020-06-17 Wed 19:52] => 0:11
CLOCK: [2020-06-17 Wed 19:05]--[2020-06-17 Wed 19:28] => 0:23
:END:
** KILL Passe 1
:LOGBOOK:
CLOCK: [2020-06-23 Tue 20:47]--[2020-06-23 Tue 22:03] => 1:16
:END:
- [X] [[https://side-sante.fr/playtest/classic/2602023][CANCERO juin 2019]]
- [X] [[https://side-sante.fr/playtest/classic/1456262][CANCERO juin 2018]]
- [X] [[https://side-sante.fr/playtest/classic/483106][CANCERO août 2017]]
- [ ] [[https://side-sante.fr/playtest/classic/455370][CANCERO juin 2017]]
- [-] [[https://side-sante.fr/playtest/classic/719723][CANCERO sept 2016]]
- [-] [[https://side-sante.fr/playtest/classic/77722][CANCERO juin 2016]]
- [-] [[https://side-sante.fr/playtest/classic/5906][CANCERO juin 2015]]
- [-] [[https://side-sante.fr/playtest/classic/6601][CANCERO sept 2015]]
** KILL Passe 2
* KILL Lire diapos + faire CC
DEADLINE: <2020-06-23 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:33
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Cancérologie
:ARCHIVE_CATEGORY: cancero
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 cancero
:END:
[[file:~/Downloads/cancero][file:~/Downloads/cancero]]
* KILL Conf+ [7/7]
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:33
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Cancérologie
:ARCHIVE_CATEGORY: cancero
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 cancero
:END:
:LOGBOOK:
CLOCK: [2020-05-25 Mon 17:37]--[2020-05-25 Mon 18:10] => 0:33
CLOCK: [2020-05-25 Mon 15:07]--[2020-05-25 Mon 15:55] => 0:48
CLOCK: [2020-05-25 Mon 12:07]--[2020-05-25 Mon 12:37] => 0:30
CLOCK: [2020-05-25 Mon 10:38]--[2020-05-25 Mon 11:51] => 1:13
CLOCK: [2020-05-24 Sun 17:34]--[2020-05-24 Sun 18:34] => 1:00
CLOCK: [2020-05-23 Sat 17:01]--[2020-05-23 Sat 18:02] => 1:01
CLOCK: [2020-05-23 Sat 16:18]--[2020-05-23 Sat 16:44] => 0:26
CLOCK: [2020-05-23 Sat 12:57]--[2020-05-23 Sat 13:03] => 0:06
CLOCK: [2020-05-22 Fri 12:49]--[2020-05-22 Fri 13:14] => 0:25
CLOCK: [2020-05-22 Fri 11:18]--[2020-05-22 Fri 11:46] => 0:28
CLOCK: [2020-05-21 Thu 18:13]--[2020-05-21 Thu 18:40] => 0:27
CLOCK: [2020-05-21 Thu 17:04]--[2020-05-21 Thu 17:23] => 0:19
CLOCK: [2020-05-21 Thu 00:10]--[2020-05-21 Thu 00:28] => 0:18
CLOCK: [2020-05-20 Wed 22:01]--[2020-05-20 Wed 22:50] => 0:49
CLOCK: [2020-05-20 Wed 16:17]--[2020-05-20 Wed 17:27] => 1:10
CLOCK: [2020-05-20 Wed 13:18]--[2020-05-20 Wed 13:58] => 0:40
CLOCK: [2020-05-20 Wed 11:37]--[2020-05-20 Wed 11:48] => 0:11
:END:
** DONE DP 1 D3
** DONE DP 2 D3
** DONE QI 1 D3
** DONE QI 2 D3
** DONE QI 3 D3
** KILL Entraînement D3
** KILL Consensus D3
* DONE Relire fiches
DEADLINE: <2020-05-29 Fri> SCHEDULED: <2020-05-24 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:33
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Cancérologie
:ARCHIVE_CATEGORY: cancero
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 cancero
:END:
:LOGBOOK:
CLOCK: [2020-06-01 Mon 15:20]--[2020-06-01 Mon 16:44] => 1:24
CLOCK: [2020-06-01 Mon 14:38]--[2020-06-01 Mon 15:03] => 0:25
CLOCK: [2020-06-01 Mon 12:27]--[2020-06-01 Mon 13:15] => 0:48
CLOCK: [2020-06-01 Mon 11:21]--[2020-06-01 Mon 12:17] => 0:56
CLOCK: [2020-05-31 Sun 23:32]--[2020-05-31 Sun 23:39] => 0:07
CLOCK: [2020-05-31 Sun 21:39]--[2020-05-31 Sun 22:46] => 1:07
CLOCK: [2020-05-31 Sun 17:59]--[2020-05-31 Sun 18:15] => 0:16
CLOCK: [2020-05-31 Sun 14:14]--[2020-05-31 Sun 15:44] => 1:30
CLOCK: [2020-05-31 Sun 11:00]--[2020-05-31 Sun 11:45] => 0:45
CLOCK: [2020-05-30 Sat 18:59]--[2020-05-30 Sat 19:24] => 0:25
CLOCK: [2020-05-30 Sat 16:17]--[2020-05-30 Sat 17:33] => 1:16
CLOCK: [2020-05-30 Sat 12:51]--[2020-05-30 Sat 13:40] => 0:49
CLOCK: [2020-05-29 Fri 21:56]--[2020-05-29 Fri 22:05] => 0:09
CLOCK: [2020-05-29 Fri 19:29]--[2020-05-29 Fri 19:51] => 0:22
CLOCK: [2020-05-27 Wed 16:11]--[2020-05-27 Wed 17:35] => 1:24
CLOCK: [2020-05-27 Wed 12:43]--[2020-05-27 Wed 13:20] => 0:37
CLOCK: [2020-05-27 Wed 12:12]--[2020-05-27 Wed 12:26] => 0:14
CLOCK: [2020-05-26 Tue 11:00]--[2020-05-26 Tue 12:00] => 1:00
CLOCK: [2020-05-25 Mon 23:06]--[2020-05-25 Mon 23:53] => 0:47
:END:
** TODO Item 307
* DONE ECN asso
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:33
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Cancérologie
:ARCHIVE_CATEGORY: cancero
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 cancero
:END:
:LOGBOOK:
CLOCK: [2020-05-31 Sun 15:28]--[2020-05-31 Sun 16:13] => 0:45
:END:
** DONE Conf du 2020-05-28
DEADLINE: <2020-05-28 Thu>
:LOGBOOK:
CLOCK: [2020-05-29 Fri 16:14]--[2020-05-29 Fri 17:24] => 1:10
CLOCK: [2020-05-28 Thu 12:23]--[2020-05-28 Thu 13:37] => 1:14
CLOCK: [2020-05-28 Thu 11:23]--[2020-05-28 Thu 11:57] => 0:34
:END:
*** DONE Faire la conf
*** DONE Relire
** DONE Conf [2020-06-17 Wed]
DEADLINE: <2020-06-17 Wed>
* KILL Exercices masson
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Gynécologie
:ARCHIVE_CATEGORY: gynéco
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 gyneco
:END:
** KILL CC [5/5]
** DONE DP [23/23]
DEADLINE: <2020-06-09 Tue> SCHEDULED: <2020-06-01 Mon>
:LOGBOOK:
CLOCK: [2020-06-10 Wed 17:33]--[2020-06-10 Wed 20:27] => 2:54
CLOCK: [2020-06-10 Wed 16:57]--[2020-06-10 Wed 17:27] => 0:30
CLOCK: [2020-06-09 Tue 21:45]--[2020-06-09 Tue 22:40] => 0:55
CLOCK: [2020-06-08 Mon 20:50]--[2020-06-08 Mon 21:14] => 0:24
CLOCK: [2020-06-08 Mon 15:40]--[2020-06-08 Mon 16:30] => 0:50
CLOCK: [2020-06-08 Mon 15:05]--[2020-06-08 Mon 15:36] => 0:31
CLOCK: [2020-06-06 Sat 21:54]--[2020-06-06 Sat 22:25] => 0:31
CLOCK: [2020-06-06 Sat 18:11]--[2020-06-06 Sat 18:25] => 0:14
CLOCK: [2020-06-06 Sat 16:22]--[2020-06-06 Sat 17:06] => 0:44
CLOCK: [2020-06-06 Sat 14:32]--[2020-06-06 Sat 15:57] => 1:25
CLOCK: [2020-06-06 Sat 13:17]--[2020-06-06 Sat 14:03] => 0:46
CLOCK: [2020-06-06 Sat 11:26]--[2020-06-06 Sat 12:10] => 0:44
CLOCK: [2020-06-05 Fri 22:51]--[2020-06-05 Fri 23:30] => 0:39
CLOCK: [2020-06-05 Fri 21:41]--[2020-06-05 Fri 22:02] => 0:21
CLOCK: [2020-06-05 Fri 12:39]--[2020-06-05 Fri 13:20] => 0:41
CLOCK: [2020-06-04 Thu 22:44]--[2020-06-04 Thu 23:45] => 1:01
CLOCK: [2020-06-04 Thu 19:46]--[2020-06-04 Thu 21:00] => 1:14
CLOCK: [2020-06-03 Wed 19:10]--[2020-06-03 Wed 19:39] => 0:29
CLOCK: [2020-06-02 Tue 21:52]--[2020-06-02 Tue 22:35] => 0:43
CLOCK: [2020-06-02 Tue 17:48]--[2020-06-02 Tue 18:48] => 1:00
CLOCK: [2020-06-02 Tue 17:10]--[2020-06-02 Tue 17:35] => 0:25
CLOCK: [2020-06-01 Mon 21:38]--[2020-06-01 Mon 23:12] => 1:34
CLOCK: [2020-06-01 Mon 18:54]--[2020-06-01 Mon 19:56] => 1:02
:END:
** KILL QI [/200]
* KILL Lire diapos et faire CC
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Gynécologie
:ARCHIVE_CATEGORY: gynéco
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 gyneco
:END:
:LOGBOOK:
CLOCK: [2020-06-21 Sun 21:55]--[2020-06-21 Sun 22:51] => 0:56
CLOCK: [2020-06-21 Sun 16:41]--[2020-06-21 Sun 17:13] => 0:32
CLOCK: [2020-06-21 Sun 15:59]--[2020-06-21 Sun 16:20] => 0:21
:END:
# [[file:~/Downloads/gyneco][file:~/Downloads/gyneco]]
- [X] [[~/Downloads/gyneco/Algies pelviennes FASM2.pdf]]
- [X] [[~/Downloads/gyneco/Allaitement et complications.pdf]]
- [X] [[~/Downloads/gyneco/Aménorrhée.pdf]]
- [X] [[~/Downloads/gyneco/cancer du col 2016.pdf]]
- [X] [[~/Downloads/gyneco/CAS CLINIQUE AMP.pptx]]
- [X] [[~/Downloads/gyneco/diabète.pdf]]
- [X] [[~/Downloads/gyneco/Douleur abdo chez la femme enceinte DU 2017.pdf]]
- [ ] [[~/Downloads/gyneco/DP douleurs pelviennes.pptx]]
- [ ] [[~/Downloads/gyneco/DP FCUK.pptx]]
- [X] [[~/Downloads/gyneco/DP fibrome.pptx]]
- [ ] [[~/Downloads/gyneco/DP Grossesse Localisation Indéterminée.pptx]]
- [ ] [[~/Downloads/gyneco/FASM2 - 35 - Contraception.pdf]]
- [ ] [[~/Downloads/gyneco/FASM2 - 36 - IVG.pdf]]
- [ ] [[~/Downloads/gyneco/FASM2 - 41 - Hémorragies génitales.pdf]]
- [ ] [[~/Downloads/gyneco/FASM2 - 42 - Tuméfactions pelviennes.pdf]]
- [ ] [[~/Downloads/gyneco/Fasm 2 doul pelv 20020.pptx]]
- [ ] [[~/Downloads/gyneco/FASM 2 MTR 2018.pdf]]
- [ ] [[~/Downloads/gyneco/FCTMAPRPM int.ppt]]
- [ ] [[~/Downloads/gyneco/Fièvre et Grossesse.pdf]]
- [ ] [[~/Downloads/gyneco/GEU FASM2.pdf]]
- [ ] [[~/Downloads/gyneco/grossesse nle et accouchement.pdf]]
- [ ] [[~/Downloads/gyneco/HTA grossesse 2018.pdf]]
- [ ] [[~/Downloads/gyneco/I26-FASM2.pdf]]
- [ ] [[~/Downloads/gyneco/IGH FASM2.pdf]]
- [ ] [[~/Downloads/gyneco/Infertilité.pdf]]
- [ ] [[~/Downloads/gyneco/Item 22 – Grossesse normale.pdf]]
- [ ] [[~/Downloads/gyneco/Item 29 _ prématurité et RCIU.pdf]]
- [ ] [[~/Downloads/gyneco/Item 339_ prééclampsie.pdf]]
- [ ] [[~/Downloads/gyneco/IVG.pdf]]
- [ ] [[~/Downloads/gyneco/Les dysplasies cervicales 2017.pdf]]
- [ ] [[~/Downloads/gyneco/MAP.RPM..pdf]]
- [ ] [[~/Downloads/gyneco/Ménopause.pdf]]
- [ ] [[~/Downloads/gyneco/nutrition et gross.pdf]]
- [ ] [[~/Downloads/gyneco/Prématurité spontanée.pdf]]
- [ ] [[~/Downloads/gyneco/Présentation HPP.pdf]]
- [ ] [[~/Downloads/gyneco/RCIU 2018.pdf]]
- [ ] [[~/Downloads/gyneco/suite de couches.pdf]]
- [ ] [[~/Downloads/gyneco/Trame CS AMP.pdf]]
- [ ] [[~/Downloads/gyneco/Troubles du cycle.pdf]]
- [ ] [[~/Downloads/gyneco/Tumeurs de l’ovaire.pdf]]
* KILL ECNI intensif (disponible en ligne)
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Gynécologie
:ARCHIVE_CATEGORY: gynéco
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 gyneco
:END:
https://www-elsevierelibrary-fr.bases-doc.univ-lorraine.fr/epubreader/gyncologieobsttrique15185761
* KILL Pôle abdominopelvien (en ligne)
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Gynécologie
:ARCHIVE_CATEGORY: gynéco
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 gyneco
:END:
https://www-elsevierelibrary-fr.bases-doc.univ-lorraine.fr/epubreader/ple-abdominopelvien-gyncologieobsttriquehpatogastroentrologiechirurgie-digestive
* KILL Annales
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Gynécologie
:ARCHIVE_CATEGORY: gynéco
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 gyneco
:END:
** KILL Passe 1
:LOGBOOK:
CLOCK: [2020-06-22 Mon 11:16]--[2020-06-22 Mon 11:52] => 0:36
CLOCK: [2020-06-21 Sun 23:43]--[2020-06-22 Mon 00:25] => 0:42
CLOCK: [2020-06-21 Sun 22:54]--[2020-06-21 Sun 23:20] => 0:26
CLOCK: [2020-06-21 Sun 18:03]--[2020-06-21 Sun 19:30] => 1:27
CLOCK: [2020-06-21 Sun 14:04]--[2020-06-21 Sun 14:40] => 0:36
CLOCK: [2020-06-21 Sun 13:14]--[2020-06-21 Sun 13:22] => 0:08
CLOCK: [2020-06-21 Sun 12:43]--[2020-06-21 Sun 12:55] => 0:12
:END:
- [X] [[https://side-sante.fr/playtest/classic/2601978][Gynecologie Juin 2019]]
- [X] [[https://side-sante.fr/playtest/classic/1456307][gyneco 26 juin 2018]]
- [X] [[https://side-sante.fr/playtest/classic/483059][GYNECO août 2017]]
- [-] [[https://side-sante.fr/playtest/classic/455371][Gyneco juin 2017]]
- [-] [[https://side-sante.fr/playtest/classic/77724][GYNECO juin 2016]]
- [-] [[https://side-sante.fr/playtest/classic/358415][GYNECO sept 2016]]
- [-] [[https://side-sante.fr/playtest/classic/11837][Gyneco juin 2015]]
- [-] [[https://side-sante.fr/playtest/classic/7136][Gyneco sept 2015]]
* Génétique
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_CATEGORY: ???
:ARCHIVE_ITAGS: revisions
:END:
Livret à la fin
Source: https://www-elsevierelibrary-fr.bases-doc.univ-lorraine.fr/epubreader/gntique-mdicale
* KILL Masson QRC [0/35]
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Gériatrie
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions geria A2
:END:
* KILL Ecn intensif DP et QI
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Gériatrie
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions geria A2
:END:
** KILL DP 10-50 QI 0-140
* KILL ECN Asso
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Maladies infectieuses
:ARCHIVE_CATEGORY: malinf
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions D1 malinf
:END:
** DONE Conf <2020-05-18 Mon>
DEADLINE: <2020-05-19 Tue>
:LOGBOOK:
CLOCK: [2020-05-19 Tue 11:29]--[2020-05-19 Tue 12:42] => 1:13
CLOCK: [2020-05-18 Mon 23:56]--[2020-05-19 Tue 00:29] => 0:33
CLOCK: [2020-05-17 Sun 22:56]--[2020-05-17 Sun 23:25] => 0:29
:END:
*** Relire
DP 1 ok
** KILL Conf <2020-05-13 Wed>
https://www.twitch.tv/videos/620892295
* KILL Conf ecn asso
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: MPR
:ARCHIVE_CATEGORY: ???
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A1 mpr
:END:
[[file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_mpr_corrige.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_mpr_corrige.pdf]]
* DONE [#B] Lire collège (cf et tag retard) [23/23]
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Nephrologie
:ARCHIVE_CATEGORY: nephro
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A1 nephro
:END:
:LOGBOOK:
CLOCK: [2020-08-19 Wed 22:31]--[2020-08-19 Wed 23:56] => 1:25
CLOCK: [2020-08-19 Wed 21:19]--[2020-08-19 Wed 21:39] => 0:20
CLOCK: [2020-08-19 Wed 18:13]--[2020-08-19 Wed 18:46] => 0:33
CLOCK: [2020-08-19 Wed 12:04]--[2020-08-19 Wed 12:18] => 0:14
CLOCK: [2020-08-19 Wed 10:42]--[2020-08-19 Wed 11:16] => 0:34
CLOCK: [2020-08-18 Tue 15:01]--[2020-08-18 Tue 16:05] => 1:04
CLOCK: [2020-08-18 Tue 13:53]--[2020-08-18 Tue 14:33] => 0:40
CLOCK: [2020-08-18 Tue 10:44]--[2020-08-18 Tue 11:48] => 1:04
CLOCK: [2020-08-17 Mon 22:28]--[2020-08-17 Mon 22:59] => 0:31
CLOCK: [2020-08-17 Mon 15:33]--[2020-08-17 Mon 15:47] => 0:14
CLOCK: [2020-08-17 Mon 14:40]--[2020-08-17 Mon 15:01] => 0:21
CLOCK: [2020-08-17 Mon 14:13]--[2020-08-17 Mon 14:32] => 0:19
CLOCK: [2020-08-17 Mon 11:52]--[2020-08-17 Mon 12:42] => 0:50
CLOCK: [2020-08-17 Mon 10:18]--[2020-08-17 Mon 11:06] => 0:48
CLOCK: [2020-07-13 Mon 23:29]--[2020-07-13 Mon 23:48] => 0:19
CLOCK: [2020-05-10 Sun 10:39]--[2020-05-10 Sun 11:50] => 1:11
:END:
** DONE [[23 Principales complications de la grossesse]]
DEADLINE: <2020-08-17 Mon>
** DONE [[126 Personne agée malade]]
** DONE [[157 Infections urinaires]]
DEADLINE: <2020-08-17 Mon>
** DONE [[190 Lupus erythémateux systémique]]
** DONE [[197 Transplantation d'organes]]
** DONE [[217 Amylose]]
** DONE [[221 HTA]]
DEADLINE: <2020-08-17 Mon>
** DONE [[245 Diabète]]
** DONE [[254 Syndromes oedemateux]]
** DONE [[255 Élévation de la créatinine]]
** DONE [[256 Protéinurie et syndrome néphrotique]]
** DONE [[257 Hématurie]]
** DONE [[258 Néphropathies glomérulaires]]
** DONE [[259 Néphropathies interstitielles chroniques]]
** DONE [[260 Néphropathies vasculaires]]
DEADLINE: <2020-08-17 Mon>
** DONE [[261 Insuffisance rénale chronique]]
** DONE [[262 Lithiase urinaire]]
** DONE [[263 Polykystose rénale]]
** DONE [[264 Diurétiques]]
** DONE [[265 Hypocalcémie, dyskaliémie, hyponatrémie]]
** DONE [[266 Hypercalcémie]]
** DONE [[317 Myélome multiple]]
** DONE [[326 Médicaments les plus courants]]
* KILL Annales
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Nephrologie
:ARCHIVE_CATEGORY: nephro
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A1 nephro
:END:
* KILL Confplus [6/6]
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Nephrologie
:ARCHIVE_CATEGORY: nephro
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A1 nephro
:END:
:LOGBOOK:
CLOCK: [2020-08-19 Wed 16:34]--[2020-08-19 Wed 17:24] => 0:50
CLOCK: [2020-08-19 Wed 16:13]--[2020-08-19 Wed 16:24] => 0:11
CLOCK: [2020-08-19 Wed 14:57]--[2020-08-19 Wed 16:04] => 1:07
CLOCK: [2020-08-18 Tue 16:54]--[2020-08-18 Tue 18:13] => 1:19
CLOCK: [2020-08-17 Mon 17:24]--[2020-08-17 Mon 18:14] => 0:50
:END:
** DONE DP 1
** DONE DP 2
DEADLINE: <2020-08-17 Mon>
** KILL DP 3
** DONE QI 1
DEADLINE: <2020-08-17 Mon>
Moitié faite
** KILL QI 2
** KILL QI 3
* KILL ECNI intensif [0/1]
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Nephrologie
:ARCHIVE_CATEGORY: nephro
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A1 nephro
:END:
** KILL CC [1/30]
*** DONE CC 1
*** KILL CC 2
*** KILL CC 3
*** KILL CC 4
*** KILL CC 5
*** KILL CC 6
*** KILL CC 7
*** KILL CC 8
*** KILL CC 9
*** KILL CC 10
*** KILL CC 11
*** KILL CC 12
*** KILL CC 13
*** KILL CC 14
*** KILL CC 15
*** KILL CC 16
*** KILL CC 17
*** KILL CC 18
*** KILL CC 19
*** KILL CC 20
*** KILL CC 21
*** KILL CC 22
*** KILL CC 23
*** KILL CC 24
*** KILL CC 25
*** KILL CC 26
*** KILL CC 27
*** KILL CC 28
*** KILL CC 29
*** KILL CC 30
* KILL Conf ecn asso
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: ORL
:ARCHIVE_CATEGORY: orl
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A1 orl
:END:
[[file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_orl_corrige_2020-03.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_orl_corrige_2020-03.pdf]]
* KILL ECNI intensif
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Orthopédie
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 ortho
:END:
** KILL 2eme passe
*** DONE DP [26/35]
*** DONE QI [70/150]
* TODO Conf+ [1/7]
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Orthopédie
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: TODO
:ARCHIVE_ITAGS: revisions A2 ortho
:END:
:LOGBOOK:
CLOCK: [2020-06-20 Sat 11:31]--[2020-06-20 Sat 12:25] => 0:54
CLOCK: [2020-06-20 Sat 09:30]--[2020-06-20 Sat 10:30] => 1:00
:END:
** DONE DP 1 D3
DEADLINE: <2020-06-20 Sat>
** TODO DP 2 D3
** TODO QI 1 D3
** TODO QI 2 D3
** TODO QI 3 D3
** TODO Entraînement D3
** TODO Consensus D3
* DONE Annales
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Orthopédie
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 ortho
:END:
:LOGBOOK:
CLOCK: [2020-06-21 Sun 00:00]--[2020-06-21 Sun 00:25] => 0:25
CLOCK: [2020-06-20 Sat 23:17]--[2020-06-20 Sat 23:33] => 0:16
CLOCK: [2020-06-20 Sat 22:08]--[2020-06-20 Sat 22:28] => 0:20
CLOCK: [2020-06-20 Sat 21:25]--[2020-06-20 Sat 21:42] => 0:17
CLOCK: [2020-06-20 Sat 18:59]--[2020-06-20 Sat 19:18] => 0:19
CLOCK: [2020-06-20 Sat 17:46]--[2020-06-20 Sat 18:09] => 0:23
CLOCK: [2020-06-20 Sat 16:39]--[2020-06-20 Sat 17:00] => 0:21
CLOCK: [2020-06-20 Sat 15:06]--[2020-06-20 Sat 16:00] => 0:54
CLOCK: [2020-06-20 Sat 13:05]--[2020-06-20 Sat 13:36] => 0:31
CLOCK: [2020-06-19 Fri 23:59]--[2020-06-20 Sat 00:47] => 0:48
:END:
** DONE Passe 1
- [X] [[https://side-sante.fr/playtest/classic/2602043][Orthopédie - Juin 2019]]
- [X] [[https://side-sante.fr/playtest/classic/1456285][orthopédie 27 juin 2018]]
- [X] [[https://side-sante.fr/playtest/classic/483083][ORTHOPEDIE août 2017]]
- [X] [[https://side-sante.fr/playtest/classic/455373][Orthopédie juin 2017]]
- [X] [[https://side-sante.fr/playtest/classic/358414][ORTHO sept 2016]]
- [X] [[https://side-sante.fr/playtest/classic/77723][ORTHOPEDIE juin 2016]]
- [-] [[https://side-sante.fr/playtest/classic/11839][Orthopédie sept 2015]]
- [-] [[https://side-sante.fr/playtest/classic/7029][Orthopédie 12 juin 2015]]
* DONE Collège
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Orthopédie
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 ortho
:END:
* KILL Conf ecn asso D2
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:35
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Psychiatrie
:ARCHIVE_CATEGORY: psy
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A1 psy
:END:
https://www.youtube.com/watch?v=0qoyLdMZmDY
* KILL Conf+ [8/8]
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:36
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Pédiatrie
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 pedia
:END:
** DONE DP1 D3
DEADLINE: <2020-05-02 Sat>
:LOGBOOK:
CLOCK: [2020-05-02 Sat 11:34]--[2020-05-02 Sat 13:13] => 1:39
CLOCK: [2020-05-02 Sat 10:33]--[2020-05-02 Sat 11:02] => 0:29
:END:
** DONE DP2 D3
:LOGBOOK:
CLOCK: [2020-05-03 Sun 21:05]--[2020-05-03 Sun 21:30] => 0:25
:END:
** DONE DP3 D3
DEADLINE: <2020-05-09 Sat>
:LOGBOOK:
CLOCK: [2020-05-09 Sat 18:16]--[2020-05-09 Sat 18:30] => 0:14
CLOCK: [2020-05-09 Sat 16:47]--[2020-05-09 Sat 17:36] => 0:49
CLOCK: [2020-05-09 Sat 14:57]--[2020-05-09 Sat 15:23] => 0:26
:END:
** KILL DP4 D3
** KILL QI 1 D3
** KILL QI 2 D3
** KILL QI 3 D3
** KILL Consensus D3
* KILL Lire diapos + faire CC
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:36
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Pédiatrie
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 pedia
:END:
[[file:~/Downloads/pedia][file:~/Downloads/pedia]]
* KILL Les dossiers ECNI 2016
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:36
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Pédiatrie
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 pedia
:END:
** DONE Refaire DP 1-10 [10/10]
SCHEDULED: <2020-05-09 Sat>
:LOGBOOK:
CLOCK: [2020-05-16 Sat 21:28]--[2020-05-16 Sat 21:43] => 0:15
CLOCK: [2020-05-16 Sat 14:48]--[2020-05-16 Sat 15:05] => 0:17
CLOCK: [2020-05-14 Thu 17:04]--[2020-05-14 Thu 17:54] => 0:50
CLOCK: [2020-05-13 Wed 16:18]--[2020-05-13 Wed 17:30] => 1:12
CLOCK: [2020-05-12 Tue 16:51]--[2020-05-12 Tue 17:33] => 0:42
CLOCK: [2020-05-12 Tue 14:40]--[2020-05-12 Tue 15:56] => 1:16
CLOCK: [2020-05-12 Tue 14:24]--[2020-05-12 Tue 14:38] => 0:14
CLOCK: [2020-05-11 Mon 22:08]--[2020-05-11 Mon 22:22] => 0:14
CLOCK: [2020-05-10 Sun 21:21]--[2020-05-10 Sun 22:09] => 0:48
CLOCK: [2020-05-10 Sun 18:33]--[2020-05-10 Sun 18:50] => 0:17
CLOCK: [2020-05-10 Sun 15:11]--[2020-05-10 Sun 16:30] => 1:19
CLOCK: [2020-05-10 Sun 14:01]--[2020-05-10 Sun 14:54] => 0:53
CLOCK: [2020-05-09 Sat 22:26]--[2020-05-09 Sat 23:00] => 0:34
CLOCK: [2020-05-09 Sat 21:38]--[2020-05-09 Sat 21:49] => 0:11
CLOCK: [2020-05-09 Sat 18:43]--[2020-05-09 Sat 19:11] => 0:28
:END:
** DONE DP 11-15 [15/15] QI [15/15]
DEADLINE: <2020-05-18 Mon>
:LOGBOOK:
CLOCK: [2020-05-19 Tue 22:30]--[2020-05-19 Tue 23:04] => 0:34
CLOCK: [2020-05-19 Tue 17:08]--[2020-05-19 Tue 18:19] => 1:11
CLOCK: [2020-05-19 Tue 15:08]--[2020-05-19 Tue 15:30] => 0:22
CLOCK: [2020-05-19 Tue 13:04]--[2020-05-19 Tue 13:21] => 0:17
CLOCK: [2020-05-18 Mon 18:34]--[2020-05-18 Mon 18:50] => 0:16
CLOCK: [2020-05-18 Mon 15:26]--[2020-05-18 Mon 16:40] => 1:14
CLOCK: [2020-05-18 Mon 15:07]--[2020-05-18 Mon 15:14] => 0:07
CLOCK: [2020-05-17 Sun 19:08]--[2020-05-17 Sun 19:55] => 0:47
CLOCK: [2020-05-17 Sun 16:59]--[2020-05-17 Sun 17:06] => 0:07
CLOCK: [2020-05-17 Sun 16:19]--[2020-05-17 Sun 16:29] => 0:10
CLOCK: [2020-05-17 Sun 14:44]--[2020-05-17 Sun 15:28] => 0:44
CLOCK: [2020-05-17 Sun 14:23]--[2020-05-17 Sun 14:36] => 0:13
CLOCK: [2020-05-17 Sun 12:13]--[2020-05-17 Sun 12:25] => 0:12
:END:
** KILL DP 16-30 QI 16-30
* KILL Annales
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:36
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Pédiatrie
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 pedia
:END:
:LOGBOOK:
CLOCK: [2020-06-22 Mon 20:32]--[2020-06-22 Mon 21:09] => 0:37
CLOCK: [2020-06-22 Mon 16:00]--[2020-06-22 Mon 18:00] => 2:00
CLOCK: [2020-06-22 Mon 14:53]--[2020-06-22 Mon 15:32] => 0:39
CLOCK: [2020-06-22 Mon 13:22]--[2020-06-22 Mon 14:07] => 0:45
CLOCK: [2020-06-22 Mon 12:40]--[2020-06-22 Mon 13:00] => 0:20
:END:
- [X] [[https://side-sante.fr/playtest/classic/2602001][Pédiatrie Juin 2019]]
- [X] [[https://side-sante.fr/playtest/classic/1456330][pédiatrie 26 juin 2018]]
- [?] [[https://side-sante.fr/playtest/classic/483036][PEDIATRIE août 2017]]
- [-] [[https://side-sante.fr/playtest/classic/455372][Pédiatrie juin 2017]]
- [-] [[https://side-sante.fr/playtest/classic/77725][PEDIATRIE juin 2016]]
- [-] [[https://side-sante.fr/playtest/classic/358406][PEDIATRIE sept.2016]]
- [-] [[https://side-sante.fr/playtest/classic/6602][Pédiatrie Sept2015]]
- [-] [[https://side-sante.fr/playtest/classic/5815][Pédiatrie juin 2015]]
* DONE Conf ECN asso du <2020-05-14 Thu>
DEADLINE: <2020-05-19 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:36
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Radiologie
:ARCHIVE_CATEGORY: ???
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions radio
:END:
:LOGBOOK:
CLOCK: [2020-05-23 Sat 11:36]--[2020-05-23 Sat 12:38] => 1:02
CLOCK: [2020-05-22 Fri 14:58]--[2020-05-22 Fri 16:45] => 1:47
:END:
https://www.twitch.tv/videos/620892295
* KILL Les dossiers ECNI
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:36
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Rhumato
:ARCHIVE_CATEGORY: rhumato
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A2 rhumato
:END:
** KILL DP 13-30 QI
* KILL Conf ecn asso
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-08 Sun 10:36
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Urologie
:ARCHIVE_CATEGORY: uro
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions A1 uro
:END:
[[file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_uro_corrige_2020-05.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_uro_corrige_2020-05.pdf]]
:PROPERTIES:
:EXPORT_OPTIONS: toc:nil
:END:
* KILL S-ecn
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-22 Sun 10:30
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf
:ARCHIVE_CATEGORY: conf
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
http://www.s-ecn.com.bases-doc.univ-lorraine.fr/cycle
2 DP et 1 QI par matière
* HOLD Conf +
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-22 Sun 10:32
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf
:ARCHIVE_CATEGORY: conf
:ARCHIVE_TODO: HOLD
:ARCHIVE_ITAGS: revisions
:END:
** HOLD Cardio
:PROPERTIES:
:CATEGORY: cardio
:END:
*** HOLD D2 [0/9]
**** HOLD DP1
**** HOLD DP2
DEADLINE: <2020-09-27 Sun 18:30>
1/2
**** HOLD [#A] DP3
DEADLINE: <2020-09-25 Fri>
1/2
**** HOLD DP4
**** HOLD DP5
DEADLINE: <2020-09-28 Mon>
**** HOLD QI 1
DEADLINE: <2020-10-03 Sat>
**** TODO QI 2
**** TODO QI 3
**** TODO QI 4
*** TODO D3 [0/9]
**** TODO DP1
**** TODO DP2
**** TODO DP3
**** TODO DP4
**** TODO DP5
**** TODO QI 1
**** TODO QI 2
**** TODO QI 3
**** TODO QI 4
** HOLD Pneumo
:PROPERTIES:
:CATEGORY: pneumo
:END:
*** TODO D2 [0/9]
**** TODO DP1
**** TODO DP2
**** TODO DP3
**** TODO DP4
**** TODO DP5
**** TODO QI 1
**** TODO QI 2
**** TODO QI 3
**** TODO QI 4
*** TODO D3 [0/9]
**** TODO DP1
**** TODO DP2
**** TODO DP3
**** TODO DP4
**** TODO DP5
**** TODO QI 1
**** TODO QI 2
**** TODO QI 3
**** TODO QI 4
** HOLD Nephro
:PROPERTIES:
:CATEGORY: nephro
:END:
*** TODO D2 [4/6]
**** DONE DP1
**** DONE DP2
**** DONE DP3
DEADLINE: <2020-09-27 Sun 21:30>
1/2
**** DONE QI 1
**** TODO QI 2
**** TODO QI 3
*** TODO D3 [0/9]
**** TODO DP1
**** TODO DP2
**** TODO DP3
**** TODO DP4
**** TODO DP5
**** TODO QI 1
**** TODO QI 2
**** TODO QI 3
**** TODO QI 4
** HOLD Neuro
:PROPERTIES:
:CATEGORY: neuro
:END:
*** TODO D2 [2/9]
**** DONE DP1
DEADLINE: <2020-10-03 Sat>
**** DONE DP2
DEADLINE: <2020-10-04 Sun>
**** TODO DP3
**** TODO DP4
**** TODO DP5
**** TODO QI 1
**** TODO QI 2
**** TODO QI 3
**** TODO QI 4
*** TODO D3 [0/9]
** HOLD ORL-maxillo
:PROPERTIES:
:CATEGORY: orl
:END:
*** TODO D2 [1/9]
**** DONE CMF DP1
DEADLINE: <2020-10-03 Sat>
**** TODO CMF DP2
**** TODO ORL DP1
**** TODO ORL DP2
**** TODO ORL DP3
**** TODO CMF QI 1
**** TODO CMF QI 2
**** TODO ORL QI 1
**** TODO QI 4
*** TODO D3 [0/9]
* KILL Lire corrigé épreuve sémio EE44EMEB
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-24 Tue 10:11
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Annales ECN
:ARCHIVE_CATEGORY: annales
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
:LOGBOOK:
CLOCK: [2020-05-09 Sat 18:38]--[2020-05-09 Sat 18:43] => 0:05
:END:
* HOLD Annales SIDES
:PROPERTIES:
:ARCHIVE_TIME: 2020-12-03 Thu 10:31
:ARCHIVE_FILE: ~/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Annales ECN
:ARCHIVE_CATEGORY: annales
:ARCHIVE_TODO: HOLD
:ARCHIVE_ITAGS: revisions
:END:
- [ ] [[https://side-sante.fr/playtest/classic/11840][iECN BLANC LCA 30/04/2015 après]]
- [ ] [[https://side-sante.fr/playtest/classic/7138][iECN BLANC 30/04/2015 matin]]
- [ ] [[https://side-sante.fr/playtest/classic/3142][EST LCA-1 juin 2015]]
- [ ] [[https://side-sante.fr/playtest/classic/6026][EST LCA-2 sept 2015]]
- [ ] [[https://side-sante.fr/playtest/classic/1910][EST-1 juin 2015]]
- [ ] [[https://side-sante.fr/playtest/classic/6025][EST-2 sept 2015]]
* Anapath
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-10 Sun 15:49
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_ITAGS: revisions
:END:
** KILL Masson https://www-elsevierelibrary-fr.bases-doc.univ-lorraine.fr/epubreader/anatomie-et-cytologie-pathologiques
* KILL Corrigé radio 2020
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-11 Mon 23:18
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Annales ECN
:ARCHIVE_CATEGORY: annales
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
https://happydoctor.learnybox.com/conference/replay/correction-des-dossiers-d-imagerie-des-ecn-2020/
* DONE Regarder corrigé [2020-09-11 Fri]
DEADLINE: <2020-09-17 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* DONE Regarder corrigé [2020-09-18 Fri]
DEADLINE: <2020-09-21 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
Nephro ok
* DONE Corrigé [2020-09-25 Fri]
DEADLINE: <2020-09-28 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* DONE Regarder corrigé LCA 2020-10-02
DEADLINE: <2020-10-12 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* DONE Regarder corrigé [2020-10-10 Sat]
DEADLINE: <2020-10-14 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* DONE Regarder corrigé [2020-10-16 Fri]
DEADLINE: <2020-10-16 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Revoir la question du trismus si corrigé
DEADLINE: <2020-10-21 Wed>
* DONE Corrigé du <2020-10-23 Fri>
DEADLINE: <2020-10-24 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
* DONE Corrigé du <2020-11-06 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Vidéo mal inf
DEADLINE: <2020-11-11 Wed>
https://drive.google.com/drive/folders/12DNBdF_TmB0jYeFWxipDg4lOrvtdyilT
-> question 10
** DONE Vidéo
DEADLINE: <2020-11-13 Fri>
* DONE Corrigé du <2020-11-13 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Vidéo
DEADLINE: <2020-11-14 Sat>
** DONE QI
DEADLINE: <2020-11-14 Sat>
* DONE Corrigé du <2020-11-20 Fri>
DEADLINE: <2021-01-12 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-17 Sun 12:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Contrôle continu
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Vidéo HGE
** DONE Lire endoc + QI
[[file:/usr/home/alex/cours/Medecine/FASM3/cc-2020-11-20.pdf][file:/usr/home/alex/cours/Medecine/FASM3/cc-2020-11-20.pdf]]
* DONE [2020-08-20 Thu] :cardio:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
:LOGBOOK:
CLOCK: [2020-08-20 Thu 13:47]--[2020-08-20 Thu 14:12] => 0:25
CLOCK: [2020-08-20 Thu 10:05]--[2020-08-20 Thu 10:33] => 0:28
:END:
** DONE Faire
** DONE Relire corrigé
** DONE MAJ Fiches ecni avec collège
*** DONE Blocs autrio-ventriculaire
** DONE Compléter avec diapos
DEADLINE: <2020-09-22 Tue>
** DONE QI
* DONE <2020-09-22 Tue> :lca:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Préparer
DEADLINE: <2020-09-20 Sun>
** DONE Conf
DEADLINE: <2020-09-22 Tue>
** DONE Relire corrigé
DEADLINE: <2020-09-23 Wed>
* DONE <2020-09-23 Wed> :malinf:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Préparer
DEADLINE: <2020-09-21 Mon>
** DONE Conf
DEADLINE: <2020-09-23 Wed>
** DONE Relire corrigé
SCHEDULED: <2020-09-27 Sun 10:45> DEADLINE: <2020-09-27 Sun 11:45>
:LOGBOOK:
CLOCK: [2020-09-27 Sun 14:48]--[2020-09-27 Sun 15:38] => 0:50
CLOCK: [2020-09-27 Sun 12:09]--[2020-09-27 Sun 12:18] => 0:09
CLOCK: [2020-09-27 Sun 10:56]--[2020-09-27 Sun 12:00] => 1:04
:END:
* DONE <2020-10-06 Tue> :hge:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Préparer
DEADLINE: <2020-10-05 Mon>
** DONE Conf
DEADLINE: <2020-10-06 Tue>
** DONE Relire corrigé
DEADLINE: <2020-10-11 Sun>
-> DP1 Q5
* DONE <2020-10-12 Mon> :orl:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Préparer
DEADLINE: <2020-10-11 Sun>
** DONE Conf
DEADLINE: <2020-10-12 Mon>
** DONE Relire corrigé
DEADLINE: <2020-10-13 Mon>
* DONE <2020-10-14 Wed> :hemato:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Preparer
DEADLINE: <2020-10-13 Tue>
DP 1 fait
** DONE Conf
DEADLINE: <2020-10-14 Wed>
** DONE Relire corrigé
DEADLINE: <2020-10-16 Fri>
+ corriger fin QI (à partir de question 10)
* DONE <2020-10-27 Tue> :medinterne:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Preparer
** DONE Conf
DEADLINE: <2020-10-29 Thu>
:LOGBOOK:
CLOCK: [2020-10-29 Thu 11:42]--[2020-10-29 Thu 12:07] => 0:25
CLOCK: [2020-10-29 Thu 11:22]--[2020-10-29 Thu 11:36] => 0:14
CLOCK: [2020-10-29 Thu 10:18]--[2020-10-29 Thu 10:40] => 0:22
CLOCK: [2020-10-29 Thu 09:21]--[2020-10-29 Thu 09:40] => 0:19
:END:
* DONE <2020-10-29 Wed> :endoc:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Preparer
DEADLINE: <2020-10-29 Thu>
** DONE Conf
DEADLINE: <2020-10-30 Fri>
* DONE <2020-11-03 Tue> :psy:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Preparer
DEADLINE: <2020-11-14 Sat>
** DONE Conf
DEADLINE: <2020-11-15 Sun>
** DONE Relire fiches
DEADLINE: <2020-11-23 Mon>
* DONE <2020-11-11 Tue> :ophtalmo:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Preparer
DEADLINE: <2020-11-11 Wed>
** DONE Conf
DEADLINE: <2020-11-11 Wed>
** DONE Relire corrigé
DEADLINE: <2020-12-17 Thu>
* DONE <2020-11-25 Wed> :rhumato:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Preparer
DEADLINE: <2020-12-30 Wed>
** DONE Conf
DEADLINE: <2020-12-30 Wed>
* DONE <2020-11-25 Wed> :dermato:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Preparer
DEADLINE: <2020-12-03 Thu>
** DONE Conf
DEADLINE: <2020-12-03 Thu>
* DONE <2020-12-02 Wed> :rea:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Vidée
DEADLINE: <2020-12-04 Fri>
* DONE <2020-12-17 Thu> :geria:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Faire sujet
DEADLINE: <2021-01-05 Tue>
** DONE Vidéo
DEADLINE: <2021-01-05 Tue>
* DONE <2021-01-07 Thu> :uro:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Faire sujet
DEADLINE: <2021-01-06 Wed>
** DONE Vidéo
DEADLINE: <2021-01-16 Sat>
* DONE [2021-01-19 Tue] :gyneco:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Live
DEADLINE: [2021-01-19 Tue>
** DONE Sujet
DEADLINE: [2021-01-19 Tue>
** DONE Relire corrigé
DEADLINE: <2021-01-20 Wed>
* DONE [2021-01-19 Tue] :cancero:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Live
DEADLINE: <2021-01-20 Wed>
** DONE Sujet
DEADLINE: <2021-01-20 Wed>
** DONE Relire corrigé
DEADLINE: <2021-01-21 Thu>
* DONE [2021-01-28 Thu] :lca:
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-16 Tue 19:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet + corrigé
DEADLINE: <2021-02-02 Tue>
* DONE Relire fiches
DEADLINE: <2020-06-10 Wed> SCHEDULED: <2020-06-10 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2021-02-24 Wed 21:36
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Pédiatrie
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions A2 pedia
:END:
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:END:
:LOGBOOK:
CLOCK: [2020-06-16 Tue 20:39]--[2020-06-16 Tue 21:09] => 0:30
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CLOCK: [2020-06-16 Tue 14:33]--[2020-06-16 Tue 14:47] => 0:14
CLOCK: [2020-06-16 Tue 13:08]--[2020-06-16 Tue 13:16] => 0:08
CLOCK: [2020-06-16 Tue 10:38]--[2020-06-16 Tue 11:20] => 0:42
CLOCK: [2020-06-15 Mon 11:23]--[2020-06-15 Mon 11:56] => 0:33
CLOCK: [2020-06-14 Sun 22:18]--[2020-06-14 Sun 23:21] => 1:03
CLOCK: [2020-06-14 Sun 21:45]--[2020-06-14 Sun 22:10] => 0:33
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CLOCK: [2020-06-14 Sun 13:20]--[2020-06-14 Sun 14:02] => 0:42
CLOCK: [2020-06-13 Sat 12:11]--[2020-06-13 Sat 12:59] => 0:48
CLOCK: [2020-06-13 Sat 11:31]--[2020-06-13 Sat 11:45] => 0:14
CLOCK: [2020-06-12 Fri 22:19]--[2020-06-12 Fri 23:12] => 0:53
CLOCK: [2020-06-12 Fri 16:39]--[2020-06-12 Fri 17:23] => 0:44
CLOCK: [2020-06-11 Thu 22:36]--[2020-06-11 Thu 23:11] => 0:35
CLOCK: [2020-06-11 Thu 22:01]--[2020-06-11 Thu 22:15] => 0:14
CLOCK: [2020-06-11 Thu 19:03]--[2020-06-11 Thu 19:28] => 0:25
CLOCK: [2020-06-11 Thu 18:03]--[2020-06-11 Thu 18:10] => 0:07
CLOCK: [2020-06-11 Thu 17:22]--[2020-06-11 Thu 17:32] => 0:10
CLOCK: [2020-06-11 Thu 16:13]--[2020-06-11 Thu 16:38] => 0:25
CLOCK: [2020-06-11 Thu 14:44]--[2020-06-11 Thu 15:05] => 0:00
CLOCK: [2020-06-11 Thu 12:51]--[2020-06-11 Thu 13:39] => 0:48
CLOCK: [2020-06-11 Thu 11:28]--[2020-06-11 Thu 11:44] => 0:16
CLOCK: [2020-06-10 Wed 22:13]--[2020-06-10 Wed 22:34] => 0:21
:END:
* KILL [#A] Annales d'oral Nancy
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-23 Tue 22:05
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Annales ECN
:ARCHIVE_CATEGORY: annales
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
[[file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/oral][file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/oral]]
** KILL 2019
DEADLINE: <2021-03-29 Mon> SCHEDULED: <2021-03-01 Mon>
:LOGBOOK:
CLOCK: [2021-03-21 Sun 22:17]--[2021-03-21 Sun 23:04] => 0:47
CLOCK: [2021-03-21 Sun 11:47]--[2021-03-21 Sun 11:55] => 0:08
CLOCK: [2021-03-21 Sun 16:49]--[2021-03-21 Sun 17:22] => 0:33
CLOCK: [2021-03-21 Sun 15:29]--[2021-03-21 Sun 16:46] => 1:17
CLOCK: [2021-03-21 Sun 12:53]--[2021-03-21 Sun 13:33] => 0:40
:END:
[[file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/oral/Oral csct 2019.pdf][file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/oral/Oral csct 2019.pdf]]
https://docs.google.com/document/d/1XWQCJp2yw9WiF4OclqqhVPgQtdQqhahck5wRnVIybfI/edit?usp=sharing
-> page 5
** DONE 2020 Passe 1
:LOGBOOK:
CLOCK: [2021-03-19 Fri 21:03]--[2021-03-19 Fri 21:59] => 0:56
CLOCK: [2021-03-19 Fri 16:09]--[2021-03-19 Fri 16:24] => 0:15
CLOCK: [2021-03-19 Fri 14:59]--[2021-03-19 Fri 15:45] => 0:46
CLOCK: [2021-03-19 Fri 11:36]--[2021-03-19 Fri 11:59] => 0:23
CLOCK: [2021-03-18 Thu 22:12]--[2021-03-18 Thu 22:32] => 0:20
CLOCK: [2021-03-18 Thu 11:03]--[2021-03-18 Thu 11:22] => 0:19
CLOCK: [2021-03-14 Sun 21:59]--[2021-03-14 Sun 22:35] => 0:36
CLOCK: [2021-03-14 Sun 15:02]--[2021-03-14 Sun 16:08] => 1:06
CLOCK: [2021-03-14 Sun 12:42]--[2021-03-14 Sun 13:05] => 0:23
CLOCK: [2021-03-14 Sun 11:22]--[2021-03-14 Sun 11:44] => 0:22
CLOCK: [2021-03-13 Sat 22:29]--[2021-03-13 Sat 23:27] => 0:58
CLOCK: [2021-03-13 Sat 19:38]--[2021-03-13 Sat 20:09] => 0:31
CLOCK: [2021-03-13 Sat 12:04]--[2021-03-13 Sat 13:01] => 0:57
CLOCK: [2021-03-12 Fri 22:06]--[2021-03-12 Fri 22:51] => 0:45
CLOCK: [2021-03-12 Fri 18:28]--[2021-03-12 Fri 19:00] => 0:32
CLOCK: [2021-03-12 Fri 18:14]--[2021-03-12 Fri 18:20] => 0:06
CLOCK: [2021-03-12 Fri 15:55]--[2021-03-12 Fri 16:52] => 0:57
CLOCK: [2021-03-12 Fri 14:50]--[2021-03-12 Fri 14:58] => 0:08
CLOCK: [2021-03-12 Fri 12:27]--[2021-03-12 Fri 12:50] => 0:23
CLOCK: [2021-03-12 Fri 11:37]--[2021-03-12 Fri 12:20] => 0:43
CLOCK: [2021-03-11 Thu 22:50]--[2021-03-11 Thu 23:55] => 1:05
CLOCK: [2021-03-11 Thu 18:00]--[2021-03-11 Thu 18:45] => 0:45
CLOCK: [2021-03-07 Sun 22:47]--[2021-03-07 Sun 23:08] => 0:21
CLOCK: [2021-03-07 Sun 22:01]--[2021-03-07 Sun 22:14] => 0:13
CLOCK: [2021-03-07 Sun 19:26]--[2021-03-07 Sun 19:55] => 0:29
CLOCK: [2021-03-07 Sun 15:00]--[2021-03-07 Sun 16:00] => 1:00
CLOCK: [2021-03-07 Sun 12:36]--[2021-03-07 Sun 13:11] => 0:35
:END:
https://docs.google.com/document/d/1qlW1-ZkNyqjqsrK9zW8GmjflG5sXWpf6_Sis4mPQ4KM/edit?usp=sharing
[[file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/oral/ORAL CSCT 2020.pdf][file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/oral/ORAL CSCT 2020.pdf]]
** KILL 2020 passe 2
DEADLINE: <2021-03-22 Mon>
:LOGBOOK:
CLOCK: [2021-03-22 Mon 21:26]--[2021-03-22 Mon 22:33] => 1:07
CLOCK: [2021-03-22 Mon 17:12]--[2021-03-22 Mon 18:20] => 1:08
CLOCK: [2021-03-22 Mon 15:38]--[2021-03-22 Mon 16:27] => 0:49
CLOCK: [2021-03-22 Mon 12:18]--[2021-03-22 Mon 12:50] => 0:32
CLOCK: [2021-03-22 Mon 11:05]--[2021-03-22 Mon 11:50] => 0:45
:END:
-> p 26
** DONE Sujet tombables à réviser
SCHEDULED: <2021-03-22 Mon>
K sein, CCR, endocardite
* DONE [2021-02-09 Tue] :pedia:
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-29 Mon 15:46
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet
** DONE Conf
** DONE Relire corrigé
DEADLINE: <2021-02-10 Wed>
* DONE [2021-02-11 Thu] :orthopédie:
DEADLINE: <2021-02-11 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-29 Mon 15:46
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet
** DONE Conf
** DONE Relire corrigé
* DONE [2021-02-17 Thu] :pneumo:
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-29 Mon 15:46
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet
DEADLINE: <2021-02-16 Tue>
** DONE Conf
DEADLINE: <2021-02-17 Wed>
** DONE Relire corrigé
DEADLINE: <2021-02-18 Thu>
* DONE [2021-03-03 Wed] :hge:
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-29 Mon 15:46
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet
DEADLINE: <2021-03-03 Wed>
:LOGBOOK:
CLOCK: [2021-03-03 Wed 12:33]--[2021-03-03 Wed 13:13] => 0:40
:END:
** DONE Live
DEADLINE: <2021-03-03 Wed>
** DONE Relire
DEADLINE: <2021-03-28 Sun>
:LOGBOOK:
CLOCK: [2021-03-28 Sun 13:56]--[2021-03-28 Sun 14:50] => 0:54
:END:
* DONE [2021-03-10 Wed] :lca:
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-29 Mon 15:46
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Faire sujet
DEADLINE: <2021-03-10 Wed>
:LOGBOOK:
CLOCK: [2021-03-10 Wed 15:52]--[2021-03-10 Wed 16:36] => 0:44
:END:
** DONE Conférence
DEADLINE: <2021-03-10 Wed>
* DONE [2021-03-25 Thu] :neuro:
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-11 Sun 12:34
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet
DEADLINE: <2021-03-25 Thu>
:LOGBOOK:
CLOCK: [2021-03-25 Thu 12:57]--[2021-03-25 Thu 13:39] => 0:42
CLOCK: [2021-03-25 Thu 12:31]--[2021-03-25 Thu 12:38] => 0:07
:END:
** DONE Conf
DEADLINE: <2021-03-25 Thu>
** DONE Relire
DEADLINE: <2021-03-26 Fri>
:LOGBOOK:
CLOCK: [2021-03-31 Wed 17:26]--[2021-03-31 Wed 17:46] => 0:20
CLOCK: [2021-03-31 Wed 16:57]--[2021-03-31 Wed 17:19] => 0:22
CLOCK: [2021-03-31 Wed 16:10]--[2021-03-31 Wed 16:41] => 0:31
:END:
* KILL Annales
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-11 Sun 12:34
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
[[file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nephro_corrige_Mauvais-calcul.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nephro_corrige_Mauvais-calcul.pdf]]
[[file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nephro_corrige_intestin-et-rein.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nephro_corrige_intestin-et-rein.pdf]]
[[file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nephro_corrige_Boire-ou-ne-pas-boire-de-leau.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nephro_corrige_Boire-ou-ne-pas-boire-de-leau.pdf]]
[[file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nephro_corrige_Attention-à-lhypertension.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nephro_corrige_Attention-à-lhypertension.pdf]]
[[file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nepho_corrige_qi.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM1/conferences/ecn_asso/D2_conf_nepho_corrige_qi.pdf]]
* DONE [2021-03-31 Wed] :rhumato:
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-11 Sun 12:34
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet
DEADLINE: <2021-03-31 Wed>
:LOGBOOK:
CLOCK: [2021-03-31 Wed 10:06]--[2021-03-31 Wed 11:52] => 1:46
:END:
** DONE Conf
DEADLINE: <2021-03-31 Wed>
** DONE Relire
DEADLINE: <2021-04-01 Thu>
-> q15
:LOGBOOK:
CLOCK: [2021-04-04 Sun 19:01]--[2021-04-04 Sun 19:20] => 0:19
CLOCK: [2021-04-04 Sun 16:45]--[2021-04-04 Sun 17:02] => 0:17
CLOCK: [2021-04-04 Sun 15:42]--[2021-04-04 Sun 16:32] => 0:50
CLOCK: [2021-04-04 Sun 12:34]--[2021-04-04 Sun 13:27] => 0:53
CLOCK: [2021-04-03 Sat 11:30]--[2021-04-03 Sat 12:00] => 0:30
CLOCK: [2021-04-02 Fri 22:55]--[2021-04-02 Fri 23:25] => 0:30
CLOCK: [2021-04-02 Fri 22:20]--[2021-04-02 Fri 22:34] => 0:14
CLOCK: [2021-04-02 Fri 18:56]--[2021-04-02 Fri 19:13] => 0:17
:END:
* KILL Contrôle continu
:PROPERTIES:
:CATEGORY: CC
:ARCHIVE_TIME: 2021-04-21 Wed 10:08
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_CATEGORY: CC
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
** DONE Corrigé du <2020-11-27 Fri>
DEADLINE: <2021-01-12 Tue>
[[file:/usr/home/alex/cours/Medecine/FASM3/cc-2020-11-27.pdf][file:/usr/home/alex/cours/Medecine/FASM3/cc-2020-11-27.pdf]]
** DONE Corrigé du <2020-12-04 Fri>
*** DONE Lire corrigé
DEADLINE: <2020-12-04 Fri>
*** DONE Correction vidéo
DEADLINE: <2021-01-12 Tue>
[[file:/usr/home/alex/cours/Medecine/FASM3/cc-2020-12-04.pdf][file:/usr/home/alex/cours/Medecine/FASM3/cc-2020-12-04.pdf]]
** DONE Corrigé du <2020-12-18 Fri>
DEADLINE: <2021-01-17 Sun>
*** DONE [[file:/usr/home/alex/cours/Medecine/FASM3/urgences-rea-therapeutique.pdf][file:/usr/home/alex/cours/Medecine/FASM3/urgences-rea-therapeutique.pdf]]
*** DONE [[file:/usr/home/alex/cours/Medecine/FASM3/sante-publique.pdf][file:/usr/home/alex/cours/Medecine/FASM3/sante-publique.pdf]]
** KILL Corrigé du <2021-01-08 Fri>
[[file:/usr/home/alex/cours/Medecine/FASM3/rattrapage-therapeutiques.pdf][file:/usr/home/alex/cours/Medecine/FASM3/rattrapage-therapeutiques.pdf]]
[[file:/usr/home/alex/cours/Medecine/FASM3/cc-2021-01-08.pdf][file:/usr/home/alex/cours/Medecine/FASM3/cc-2021-01-08.pdf]]
** KILL Autres corrigés
** KILL Annales urgences-thérapeutiques-santé publique Nancy
DEADLINE: <2021-01-07 Thu> SCHEDULED: <2021-01-06 Wed>
*** DONE Santé publique - 20/12/2019 https://side-sante.fr/playtest/classic/3184594
*** DONE Urgences Réa Thérapeutiques - 20/12/2019 https://side-sante.fr/playtest/classic/3160416
*** DONE Urgences Réa 2ème session mars 2019 https://side-sante.fr/playtest/classic/2210752
*** DONE Santé publique 2ème session mars 2019 https://side-sante.fr/playtest/classic/2210728
*** DONE Santé publique 21/12/2018 https://side-sante.fr/playtest/classic/1878604
*** DONE Urgences/Réa/Thérapeutiques du 21/12/2018 https://side-sante.fr/playtest/classic/1878580
*** DONE SANTE PUBLIQUE du 12 janv 2018 https://side-sante.fr/playtest/classic/817568
*** KILL URGENCE REA THERAPEUTIQUE du 12 janv 2018 https://side-sante.fr/playtest/classic/777476
*** KILL Thérapeutique et Urgences fév.2017 https://side-sante.fr/playtest/classic/223462
*** KILL Santé Publique / Gériatrie nov.2016 https://side-sante.fr/playtest/classic/127605
*** KILL ?? https://side-sante.fr/playtest/classic/30393
* DONE Test de charge
:PROPERTIES:
:CATEGORY: testdecharge
:ARCHIVE_TIME: 2021-04-21 Wed 10:09
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Annales ECN
:ARCHIVE_CATEGORY: testdecharge
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Faire examens
** DONE Corrigé
SCHEDULED: <2021-02-22 Mon> DEADLINE: <2021-01-30 Sat>
:LOGBOOK:
CLOCK: [2021-03-14 Sun 17:00]--[2021-03-14 Sun 17:34] => 0:34
CLOCK: [2021-02-24 Wed 13:32]--[2021-02-24 Wed 14:17] => 0:45
CLOCK: [2021-02-23 Tue 21:42]--[2021-02-23 Tue 23:58] => 2:16
CLOCK: [2021-02-23 Tue 16:05]--[2021-02-23 Tue 17:15] => 1:10
CLOCK: [2021-02-18 Thu 21:31]--[2021-02-18 Thu 21:36] => 0:05
CLOCK: [2021-02-18 Thu 14:42]--[2021-02-18 Thu 17:12] => 2:30
CLOCK: [2021-02-18 Thu 14:27]--[2021-02-18 Thu 14:32] => 0:05
CLOCK: [2021-02-18 Thu 11:43]--[2021-02-18 Thu 12:02] => 0:19
CLOCK: [2021-02-18 Thu 11:09]--[2021-02-18 Thu 11:29] => 0:20
:END:
DP ok
[[file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/test_charge/praga-alexis-31713741-ecni-test-de-charge-national-et-epreuve-2-des-ecni-regionales-aura-apres-midi-8t2u3hb6.pdf][file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/test_charge/praga-alexis-31713741-ecni-test-de-charge-national-et-epreuve-2-des-ecni-regionales-aura-apres-midi-8t2u3hb6.pdf]]
* KILL Entraînement LCA D1
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-21 Wed 10:09
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Annales ECN
:ARCHIVE_CATEGORY: annales
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
[[notmuch:id:1548439400.1013668.1611831963411.JavaMail.zimbra@univ-lorraine.fr][Email from Anne Cioni: [medecine-fasm-3-2021] URGENT: Mise en place d'entrainements LCA FASM3]]
** KILL [2021-02-01 Mon]
*** DONE Épreuve
*** KILL Corrigé
DEADLINE: <2021-03-29 Mon>
- Question 3 : pas de mention de plusieurs centres...
- Question 5 : "read by a single radiographer" => pas de double lecture...
** KILL <2021-03-01 Mon>
** KILL <2021-04-12 Mon>
** KILL <2021-04-21 Mon>
** KILL <2021-05-12 Mon>
* DONE Lille génétique
DEADLINE: <2021-01-30 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-21 Wed 10:09
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Annales ECN
:ARCHIVE_CATEGORY: annales
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
[[file:/usr/home/alex/backups/hubic/Public/Cours/Medecine/autres/correction_conference_genetique_internat_Med6_2020_1.docx][file:/usr/home/alex/backups/hubic/Public/Cours/Medecine/autres/correction_conference_genetique_internat_Med6_2020_1.docx]]
* DONE Lille génétique
DEADLINE: <2021-01-30 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-21 Wed 10:09
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/revisions.org
:ARCHIVE_OLPATH: Annales ECN
:ARCHIVE_CATEGORY: annales
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
[[file:/usr/home/alex/backups/hubic/Public/Cours/Medecine/autres/correction_conference_genetique_internat_Med6_2020_1.docx][file:/usr/home/alex/backups/hubic/Public/Cours/Medecine/autres/correction_conference_genetique_internat_Med6_2020_1.docx]]
* DONE [2021-04-08 Thu] :endoc:
:PROPERTIES:
:CATEGORY: endocrino
:ARCHIVE_TIME: 2021-05-20 Thu 10:13
:ARCHIVE_FILE: /usr/home/alex/projects/blog/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: endocrino
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
:LOGBOOK:
CLOCK: [2021-04-11 Sun 12:35]--[2021-04-11 Sun 13:19] => 0:44
CLOCK: [2021-04-11 Sun 11:37]--[2021-04-11 Sun 12:13] => 0:36
:END:
** DONE Sujet
DEADLINE: <2021-04-08 Thu>
:LOGBOOK:
CLOCK: [2021-04-08 Thu 17:07]--[2021-04-08 Thu 17:31] => 0:24
:END:
** DONE Conf
DEADLINE: <2021-04-08 Thu>
** DONE Relire
DEADLINE: <2021-04-09 Fri>
* DONE [2021-04-09 Fri] :santepub:
:PROPERTIES:
:CATEGORY: santepub
:ARCHIVE_TIME: 2021-05-20 Thu 10:13
:ARCHIVE_FILE: /usr/home/alex/projects/blog/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: santepub
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet
DEADLINE: <2021-04-11 Sun>
:LOGBOOK:
CLOCK: [2021-04-11 Sun 14:57]--[2021-04-11 Sun 15:27] => 0:30
:END:
** DONE Corrigé
DEADLINE: <2021-04-11 Sun>
:LOGBOOK:
CLOCK: [2021-04-11 Sun 19:12]--[2021-04-11 Sun 19:22] => 0:10
CLOCK: [2021-04-11 Sun 18:06]--[2021-04-11 Sun 18:20] => 0:14
CLOCK: [2021-04-11 Sun 16:20]--[2021-04-11 Sun 17:56] => 1:36
CLOCK: [2021-04-11 Sun 15:43]--[2021-04-11 Sun 16:37] => 0:54
:END:
* DONE [2021-04-12 Mon] :psy:
:PROPERTIES:
:CATEGORY: psy
:ARCHIVE_TIME: 2021-05-20 Thu 10:13
:ARCHIVE_FILE: /usr/home/alex/projects/blog/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: psy
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet
DEADLINE: <2000-04-11 Tue>
:LOGBOOK:
CLOCK: [2021-04-12 Mon 11:07]--[2021-04-12 Mon 11:26] => 0:19
:END:
** DONE Conf
DEADLINE: <2000-04-11 Tue>
** DONE Corrigé
DEADLINE: <2021-04-13 Tue>
:LOGBOOK:
CLOCK: [2021-04-15 Thu 15:19]--[2021-04-15 Thu 15:47] => 0:28
:END:
* DONE [2021-04-15 Thu] :nephro:
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-20 Thu 10:13
:ARCHIVE_FILE: /usr/home/alex/projects/blog/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
** DONE Sujet
DEADLINE: <2021-04-15 Thu>
:LOGBOOK:
CLOCK: [2021-04-15 Thu 14:06]--[2021-04-15 Thu 15:00] => 0:54
:END:
** DONE Conf
DEADLINE: <2021-04-16 Fri>
:LOGBOOK:
CLOCK: [2021-04-16 Fri 20:07]--[2021-04-16 Fri 20:45] => 0:38
CLOCK: [2021-04-16 Fri 19:26]--[2021-04-16 Fri 19:40] => 0:14
CLOCK: [2021-04-16 Fri 17:19]--[2021-04-16 Fri 17:39] => 0:20
CLOCK: [2021-04-16 Fri 15:25]--[2021-04-16 Fri 16:40] => 1:15
CLOCK: [2021-04-16 Fri 14:13]--[2021-04-16 Fri 14:59] => 0:46
CLOCK: [2021-04-16 Fri 13:03]--[2021-04-16 Fri 13:44] => 0:41
CLOCK: [2021-04-16 Fri 11:54]--[2021-04-16 Fri 12:42] => 0:48
CLOCK: [2021-04-16 Fri 11:02]--[2021-04-16 Fri 11:20] => 0:18
:END:
* DONE [2021-05-02 Sun] :lca:
DEADLINE: <2021-05-10 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-20 Thu 10:13
:ARCHIVE_FILE: /usr/home/alex/projects/blog/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: revisions
:END:
:LOGBOOK:
CLOCK: [2021-05-11 Tue 13:01]--[2021-05-11 Tue 14:00] => 0:59
CLOCK: [2021-05-10 Mon 23:56]--[2021-05-11 Tue 00:45] => 0:49
CLOCK: [2021-05-10 Mon 22:29]--[2021-05-10 Mon 22:42] => 0:13
:END:
* KILL [2021-05-11 Tue] :cardio:
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-20 Thu 10:13
:ARCHIVE_FILE: /usr/home/alex/projects/blog/revisions.org
:ARCHIVE_OLPATH: Conf/Ecn asso
:ARCHIVE_CATEGORY: ecn-asso
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
** DONE Conf
DEADLINE: <2021-05-11 Tue>
** KILL Relire
DEADLINE: <2021-05-11 Tue>
* KILL Abrégé des très bien classés [11/30] :abrégé:
:PROPERTIES:
:CATEGORY: ATBC
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: ATBC
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
** DONE Santé publique
DEADLINE: <2020-11-22 Sun>
-> item 11
** DONE Pédiatrie
SCHEDULED: <2021-05-25 Tue> DEADLINE: <2021-05-26 Wed>
:LOGBOOK:
CLOCK: [2021-05-28 Fri 13:08]--[2021-05-28 Fri 13:25] => 0:17
CLOCK: [2021-05-28 Fri 12:38]--[2021-05-28 Fri 12:59] => 0:21
CLOCK: [2021-05-28 Fri 12:12]--[2021-05-28 Fri 12:31] => 0:19
CLOCK: [2021-05-28 Fri 11:21]--[2021-05-28 Fri 11:45] => 0:30
CLOCK: [2021-05-28 Fri 00:11]--[2021-05-28 Fri 00:51] => 0:40
CLOCK: [2021-05-27 Thu 19:07]--[2021-05-27 Thu 19:54] => 0:47
CLOCK: [2021-05-27 Thu 13:09]--[2021-05-27 Thu 13:51] => 0:42
CLOCK: [2021-05-27 Thu 12:58]--[2021-05-27 Thu 13:00] => 0:02
CLOCK: [2021-05-26 Wed 23:25]--[2021-05-26 Wed 23:30] => 0:05
CLOCK: [2021-05-26 Wed 22:06]--[2021-05-26 Wed 23:06] => 1:00
CLOCK: [2021-05-26 Wed 18:41]--[2021-05-26 Wed 18:50] => 0:09
CLOCK: [2021-05-26 Wed 18:14]--[2021-05-26 Wed 18:32] => 0:18
CLOCK: [2021-05-26 Wed 17:18]--[2021-05-26 Wed 17:42] => 0:24
CLOCK: [2021-05-26 Wed 16:18]--[2021-05-26 Wed 17:06] => 0:48
CLOCK: [2021-05-26 Wed 12:58]--[2021-05-26 Wed 14:02] => 1:04
CLOCK: [2021-05-25 Tue 23:23]--[2021-05-25 Tue 23:53] => 0:30
CLOCK: [2021-05-25 Tue 18:17]--[2021-05-25 Tue 19:00] => 0:43
CLOCK: [2021-05-25 Tue 18:06]--[2021-05-25 Tue 18:08] => 0:02
CLOCK: [2021-05-25 Tue 16:35]--[2021-05-25 Tue 16:50] => 0:15
CLOCK: [2021-05-25 Tue 13:04]--[2021-05-25 Tue 13:48] => 0:44
:END:
*** DONE Item 29,31
** KILL Gynéco
DEADLINE: <2021-06-11 Fri>
** KILL Psychiatrie
** DONE Dermatologie
DEADLINE: <2021-05-16 Sun> SCHEDULED: <2021-05-12 Wed>
:LOGBOOK:
CLOCK: [2021-05-15 Sat 14:40]--[2021-05-15 Sat 15:12] => 0:32
CLOCK: [2021-05-15 Sat 11:57]--[2021-05-15 Sat 13:10] => 1:13
CLOCK: [2021-05-14 Fri 16:03]--[2021-05-14 Fri 17:00] => 0:57
CLOCK: [2021-05-14 Fri 14:59]--[2021-05-14 Fri 15:21] => 0:22
CLOCK: [2021-05-14 Fri 11:08]--[2021-05-14 Fri 11:40] => 0:32
CLOCK: [2021-05-14 Fri 10:37]--[2021-05-14 Fri 11:02] => 0:25
CLOCK: [2021-05-14 Fri 00:13]--[2021-05-14 Fri 00:39] => 0:26
CLOCK: [2021-05-13 Thu 17:57]--[2021-05-13 Thu 18:31] => 0:34
:END:
*** DONE Item 109
*** DONE Item 110
*** DONE Item 111
*** DONE Item 112
*** DONE Item 113
*** DONE Item 114
*** DONE Item 183
*** DONE Item 299
*** DONE Item 345
*** DONE Item 211
** KILL Neurologie
** KILL Opthalmo
** KILL ORL
** KILL Chir maxillo
** KILL Anesth
** DONE Gériatrie
DEADLINE: <2021-06-02 Wed>
:LOGBOOK:
CLOCK: [2021-06-02 Wed 12:07]--[2021-06-02 Wed 12:12] => 0:05
:END:
** KILL MPR
** KILL Médecine du traval
** DONE Maladies infectieuses
DEADLINE: <2021-04-20 Tue>
:LOGBOOK:
CLOCK: [2021-04-23 Fri 16:42]--[2021-04-23 Fri 16:55] => 0:13
CLOCK: [2021-04-23 Fri 13:08]--[2021-04-23 Fri 14:10] => 1:02
CLOCK: [2021-04-22 Thu 20:56]--[2021-04-22 Thu 21:21] => 0:25
CLOCK: [2021-04-22 Thu 18:18]--[2021-04-22 Thu 18:41] => 0:23
CLOCK: [2021-04-22 Thu 15:34]--[2021-04-22 Thu 16:47] => 1:13
CLOCK: [2021-04-20 Tue 11:43]--[2021-04-20 Tue 12:08] => 0:25
:END:
*** DONE 142
*** DONE 143
*** DONE 144
*** DONE 148
*** DONE 149
*** DONE 151
*** DONE 152
*** DONE 153
*** DONE 154
*** DONE 156
*** DONE 157
*** DONE 158
*** DONE 161
*** DONE 162
*** DONE 163
*** DONE 164
*** DONE 165
*** DONE 169
*** DONE 170
*** DONE 171
*** DONE 172
*** DONE 173
*** DONE 174
** DONE Parasitologie
DEADLINE: <2021-04-23 Fri>
:LOGBOOK:
CLOCK: [2021-04-24 Sat 21:11]--[2021-04-24 Sat 21:27] => 0:16
CLOCK: [2021-04-24 Sat 17:29]--[2021-04-24 Sat 18:46] => 1:17
CLOCK: [2021-04-24 Sat 12:23]--[2021-04-24 Sat 12:50] => 0:27
:END:
*** DONE 152
** KILL Hémato
** KILL Médecine interne
*** DONE 187
** KILL Pneumo
** KILL Cardio
** KILL Rhumato
** DONE Endocrino
DEADLINE: <2021-06-11 Fri>
:LOGBOOK:
CLOCK: [2021-06-12 Sat 10:56]--[2021-06-12 Sat 11:24] => 0:28
:END:
** KILL Nephro
** KILL Nutrition
** DONE HGE + chir digestive
DEADLINE: <2021-04-26 Mon>
:LOGBOOK:
CLOCK: [2021-05-10 Mon 17:43]--[2021-05-10 Mon 19:03] => 1:20
CLOCK: [2021-05-02 Sun 17:36]--[2021-05-02 Sun 18:01] => 0:25
CLOCK: [2021-05-02 Sun 13:00]--[2021-05-02 Sun 13:45] => 0:45
CLOCK: [2021-04-30 Fri 22:49]--[2021-04-30 Fri 23:33] => 0:44
CLOCK: [2021-04-30 Fri 18:06]--[2021-04-30 Fri 19:08] => 1:02
CLOCK: [2021-04-30 Fri 16:38]--[2021-04-30 Fri 17:47] => 1:09
CLOCK: [2021-04-30 Fri 12:40]--[2021-04-30 Fri 13:12] => 0:32
CLOCK: [2021-04-29 Thu 23:26]--[2021-04-29 Thu 23:35] => 0:09
CLOCK: [2021-04-29 Thu 22:28]--[2021-04-29 Thu 22:40] => 0:12
CLOCK: [2021-04-29 Thu 17:41]--[2021-04-29 Thu 18:06] => 0:25
CLOCK: [2021-04-29 Thu 16:21]--[2021-04-29 Thu 17:10] => 0:49
CLOCK: [2021-04-29 Thu 12:15]--[2021-04-29 Thu 13:06] => 0:51
CLOCK: [2021-04-28 Wed 22:51]--[2021-04-28 Wed 23:32] => 0:41
CLOCK: [2021-04-28 Wed 18:14]--[2021-04-28 Wed 19:01] => 0:47
CLOCK: [2021-04-28 Wed 17:18]--[2021-04-28 Wed 17:51] => 0:33
CLOCK: [2021-04-28 Wed 11:57]--[2021-04-28 Wed 12:02] => 0:05
CLOCK: [2021-04-28 Wed 11:31]--[2021-04-28 Wed 11:46] => 0:15
CLOCK: [2021-04-27 Tue 23:22]--[2021-04-27 Tue 23:52] => 0:30
CLOCK: [2021-04-27 Tue 23:04]--[2021-04-27 Tue 23:09] => 0:05
CLOCK: [2021-04-27 Tue 16:45]--[2021-04-27 Tue 17:06] => 0:21
CLOCK: [2021-04-27 Tue 14:00]--[2021-04-27 Tue 15:00] => 1:00
CLOCK: [2021-04-27 Tue 13:07]--[2021-04-27 Tue 13:37] => 0:30
CLOCK: [2021-04-26 Mon 21:37]--[2021-04-26 Mon 22:48] => 1:11
CLOCK: [2021-04-26 Mon 18:10]--[2021-04-26 Mon 18:31] => 0:21
CLOCK: [2021-04-26 Mon 16:42]--[2021-04-26 Mon 17:34] => 0:52
CLOCK: [2021-04-26 Mon 15:38]--[2021-04-26 Mon 15:54] => 0:16
CLOCK: [2021-04-26 Mon 15:20]--[2021-04-26 Mon 15:30] => 0:10
CLOCK: [2021-04-26 Mon 12:30]--[2021-04-26 Mon 12:52] => 0:22
:END:
*** DONE Item 267
*** DONE Item 268
*** DONE Item 269
*** DONE Item 270
*** DONE Item 271
*** DONE Item 272
*** DONE Item 273
*** DONE Item 274
*** DONE Item 275
*** DONE Item 276
*** DONE Item 277
*** DONE Item 278
*** DONE Item 279
*** DONE Item 280
*** DONE Item 281
*** DONE Item 282
*** DONE Item 350
*** DONE Item 353
*** DONE Item 284
*** DONE Item 285
*** DONE Item 286
*** DONE Item 298
*** DONE Item 300
*** DONE Item 301
*** DONE Item 302
*** DONE Item 305
*** DONE Item 329
*** DONE Item 349
*** DONE Item 351
*** DONE : Item 352
** DONE Urologie
DEADLINE: <2021-06-11 Fri>
:LOGBOOK:
CLOCK: [2021-06-11 Fri 11:50]--[2021-06-11 Fri 11:58] => 0:08
CLOCK: [2021-06-11 Fri 10:36]--[2021-06-11 Fri 11:09] => 0:33
:END:
** DONE Oncologie
** KILL Pharmaco
** KILL Réa
** DONE Ortho
DEADLINE: <2021-06-07 Mon>
:LOGBOOK:
CLOCK: [2021-06-07 Mon 17:03]--[2021-06-07 Mon 17:50] => 0:47
CLOCK: [2021-06-07 Mon 16:00]--[2021-06-07 Mon 16:35] => 0:35
:END:
** KILL LCA
* Anesthésie-Rea :anesth:
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_ITAGS: revisions
:END:
PDF [[file:~/backups/hubic/Public/Cours/Medecine/referentiels/Anesth_college_2018.pdf][file:~/backups/hubic/Public/Cours/Medecine/referentiels/Anesth_college_2018.pdf]]
https://drive.google.com/drive/folders/1PKMHd9yq-clAB5P1lLSnMRd7rtfOjvO7
* Annales ECN [13/13] :annales:
:PROPERTIES:
:CATEGORY: annales
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: annales
:ARCHIVE_ITAGS: revisions
:END:
** Sources
- Annales/QI des très bien classés/asclepia
- Pezel/LC des très bien classés
** KILL 2021 blancs [0/3]
*** KILL DP [0/3]
**** KILL DCP 1 [0/6]
***** KILL DP 1
***** KILL DP 2
***** KILL DP 3
***** KILL DP 4
***** KILL DP 5
***** KILL DP 6
**** KILL DCP 2 [0/6]
***** KILL DP 1
***** KILL DP 2
***** KILL DP 3
***** KILL DP 4
***** KILL DP 5
***** KILL DP 6
**** KILL DCP 3 [0/6]
***** KILL DP 1
***** KILL DP 2
***** KILL DP 3
***** KILL DP 4
***** KILL DP 5
***** KILL DP 6
*** KILL QI
*** KILL LCA [0/2]
**** KILL Article 1
**** KILL Article 2
** KILL 2020 [3/5]
*** DONE DCP 1 [6/6]
**** DONE Dossier 1
:LOGBOOK:
CLOCK: [2021-04-03 Sat 20:10]--[2021-04-03 Sat 22:03] => 1:53
CLOCK: [2021-04-03 Sat 17:40]--[2021-04-03 Sat 19:43] => 2:03
CLOCK: [2021-04-03 Sat 12:00]--[2021-04-03 Sat 12:35] => 0:35
:END:
**** DONE Dossier 2
DEADLINE: <2021-04-10 Sat>
:LOGBOOK:
CLOCK: [2021-04-10 Sat 16:50]--[2021-04-10 Sat 17:38] => 0:48
CLOCK: [2021-04-10 Sat 13:08]--[2021-04-10 Sat 13:22] => 0:14
:END:
**** DONE Dossier 3
DEADLINE: <2021-04-17 Sat>
**** DONE Dossier 4
DEADLINE: <2021-05-08 Sat>
:LOGBOOK:
CLOCK: [2021-05-08 Sat 18:08]--[2021-05-08 Sat 19:00] => 0:52
CLOCK: [2021-05-08 Sat 16:58]--[2021-05-08 Sat 17:10] => 0:12
:END:
**** DONE Dossier 5
SCHEDULED: <2021-05-14 Fri> DEADLINE: <2021-05-16 Sun>
:LOGBOOK:
CLOCK: [2021-05-16 Sun 13:35]--[2021-05-16 Sun 13:47] => 0:12
CLOCK: [2021-05-16 Sun 10:53]--[2021-05-16 Sun 11:55] => 1:02
CLOCK: [2021-05-15 Sat 22:37]--[2021-05-15 Sat 22:52] => 0:15
:END:
**** DONE Dossier 6
SCHEDULED: <2021-05-14 Fri> DEADLINE: <2021-05-16 Sun>
:LOGBOOK:
CLOCK: [2021-05-16 Sun 22:07]--[2021-05-16 Sun 22:40] => 0:33
CLOCK: [2021-05-16 Sun 15:01]--[2021-05-16 Sun 16:06] => 1:05
:END:
*** DONE DCP 2 [6/6]
**** DONE Dossier 7
DEADLINE: <2021-05-22 Sat>
:LOGBOOK:
CLOCK: [2021-05-23 Sun 12:23]--[2021-05-23 Sun 13:18] => 0:55
CLOCK: [2021-05-23 Sun 11:55]--[2021-05-23 Sun 12:02] => 0:07
CLOCK: [2021-05-22 Sat 22:20]--[2021-05-22 Sat 22:40] => 0:20
:END:
**** DONE Dossier 8
DEADLINE: <2021-05-22 Sat>
:LOGBOOK:
CLOCK: [2021-05-23 Sun 13:22]--[2021-05-23 Sun 14:10] => 0:48
:END:
Déjà fait sur asclepia ?
https://www.facebook.com/watch/live/?v=684259552250242
DEADLINE: <2021-05-22 Sat>
**** DONE Dossier 9
DEADLINE: <2021-05-29 Sat>
:LOGBOOK:
CLOCK: [2021-05-29 Sat 23:09]--[2021-05-29 Sat 23:39] => 0:30
CLOCK: [2021-05-29 Sat 19:23]--[2021-05-29 Sat 20:17] => 0:54
CLOCK: [2021-05-29 Sat 18:03]--[2021-05-29 Sat 19:20] => 1:17
CLOCK: [2021-05-29 Sat 15:15]--[2021-05-29 Sat 17:13] => 1:58
CLOCK: [2021-05-29 Sat 14:50]--[2021-05-29 Sat 15:00] => 0:10
CLOCK: [2021-05-29 Sat 12:34]--[2021-05-29 Sat 12:49] => 0:15
:END:
**** DONE Dossier 10
:LOGBOOK:
CLOCK: [2021-05-29 Sat 23:47]--[2021-05-30 Sun 00:18] => 0:31
CLOCK: [2021-05-30 Sun 12:15]--[2021-05-30 Sun 12:58] => 0:43
CLOCK: [2021-05-30 Sun 10:59]--[2021-05-30 Sun 12:04] => 1:05
:END:
**** DONE Dossier 11
DEADLINE: <2021-06-05 Sat>
:LOGBOOK:
CLOCK: [2021-06-05 Sat 21:51]--[2021-06-05 Sat 22:28] => 0:37
CLOCK: [2021-06-05 Sat 18:51]--[2021-06-05 Sat 19:59] => 1:08
:END:
**** DONE Dossier 12
DEADLINE: <2021-06-05 Sat>
*** KILL DCP 3 [5/6]
DEADLINE: <2021-06-10 Thu>
:LOGBOOK:
CLOCK: [2021-06-12 Sat 19:58]--[2021-06-12 Sat 20:35] => 0:37
CLOCK: [2021-06-12 Sat 19:48]--[2021-06-12 Sat 19:56] => 0:08
CLOCK: [2021-06-12 Sat 12:49]--[2021-06-12 Sat 13:17] => 0:28
CLOCK: [2021-06-12 Sat 11:40]--[2021-06-12 Sat 12:22] => 0:42
CLOCK: [2021-06-11 Fri 23:42]--[2021-06-12 Sat 00:14] => 0:32
CLOCK: [2021-06-11 Fri 23:20]--[2021-06-11 Fri 23:30] => 0:10
CLOCK: [2021-06-11 Fri 22:15]--[2021-06-11 Fri 22:52] => 0:37
CLOCK: [2021-06-11 Fri 21:44]--[2021-06-11 Fri 22:07] => 0:23
:END:
**** DONE Dossier 13
**** DONE Dossier 14
**** DONE Dossier 15
**** DONE Dossier 16
**** DONE Dossier 17
**** KILL Dossier 18
*** KILL QI
DEADLINE: <2021-06-11 Fri>
*** DONE LCA [2/2]
**** DONE Article 1
**** DONE Article 2
** DONE 2020 blancs [1/1]
*** DONE LCA [2/2]
**** DONE Article 1
SCHEDULED: <2021-05-14 Fri> DEADLINE: <2021-05-16 Sun>
:LOGBOOK:
CLOCK: [2021-05-15 Sat 22:31]--[2021-05-15 Sat 22:31] => 0:00
CLOCK: [2021-05-15 Sat 22:18]--[2021-05-15 Sat 22:31] => 0:13
CLOCK: [2021-05-15 Sat 21:42]--[2021-05-15 Sat 21:55] => 0:13
CLOCK: [2021-05-15 Sat 19:15]--[2021-05-15 Sat 19:42] => 0:27
CLOCK: [2021-05-15 Sat 18:17]--[2021-05-15 Sat 18:35] => 0:18
CLOCK: [2021-05-15 Sat 18:11]--[2021-05-15 Sat 18:14] => 0:03
CLOCK: [2021-05-15 Sat 17:32]--[2021-05-15 Sat 17:54] => 0:22
CLOCK: [2021-05-15 Sat 15:41]--[2021-05-15 Sat 16:50] => 1:09
:END:
**** DONE Article 2
DEADLINE: <2021-05-22 Sat>
** DONE 2019 [3/3]
*** DONE DP [18/18]
**** DONE Dossier 1
DEADLINE: <2020-10-10 Sat>
**** DONE Dossier 2
DEADLINE: <2020-10-10 Sat>
**** DONE Dossier 3
DEADLINE: <2020-10-10 Sat>
**** DONE Dossier 4
DEADLINE: <2020-10-10 Sat>
**** DONE Dossier 5
DEADLINE: <2020-10-10 Sat>
**** DONE Dossier 6
DEADLINE: <2020-10-17 Sat>
**** DONE Dossier 7
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 8
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 9
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 10
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 11
**** DONE Dossier 12
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 13
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 14
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 15
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 16
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 17
DEADLINE: <2020-10-26 Mon>
**** DONE Dossier 18
DEADLINE: <2020-10-26 Mon>
*** DONE QI [2/2]
**** DONE 1-60
DEADLINE: <2020-10-19 Mon>
**** DONE 61-120
DEADLINE: <2020-10-31 Sat>
*** DONE LCA
<<<<<<< HEAD
** DONE 2019 blancs [1/1]
*** DONE LCA
**** DONE Article 1
DEADLINE: <2021-05-29 Sat>
**** DONE Article 2
DEADLINE: <2021-06-05 Sat>
:LOGBOOK:
CLOCK: [2021-06-06 Sun 13:03]--[2021-06-06 Sun 13:15] => 0:12
CLOCK: [2021-06-06 Sun 12:02]--[2021-06-06 Sun 12:40] => 0:38
CLOCK: [2021-06-05 Sat 23:17]--[2021-06-06 Sun 00:03] => 0:46
:END:
** DONE 2018 [3/3]
*** DONE LCA
DEADLINE: <2021-05-08 Sat>
:LOGBOOK:
CLOCK: [2021-05-09 Sun 16:02]--[2021-05-09 Sun 17:00] => 0:58
CLOCK: [2021-05-09 Sun 15:13]--[2021-05-09 Sun 15:45] => 0:32
:END:
relire
*** DONE DP [3/3]
**** DONE DCP 1 [6/6]
***** DONE DP 1
***** DONE DP 2
***** DONE DP 3
***** DONE DP 4
***** DONE DP 5
***** DONE DP 6
**** DONE DCP 2 [0/6]
***** DONE DP 1
***** DONE DP 2
***** DONE DP 3
***** DONE DP 4
***** DONE DP 5
***** DONE DP 6
**** DONE DCP 3 [6/6]
***** DONE DP 1
***** DONE DP 2
***** DONE DP 3
***** DONE DP 4
***** DONE DP 5
***** DONE DP 6
*** DONE QI
** DONE 2018 blancs [1/1]
*** DONE LCA [2/2]
**** DONE Article 1
**** DONE Article 2
** DONE 2017 [3/3]
DEADLINE: <2021-06-04 Fri> SCHEDULED: <2021-06-02 Wed>
:PROPERTIES:
:CATEGORY: 2017
:END:
*** DONE DP [3/3]
**** DONE DCP 1 [6/6]
***** DONE DP 1
***** DONE DP 2
***** DONE DP 3
***** DONE DP 4
***** DONE DP 5
***** DONE DP 6
**** DONE DCP 2 [6/6]
***** DONE DP 1
***** DONE DP 2
***** DONE DP 3
***** DONE DP 4
***** DONE DP 5
***** DONE DP 6
**** DONE DCP 3 [4/6]
DEADLINE: <2021-06-08 Tue> SCHEDULED: <2021-06-05 Sat>
:LOGBOOK:
CLOCK: [2021-06-10 Thu 23:27]--[2021-06-11 Fri 00:00] => 0:33
CLOCK: [2021-06-10 Thu 22:45]--[2021-06-10 Thu 23:01] => 0:16
CLOCK: [2021-06-10 Thu 22:09]--[2021-06-10 Thu 22:37] => 0:28
CLOCK: [2021-06-10 Thu 21:46]--[2021-06-10 Thu 21:54] => 0:08
CLOCK: [2021-06-10 Thu 20:00]--[2021-06-10 Thu 20:05] => 0:05
CLOCK: [2021-06-10 Thu 18:48]--[2021-06-10 Thu 19:15] => 0:27
CLOCK: [2021-06-10 Thu 13:11]--[2021-06-10 Thu 13:32] => 0:21
CLOCK: [2021-06-10 Thu 12:15]--[2021-06-10 Thu 12:40] => 0:25
CLOCK: [2021-06-10 Thu 11:36]--[2021-06-10 Thu 11:58] => 0:22
CLOCK: [2021-06-10 Thu 11:08]--[2021-06-10 Thu 11:27] => 0:19
CLOCK: [2021-06-07 Mon 15:02]--[2021-06-07 Mon 15:28] => 0:26
CLOCK: [2021-06-07 Mon 12:21]--[2021-06-07 Mon 13:20] => 0:59
CLOCK: [2021-06-07 Mon 10:54]--[2021-06-07 Mon 11:30] => 0:36
CLOCK: [2021-06-06 Sun 19:06]--[2021-06-06 Sun 21:59] => 2:53
CLOCK: [2021-06-06 Sun 18:16]--[2021-06-06 Sun 18:35] => 0:19
CLOCK: [2021-06-05 Sat 18:05]--[2021-06-05 Sat 18:26] => 0:21
CLOCK: [2021-06-05 Sat 16:45]--[2021-06-05 Sat 17:50] => 1:05
CLOCK: [2021-06-05 Sat 14:49]--[2021-06-05 Sat 15:09] => 0:20
CLOCK: [2021-06-05 Sat 11:34]--[2021-06-05 Sat 11:55] => 0:21
CLOCK: [2021-06-05 Sat 10:45]--[2021-06-05 Sat 10:55] => 0:10
CLOCK: [2021-06-05 Sat 10:04]--[2021-06-05 Sat 10:37] => 0:33
CLOCK: [2021-06-04 Fri 23:36]--[2021-06-04 Fri 23:50] => 0:14
CLOCK: [2021-06-04 Fri 23:06]--[2021-06-04 Fri 23:10] => 0:04
CLOCK: [2021-06-04 Fri 22:18]--[2021-06-04 Fri 22:40] => 0:22
CLOCK: [2021-06-04 Fri 17:46]--[2021-06-04 Fri 18:25] => 0:39
CLOCK: [2021-06-04 Fri 17:02]--[2021-06-04 Fri 17:35] => 0:33
CLOCK: [2021-06-04 Fri 16:40]--[2021-06-04 Fri 16:53] => 0:13
CLOCK: [2021-06-04 Fri 16:30]--[2021-06-04 Fri 16:37] => 0:07
CLOCK: [2021-06-04 Fri 15:07]--[2021-06-04 Fri 15:22] => 0:15
CLOCK: [2021-06-04 Fri 12:46]--[2021-06-04 Fri 13:00] => 0:14
CLOCK: [2021-06-04 Fri 11:32]--[2021-06-04 Fri 11:45] => 0:13
CLOCK: [2021-06-04 Fri 10:55]--[2021-06-04 Fri 11:15] => 0:20
CLOCK: [2021-06-03 Thu 23:15]--[2021-06-03 Thu 23:49] => 0:34
CLOCK: [2021-06-03 Thu 22:09]--[2021-06-03 Thu 23:02] => 0:53
CLOCK: [2021-06-03 Thu 17:53]--[2021-06-03 Thu 18:30] => 0:37
CLOCK: [2021-06-03 Thu 17:10]--[2021-06-03 Thu 17:36] => 0:26
CLOCK: [2021-06-03 Thu 13:31]--[2021-06-03 Thu 13:47] => 0:16
CLOCK: [2021-06-03 Thu 12:22]--[2021-06-03 Thu 12:58] => 0:36
CLOCK: [2021-06-03 Thu 11:54]--[2021-06-03 Thu 11:59] => 0:05
:END:
***** DONE DP 1
***** DONE DP 2
***** DONE DP 3
***** DONE DP 4
***** KILL DP 5
***** KILL DP 6
*** DONE QI
SCHEDULED: <2021-06-07 Mon> DEADLINE: <2021-06-08 Tue>
:LOGBOOK:
CLOCK: [2021-06-09 Wed 23:23]--[2021-06-09 Wed 23:58] => 0:35
CLOCK: [2021-06-09 Wed 21:58]--[2021-06-09 Wed 22:55] => 0:57
CLOCK: [2021-06-09 Wed 20:38]--[2021-06-09 Wed 20:44] => 0:06
CLOCK: [2021-06-09 Wed 20:13]--[2021-06-09 Wed 20:20] => 0:07
CLOCK: [2021-06-09 Wed 19:57]--[2021-06-09 Wed 20:05] => 0:08
CLOCK: [2021-06-09 Wed 17:44]--[2021-06-09 Wed 18:25] => 0:41
CLOCK: [2021-06-09 Wed 17:03]--[2021-06-09 Wed 17:24] => 0:21
CLOCK: [2021-06-09 Wed 16:47]--[2021-06-09 Wed 16:55] => 0:08
CLOCK: [2021-06-09 Wed 15:17]--[2021-06-09 Wed 16:15] => 0:58
CLOCK: [2021-06-09 Wed 13:54]--[2021-06-09 Wed 15:00] => 1:06
CLOCK: [2021-06-09 Wed 13:17]--[2021-06-09 Wed 13:44] => 0:27
CLOCK: [2021-06-09 Wed 12:01]--[2021-06-09 Wed 12:40] => 0:39
CLOCK: [2021-06-09 Wed 11:01]--[2021-06-09 Wed 11:45] => 0:44
CLOCK: [2021-06-08 Tue 23:36]--[2021-06-09 Wed 00:11] => 0:35
CLOCK: [2021-06-08 Tue 22:33]--[2021-06-08 Tue 22:59] => 0:26
CLOCK: [2021-06-08 Tue 21:14]--[2021-06-08 Tue 22:16i] => 1:02
CLOCK: [2021-06-08 Tue 17:49]--[2021-06-08 Tue 19:21] => 1:32
CLOCK: [2021-06-08 Tue 16:58]--[2021-06-08 Tue 17:13] => 0:15
CLOCK: [2021-06-08 Tue 14:46]--[2021-06-08 Tue 16:01] => 1:15
CLOCK: [2021-06-08 Tue 11:10]--[2021-06-08 Tue 11:42] => 0:32
CLOCK: [2021-06-08 Tue 10:20]--[2021-06-08 Tue 11:05] => 0:45
CLOCK: [2021-06-07 Mon 20:22]--[2021-06-07 Mon 21:44] => 1:22
CLOCK: [2021-06-07 Mon 18:54]--[2021-06-07 Mon 19:13] => 0:19
:END:
*** DONE LCA
** KILL 2017 blancs [0/2]
:PROPERTIES:
:CATEGORY: 2017blanc
:END:
*** KILL DP [0/3]
SCHEDULED: <2021-06-12 Sat> DEADLINE: <2021-06-13 Sun>
**** KILL DCP 1 [0/6]
***** KILL DP 1
***** KILL DP 2
***** KILL DP 3
***** KILL DP 4
***** KILL DP 5
***** KILL DP 6
**** KILL DCP 2 [0/6]
***** KILL DP 1
***** KILL DP 2
***** KILL DP 3
***** KILL DP 4
***** KILL DP 5
***** KILL DP 6
**** KILL DCP 3 [0/6]
***** KILL DP 1
***** KILL DP 2
***** KILL DP 3
***** KILL DP 4
***** KILL DP 5
***** KILL DP 6
*** KILL LCA
** KILL 2016 blancs
:PROPERTIES:
:CATEGORY: 2016blanc
:END:
*** KILL DP [0/3]
**** KILL DCP 1 [0/6]
***** KILL DP 1
***** KILL DP 2
***** KILL DP 3
***** KILL DP 4
***** KILL DP 5
***** KILL DP 6
**** KILL DCP 2 [0/6]
***** KILL DP 1
***** KILL DP 2
***** KILL DP 3
***** KILL DP 4
***** KILL DP 5
***** KILL DP 6
**** KILL DCP 3 [0/6]
***** KILL DP 1
***** KILL DP 2
***** KILL DP 3
***** KILL DP 4
***** KILL DP 5
***** KILL DP 6
*** KILL LCA
** DONE 2016 [3/3]
:PROPERTIES:
:CATEGORY: 2016
:END:
*** DONE [#A] DP [3/3]
DEADLINE: <2021-05-19 Wed> SCHEDULED: <2021-04-05 Mon>
:LOGBOOK:
CLOCK: [2021-05-19 Wed 22:22]--[2021-05-19 Wed 23:00] => 0:38
CLOCK: [2021-05-19 Wed 19:45]--[2021-05-19 Wed 20:13] => 0:28
CLOCK: [2021-05-19 Wed 15:28]--[2021-05-19 Wed 15:46] => 0:18
CLOCK: [2021-05-19 Wed 13:11]--[2021-05-19 Wed 13:49] => 0:38
CLOCK: [2021-05-19 Wed 11:25]--[2021-05-19 Wed 11:32] => 0:07
CLOCK: [2021-05-19 Wed 10:50]--[2021-05-19 Wed 11:25] => 0:35
CLOCK: [2021-05-18 Tue 21:53]--[2021-05-18 Tue 23:02] => 1:09
CLOCK: [2021-05-18 Tue 18:13]--[2021-05-18 Tue 19:00] => 0:47
CLOCK: [2021-05-18 Tue 17:18]--[2021-05-18 Tue 17:30] => 0:12
CLOCK: [2021-05-18 Tue 14:00]--[2021-05-18 Tue 15:15] => 1:15
CLOCK: [2021-05-18 Tue 12:03]--[2021-05-18 Tue 12:40] => 0:37
CLOCK: [2021-05-17 Mon 22:39]--[2021-05-17 Mon 23:16] => 0:37
CLOCK: [2021-04-11 Sun 20:30]--[2021-04-11 Sun 21:46] => 1:16
CLOCK: [2021-04-05 Mon 21:05]--[2021-04-05 Mon 22:11] => 1:06
CLOCK: [2021-04-05 Mon 18:28]--[2021-04-05 Mon 19:12] => 0:54
CLOCK: [2021-04-05 Mon 15:50]--[2021-04-05 Mon 16:50] => 1:00
CLOCK: [2021-04-05 Mon 14:33]--[2021-04-05 Mon 15:34] => 1:01
CLOCK: [2021-04-05 Mon 11:42]--[2021-04-05 Mon 12:45] => 1:03
CLOCK: [2021-04-05 Mon 10:52]--[2021-04-05 Mon 11:13] => 0:21
:END:
**** DONE DCP 1 [6/6]
***** DONE DP 1
***** DONE DP 2
***** DONE DP 3
***** DONE DP 4
***** DONE DP 5
***** DONE DP 6
**** DONE DCP 2 [6/6]
DEADLINE: <2021-04-19 Mon>
:LOGBOOK:
CLOCK: [2021-04-21 Wed 22:16]--[2021-04-21 Wed 22:31] => 0:15
CLOCK: [2021-04-21 Wed 21:15]--[2021-04-21 Wed 21:45] => 0:30
CLOCK: [2021-04-21 Wed 20:55]--[2021-04-21 Wed 21:01] => 0:06
CLOCK: [2021-04-21 Wed 18:56]--[2021-04-21 Wed 19:07] => 0:11
CLOCK: [2021-04-21 Wed 17:14]--[2021-04-21 Wed 18:11] => 0:57
CLOCK: [2021-04-21 Wed 11:40]--[2021-04-21 Wed 13:00] => 1:20
CLOCK: [2021-04-21 Wed 11:18]--[2021-04-21 Wed 11:27] => 0:09
CLOCK: [2021-04-15 Thu 17:42]--[2021-04-15 Thu 17:59] => 0:17
CLOCK: [2021-04-15 Thu 16:57]--[2021-04-15 Thu 17:13] => 0:16
CLOCK: [2021-04-15 Thu 12:55]--[2021-04-15 Thu 12:58] => 0:03
CLOCK: [2021-04-15 Thu 10:52]--[2021-04-15 Thu 12:10] => 1:18
:END:
***** DONE DP 1
***** DONE DP 2
***** DONE DP 3
***** DONE DP 4
***** DONE DP 5
***** DONE DP 6
**** DONE DCP 3 [6/6]
***** DONE DP 1
***** DONE DP 2
***** DONE DP 3
***** DONE DP 4
***** DONE DP 5
***** DONE DP 6
*** DONE QI
SCHEDULED: <2021-05-19 Wed> DEADLINE: <2021-05-20 Thu>
:LOGBOOK:
CLOCK: [2021-05-24 Mon 18:17]--[2021-05-24 Mon 18:44] => 0:27
CLOCK: [2021-05-24 Mon 17:40]--[2021-05-24 Mon 18:00] => 0:20
CLOCK: [2021-05-24 Mon 16:17]--[2021-05-24 Mon 17:10] => 0:53
CLOCK: [2021-05-24 Mon 13:17]--[2021-05-24 Mon 14:00] => 0:43
CLOCK: [2021-05-22 Sat 21:07]--[2021-05-22 Sat 21:50] => 0:43
CLOCK: [2021-05-22 Sat 20:24]--[2021-05-22 Sat 20:58] => 0:34
CLOCK: [2021-05-22 Sat 17:09]--[2021-05-22 Sat 18:14] => 1:05
CLOCK: [2021-05-22 Sat 16:44]--[2021-05-22 Sat 16:52] => 0:08
CLOCK: [2021-05-22 Sat 16:09]--[2021-05-22 Sat 16:30 ] => 0:21
CLOCK: [2021-05-22 Sat 15:52]--[2021-05-22 Sat 16:00] => 0:08
CLOCK: [2021-05-22 Sat 15:13]--[2021-05-22 Sat 15:35] => 0:22
CLOCK: [2021-05-22 Sat 14:35]--[2021-05-22 Sat 14:50] => 0:15
CLOCK: [2021-05-22 Sat 11:48]--[2021-05-22 Sat 12:55] => 1:07
CLOCK: [2021-05-21 Fri 21:37]--[2021-05-21 Fri 21:55] => 0:18
CLOCK: [2021-05-21 Fri 18:40]--[2021-05-21 Fri 19:51] => 1:11
CLOCK: [2021-05-21 Fri 17:03]--[2021-05-21 Fri 17:45] => 0:42
CLOCK: [2021-05-21 Fri 16:31]--[2021-05-21 Fri 17:02] => 0:31
CLOCK: [2021-05-20 Thu 18:18]--[2021-05-20 Thu 18:39] => 0:21
CLOCK: [2021-05-20 Thu 15:50]--[2021-05-20 Thu 16:33] => 0:43
:END:
*** DONE LCA
** KILL LCA [7/7]
:PROPERTIES:
:CATEGORY: lca
:END:
Utiliser les annales du collège après 2011
*** DONE 2015
DEADLINE: <2020-12-03 Thu> SCHEDULED: <2020-11-30 Mon>
*** DONE 2014
SCHEDULED: <2021-01-09 Sat> DEADLINE: <2021-01-09 Sat>
*** DONE 2013
*** DONE 2012
DEADLINE: <2021-02-03 Wed>
*** DONE 2011
*** DONE 2010
DEADLINE: <2021-06-11 Fri>
:LOGBOOK:
CLOCK: [2021-06-11 Fri 19:42]--[2021-06-11 Fri 20:02] => 0:20
CLOCK: [2021-06-11 Fri 18:43]--[2021-06-11 Fri 19:12] => 0:29
CLOCK: [2021-06-11 Fri 17:19]--[2021-06-11 Fri 17:58] => 0:39
:END:
*** DONE 2009
DEADLINE: <2021-06-12 Sat>
:LOGBOOK:
CLOCK: [2021-06-12 Sat 17:02]--[2021-06-12 Sat 17:16] => 0:14
CLOCK: [2021-06-12 Sat 16:22]--[2021-06-12 Sat 16:30] => 0:08
CLOCK: [2021-06-12 Sat 14:59]--[2021-06-12 Sat 15:20] => 0:21
CLOCK: [2021-06-12 Sat 14:08]--[2021-06-12 Sat 14:42] => 0:34
:END:
** DONE Interfac décembre
:PROPERTIES:
:CATEGORY: inter-fac
:END:
*** DONE Faire examens
*** DONE Corrigé
SCHEDULED: <2021-02-22 Mon> DEADLINE: <2021-01-10 Sun>
**** DONE LCA
DEADLINE: <2021-02-09 Tue>
[[file:/usr/home/alex/backups/hubic/Public/Cours/Medecine/FASM3/interfac/interufr-dec2020-lca.pdf][file:/usr/home/alex/backups/hubic/Public/Cours/Medecine/FASM3/interfac/interufr-dec2020-lca.pdf]]
**** DONE QI
DEADLINE: <2021-04-11 Sun>
:LOGBOOK:
CLOCK: [2021-04-14 Wed 22:14]--[2021-04-14 Wed 22:40] => 0:26
CLOCK: [2021-04-14 Wed 21:53]--[2021-04-14 Wed 22:07] => 0:14
CLOCK: [2021-04-14 Wed 20:47]--[2021-04-14 Wed 21:14] => 0:27
CLOCK: [2021-04-14 Wed 17:24]--[2021-04-14 Wed 17:28] => 0:04
CLOCK: [2021-04-14 Wed 15:42]--[2021-04-14 Wed 16:24] => 0:42
CLOCK: [2021-04-14 Wed 12:28]--[2021-04-14 Wed 13:24] => 0:56
CLOCK: [2021-04-14 Wed 11:47]--[2021-04-14 Wed 12:18] => 0:31
CLOCK: [2021-04-13 Tue 22:14]--[2021-04-13 Tue 23:10] => 0:56
CLOCK: [2021-04-13 Tue 17:16]--[2021-04-13 Tue 17:53] => 0:37
CLOCK: [2021-04-13 Tue 15:06]--[2021-04-13 Tue 16:09] => 1:03
CLOCK: [2021-04-13 Tue 12:32]--[2021-04-13 Tue 13:46] => 1:14
CLOCK: [2021-04-12 Mon 22:03]--[2021-04-12 Mon 22:22] => 0:19
CLOCK: [2021-04-12 Mon 15:00]--[2021-04-12 Mon 15:55] => 0:55
CLOCK: [2021-04-12 Mon 12:33]--[2021-04-12 Mon 14:09] => 1:36
CLOCK: [2021-03-10 Wed 14:18]--[2021-03-10 Wed 15:29] => 1:11
CLOCK: [2021-03-10 Wed 11:37]--[2021-03-10 Wed 12:35] => 0:58
:END:
[[file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/interfac/interufr-dec2020-qi.pdf][file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/interfac/interufr-dec2020-qi.pdf]]
-> Q92
**** DONE DP1
DEADLINE: <2021-01-05 Tue>
[[file:/usr/home/alex/Cours/Medecine/FASM3/interfac/interufr-dec2020-dcp1.pdf][file:/usr/home/alex/Cours/Medecine/FASM3/interfac/interufr-dec2020-dcp1.pdf]]
Moitié faite
=> on reprend depuis le début
p 43/66
**** DONE DP2
SCHEDULED: <2021-01-22 Fri> DEADLINE: <2021-01-17 Sun>
[[file:/usr/home/alex/backups/hubic/Public/Cours/Medecine/FASM3/interfac/interufr-dec2020-dcp2.pdf][file:/usr/home/alex/backups/hubic/Public/Cours/Medecine/FASM3/interfac/interufr-dec2020-dcp2.pdf]]
**** DONE DP3
SCHEDULED: <2021-02-22 Mon> DEADLINE: <2021-01-26 Tue>
:LOGBOOK:
CLOCK: [2021-03-01 Mon 12:31]--[2021-03-01 Mon 13:25] => 0:54
CLOCK: [2021-02-28 Sun 22:53]--[2021-02-28 Sun 23:15] => 0:22
CLOCK: [2021-02-28 Sun 18:36]--[2021-02-28 Sun 19:21] => 0:45
CLOCK: [2021-02-28 Sun 15:10]--[2021-02-28 Sun 16:15] => 1:05
:END:
[[file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/interfac/interufr-dec2020-dcp3.pdf][file:/usr/home/alex/backups/hubic/public/cours/Medecine/FASM3/interfac/interufr-dec2020-dcp3.pdf]]
* TOUR1 Cancérologie :cancero:
:PROPERTIES:
:CATEGORY: cancero
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: cancero
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** TOUR1 Relire fiches
:LOGBOOK:
CLOCK: [2021-06-10 Thu 16:19]--[2021-06-10 Thu 16:43] => 0:24
CLOCK: [2021-06-10 Thu 15:24]--[2021-06-10 Thu 16:05] => 0:41
CLOCK: [2021-04-04 Sun 11:34]--[2021-04-04 Sun 12:04] => 0:30
:END:
:DEADLINE: <2021-06-10 Thu>
Minimum:
- [ ] 5 cancers
- [ ] Effets secondaires
** DONE MAJ effets secondaires chimio
DEADLINE: <2021-05-24 Mon>
:LOGBOOK:
CLOCK: [2021-05-24 Mon 11:54]--[2021-05-24 Mon 12:15] => 0:21
:END:
* TOUR1 Cardiologie :D1:
:PROPERTIES:
:CATEGORY: cardiologie
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: cardiologie
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches pour CC
SCHEDULED: <2020-09-26 Sat 11:30> DEADLINE: <2020-09-26 Sat 12:30>
:LOGBOOK:
CLOCK: [2020-09-26 Sat 17:23]--[2020-09-26 Sat 18:16] => 0:53
CLOCK: [2020-09-26 Sat 14:45]--[2020-09-26 Sat 17:08] => 2:23
CLOCK: [2020-09-26 Sat 12:29]--[2020-09-26 Sat 12:45] => 0:16
CLOCK: [2020-09-26 Sat 12:18]--[2020-09-26 Sat 12:26] => 0:08
CLOCK: [2020-09-26 Sat 11:36]--[2020-09-26 Sat 12:07] => 0:31
:END:
SCHEDULED: <2020-09-26 Sat 14:00> DEADLINE: <2020-09-26 Sat 15:00>
** KILL LITFL top 100 ECG [23/120]
https://litfl.com/top-100/ecg/
:PROPERTIES:
:LAST_REPEAT: [2020-10-13 Tue 09:45]
:END:
- [ ] ECG 1
- [ ] ECG 2
- [ ] ECG 3
- [ ] ECG 4
- [ ] ECG 5
- [ ] ECG 6
- [ ] ECG 7
- [ ] ECG 8
- [ ] ECG 9
- [ ] ECG 10
- [ ] ECG 11
- [ ] ECG 12
- [ ] ECG 13
- [ ] ECG 14
- [ ] ECG 15
- [ ] ECG 16
- [ ] ECG 17
- [ ] ECG 18
- [ ] ECG 19
- [ ] ECG 20
- [ ] ECG 21
- [ ] ECG 22
- [ ] ECG 23
- [ ] ECG 24
- [ ] ECG 25
- [ ] ECG 26
- [ ] ECG 27
- [ ] ECG 28
- [ ] ECG 29
- [ ] ECG 30
- [ ] ECG 31
- [ ] ECG 32
- [ ] ECG 33
- [ ] ECG 34
- [ ] ECG 35
- [ ] ECG 36
- [ ] ECG 37
- [ ] ECG 38
- [ ] ECG 39
- [ ] ECG 40
- [ ] ECG 41
- [ ] ECG 42
- [ ] ECG 43
- [ ] ECG 44
- [ ] ECG 45
- [ ] ECG 46
- [ ] ECG 47
- [ ] ECG 48
- [ ] ECG 49
- [ ] ECG 50
- [ ] ECG 51
- [ ] ECG 52
- [ ] ECG 53
- [ ] ECG 54
- [ ] ECG 55
- [ ] ECG 56
- [ ] ECG 57
- [ ] ECG 58
- [ ] ECG 59
- [ ] ECG 60
- [ ] ECG 61
- [ ] ECG 62
- [ ] ECG 63
- [ ] ECG 64
- [ ] ECG 65
- [ ] ECG 66
- [ ] ECG 67
- [ ] ECG 68
- [ ] ECG 69
- [ ] ECG 70
- [ ] ECG 71
- [ ] ECG 72
- [ ] ECG 73
- [ ] ECG 74
- [ ] ECG 75
- [ ] ECG 76
- [ ] ECG 77
- [ ] ECG 78
- [ ] ECG 79
- [ ] ECG 80
- [ ] ECG 81
- [ ] ECG 82
- [ ] ECG 83
- [ ] ECG 84
- [ ] ECG 85
- [ ] ECG 86
- [ ] ECG 87
- [ ] ECG 88
- [ ] ECG 89
- [ ] ECG 90
- [ ] ECG 91
- [ ] ECG 92
- [ ] ECG 93
- [ ] ECG 94
- [ ] ECG 95
- [X] ECG 96
- [X] ECG 97
- [X] ECG 98
- [X] ECG 99
- [X] ECG 100
- [X] ECG 101
- [X] ECG 102
- [X] ECG 103
- [X] ECG 104
- [X] ECG 105
- [X] ECG 106
- [X] ECG 107
- [X] ECG 108
- [X] ECG 109
- [X] ECG 110
- [X] ECG 111
- [X] ECG 112
- [X] ECG 113
- [X] ECG 114
- [X] ECG 115
- [X] ECG 116
- [X] ECG 117
- [X] ECG 118
- [ ] ECG 119
- [ ] ECG 120
** KILL [#B] 150 ECGs Hampton [3/150]
:LOGBOOK:
CLOCK: [2021-04-30 Fri 22:49]--[2021-04-30 Fri 22:49] => 0:00
CLOCK: [2021-04-11 Sun 11:09]--[2021-04-11 Sun 11:20] => 0:11
:END:
[[file:/media/books/medecine/150 ECG Problems, 4th Edition/150 ECG Problems, 4th.pdf][file:/media/books/medecine/150 ECG Problems, 4th Edition/150 ECG Problems, 4th.pdf]]
- [X] ECG 1
- [X] ECG 2
- [X] ECG 3
- [ ] ECG 4
- [ ] ECG 5
- [ ] ECG 6
- [ ] ECG 7
- [ ] ECG 8
- [ ] ECG 9
- [ ] ECG 10
- [ ] ECG 11
- [ ] ECG 12
- [ ] ECG 13
- [ ] ECG 14
- [ ] ECG 15
- [ ] ECG 16
- [ ] ECG 17
- [ ] ECG 18
- [ ] ECG 19
- [ ] ECG 20
- [ ] ECG 21
- [ ] ECG 22
- [ ] ECG 23
- [ ] ECG 24
- [ ] ECG 25
- [ ] ECG 26
- [ ] ECG 27
- [ ] ECG 28
- [ ] ECG 29
- [ ] ECG 30
- [ ] ECG 31
- [ ] ECG 32
- [ ] ECG 33
- [ ] ECG 34
- [ ] ECG 35
- [ ] ECG 36
- [ ] ECG 37
- [ ] ECG 38
- [ ] ECG 39
- [ ] ECG 40
- [ ] ECG 41
- [ ] ECG 42
- [ ] ECG 43
- [ ] ECG 44
- [ ] ECG 45
- [ ] ECG 46
- [ ] ECG 47
- [ ] ECG 48
- [ ] ECG 49
- [ ] ECG 50
- [ ] ECG 51
- [ ] ECG 52
- [ ] ECG 53
- [ ] ECG 54
- [ ] ECG 55
- [ ] ECG 56
- [ ] ECG 57
- [ ] ECG 58
- [ ] ECG 59
- [ ] ECG 60
- [ ] ECG 61
- [ ] ECG 62
- [ ] ECG 63
- [ ] ECG 64
- [ ] ECG 65
- [ ] ECG 66
- [ ] ECG 67
- [ ] ECG 68
- [ ] ECG 69
- [ ] ECG 70
- [ ] ECG 71
- [ ] ECG 72
- [ ] ECG 73
- [ ] ECG 74
- [ ] ECG 75
- [ ] ECG 76
- [ ] ECG 77
- [ ] ECG 78
- [ ] ECG 79
- [ ] ECG 80
- [ ] ECG 81
- [ ] ECG 82
- [ ] ECG 83
- [ ] ECG 84
- [ ] ECG 85
- [ ] ECG 86
- [ ] ECG 87
- [ ] ECG 88
- [ ] ECG 89
- [ ] ECG 90
- [ ] ECG 91
- [ ] ECG 92
- [ ] ECG 93
- [ ] ECG 94
- [ ] ECG 95
- [ ] ECG 96
- [ ] ECG 97
- [ ] ECG 98
- [ ] ECG 99
- [ ] ECG 100
- [ ] ECG 101
- [ ] ECG 102
- [ ] ECG 103
- [ ] ECG 104
- [ ] ECG 105
- [ ] ECG 106
- [ ] ECG 107
- [ ] ECG 108
- [ ] ECG 109
- [ ] ECG 110
- [ ] ECG 111
- [ ] ECG 112
- [ ] ECG 113
- [ ] ECG 114
- [ ] ECG 115
- [ ] ECG 116
- [ ] ECG 117
- [ ] ECG 118
- [ ] ECG 119
- [ ] ECG 120
- [ ] ECG 121
- [ ] ECG 122
- [ ] ECG 123
- [ ] ECG 124
- [ ] ECG 125
- [ ] ECG 126
- [ ] ECG 127
- [ ] ECG 128
- [ ] ECG 129
- [ ] ECG 130
- [ ] ECG 131
- [ ] ECG 132
- [ ] ECG 133
- [ ] ECG 134
- [ ] ECG 135
- [ ] ECG 136
- [ ] ECG 137
- [ ] ECG 138
- [ ] ECG 139
- [ ] ECG 140
- [ ] ECG 141
- [ ] ECG 142
- [ ] ECG 143
- [ ] ECG 144
- [ ] ECG 145
- [ ] ECG 146
- [ ] ECG 147
- [ ] ECG 148
- [ ] ECG 149
- [ ] ECG 150
** KILL ECG made easy
:LOGBOOK:
CLOCK: [2021-04-13 Tue 11:42]--[2021-04-13 Tue 12:26] => 0:44
:END:
* KILL Chir vasculaire
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
Source: [[file:~/backups/hubic/Public/Cours/Medecine/referentiels/chir_vasculaire.pdf][file:~/backups/hubic/Public/Cours/Medecine/referentiels/chir_vasculaire.pdf]]
En ligne : http://cemv.web-plateform.net/ECN_Poly_ConsultEcran.pdf
https://drive.google.com/drive/folders/1PKMHd9yq-clAB5P1lLSnMRd7rtfOjvO7
** KILL TVP
** KILL AOMI
** KILL Insuffisance veineuse
* TOUR1 Chirurgie maxillo-faciale :maxillo:
:PROPERTIES:
:CATEGORY: maxillo
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: maxillo
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches pour CC
SCHEDULED: <2020-10-05 Mon> DEADLINE: <2020-10-06 Tue>
*** DONE Anatomie craniofaciale
*** DONE Examen de la face et de la cavité buccale
*** DONE Item 46 – Développement buccodentaire et anomalies
*** DONE Items 329, 330, 360 – Traumatologie maxillofaciale
*** DONE Item 88 – Pathologie des glandes salivaires
*** DONE Item 295 – Tumeurs de la cavité buccale
*** DONE Item 304 – Tumeurs des os de la face primitives et secondaires
*** DONE Item 299 – Tumeurs cutanées
*** DONE Item 111 – Angiomes de la face et de la cavité buccale
*** DONE Item 344 – Infections aiguës des parties molles d'origine dentaire
*** DONE Items 152, 164 – Pathologie non tumorale de la muqueuse buccale
*** DONE Item 97 – Diagnostic différentiel des migraines, névralgies trijéminales, algies de la face : douleurs buccales
*** DONE Item 133 – Anesthésie locale, régionale et générale dans le cadre de la chirurgie maxillofaciale
*** DONE Item 198 – Allotransplantation de tissu composite : greffe de visage
* Conf
:PROPERTIES:
:CATEGORY: conf
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: conf
:ARCHIVE_ITAGS: revisions
:END:
** KILL Ecn asso
:PROPERTIES:
:CATEGORY: ecn-asso
:END:
*** DONE [2021-05-13 Thu] :pédia:
**** DONE Sujet
DEADLINE: <2021-05-13 Thu>
:LOGBOOK:
CLOCK: [2021-05-13 Thu 13:28]--[2021-05-13 Thu 13:51] => 0:23
CLOCK: [2021-05-13 Thu 11:00]--[2021-05-13 Thu 12:00] => 1:00
:END:
**** DONE Conf
DEADLINE: <2021-05-13 Thu>
:LOGBOOK:
CLOCK: [2021-05-14 Fri 21:43]--[2021-05-14 Fri 22:23] => 0:40
CLOCK: [2021-05-14 Fri 18:21]--[2021-05-14 Fri 19:52] => 1:31
:END:
**** DONE Relire
*** KILL [2021-05-20 Thu] :gyneco:
**** DONE Sujet
DEADLINE: <2021-05-20 Thu>
:LOGBOOK:
CLOCK: [2021-05-20 Thu 13:24]--[2021-05-20 Thu 13:38] => 0:14
CLOCK: [2021-05-20 Thu 12:36]--[2021-05-20 Thu 13:00] => 0:24
CLOCK: [2021-05-20 Thu 11:15]--[2021-05-20 Thu 11:54] => 0:39
:END:
**** DONE Correction
DEADLINE: <2021-05-20 Thu>
**** DONE Relire
DEADLINE: <2021-05-21 Fri>
:LOGBOOK:
CLOCK: [2021-05-21 Fri 12:00]--[2021-05-21 Fri 13:10] => 1:10
:END:
* TOUR1 Dermato :dermato:
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE [#A] Relire fiches
DEADLINE: <2021-05-16 Sun> SCHEDULED: <2021-05-12 Wed>
:PROPERTIES:
:CATEGORY: dermato
:END:
:LOGBOOK:
CLOCK: [2021-05-17 Mon 18:00]--[2021-05-17 Mon 18:40] => 0:40
CLOCK: [2021-05-17 Mon 14:57]--[2021-05-17 Mon 15:53] => 0:56
CLOCK: [2021-05-17 Mon 12:39]--[2021-05-17 Mon 13:17] => 0:38
CLOCK: [2021-05-12 Wed 22:56]--[2021-05-12 Wed 23:41] => 0:45
CLOCK: [2021-05-12 Wed 19:19]--[2021-05-12 Wed 19:45] => 0:26
:END:
** DONE Images commentées
DEADLINE: <2021-05-12 Wed>
* Dernières reco (HAS)
:PROPERTIES:
:CATEGORY: inter-fac
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: inter-fac
:ARCHIVE_ITAGS: revisions
:END:
* Endocrino :endocrino:
:PROPERTIES:
:CATEGORY: endocrino
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: endocrino
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches
DEADLINE: <2021-06-11 Fri>
:LOGBOOK:
CLOCK: [2021-06-12 Sat 17:36]--[2021-06-12 Sat 18:12] => 0:36
:END:
* Garde
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_ITAGS: revisions
:END:
** Urgences
*** KILL Positionnement ECG
*** KILL Gas du sang
*** KILL Examen clinique
**** KILL Urgences vitale (ABCDe)
*** KILL Collège d'urgence
*** KILL Pathologies
Colique néphrétique
Colique hépatique
Uro
** KILL Examen clinique
:PROPERTIES:
:CATEGORY: sémiologie
:END:
* Gynécologie :gyneco:
:PROPERTIES:
:CATEGORY: gynéco
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: gynéco
:ARCHIVE_ITAGS: revisions
:END:
** KILL Relire fiches
DEADLINE: <2021-06-11 Fri>
* Génétique
:PROPERTIES:
:CATEGORY: génétique
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: génétique
:ARCHIVE_ITAGS: revisions
:END:
** DONE Exercices
DEADLINE: <2021-06-12 Sat>
:LOGBOOK:
CLOCK: [2021-06-12 Sat 18:17]--[2021-06-12 Sat 19:01] => 0:44
:END:
Livret à la fin
Source: https://www-elsevierelibrary-fr.bases-doc.univ-lorraine.fr/epubreader/gntique-mdicale
* TOUR1 Gériatrie :geria:
:PROPERTIES:
:CATEGORY: géria
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: géria
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches :geria:
DEADLINE: <2021-06-02 Wed> SCHEDULED: <2021-06-02 Wed>
:PROPERTIES:
:ORDERED: t
:END:
:LOGBOOK:
CLOCK: [2021-06-02 Wed 22:25]--[2021-06-02 Wed 22:45] => 0:20
CLOCK: [2021-06-02 Wed 21:56]--[2021-06-02 Wed 22:16] => 0:20
CLOCK: [2021-06-02 Wed 18:50]--[2021-06-02 Wed 19:10] => 0:20
CLOCK: [2021-06-02 Wed 17:36]--[2021-06-02 Wed 18:27] => 0:51
CLOCK: [2021-06-02 Wed 15:20]--[2021-06-02 Wed 16:38] => 1:18
CLOCK: [2021-06-02 Wed 12:12]--[2021-06-02 Wed 12:37] => 0:25
:END:
* TOUR1 Hémato :hémato:
:PROPERTIES:
:CATEGORY: hémato
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: hémato
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches
DEADLINE: <2021-01-16 Sat> SCHEDULED: <2021-01-12 Tue>
* TOUR1 Hépato-Gastro :hge:
:PROPERTIES:
:COLUMNS: %25ITEM %Lu %Fiche %QI
:QI_source: 1000 QROC
:CATEGORY: HGE
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: HGE
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches
DEADLINE: <2021-04-27 Tue> SCHEDULED: <2021-04-22 Sat>
:LOGBOOK:
CLOCK: [2021-05-12 Wed 16:23]--[2021-05-12 Wed 17:10] => 0:47
CLOCK: [2021-05-09 Sun 22:50]--[2021-05-09 Sun 22:53] => 0:03
CLOCK: [2021-05-02 Sun 11:45]--[2021-05-02 Sun 12:55] => 1:10
CLOCK: [2021-04-28 Wed 16:56]--[2021-04-28 Wed 17:01] => 0:05
CLOCK: [2021-04-28 Wed 12:10]--[2021-04-28 Wed 13:24] => 1:14
CLOCK: [2021-04-26 Mon 12:02]--[2021-04-26 Mon 12:29] => 0:27
CLOCK: [2021-04-26 Mon 11:22]--[2021-04-26 Mon 11:38] => 0:16
CLOCK: [2021-04-25 Sun 22:25]--[2021-04-25 Sun 22:44] => 0:19
CLOCK: [2021-04-25 Sun 21:20]--[2021-04-25 Sun 21:55] => 0:35
CLOCK: [2021-04-25 Sun 19:54]--[2021-04-25 Sun 20:01] => 0:07
CLOCK: [2021-04-25 Sun 18:49]--[2021-04-25 Sun 19:05] => 0:16
CLOCK: [2021-04-25 Sun 18:28]--[2021-04-25 Sun 18:40] => 0:12
CLOCK: [2021-04-25 Sun 16:00]--[2021-04-25 Sun 16:41] => 0:41
CLOCK: [2021-04-25 Sun 15:24]--[2021-04-25 Sun 15:45] => 0:21
CLOCK: [2021-04-25 Sun 14:41]--[2021-04-25 Sun 14:58] => 0:17
:END:
* Imagerie
:PROPERTIES:
:CATEGORY: imagerie
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: imagerie
:ARCHIVE_ITAGS: revisions
:END:
** Tuto radio
Source
*** KILL [[https://www.youtube.com/watch?v=BzAuXu1ibrM][#10: Cholécystite Aigüe !]]
[[file:~/TV_Shows/Tuto_radio/Conf Tuto Radio #10 - Cholécystite Aiguë !-BzAuXu1ibrM.webm][file:~/TV_Shows/Tuto_radio/Conf Tuto Radio #10 - Cholécystite Aiguë !-BzAuXu1ibrM.webm]]
DEADLINE: <2020-10-09 Fri>
*** DONE [[https://www.youtube.com/watch?v=1G7P9V3s0Ao][#9 : Radiculalgie et Hernie Discale !]]
DEADLINE: <2020-10-05 Mon>
*** DONE [[https://www.youtube.com/watch?v=uTGvhzjW_dM][#8: Pancréatite Aigue !]]
DEADLINE: <2020-10-12 Mon>
[[file:~/TV_Shows/Tuto_radio/Conf Tuto Radio #8 - Pancréatite Aigue !-uTGvhzjW_dM.webm][file:~/TV_Shows/Tuto_radio/Conf Tuto Radio #8 - Pancréatite Aigue !-uTGvhzjW_dM.webm]]
*** DONE [[https://www.youtube.com/watch?v=TcEQSUFPUzA][#7: Hémorragie méningée non traumatique !]]
DEADLINE: <2020-10-07 Wed>
*** KILL [[https://www.youtube.com/watch?v=sZrr_2vbDY4][#6 : Grossesse Extra-Utérine !]]
[[file:~/TV_Shows/Tuto_radio/Conf Tuto Radio #6 - Grossesse Extra-Utérine !-sZrr_2vbDY4.mkv][file:~/TV_Shows/Tuto_radio/Conf Tuto Radio #6 - Grossesse Extra-Utérine !-sZrr_2vbDY4.mkv]]
DEADLINE: <2020-10-14 Wed>
*** DONE [[https://www.youtube.com/watch?v=M57Sbl8k058][#5: Diverticulite aigüe !]]
DEADLINE: <2020-10-11 Sun>
*** DONE [[https://www.youtube.com/watch?v=i5Jb22kwVBQ][#4: Spondylodiscite infectieuse !]]
*** DONE [[https://www.youtube.com/watch?v=6zIZq-xRus4][#3 : la Colique Néphr\u00e9tique !]]
*** DONE [[https://www.youtube.com/watch?v=UQgKuIoVotM][#2: Appendicite]]
*** DONE [[https://www.youtube.com/watch?v=K1Gw99I0zPU][#1 : Embolie pulmonaire]]
* Items
:PROPERTIES:
:COLUMNS: %KILL% %25ITEM %neuro% %neurochir%
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_ITAGS: revisions
:END:
** KILL 1 La relation médecin-malade :psy:
** KILL 2 Les valeurs professionnelles du médecin et des autres professions de santé
** TOUR1 3 Le raisonnement et la décision en médecine :santepub:
:PROPERTIES:
:santepub: t
:END:
** TOUR1 4 La sécurité du patient :malinf:santepub:
:PROPERTIES:
:malinf: t
:santepub: t
:END:
** KILL 5 La gestion des erreurs et des plaintes ; l'aléa thérapeutique
** KILL 6 Organisation de l'exercice clinique
:PROPERTIES:
:ECNI: 1
:ID: 579495ad-c582-4d21-84da-47e05e4cfce2
:END:
** TOUR1 7 Droits du patients :medecinelegale:
:PROPERTIES:
:ECNI: 1
:ID: 75ef52fb-e149-424d-9e37-0045d8cc6576
:END:
** KILL 8 Éthique médicale :gyneco:mpr:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:ID: 30960cb5-7cd8-49b9-a30c-d6ff6db8f70b
:mpr: t
:END:
** TOUR1 9 Certificats médicaux :medecinelegale:ophtalmo:
** TOUR1 10 Violences sexuelles :gyneco:medecinelegale:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:ID: 6142ee88-d6a8-48db-b6e7-264b18ff1c16
:legal: t
:END:
** TOUR1 11 Soins psychiatriques sans consentement :psy:
:PROPERTIES:
:psy: t
:END:
** KILL 12 Responsabilités médicale pénale, civile, administrative et disciplinaire
** TOUR1 13 Qualité des soins
:PROPERTIES:
:santepub: t
:END:
** TOUR1 14 Formation tout au lon de la vie :pedia:santepub:
:PROPERTIES:
:santepub: t
:END:
** TOUR1 15 Organisation du système de soins :pedia:santepub:
:PROPERTIES:
:santepub: t
:END:
** KILL 16 La sécurité sociale. L'assurance maladie
** TOUR1 17 Convention médicale :pedia:santepub:
:PROPERTIES:
:santepub: t
:END:
** TOUR1 18 Méthodologie de la recherche :pedia:santepub:
:PROPERTIES:
:santepub: t
:END:
** TOUR1 19 Mesure de l'état de santé :pedia:mpr:santepub:
:PROPERTIES:
:santepub: t
:mpr: t
:END:
** TOUR1 20 Interprétation d'une enquête épidémiologique :pedia:santepub:
** KILL 21 Examen pré-nuptial :pedia:gyneco:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:ID: b7075897-bbf4-4fd1-a808-cccc6ff7a771
:END:
** KILL 22 Grossesse normale :pedia:gyneco:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:ID: 25641206-7d98-48de-8fa4-999edafef11d
:END:
** KILL 23 Principales complications de la grossesse :pedia:gyneco:nephro:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:ID: 64e346d3-7ba2-4a7c-976a-2e69c6f50e88
:END:
** KILL 24 Grossesse extra-utérine :pedia:gyneco:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:ID: ca2f6611-cab2-4ecc-adb9-9596ef21472a
:END:
** KILL 25 Douleurs abdominales chez la femme enceinte :pedia:gyneco:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** KILL [#A] 26 Prévention des risques foetaux :pedia:gyneco:malinf:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:malinf: t
:END:
** TOUR1 27 Infections urinaires pendant la grossesse :pedia:gyneco:malinf:
:PROPERTIES:
:malinf: t
:END:
** KILL 28 Risques pour la maternité :pedia:gyneco:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 29 Prématurité et RCIU :pedia:gyneco:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:pedia: t
:gyneco: t
:END:
** KILL 30 Accouchement normal :pedia:gyneco:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 31 Évalution du nouveau-né :pedia:gyneco:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:pedia: t
:END:
** KILL 32 Allaitement maternel :pedia:gyneco:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:END:
** KILL 33 Suites de couches pathologiques :pedia:gyneco:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** KILL 34 Anomalises du cycle mestruel :pedia:gyneco:
** KILL 35 Contraception :pedia:endoc:gyneco:uro:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:END:
** TOUR1 36 IVG :pedia:gyneco:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:gyneco: t
:END:
** TOUR1 37 Stérilité couple :pedia:endoc:gyneco:uro:retard:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:END:
** KILL 38 Assistance médicale à la procréation :pedia:gyneco:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** KILL 39 Algies pelviennes chez la femme :pedia:gyneco:uro:retard:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** KILL 40 Aménorrhée :pedia:endoc:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:END:
** KILL 41 Hémorragie génitale chez la femme :pedia:gyneco:
** KILL 42 Tuméfaction pelvienne chez la femme :pedia:gyneco:uro:retard:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 43 Trisomie 21, syndrome de l'X fragile :pedia:gyneco:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 4
:pedia: t
:END:
** TOUR1 44 Suivi d'un nourrisson. Dépistage des anomalies orthopédiques, auditives, visuelle :pedia:ophtalmo:orl:ortho:
:PROPERTIES:
:ECNI: 3
:COLLEGE: 2
:ORL: t
:pedia: t
:END:
** TOUR1 45 Alimentation du nourrisson et de l'enfant
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:END:
** TOUR1 46 Développement bucco-dentaire
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:pedia: t
:END:
** TOUR1 47 Puberté :pedia:gyneco:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 3
:pedia: t
:endoc: t
:END:
** TOUR1 48 Cryptorchidie :pedia:endoc:uro:retard:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 2
:END:
** TOUR1 49 Troubles de la miction chez l'enfant
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:pedia: t
:END:
** TOUR1 50 Strabisme chez l'enfant :pedia:ophtalmo:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 2
:ophtalmo: t
:END:
** TOUR1 51 retard de croissance :pedia:endoc:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 3
:END:
** TOUR1 52 Boiteries de l'enfant :pedia:ortho:rhumato:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 3
:END:
** TOUR1 53 Développement psychomoteur :pedia:pédia:psy:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:pedia: t
:END:
** TOUR1 54 L'enfant handicapé :pedia:mpr:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 2
:mpr: t
:END:
** TOUR1 55 Maltraitance :pedia:medecinelegale:pédia:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 2
:legal: t
:END:
** TOUR1 56 Sexualité normale et ses troubles :pedia:gyneco:psy:uro:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:psy: t
:END:
** TOUR1 57 Sujets en situation de précarité :pedia:psy:santepub:
:PROPERTIES:
:santepub: t
:psy: t
:END:
** TOUR1 58 Facteurs de risques des troubles mentaux :pedia:psy:
** TOUR1 59 Classification des troubles mentaux :pedia:psy:
:PROPERTIES:
:psy: t
:END:
** TOUR1 60 Offres de soins en psychiatrie :pedia:psy:
** TOUR1 61 Trouble schizophrenique :pedia:psy:
:PROPERTIES:
:psy: t
:END:
** TOUR1 62 Trouble bipolaire :pedia:psy:
:PROPERTIES:
:psy: t
:END:
** KILL 63 Trouble délirant persistant :pedia:psy:
** TOUR1 63 Troubles délirants persistants
:PROPERTIES:
:psy: t
:END:
** TOUR1 64 Trouble dépressif, anxieux généralisé... :pedia:psy:
** TOUR1 65 Troubles envahissants du développements :pedia:psy:
** TOUR1 66 Trouble de personnalité :pedia:psy:
:PROPERTIES:
:ECNI: 1
:END:
** TOUR1 67 Troubles psychique de la grossesse et du post-partum :pedia:gyneco:psy:
** TOUR1 68 Troubles psychique du sujet âgé :pedia:psy:
:pedia:PROPERTIES:
:pedia:COLLEGE: 1
:pedia:ECNI: 1
:pedia:END:
** TOUR1 69 Troubles des conduites alimentaires :pedia:psy:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 70 Troubles somatoformes :pedia:psy:
:PROPERTIES:
:psy: t
:END:
** TOUR1 71 Techniques psychothérapeutiques :pedia:psy:
:PROPERTIES:
:psy: t
:END:
** TOUR1 72 Prescription des psychotropes :pedia:psy:
:PROPERTIES:
:COLLEGE: 1
:psy: t
:END:
** TOUR1 73 Addiction au tabac :pedia:pneumo:psy:
:PROPERTIES:
:ID: 4b29a074-b19a-4ca1-a5ee-c1b7419373f8
:santepub: t
:END:
** TOUR1 74 Addiction à l'alcool :pedia:neuro:psy:
:PROPERTIES:
:santepub: t
:psy: t
:END:
** TOUR1 75 Addictions aux psychotropes :pedia:psy:
:PROPERTIES:
:santepub: t
:psy: t
:END:
** TOUR1 76 Addiction au cannabis etc :pedia:psy:
:PROPERTIES:
:psy: t
:END:
** TOUR1 77 Addictions comportementales :pedia:psy:
** TOUR1 78 Dopage :pedia:endoc:psy:
** TOUR1 79 Altération de la fonction visuelle :pedia:ophtalmo:
:PROPERTIES:
:ophtalmo: t
:END:
** TOUR1 80 Anomalies de la vision d'apparition brutale :pedia:neuro:ophtalmo:
:PROPERTIES:
:ophtalmo: t
:END:
** TOUR1 81 Oeil rouge/douloureux :pedia:ophtalmo:
** TOUR1 82 Glaucome chronique :pedia:ophtalmo:
:PROPERTIES:
:ophtalmo: t
:END:
** TOUR1 83 Troubles de la réfraction :pedia:ophtalmo:
:PROPERTIES:
:ophtalmo: t
:END:
** TOUR1 84 Pathologies des paupières :pedia:ophtalmo:
** TOUR1 85 Épistaxis :pedia:orl:
:PROPERTIES:
:ORL: t
:END:
** TOUR1 86 Trouble aigu de la parole. Dysphonie :pedia:orl:neuro:
:PROPERTIES:
:ORL: t
:neuro: t
:END:
** TOUR1 87 Altération de la fonction auditive :pedia:orl:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 88 Pathologie des glandes salivaires :pedia:anapath:orl:
:PROPERTIES:
:anapath: t
:END:
** TOUR1 89 Déficit neurologique récent :pedia:neuro:
:PROPERTIES:
:neuro: t
:END:
** TOUR1 90 Déficit moteur et/ou sensitif des membres :pedia:neuro:
:PROPERTIES:
:neuro: t
:END:
** TOUR1 91 Compression médullaire non traumatique :pedia:mpr:neuro:ortho:rhumato:neurochir:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:neurochir: t
:END:
** TOUR1 92 Rachialgies :pedia:mpr:ortho:rhumato:
:pedia:PROPERTIES:
:pedia:ECNI: 2
:pedia:COLLEGE: 2
:pedia:mpr: t
:pedia:END:
** TOUR1 93 Radiculalgies :pedia:neuro:ortho:rhumato:neurochir:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:neurochir: t
:END:
** TOUR1 94 Neuropathies périphériques :pedia:neuro:
:PROPERTIES:
:neuro: t
:END:
** TOUR1 95 Polyradiculonévrite aigüe inflammatoire (syndrome de Guillain-Barré) :pedia:neuro:
:PROPERTIES:
:neuro: t
:END:
** TOUR1 [#C] 96 Myasthénies :pedia:neuro:
** TOUR1 97 Migraine, névralgie du trijumeau et algies de la face :pedia:orl:neuro:
:PROPERTIES:
:neuro: t
:END:
** TOUR1 98 Céphalée aigüe et chronique chez l'adulte et l'enfant :pedia:neuro:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:neuro: t
:END:
** TOUR1 Item 99 – Paralysie faciale :pedia:orl:neuro:
** TOUR1 100 Diplopie :pedia:neuro:ophtalmo:
** TOUR1 101 Vertige :pedia:anapath:orl:neuro:
** TOUR1 102 Sclérose en plaque :pedia:neuro:ophtalmo:
:PROPERTIES:
:neuro: t
:ophtalmo: t
:END:
** TOUR1 103 Epilepsie :pedia:neuro:
** TOUR1 104 Maladie de Parkinson :pedia:mpr:neuro:
:PROPERTIES:
:neuro: t
:END:
** TOUR1 105 Mouvements anormaux :pedia:neuro:
:PROPERTIES:
:neuro: t
:END:
** DONE 106 Confusion, démence :pedia:neuro:
** TOUR1 107 Trouble de la marche et de l'équilibre :pedia:mpr:neuro:rhumato:
:PROPERTIES:
:neuro: t
:END:
** TOUR1 108 Troubles du sommeil :pedia:neuro:orl:pneumo:psy:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:ID: aef7082d-145a-4513-aeab-808a4a8f74e7
:END:
** TOUR1 109 Dermatoses faciales :dermato:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 110 Dermatoses bulleuses :dermato:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 111 Angiomes :dermato:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 112 Exanthèmes :dermato:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 113 Prurit :dermato:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 114 Psoriasis :pedia:rhumato:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:END:
** TOUR1 115 Évaluation clinique et fonctionnelle d'un handicap cognitif :pedia:mpr:neuro:orl:
:PROPERTIES:
:ORL: t
:neuro: t
:mpr: t
:END:
** TOUR1 116 Conplication de l'immobilité :pedia:mpr:
:PROPERTIES:
:mpr: t
:END:
** KILL 117 Handicap psychique
** TOUR1 118 Rééducation :pedia:mpr:orl:rhumato:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:mpr: t
:END:
** TOUR1 119 Vieillissement normal
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:mpr: t
:END:
** TOUR1 120 Ménopause, andropause :pedia:endoc:gyneco:uro:retard:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:END:
** KILL 121 Trouble de la miction :pedia:endoc:gyneco:mpr:uro:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 3
:mpr: t
:END:
** KILL 122 Troubles de l'érection :pedia:uro:retard:
:PROPERTIES:
:COLLEGE: 1
:END:
** TOUR1 123 Hypertrophie bénigne de la prostate :pedia:uro:retard:
:PROPERTIES:
:uro: t
:END:
** TOUR1 124 Ostéopathies fragilisantes :pedia:endoc:rhumato:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 2
:END:
** TOUR1 125 Arthrose :pedia:mpr:rhumato:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:END:
** TOUR1 126 Personne agée malade
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 127 Déficit neurosensoriel chez la personne âgée :pedia:ophtalmo:orl:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:ORL: t
:ophtalmo: t
:END:
** TOUR1 128 Troubles de la marche et de l'équilibre chez le sujet âgé :pedia:neuro:rhumato:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:neuro: t
:END:
** TOUR1 129 Trouble cognitifs du sujet âgé :pedia:neuro:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 130 Autonomie du sujet âgé
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** KILL 131 Physiopathologie de la douleur :pedia:neuro:rhumato:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:neuro: t
:END:
** KILL 132 Thérapeutiques antalgiques :pedia:neuro:rhumato:neurochir:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:neurochir: t
:neuro: t
:END:
** TOUR1 133 – Anesthésie locale, régionale et générale :pedia:douleur:
:PROPERTIES:
:douleur: t
:END:
** KILL 134 Douleur chez l'enfant
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:END:
** TOUR1 135 Douleur en santé mentale :pedia:psy:
** KILL 136 Soins palliatifs
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** KILL 137 Soins palliatifs
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** KILL 138 Soins palliatifs
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** KILL 140 Connaître les aspects spécifiques des soins palliatifs en réanimation
** TOUR1 141 Deuil :pedia:psy:
** TOUR1 142 Surveillance des maladies infectieuses transmissibles :pedia:malinf:
:PROPERTIES:
:malinf: t
:END:
** TOUR1 143 Vaccinations :pedia:malinf:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:malinf: t
:santepub: t
:END:
** TOUR1 144 Fièvre aiguë :pedia:malinf:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:malinf: t
:END:
** TOUR1 145 Infections nasosinusiennes de l'enfant et de l'adulte :pedia:malinf:orl:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:ORL: t
:END:
** TOUR1 146 Rhinopharyngite, angine :pedia:malinf:orl:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:pedia: t
:END:
** TOUR1 147 Otites infectieuses de l'adulte et de l'enfant :pedia:malinf:orl:
:PROPERTIES:
:pedia: t
:END:
** TOUR1 148 Méningites :pedia:malinf:neuro:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:neuro: t
:malinf: t
:END:
** TOUR1 149 Endocardite infectieuse :pedia:cardio:malinf:
:PROPERTIES:
:ID: a15898d5-f3bf-42d9-b89a-44054a8363c4
:TOUR1: 2020-09-26
:MAITRISE: 2
:END:
** TOUR1 150 Surveillance des porteurs de valves :pedia:cardio:malinf:
:PROPERTIES:
:ID: 9bd61c36-6d14-40a5-bf8b-5874face3579
:END:
** TOUR1 151 Infections bronchopulmonaire communautaires :pedia:malinf:pneumo:urgences:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 2
:ID: a549a6c6-454d-49fe-986f-f4d74822e9ee
:END:
** TOUR1 152 Infections cutanéo-muqueuses :pedia:dermato:malinf:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:END:
** TOUR1 153 Infections ostéoarticulaires :pedia:malinf:ortho:rhumato:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 2
:END:
** TOUR1 154 Septicémie :pedia:malinf:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 155 Tuberculose :pedia:anapath:malinf:pneumo:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:ID: 3166373c-50bd-41b3-9f68-c791bcb31cd0
:END:
** TOUR1 156 Tétanos :pedia:malinf:
** TOUR1 157 Infections urinaires :pedia:malinf:nephro:uro:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:END:
** TOUR1 158 IST :dermato:pedia:gyneco:malinf:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 3
:malinf: t
:END:
** TOUR1 159 Coqueluche :pedia:malinf:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:pedia: t
:END:
** TOUR1 160 Éruptions fébriles
:PROPERTIES:
:COLLEGE: 1
:ECNI: 2
:END:
** TOUR1 162 Grippe :pedia:malinf:
** TOUR1 161 Oreillons :pedia:malinf:
** TOUR1 163 Hépatites virales :pedia:anapath:hge:malinf:
:LOGBOOK:
CLOCK: [2021-04-15 Thu 21:33]--[2021-04-15 Thu 22:45] => 1:12
CLOCK: [2021-04-15 Thu 20:24]--[2021-04-15 Thu 20:45] => 0:21
:END:
** TOUR1 164 HSV :dermato:pedia:malinf:neuro:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:neuro: t
:END:
** TOUR1 165 VIH :dermato:pedia:malinf:neuro:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 166 Paludisme :pedia:malinf:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 167 Gale, pediculose :dermato:pedia:malinf:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 168 Parasitoses digestives :pedia:malinf:
** TOUR1 169 Zoonoses :pedia:malinf:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 170 Pathologies infectieuses chez le migrant :pedia:malinf:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 171 Voyage en pays tropical :pedia:malinf:
:PROPERTIES:
:malinf: t
:END:
** TOUR1 172 Diarrhées infectieuses :pedia:malinf:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:santepub: t
:END:
** TOUR1 173 Anti-infectieux :pedia:malinf:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:santepub: t
:END:
** TOUR1 174 Bioterrorisme :pedia:malinf:
** TOUR1 175 Risques sanitaires liés à l'eau et à l'alimentation. Toxi-infections alimentaires :pedia:malinf:
** TOUR1 176 Risques sanitaires liés aux irradiations :pedia:medecinetravail:
:PROPERTIES:
:medecineTravail: t
:END:
** TOUR1 177 Sécurité sanitaire, veille sanitaire :pedia:medecinetravail:
:PROPERTIES:
:medecineTravail: t
:END:
** TOUR1 178 Environnement professionnel :pedia:medecinetravail:
:PROPERTIES:
:medecinetravail: t
:END:
** TOUR1 179 Organisation de la médecine du travail :pedia:medecinetravail:
:PROPERTIES:
:medecinetravail: t
:END:
** TOUR1 180 Accidents du travail :pedia:pneumo:
:PROPERTIES:
:COLLEGE: 1
:ID: 46643f3d-643c-4446-8be1-27d37ffcd724
:END:
** TOUR1 181 Réaction inflammatoire :pedia:rhumato:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:END:
** TOUR1 182 Hypersensibilités et allergies :pedia:pneumo:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 3
:ID: 5129e4fe-86ee-4065-a213-dbf2003a67ee
:END:
** TOUR1 183 Hypersensibilités et allergies cutanéomuqueuses :dermato:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:END:
** TOUR1 184 Hypersensibilités et allergies respiratoires. Asthme, rhinite :pedia:pneumo:urgences:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:ID: 12dff8dd-eb2f-4919-9081-0806b9f0497a
:END:
** TOUR1 185 Déficit immunitaire
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:END:
** TOUR1 186 Fièvre prolongée :pedia:malinf:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 187 Fièvre chez immunodéprimé :pedia:malinf:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:ATBC: t
:END:
** KILL 188 Pathologies auto-immunes :pedia:anapath:dermato:pneumo:rhumato:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 3
:ID: 86aef5f5-4724-4a2f-821f-a9e4e720bebe
:END:
** KILL 189 Vascularite systémique :pedia:pneumo:rhumato:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:ID: 8c07dc68-0ef5-48de-991a-c3c6a6ad8dd8
:END:
** TOUR1 190 Lupus erythémateux systémique :anapath:dermato:pedia:nephro:rhumato:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 3
:anapath: t
:END:
** TOUR1 191 Artérite à cellules géantes :pedia:anapath:hemato:rhumato:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:rhumato: t
:END:
** TOUR1 192 Polyrarthrite rhymatoïde :pedia:mpr:rhumato:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:rhumato: t
:END:
** TOUR1 193 Spondylarthrite inflammatoire :pedia:mpr:rhumato:
:PROPERTIES:
:COLLEGE: 1
:rhumato: t
:END:
** KILL 194 Arthropathie microcristalline :pedia:rhumato:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 195 Syndrome douloureux régional complexe :pedia:mpr:ortho:rhumato:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:mpr: t
:rhumato: t
:END:
** KILL 196 Épanchement articulaire :pedia:ortho:rhumato:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:END:
** TOUR1 197 Transplantation d'organes :dermato:pedia:nephro:ophtalmo:uro:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:ophtalmo: t
:END:
** TOUR1 198 Biothérapies :pedia:hemato:rhumato:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:hemato: t
:rhumato: t
:END:
** TOUR1 199 Dyspnée :pedia:anapath:cardio:pneumo:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:ID: a6ae72dd-a1c1-4084-8b7f-7ea5764366c1
:TOUR1: 2020-09-26
:MAITRISE: 4
:END:
** TOUR1 200 Toux :pedia:pneumo:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:ID: d45f6adf-02f5-429b-874f-850d2c05a2e9
:END:
** TOUR1 201 Hémoptysie :pedia:pneumo:urgences:
:PROPERTIES:
:COLLEGE: 1
:ID: 528fddbb-b254-4519-9b8f-1af45d4c3671
:END:
** TOUR1 202 Épanchement pleural :pedia:anapath:pneumo:urgences:
:PROPERTIES:
:COLLEGE: 1
:ID: e2079996-6fa5-479b-b01b-b326243ac528
:END:
** TOUR1 203 Opacités et masses intrathoraciques :pedia:anapath:pneumo:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:ID: 3fd385fc-a7a1-4196-9568-e7e0f97e5e07
:END:
** TOUR1 204 Insuffisance respiratoire chronique :pedia:pneumo:
:PROPERTIES:
:COLLEGE: 1
:ID: 02570aa0-2b78-493a-bcd8-0e257dfbd80d
:END:
** TOUR1 205 BPCO :pedia:pneumo:urgences:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:ID: 99241469-d05a-474f-af15-32f1572cb303
:END:
** TOUR1 206 Pneumopathies interstitielles diffuses :pedia:anapath:pneumo:
:PROPERTIES:
:ID: 4a0593d0-8ba3-44c4-89a4-0fa4f3650243
:END:
** KILL 207 Sarcoidose :dermato:pedia:anapath:endoc:pneumo:rhumato:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 2
:ID: 7790cf6a-bc2e-4256-a623-6eedc334df4f
:END:
** TOUR1 208 Hémogramme :pedia:hemato:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 209 Anémie :pedia:hemato:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:END:
** TOUR1 210 Thrombopénie :pedia:hemato:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 211 Purpura :pedia:dermato:hemato:malinf:
:PROPERTIES:
:COLLEGE: 3
:ECNI: 3
:hemato: t
:END:
** TOUR1 212 Syndrome hémorragique :pedia:hemato:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 213 Syndrome mononucléosique :pedia:hemato:malinf:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 214 Éosinophilie :pedia:hemato:malinf:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 215 Pathologie du fer :pedia:anapath:endoc:hemato:hge:rhumato:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:endoc: t
:END:
** TOUR1 216 Adénopathies superficielles :pedia:anapath:hemato:malinf:orl:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:END:
** TOUR1 217 Amylose :pedia:anapath:hemato:nephro:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:nephro: t
:END:
** TOUR1 218 Athérome :pedia:cardio:pneumo:
:PROPERTIES:
:ID: 2cf00cdb-091a-4af2-9843-c5b72ec824fe
:TOUR1: 2020-09-26
:MAITRISE: 3
:santepub: t
:END:
** TOUR1 219, 222 Facteurs de risque cardio-vasculaire :pedia:cardio:endoc:
:PROPERTIES:
:COLLEGE: 1
:ID: 6e5753ed-c6f5-4832-abbf-596bc2d29ebb
:TOUR1: 2020-09-26
:MAITRISE: 4
:santepub: t
:END:
** TOUR1 220 Dyslipidémies :pedia:cardio:
:PROPERTIES:
:ID: f707a3ae-ad40-4853-93e0-67e351906d71
:TOUR1: 2020-09-26
:MAITRISE: 2
:END:
** KILL 221 HTA :pedia:cardio:endoc:nephro:ophtalmo:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:ID: 06ba2075-95e2-496c-b178-0298ae378fa4
:MAITRISE: 4
:ophtalmo: t
:cardio: t
:END:
** TOUR1 222 Hypertension artérielle pulmonaire :pedia:cardio:pneumo:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:ID: 4e71e90f-d5ae-43c8-a750-248d98e6e95c
:END:
** TOUR1 223 Arétoriopathie oblitérante de l'aorte, des membres inférieurs :pedia:cardio:
:PROPERTIES:
:ID: 4afdc3aa-f6de-43e5-b5a0-8d87f16fccd8
:END:
** TOUR1 224 Embolie pulmonaire :pedia:cardio:pneumo:
:PROPERTIES:
:ID: 8c1d14da-7657-4720-8e11-90e38a7077b5
:END:
** TOUR1 225 Insuffisance veineuse chronique :pedia:cardio:pneumo:
:PROPERTIES:
:ID: cad87837-907a-4e06-91ed-a7096eedb4f7
:END:
** TOUR1 226 Ulcère de jambe :dermato:pedia:cardio:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 227 Abords veineux :pedia:urgences:
** TOUR1 228 Douleur thoracique :pedia:cardio:
:PROPERTIES:
:COLLEGE: 1
:ID: ac892a52-b2b0-448f-b093-04b2e0c930dc
:END:
** TOUR1 229 Électrocardioramme :pedia:cardio:
:PROPERTIES:
:ID: 8fa9421e-51b6-43c6-b08c-57e01a4fa7a5
:END:
** TOUR1 230 Fibrillation atriale :pedia:cardio:
:PROPERTIES:
:ID: 36873dd8-3c1e-47c7-8ede-29eefde6ada2
:END:
** TOUR1 231 Valvulopathies :pedia:cardio:
:PROPERTIES:
:ID: 1f662d8a-119c-43df-9d35-746b06e18347
:END:
** TOUR1 232 Insuffisance cardiaque de l'adulte :pedia:cardio:
:PROPERTIES:
:ID: 159070c9-386e-410f-a353-5ca0a869d9a4
:END:
** TOUR1 233 Péricardite aigüe :pedia:cardio:
:PROPERTIES:
:ID: 62498c4a-3aca-41e4-885e-7057d5c199d1
:END:
** TOUR1 234 Troubles de la conduction intracardiaque :pedia:cardio:
:PROPERTIES:
:ID: cca3ecf0-9168-46c1-8d63-3556329d42cc
:END:
** TOUR1 235 Palpitations :pedia:cardio:
:PROPERTIES:
:ID: 4d2611f9-8011-46bb-aa7e-de17a29615b0
:END:
** TOUR1 236 Souffle cardiaque chez l'enfant :pedia:cardio:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:ID: 88fc644b-e045-4c65-b07d-2112e06afdfc
:END:
** TOUR1 237 Acrosyndrome :dermato:
:PROPERTIES:
:COLLEGE: 1
:END:
** TOUR1 238 Hypoglycémie :pedia:endoc:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 2
:END:
** TOUR1 239 Goitre, nodules thyroïdiens et cancers thyroïdiens :pedia:anapath:endoc:
:PROPERTIES:
:anapath: t
:endoc: t
:END:
** KILL 240 Hyperthyroïdie :pedia:endoc:ophtalmo:
:PROPERTIES:
:COLLEGE: 1
:END:
** KILL 241 Hypothyroïdie :pedia:endoc:
:PROPERTIES:
:COLLEGE: 1
:ID: a4b9a99d-7ce7-4400-8cbe-6352dea489de
:ECNI: 1
:END:
** KILL 242 Adénome hypophysaire :pedia:endoc:neurochir:
:PROPERTIES:
:COLLEGE: 1
:neurochir: t
:END:
** KILL 243 Insuffisance surrénale :pedia:endoc:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:END:
** KILL 244 Gynécomastie :pedia:endoc:
:PROPERTIES:
:COLLEGE: 1
:END:
** KILL 245 Diabète :pedia:gyneco:nephro:ophtalmo:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 2
:ophtalmo: t
:END:
** KILL 246 Prévention primaire par la nutrition chez l'adulte et l'enfant
** KILL 247 Modifications thérapeutiques du mode de vie (alimentation et activité physique) chez l'adulte et l'enfant :pedia:mpr:
** KILL 248 Dénutrition :pedia:endoc:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** KILL 249 Amaigrissement :pedia:endoc:
:PROPERTIES:
:COLLEGE: 1
:END:
** TOUR1 250 Troubles nutritionnels chez le sujet âgé :pedia:endoc:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** KILL 251 Obésité :pedia:endoc:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:END:
** KILL 252 Nutrition et grossesse. Diabète gestationnel :pedia:endoc:gyneco:
:PROPERTIES:
:COLLEGE: 2
:ECNI: 1
:END:
** KILL 253 Aptitude au sport, nutrition chez le sportif :pedia:cardio:endoc:mpr:rhumato:
:PROPERTIES:
:COLLEGE: 1
:ID: c070cef8-71c1-4940-a28e-78e78c8f5165
:END:
** KILL 254 Syndromes oedemateux :pedia:nephro:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:ID: ee86068b-6b6b-48dc-b1e8-c6e9935dc470
:END:
** KILL 255 Élévation de la créatinine :pedia:nephro:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** KILL 256 Protéinurie et syndrome néphrotique :pedia:nephro:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:END:
** TOUR1 257 Hématurie :pedia:nephro:retard:uro:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** KILL 258 Néphropathies glomérulaires :pedia:anapath:nephro:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** KILL 259 Néphropathies interstitielles chroniques :pedia:nephro:
** KILL 260 Néphropathies vasculaires :pedia:anapath:nephro:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** KILL 261 Insuffisance rénale chronique :pedia:nephro:
:PROPERTIES:
:ECNI: 2
:COLLEGE: 1
:END:
** TOUR1 262 Lithiase urinaire :pedia:nephro:uro:retard:
:PROPERTIES:
:uro: t
:ECNI: 1
:COLLEGE: 1
:END:
** KILL 263 Polykystose rénale :pedia:nephro:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:END:
** TOUR1 264 Diurétiques :pedia:nephro:
:PROPERTIES:
:ECNI: 1
:COLLEGE: 1
:ID: d734cf6f-938a-4b93-a2cf-3e23bc4f2b53
:END:
** TOUR1 265 Hypocalcémie, dyskaliémie, hyponatrémie :pedia:endoc:nephro:
:PROPERTIES:
:COLLEGE: 1
:ECNI: 1
:END:
** TOUR1 266 Hypercalcémie :pedia:endoc:nephro:rhumato:
:PROPERTIES:
:rhumato: t
:END:
** TOUR1 267 Douleurs abdominales aigües :pedia:hge:
:PROPERTIES:
:hge: t
:END:
** TOUR1 268 Reflux gastro-œsophagien chez le nourrisson, chez l'enfant et chez l'adulte. Hernie hiatale :pedia:anapath:hge:
:PROPERTIES:
:hge: t
:END:
** TOUR1 269 Ulcère gastroduodénal, gastrites :pedia:anapath:hge:
Gastrite à faire
** TOUR1 270 Dysphagie :pedia:orl:
** TOUR1 271 Vomissements du nourrisson, de l'enfant et de l'adulte
** TOUR1 272 Splénomégalie :pedia:anapath:hemato:
:PROPERTIES:
:hemato: t
:END:
** TOUR1 273 Hépatomégalie et masse abdominale
** TOUR1 274 Lithiase biliaire et complications
:PROPERTIES:
:hge: t
:END:
** TOUR1 275 Ictère
** TOUR1 276 Cirrhose et complications :pedia:anapath:hge:
** TOUR1 277 Ascite
** TOUR1 278 Pancréatite chronique
** TOUR1 279 Maladies inflammatoires chroniques de l'intestin (MICI) chez l'adulte et l'enfant :pedia:anapath:hge:
** TOUR1 280 Constipation chez l'enfant et l'adulte (avec le traitement)
** TOUR1 281 Colopathie fonctionnelle
** TOUR1 282 Diarrhée chronique chez l'adulte et l'enfant :pedia:anapath:hge:
** TOUR1 283 Diarrhée aiguë et déshydratation chez le nourrisson, l'enfant et l'adulte
** TOUR1 284 Diverticulose colique et diverticulite aiguë du sigmoïde
** TOUR1 285 Pathologie hémorroïdaire
** TOUR1 286 Hernie pariétale chez l'enfant et l'adulte
** KILL 287 Épidémiologie des cancers :pedia:cancero:gyneco:
:PROPERTIES:
:santepub: t
:END:
** KILL 288 Cancer :pedia: cancérogénèse, oncogénétique
** KILL 289 Diagnostic des cancers :pedia: signes d'appel et investigations para-cliniques ; caractérisation du stade ; pronostic
** KILL 290 Le médecin préleveur de cellules et/ou tissus pour des examens d'anatomie et de cytologie pathologiques: :pedia:anapath:cancero:
:PROPERTIES:
:anapath: t
:END:
** KILL 291- Traitement des cancers :pedia: chirurgie, radiothérapie, traitements médicaux des cancers
** KILL 292- Prise en charge et accompagnement d'un malade cancéreux à tous les stades de la maladie dont le stade de soins palliatifs
** TOUR1 293 Agranulocytose médicamenteuse :pedia:hemato:
:PROPERTIES:
:hemato: t
:END:
** TOUR1 294 Principaux cancers de l'enfant :pedia:anapath:cancero:
:PROPERTIES:
:santepub: t
:END:
** KILL 295 Tumeurs de la cavité buccale, nasosinusiennes et du cavum, et des voies aérodigestives supérieures :pedia:anapath:cancero:orl:
:PROPERTIES:
:ORL: t
:anapath: t
:END:
** TOUR1 296 Tumeurs intracrâniennes :pedia:anapath:cancero:neuro:neurochir:
:PROPERTIES:
:neurochir: t
:anapath: t
:END:
** KILL 297 Tumeurs du col utérin :pedia:anapath:cancero:gyneco:
** TOUR1 298 Tumeurs du côlon et du rectum :pedia:anapath:cancero:hge:
** TOUR1 299 Tumeurs cutanées, épithéliales et mélaniques :anapath:cancero:dermato:pedia:
** TOUR1 300 Tumeurs de l'estomac :pedia:anapath:cancero:hge:
** TOUR1 301 Tumeurs du foie primitives et secondaires :pedia:anapath:cancero:hge:
** TOUR1 302 Tumeurs de l'œsophage :pedia:anapath:cancero:hge:
** TOUR1 303 Tumeurs de l'ovaire :pedia:anapath:cancero:endoc:gyneco:
:PROPERTIES:
:gyneco: t
:END:
** TOUR1 304 Tumeurs des os primitives et secondaires :pedia:anapath:cancero:ortho:rhumato:
:PROPERTIES:
:anapath: t
:END:
** TOUR1 305 Tumeurs du pancréas :pedia:anapath:cancero:endoc:hge:
** TOUR1 306 Tumeurs du poumon :pedia:anapath:cancero:pneumo:
:PROPERTIES:
:ID: e8719a4c-493c-4902-a9ae-88171cbefc45
:END:
** TOUR1 307 Tumeurs de la prostate :pedia:anapath:cancero:uro:
** KILL 308 Tumeurs du rein :pedia:anapath:cancero:nephro:
** TOUR1 309 Tumeurs du sein :pedia:anapath:cancero:gyneco:
:PROPERTIES:
:gyneco: t
:END:
** TOUR1 310 Tumeurs du testicule :pedia:anapath:cancero:endoc:uro:
:PROPERTIES:
:anapath: t
:END:
** KILL 311 Tumeurs vésicales :pedia:anapath:cancero:uro:
** TOUR1 312 Leucméies aigües :pedia:hemato:
:PROPERTIES:
:hemato: t
:END:
** TOUR1 313 Syndromes myélodysplasique :pedia:hemato:
:PROPERTIES:
:hemato: t
:END:
** TOUR1 314 Syndromes myéloprolifératifs :pedia:hemato:
:PROPERTIES:
:hemato: t
:END:
** TOUR1 315 Leucémies lymphoïdes chroniques :pedia:anapath:cancero:hemato:
:PROPERTIES:
:hemato: t
:END:
** TOUR1 316 Lymphomes malins :anapath:cancero:dermato:pedia:hemato:
:PROPERTIES:
:hemato: t
:END:
** TOUR1 317 Myélome multiple des os :pedia:anapath:cancero:hemato:nephro:rhumato:
:PROPERTIES:
:rhumato: t
:END:
** KILL 318 Iatrogénie :pedia:nephro:
** KILL 319 La décision thérapeutique personnalisée :pedia: bon usage dans des situations à risque
** TOUR1 320 Analyses les résultats des études cliniques :pedia:santepub:
:PROPERTIES:
:santepub: t
:END:
** KILL 321 Éducation thérapeutique, observance et automédication
** KILL 322 Identification et gestion des risques liés aux médicaments et aux biomatériaux, risque iatrogène, erreur médicamenteuse :dermato:
** KILL 323 Cadre réglementaire de la prescription thérapeutique et recommandations pour le bon usage
** KILL 324 Thérapeutiques non médicamenteuses et dispositifs médicaux :pedia:mpr:
** KILL 325 Transfusions
** TOUR1 326 Antithrombotiques :cardio:dermato:pedia:hemato:
:PROPERTIES:
:ID: 026482df-0663-4531-b680-84ea489af70f
:END:
** TOUR1 327 Arrêt cardiocirculatoire :pedia:cardio:
:PROPERTIES:
:ID: 3eca661c-3b75-4e26-9d97-2dce9f1ed362
:END:
** TOUR1 328 État de choc :pedia:cardio:
:PROPERTIES:
:ID: cc13f354-7dac-4510-b040-005dde4e772f
:END:
** TOUR1 329 Polytraumatisé :pedia:ortho:urgences:neurochir:ortho:
:PROPERTIES:
:urgences: t
:END:
** KILL 330 Prise en charge d'un traumatisé crânien :pedia:ophtalmo:orl:neurochir:
:PROPERTIES:
:neurochir: t
:ORL: t
:END:
** TOUR1 331 Comas non traumatiques chez l'adulte :pedia:neuro:
** TOUR1 332 Intoxications :pedia:urgences:
:PROPERTIES:
:urgences: t
:END:
** TOUR1 333 Oedème de Quincke et anaphylaxie :pedia:pneumo:
:PROPERTIES:
:ID: 24a5127a-47b4-4b24-8449-4a1689f61be1
:END:
** TOUR1 334 Cardiopathie icshémique :pedia:cardio:mpr:
:PROPERTIES:
:ID: 101d691f-a6e3-4c45-9364-4442d2b8419d
:END:
** KILL 335 Accidents vasculaires cérébraux :pedia:mpr:neuro:neurochir:
:PROPERTIES:
:neurochir: t
:END:
** TOUR1 336 Hémorragie méningée non traumatique :pedia:neuro:neurochir:
:PROPERTIES:
:neurochir: t
:END:
** TOUR1 337 Malaise, perte de connaissance :pedia:neuro:cardio:
:PROPERTIES:
:ID: 642d2b2b-e83b-48af-be8e-cbc3f83ab6cf
:END:
** TOUR1 338 Confusion :pedia:neuro:
** TOUR1 339 Prééclampsie :pedia:gyneco:
:PROPERTIES:
:gyneco: t
:END:
** TOUR1 340 Agitation et délires aigüs :pedia:psy:
** TOUR1 341 Convulsions chez le nourrisson et chez l'enfant
** TOUR1 342 Rétention aiguë d'urine
:PROPERTIES:
:uro: t
:END:
** TOUR1 343 Insuffisance rénale aigüe :pedia:nephro:
:PROPERTIES:
:nephro: t
:END:
** KILL 344 Infection aiguë des parties molles (abcès, panaris, phlegmon des gaines) :pedia:ortho:
** TOUR1 345 Grosse jambe rouge aiguë :dermato:
:PROPERTIES:
:malinf: t
:END:
** TOUR1 346 Agitation et délire aiguë :pedia:psy:
** TOUR1 347 Crise d'angoisse, attaque de panique :pedia:psy:
** KILL 348 Risque et conduite suicidaire :pedia:psy:
** KILL 349 Syndrome occlusif de l'enfant et de l'adulte
:PROPERTIES:
:hge: t
:END:
** TOUR1 350 Hémorragie digestive :pedia:hge:
:PROPERTIES:
:hge: t
:END:
** TOUR1 351 Appendicite de l'enfant et de l'adulte :pedia:anapath:hge:
** TOUR1 352 Péritonite aigüe :pedia:hge:malinf:
** TOUR1 353 Pancréatite aiguë :pedia:hemato:
:PROPERTIES:
:hge: t
:END:
** TOUR1 354 Détresse respiratoire, corps étranger :pedia:orl:pneumo:urgences:
:PROPERTIES:
:ID: 69e0219b-70a7-49d1-b9eb-08483eb1c4f1
:END:
** KILL 355 Insuffisance respiratoire aigüe :pedia:urgences:
** TOUR1 356 Pneumothorax :pedia:pneumo:cardio:
** TOUR1 357 Lésions du genou, de l'épaule, de la cheville :pedia:mpr:ortho:rhumato:
:PROPERTIES:
:ortho: t
:END:
** KILL 358 Prothèses et ostéosynthèses :pedia:ortho:
** KILL 359 Fractures fréquentes de l'adulte et du sujet âgé :ortho:
** KILL 360 Fractures chez l'enfant : particularités épidémiologiques, diagnostiques et thérapeutiques :ortho:
** KILL 361 Surveillance d'un malade sous plâtre, diagnostiquer une complication :ortho:
** TOUR1 362 Accident d'exposition aux liquides biologiques :hemato:malinf:
:PROPERTIES:
:ID: 2e01b144-1666-458a-b763-3c1918dd416a
:END:
* LCA :lca:
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_ITAGS: revisions
:END:
** DONE Lire LCA de Théo Pezel
** KILL Entraînement sur le Masson
https://www-elsevierelibrary-fr.bases-doc.univ-lorraine.fr/epubreader/matriser-la-lca-en-anglais
* TOUR1 Maladies infectieuses :D1:malinf:
:PROPERTIES:
:CATEGORY: malinf
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: malinf
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches
DEADLINE: <2021-04-18 Sun> SCHEDULED: <2021-04-01 Thu>
:LOGBOOK:
CLOCK: [2021-04-20 Tue 21:57]--[2021-04-20 Tue 22:23] => 0:26
CLOCK: [2021-04-20 Tue 21:37]--[2021-04-20 Tue 21:54] => 0:17
CLOCK: [2021-04-20 Tue 19:17]--[2021-04-20 Tue 19:42] => 0:25
CLOCK: [2021-04-20 Tue 17:13]--[2021-04-20 Tue 17:47] => 0:34
CLOCK: [2021-04-20 Tue 16:45]--[2021-04-20 Tue 16:50] => 0:16
CLOCK: [2021-04-20 Tue 12:50]--[2021-04-20 Tue 13:10] => 0:20
CLOCK: [2021-04-20 Tue 11:19]--[2021-04-20 Tue 11:43] => 0:24
CLOCK: [2021-04-19 Mon 17:30]--[2021-04-19 Mon 18:16] => 0:46
CLOCK: [2021-04-19 Mon 15:49]--[2021-04-19 Mon 16:04] => 0:15
CLOCK: [2021-04-19 Mon 15:02]--[2021-04-19 Mon 15:40] => 0:38
CLOCK: [2021-04-19 Mon 12:25]--[2021-04-19 Mon 12:35] => 0:10
CLOCK: [2021-04-19 Mon 11:08]--[2021-04-19 Mon 11:57] => 0:49
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CLOCK: [2021-04-18 Sun 21:46]--[2021-04-18 Sun 22:04] => 0:18
CLOCK: [2021-04-18 Sun 17:13]--[2021-04-18 Sun 18:25] => 1:50
CLOCK: [2021-04-18 Sun 15:11]--[2021-04-18 Sun 16:08] => 0:57
CLOCK: [2021-04-18 Sun 14:49]--[2021-04-18 Sun 15:02] => 0:13
CLOCK: [2021-04-18 Sun 11:31]--[2021-04-18 Sun 11:50] => 0:19
:END:
-> tuberculose (inclus)
* Médecine interne :immuno:
:PROPERTIES:
:CATEGORY: immuno
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: immuno
:ARCHIVE_ITAGS: revisions
:END:
** KILL Relire fiches
DEADLINE: <2021-06-12 Sat>
* KILL Médecine légale, médecine du travail
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
** DONE Lire collège
DEADLINE: <2020-12-15 Tue>
** DONE Fiches + abrégés des très bien classés
** DONE DP + QI collège
DEADLINE: <2021-05-31 Mon>
:LOGBOOK:
CLOCK: [2021-06-01 Tue 13:55]--[2021-06-01 Tue 14:14] => 0:19
CLOCK: [2021-06-01 Tue 13:19]--[2021-06-01 Tue 13:24] => 0:05
CLOCK: [2021-06-01 Tue 12:57]--[2021-06-01 Tue 13:16] => 0:19
CLOCK: [2021-06-01 Tue 11:33]--[2021-06-01 Tue 12:38] => 1:05
CLOCK: [2021-06-01 Tue 00:21]--[2021-06-01 Tue 00:25] => 0:04
CLOCK: [2021-05-31 Mon 23:14]--[2021-05-31 Mon 23:46] => 0:32
CLOCK: [2021-05-31 Mon 19:48]--[2021-05-31 Mon 20:13] => 0:25
CLOCK: [2021-05-31 Mon 17:37]--[2021-05-31 Mon 18:36] => 0:59
CLOCK: [2021-05-31 Mon 16:00]--[2021-05-31 Mon 16:20] => 0:20
CLOCK: [2021-05-31 Mon 15:40]--[2021-05-31 Mon 15:48] => 0:08
CLOCK: [2021-05-31 Mon 15:10]--[2021-05-31 Mon 15:31] => 0:21
:END:
*** DONE Médecine du travail
*** KILL Médecine légale
* TOUR1 MPR :mpr:
:PROPERTIES:
:CATEGORY: mpr
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: mpr
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire collège et compléter fiches
DEADLINE: <2021-02-18 Thu> SCHEDULED: <2021-02-11 Thu>
:LOGBOOK:
CLOCK: [2021-02-18 Thu 21:54]--[2021-02-18 Thu 22:43] => 0:49
:END:
* Nephrologie :nephro:
:PROPERTIES:
:CATEGORY: nephro
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: nephro
:ARCHIVE_ITAGS: revisions
:END:
** KILL Relire fiches
* TOUR1 Neurochirurgie :neurochir:
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Lire chapitres "neurochir" du Masson
DEADLINE: <2020-10-19 Mon> SCHEDULED: <2020-10-10 Sat>
PDF [[file:~/backups/hubic/Public/Cours/Medecine/referentiels/Neurochirurgie_college_2019.pdf][file:~/backups/hubic/Public/Cours/Medecine/referentiels/Neurochirurgie_college_2019.pdf]]
Enligne
https://drive.google.com/drive/folders/1PKMHd9yq-clAB5P1lLSnMRd7rtfOjvO7
https://www-elsevierelibrary-fr.bases-doc.univ-lorraine.fr/epubreader/neurochirurgie15187914
* TOUR1 Neurologie
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: revisions
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches
DEADLINE: <2020-10-17 Sat> SCHEDULED: <2020-10-10 Sat>
:PROPERTIES:
:CATEGORY: neuro
:END:
* TOUR1 Ophtalmologie :ophtalmo:
:PROPERTIES:
:CATEGORY: ophtalmo
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: ophtalmo
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches pour CC
DEADLINE: <2020-11-26 Thu> SCHEDULED: <2020-11-26 Thu>
*** DONE Sémiologie oculaire
* TOUR1 ORL :orl:
:PROPERTIES:
:CATEGORY: orl
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: orl
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches pour CC
DEADLINE: <2020-10-05 Mon> SCHEDULED: <2020-10-05 Mon>
* TOUR1 Orthopédie :ortho:
:PROPERTIES:
:CATEGORY: ortho
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: ortho
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Lire diapos et faire CC
DEADLINE: <2020-06-20 Sat>
:LOGBOOK:
CLOCK: [2020-06-21 Sun 11:47]--[2020-06-21 Sun 12:32] => 0:45
CLOCK: [2020-06-21 Sun 00:32]--[2020-06-21 Sun 00:57] => 0:25
CLOCK: [2020-06-20 Sat 22:59]--[2020-06-20 Sat 23:16] => 0:17
CLOCK: [2020-06-20 Sat 19:21]--[2020-06-20 Sat 19:40] => 0:19
CLOCK: [2020-06-20 Sat 17:18]--[2020-06-20 Sat 17:38] => 0:20
:END:
[[file:~/Downloads/ortho][file:~/Downloads/ortho]]
- [X] [[file:~/Downloads/ortho/329- CM - PEC hospitalière immédiate préhospitalière chez le traumatisé - Galois.pdf]]
- [X] [[file:~/Downloads/ortho/357- CM - Pathologie de lépaule - Sirveaux.pdf]]
- [X] [[file:~/Downloads/ortho/357- CM - Ruptures de l’appareil extenseur - Galois.pdf]]
- [X] [[file:~/Downloads/ortho/357- CM - lésions ligam-méniscales genou - Galois.pdf]]
- [X] [[file:~/Downloads/ortho/358- CM - Consolidation osseuse - Gallois.pdf]]
- [X] [[file:~/Downloads/ortho/358- CM - Ostéosynthèse - Sirveaux.pdf]]
- [X] [[file:~/Downloads/ortho/358- CM - Prothèses - Sirveaux.pdf]]
- [X] [[file:~/Downloads/ortho/359- CM - Fractures de cheville - Galois.pdf]]
- [X] [[file:~/Downloads/ortho/359- CM - Fractures extrémité supérieure fémur - Galois.pdf]]
- [X] [[file:~/Downloads/ortho/359- CM-CC - Fractures des membres supérieurs - Sirveaux.pdf]]
- [X] [[file:~/Downloads/ortho/361- CM-CC - Surveillance d’un malade sous plâtre - Sirveaux.pdf]]
** KILL Relire fiches
:LOGBOOK:
CLOCK: [2021-02-22 Mon 17:45]--[2021-02-22 Mon 18:13] => 0:28
:END:
* TOUR1 Pneumologie :pneumo:
:PROPERTIES:
:CATEGORY: pneumo
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: pneumo
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches pour CC
DEADLINE: <2020-09-27 Sun 12:55> SCHEDULED: <2020-09-27 Sun 11:55>
DEADLINE: <2020-09-27 Sun 14:55> SCHEDULED: <2020-09-27 Sun 13:55>
** DONE Sémiologie des enseignants
DEADLINE: <2020-11-23 Mon>
https://semiologiepneumologique.com/
** KILL Dossiers progressif du CEP (2017)
[[file:~/backups/hubic/Public/Cours/Medecine/FASM3/dp_pneumo_cep/2017][file:~/backups/hubic/Public/Cours/Medecine/FASM3/dp_pneumo_cep/2017]]
** KILL Questions EFR + gaz du sang
[[file:~/backups/hubic/Public/Cours/Medecine/FASM3/dp_pneumo_cep/EFR-pourECN2017.pdf][file:~/backups/hubic/Public/Cours/Medecine/FASM3/dp_pneumo_cep/EFR-pourECN2017.pdf]]
* TOUR1 Psychiatrie :psy:
:PROPERTIES:
:CATEGORY: psy
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: psy
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches
DEADLINE: <2021-01-26 Tue> SCHEDULED: <2021-01-21 Thu>
** DONE Cecil goldman
DEADLINE: <2021-01-03 Sun>
* TOUR1 Pédiatrie :pedia:
:PROPERTIES:
:CATEGORY: pédia
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: pédia
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** DONE Relire fiches
SCHEDULED: <2021-05-24 Mon> DEADLINE: <2021-05-24 Mon>
:LOGBOOK:
CLOCK: [2021-05-28 Fri 23:27]--[2021-05-28 Fri 23:38] => 0:11
CLOCK: [2021-05-28 Fri 22:55]--[2021-05-28 Fri 23:12] => 0:17
CLOCK: [2021-05-28 Fri 22:10]--[2021-05-28 Fri 22:34] => 0:24
CLOCK: [2021-05-28 Fri 19:42]--[2021-05-28 Fri 20:12] => 0:30
CLOCK: [2021-05-28 Fri 17:30]--[2021-05-28 Fri 18:10] => 0:40
CLOCK: [2021-05-28 Fri 14:12]--[2021-05-28 Fri 15:09] => 0:57
CLOCK: [2021-05-25 Tue 12:53]--[2021-05-25 Tue 12:56] => 0:03
CLOCK: [2021-05-24 Mon 22:50]--[2021-05-24 Mon 23:00] => 0:10
CLOCK: [2021-05-24 Mon 21:59]--[2021-05-24 Mon 22:08] => 0:09
CLOCK: [2021-03-03 Wed 15:06]--[2021-03-03 Wed 16:03] => 0:57
CLOCK: [2021-03-01 Mon 16:43]--[2021-03-01 Mon 16:54] => 0:11
CLOCK: [2021-03-01 Mon 15:39]--[2021-03-01 Mon 16:05] => 0:26
CLOCK: [2021-02-26 Fri 11:15]--[2021-02-26 Fri 11:36] => 0:21
CLOCK: [2021-02-25 Thu 21:18]--[2021-02-25 Thu 22:21] => 1:03
CLOCK: [2021-02-24 Wed 21:36]--[2021-02-24 Wed 22:39] => 1:03
:END:
* Rhumato :rhumato:
:PROPERTIES:
:CATEGORY: rhumato
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: rhumato
:ARCHIVE_ITAGS: revisions
:END:
** KILL Relire fiches
* KILL Santé publique
:PROPERTIES:
:CATEGORY: santepub
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: santepub
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: revisions
:END:
** DONE Lire Masson
*** DONE Chapitre 1-6
*** DONE Chapitre 7-11
DEADLINE: <2020-11-24 Tue>
*** DONE Chapitre 12-16
DEADLINE: <2020-12-03 Thu>
*** DONE Chapitre 17-19
*** DONE Chapitre 20-24
*** DONE Chapitre 25-27
** KILL DP et QI du collège
:LOGBOOK:
CLOCK: [2021-06-01 Tue 20:07]--[2021-06-01 Tue 20:36] => 0:29
CLOCK: [2021-06-01 Tue 17:36]--[2021-06-01 Tue 17:49] => 0:13
:END:
*** DONE DP
DEADLINE: <2021-06-01 Tue>
:LOGBOOK:
CLOCK: [2021-06-01 Tue 22:56]--[2021-06-02 Wed 00:05] => 1:09
CLOCK: [2021-06-01 Tue 21:57]--[2021-06-01 Tue 22:32] => 0:35
CLOCK: [2021-06-01 Tue 21:26]--[2021-06-01 Tue 21:51] => 0:25
:END:
*** KILL Cas cliniques
*** KILL Qi
* Thérapeutique
:PROPERTIES:
:CATEGORY: therapeutique
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: therapeutique
:ARCHIVE_ITAGS: revisions
:END:
** KILL Lire collège
** KILL Lire [[file:/usr/home/alex/backups/hubic/public/cours/Medecine/referentiels/L_essentiel ECNi Médicaments - 2018.pdf][L_essentiel ECNi Médicaments - 2018.pdf]]
:LOGBOOK:
CLOCK: [2021-04-23 Fri 17:28]--[2021-04-23 Fri 17:51] => 0:23
:END:
TOUR1 Urgences
:PROPERTIES:
:CATEGORY: urgences
:END:
** DONE Lire Masson (rapidement sur item déjà traités)
DEADLINE: <2020-12-06 Sun>
*** DONE Respi
DEADLINE: <2020-11-22 Sun>
**** DONE IRA
**** DONE Infection pulmonaire
**** DONE Asthme aigu grave
**** DONE BPCO
**** DONE SDRA
**** DONE Epanchmenet pleuraux
**** DONE Hémoptysie
*** DONE Défaillance
DEADLINE: <2020-12-06 Sun>
*** DONE Neuro
DEADLINE: <2020-11-29 Sun>
**** DONE Coma non traumatique
**** DONE Accidents vasculaires cérébraux
**** DONE Convulsions et état de mal épileptique
**** DONE Paralysies extensives : syndrome de Guillain-Barré et myasthénie
**** DONE HSA
**** DONE Agitation
*** DONE Metabolique
DEADLINE: <2020-12-04 Fri>
*** DONE HGE
DEADLINE: <2020-11-29 Sun>
**** DONE Hémorragie digestive
**** DONE Insuffisance hépatocellulaire
**** DONE Pancréatite aiguë
*** DONE Hémato
DEADLINE: <2020-11-29 Sun>
*** DONE Intoxication aigüe
DEADLINE: <2020-12-04 Fri>
*** DONE Environnement
DEADLINE: <2020-12-03 Thu>
*** DONE Infectio
DEADLINE: <2020-11-15 Sun> SCHEDULED: <2020-11-14 Sat>
**** DONE Septicémie, bactériémie, fongémie de l'adulte
**** DONE Endocardite infectieuse
**** DONE Infections cutanéomuqueuses, dermohypodermites bactériennes graves
**** DONE Antibiothérapie en urgence
**** DONE Fièvre chez un patient immunodéprimé
**** DONE Paludisme grave
**** DONE Méningites et méningoencéphalites de l'adulte
Auto immune surtout
*** DONE Complications graves de la grossesse : pré-éclampsie
DEADLINE: <2020-12-05 Sat>
*** DONE Iatrogénique, qualité
DEADLINE: <2020-12-05 Sat>
*** DONE Éthique des soins en réanimation, soins palliatifs
DEADLINE: <2020-12-05 Sat>
*** DONE Chariot d'urgence et matériel de suppléance en réanimation
DEADLINE: <2020-12-05 Sat>
* TOUR1 Urologie :uro:
:PROPERTIES:
:CATEGORY: uro
:ARCHIVE_TIME: 2021-06-17 Thu 22:24
:ARCHIVE_FILE: ~/projects/blog/revisions.org
:ARCHIVE_CATEGORY: uro
:ARCHIVE_TODO: TOUR1
:ARCHIVE_ITAGS: revisions
:END:
** TOUR1 Relire fiches
DEADLINE: <2021-06-11 Fri>
:LOGBOOK:
CLOCK: [2021-06-11 Fri 12:54]--[2021-06-11 Fri 13:00] => 0:06
CLOCK: [2021-06-11 Fri 12:05]--[2021-06-11 Fri 12:45] => 0:40
:END:
# -*- mode: org -*-
Archived entries from file /home/alex/projects/tasks/todo.org
* DONE Assurance C5
:PROPERTIES:
:ARCHIVE_TIME: 2019-04-18 Thu 10:24
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** WAITING Yvain comme 2eme conducteur
** WAITING Véhicule de prêt
Archived entries from file /home/alex/projects/tasks/todo.org
* DONE Mail Marie Piazza
:PROPERTIES:
:ARCHIVE_TIME: 2019-04-18 Thu 10:24
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Archived entries from file /home/alex/projects/tasks/todo.org
* DONE Résilier taxe d'habitation Toulon
:PROPERTIES:
:ARCHIVE_TIME: 2019-04-18 Thu 10:25
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Clôtures mensualisation
** DONE Les impôts vont contacter le proprio. Remboursement pour 2018 ?
* Archive
** DONE Appel généraliste pour stage
CLOSED: [2019-05-05 Sun 18:21]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-05 Sun 18:21
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Relancer assurance
CLOSED: [2019-04-29 Mon 15:18]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-05 Sun 18:22
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison/Mazda 5
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Réparer chauffage
CLOSED: [2019-05-06 Mon 12:07]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-06 Mon 12:07
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
*** DONE Relancer bouygues au 614
*** DONE Appel électricien demain si pas de nouvelles
CLOSED: [2019-05-06 Mon 10:10] DEADLINE: <2019-05-06 Mon>
SIEG : voir avec 0645115958 (Spanagel)
Lorraine elec 57
** DONE Vérifier si frais de résiliations ont été prélevé (39€)
CLOSED: [2019-05-06 Mon 14:43]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-06 Mon 14:43
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison/Passer à bouygues
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Souscription
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-06 Mon 14:43
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison/Passer à bouygues
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Résiliation SFR
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-06 Mon 14:43
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison/Passer à bouygues
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Renvoyer box sfr
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-06 Mon 14:43
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison/Passer à bouygues
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Renvoyer clé 4g bouygues
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-06 Mon 14:43
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison/Passer à bouygues
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Vérifier Laure est bien bénéficiaire mutuelle
CLOSED: [2019-04-29 Mon 21:43]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-06 Mon 23:51
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Mail envoyé
** DONE Vidange moto à 35 500km
CLOSED: [2019-04-29 Mon 21:44]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-06 Mon 23:51
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Renvoyer contrat Allianz signé
CLOSED: [2019-05-09 Thu 19:23]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-09 Thu 19:23
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE [[mu4e:msgid:0ea3f5ed-f06d-5949-e65c-e3db0ae2c78a@chimie.ups-tlse.fr][Re: Ligne droite]]
CLOSED: [2019-05-10 Fri 09:32]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-10 Fri 09:32
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Mail
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE [[mu4e:msgid:983070460.420685.1557136487977.JavaMail.open-xchange@opme11oxm28nd1.rouen.francetelecom.fr][Re: Natation]]
CLOSED: [2019-05-10 Fri 09:42]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-10 Fri 09:42
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Mail
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Mazda 5
CLOSED: [2019-05-16 Thu 10:04]
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-16 Thu 10:04
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
*** DONE Changer amortisseur arrière + pneu avants
CLOSED: [2019-05-09 Thu 11:18]
Pièce reçue, RV pris
*** DONE Refaire CT
CLOSED: [2019-05-16 Thu 10:04]
RV pris
** DONE Relire dossier elise
CLOSED: [2019-05-16 Thu 10:04] SCHEDULED: <2019-05-10 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-16 Thu 10:04
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Prendre RV dentiste
CLOSED: [2019-05-17 Fri 10:24] SCHEDULED: <2019-05-16 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-24 Fri 10:30
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** TODO Bague pour Laure
SCHEDULED: <2019-06-05 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2019-05-24 Fri 10:30
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: TODO
:END:
** DONE Relire rapport Elise
CLOSED: [2019-06-02 Sun 18:13] DEADLINE: <2019-05-31 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2019-06-02 Sun 18:13
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Prendre RV dentiste
CLOSED: [2019-05-17 Fri 10:24] SCHEDULED: <2019-05-16 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2019-06-10 Mon 21:18
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Bague pour Laure
CLOSED: [2019-06-08 Sat 12:02] SCHEDULED: <2019-06-05 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2019-06-10 Mon 21:18
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Rendre livres BU
CLOSED: [2019-06-06 Thu 21:11] SCHEDULED: <2019-06-06 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2019-06-10 Mon 21:18
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Regarder openmp + fftw
CLOSED: [2019-06-06 Thu 21:11] SCHEDULED: <2019-06-06 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2019-06-10 Mon 21:18
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Relire rapport yvain
CLOSED: [2019-06-22 Sat 11:35]
:PROPERTIES:
:ARCHIVE_TIME: 2019-06-22 Sat 11:35
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Recoudre trampoline
CLOSED: [2019-07-01 Mon 13:52] SCHEDULED: <2019-05-16 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2019-07-01 Mon 13:52
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Recoudre 2 t-shirt
CLOSED: [2019-06-10 Mon 09:46] SCHEDULED: <2019-06-08 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2019-07-01 Mon 13:52
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** CANCELLED Corriger lettre alternance yvain
CLOSED: [2019-06-10 Mon 21:18]
:PROPERTIES:
:ARCHIVE_TIME: 2019-07-01 Mon 13:52
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:END:
** DONE Envoyer contrat assurance
CLOSED: [2019-06-13 Thu 16:10] DEADLINE: <2019-06-11 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2019-07-01 Mon 13:52
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Prendre RV
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:08
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Faire dossier
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:08
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* CANCELLED Déposer dossier
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:08
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:END:
* DONE Refaire demande bourse normale
CLOSED: [2019-07-09 Tue 12:19]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:08
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Demande en ligne
** DONE Payer
** DONE Envoyer documents
** DONE Expliquer pour Yvain
CLOSED: [2019-05-24 Fri 10:51]
* DONE Demander attestation de fin de droits à pôle emploi
CLOSED: [2019-06-13 Thu 16:00]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:08
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Mail pour avoir des infos
CLOSED: [2019-06-10 Mon 21:29]
sur la notification d'ouverture de droits
* DONE Prendre RV
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:11
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Faire dossier
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:13
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* CANCELLED Déposer dossier
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:13
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:END:
* DONE Refaire demande bourse normale
CLOSED: [2019-07-09 Tue 12:19]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:13
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Demande en ligne
** DONE Payer
** DONE Envoyer documents
** DONE Expliquer pour Yvain
CLOSED: [2019-05-24 Fri 10:51]
* DONE Demander attestation de fin de droits à pôle emploi
CLOSED: [2019-06-13 Thu 16:00]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:13
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Mail pour avoir des infos
CLOSED: [2019-06-10 Mon 21:29]
sur la notification d'ouverture de droits
* DONE Revoir assistante sociale en juin
CLOSED: [2019-07-09 Tue 12:19]
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:13
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac/Demande bourse (aide spécifique allocation annuelle)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
RV pris
* DONE Grammaire N4
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:13
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Japanese
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Vocabulaire N4
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-09 Fri 11:13
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Japanese
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Passer à bouygues
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-23 Fri 17:50
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Remboursement frais résilation
CLOSED: [2019-05-07 Tue 21:16]
Demande faite, à suivre
** DONE Payer frais de résiliations (39€)
CLOSED: [2019-05-09 Thu 11:18]
** DONE Demander remboursement électricien
CLOSED: [2019-05-17 Fri 00:00] SCHEDULED: <2019-05-16 Thu>
** DONE Vérifier remboursement
*** DONE Répondre appel
CLOSED: [2019-05-24 Fri 10:30]
*** TODO Devrait passer jeudi/vendredi pour payer en ... liquide
** CANCELLED Passer par médiateur
*** DONE Dernière chance : appel 15/07/2019 -> demande facture -> envoyée jour même
*** DONE Attendre remboursement
Appel 07/08 : demandent à nouveau la facture... Renvoyé par mail à
ca.installreseaux@gmail.com (déjà la bonne adresse la dernière fois...)
*** DONE demande médiateur
* DONE Jeter meuble salle de bain :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-23 Fri 17:50
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Remettre volet en place
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-23 Fri 17:50
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
2eme fois... On met une vis en L pour faire une sorte de cheville. Si ça ne
tient pas, mettre vis+écrou
* DONE Retour cadeaux Loraine
DEADLINE: <2019-08-14 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:17
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Résilier carde cdiscount
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:17
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Rendre livres en retard
SCHEDULED: <2019-08-20 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:17
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Rendre livres en retard
SCHEDULED: <2019-08-20 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2019-08-31 Sat 09:17
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Taxe foncière
DEADLINE: <2019-09-25 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2019-09-25 Wed 14:38
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Remboursement anneaux de gymnastique
:PROPERTIES:
:ARCHIVE_TIME: 2019-11-11 Mon 18:29
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Mail envoyé <2019-10-15 Tue>
* DONE Vider chambre élise :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2019-12-06 Fri 10:58
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
A moitié fait
Élise en a fait une partie
* DONE Finir d'enlever rouille barbecue :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2019-12-06 Fri 10:58
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* CANCELLED Louer chambre d'Élise
:PROPERTIES:
:ARCHIVE_TIME: 2019-12-06 Fri 10:58
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:END:
** DONE Annonce leboncoin
* DONE Suivre commande Cecil-Goldman
:PROPERTIES:
:ARCHIVE_TIME: 2020-02-27 Thu 16:27
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Appel Elsevier fr
Commande sur site anglais mais paiement par chèque envoyé le 29/11 au service
français.
Appel le 06/12 : pas de traces du chèque. Il sera soit transféré à elsevier GB,
soit retourné par courrier
=> attendre, rappeller dans 1 semaine si chèque non encaissé ou pas de courrier
** DONE Appel Elsevier UK
Pas de trace du chèque. Va annuler la commande : transfert au service compétent,
devrait me recontacter par mail.
Chèque annulé auprès de la banque <2019-12-13 Fri>
** DONE Recommande
Attendre annulation de la commande avant de recommander.
* DONE Changer fermeture éclair manteau :couture:
:PROPERTIES:
:ARCHIVE_TIME: 2020-02-27 Thu 16:28
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Trouver des entreprises pour Yvain
SCHEDULED: <2019-09-01 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2020-02-27 Thu 16:28
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Stage parapente :parapente:
:PROPERTIES:
:ARCHIVE_TIME: 2020-02-27 Thu 16:28
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** TODO Avec Loraine ? : seule date disponible
Problème : perf = en semaine et découverte = week-end
Cumulus parapente : compatible en septembre mais Loraine ne peut que le lundi =>
perf 1 journée est seulement en dernière minute. Envoyer un mail 3 jours avant...
https://docs.google.com/spreadsheets/d/172fsKPtWZi6UV-6eX5PZQ_GYHVs6vu6tM9qTgrdS_fQ/pubhtml?gid=1726871643&headers=false&range=a1%3Aao37&chrome=false
Bol d'air : pas compatible d'après planning https://www.bol-d-air.fr/medias/pdf/calendrier_parapente.pdf
Vosges parapente non plus https://vosges-parapente.fr/programme-parapente-vosges/
Argantair non plus et trop cher
* DONE Lire mémoire Jean-Philippe
SCHEDULED: <2019-09-01 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-07 Tue 14:06
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Notes/remarques
- pillards volent les pièce ... avant les fouillées (premières pages) ?
- vérifier le calcul de probab pour la distribution aléatoire des lamelles
* DONE Inscriptions listes électorales
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-12 Sun 10:49
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE Demande en ligne
CLOSED: [2019-06-16 Sun 10:26]
En attente
** DONE En attente de la mairie
* CANCELLED Bar hang
SCHEDULED: <2019-12-02 Mon .+1d>
:PROPERTIES:
:LOGGING: lognoterepeat
:LAST_REPEAT: [2019-12-01 Sun 12:36]
:ARCHIVE_TIME: 2020-04-26 Sun 11:53
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Gymnastics
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: gym
:END:
- State "DONE" from "TODO" [2019-09-29 Sun 19:47] \\
4x40s en actif
- State "DONE" from "TODO" [2019-09-26 Thu 13:21] \\
Actif 4x30
Passif 51s
- State "DONE" from "TODO" [2019-09-23 Mon 22:59]\\
2min actif, 20s + pause 10-15s
45s passif
- State "DONE" from "TODO" [2019-09-22 Sun 22:59]
2min30 actif, 10s + pause 10-15s
1min passif
* CANCELLED Front split
:PROPERTIES:
:LOGGING: lognoterepeat
:LAST_REPEAT: [2018-10-26 Fri 17:34]
:ARCHIVE_TIME: 2020-04-26 Sun 11:53
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Gymnastics
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: gym
:END:
- State "DONE" from "TODO" [2018-10-25 Thu 17:34] \\
30s chaque
- State "DONE" from "TODO" [2018-10-21 Mon 23:24] \\
Quadri rapide, 30s split (à gauche, pas sur les poings)
- State "DONE" from "TODO" [2018-10-20 Sat 22:53] \\
Fléchisseur 30, écart 60s (!) sur les blocs mais avec les poings
- State "DONE" from "TODO" [2018-10-20 Sat 18:46] \\
1x30s
* TODO Pancake split :daily:
SCHEDULED: <2020-04-17 Fri .+1d>
:PROPERTIES:
:LOGGING: lognoterepeat
:STYLE: habit
:LAST_REPEAT: [2020-04-16 Thu 12:04]
:ARCHIVE_TIME: 2020-04-26 Sun 11:53
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Gymnastics
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: TODO
:ARCHIVE_ITAGS: gym
:END:
- State "DONE" from "TODO" [2020-04-16 Thu 12:04]
Standing 60s-70
- State "DONE" from "TODO" [2020-04-11 Sat 23:26]
- State "DONE" from "WAITING" [2020-04-04 Sat 22:43]
- State "DONE" from "WAITING" [2020-03-19 Thu 22:43]
- State "DONE" from "WAITING" [2020-03-19 Thu 22:43]
- State "DONE" from "TODO" [2019-12-12 Thu 20:36]
Standing 120s
Frog 60s
Side 60s each
Standing straight back 60s
- State "DONE" from "TODO" [2019-10-16 Wed 21:42]
- State "DONE" from "TODO" [2019-09-24 Tue 23:51]
- State "DONE" from "TODO" [2019-08-17 Sat 20:59]
- State "DONE" from "TODO" [2019-05-25 Sat 10:41]
- State "DONE" from "TODO" [2019-05-25 Sat 22:52]
- State "DONE" from "TODO" [2019-02-02 Sat 22:52] \\
1min debout, 1min debout dos courbé, 30s debout dos droit
- State "DONE" from "TODO" [2018-10-25 Thu 17:33] \\
2x60s
- State "DONE" from "TODO" [2018-10-24 Wed 00:03] \\
2x30
- State "DONE" from "TODO" [2018-10-21 Sun 23:47] \\
2x60s escalier
- State "DONE" from "TODO" [2018-10-20 Sat 22:46] \\
60s escalire, 20s bloc yoga (dur !!)
- State "DONE" from "TODO" [2018-10-19 Fri 18:46] \\
1x30
* CANCELLED Stage Kanazawa
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-26 Sun 15:53
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: fac
:END:
** DONE Candidater
** DONE Appeler Mme Ruban
1 mois (probablement juillet)
Studio fourni + 1 vélo
visite de différents services (observation++)
Contacté Clément Guidarelli pour info
** DONE Demande diplôme de licence d'histoire
Envoyé lettre <2019-12-12 Thu>
** CANCELLED Formalités Kanazawa
*** DONE Signer convention
*** CANCELLED Billet d'avion
*** CANCELLED Documents
- attestation de responsabilité civile (mentionnant "étudiant hospitalier" comme
status) + destination [FAC, HMK]
- assistance rapatriement [FAC]
- copie billet d'avion [FAC]
- CV en anglais [HMK]
- copie de carte d'étudiant [HMK]
- copie de votre passeport [HMK]
- certificat médical [HMK] (! radio, ECG, bilan bio...)
- certificat de vaccination [HMK]
*** CANCELLED Assurance rapatriement
*** CANCELLED Certificat médical
! ECG, bio, RX...
*** CANCELLED Protection sociale ???
* DONE Rendre épargne à Élise
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-26 Sun 15:53
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: banque
:END:
* DONE Importer comptes Boursorama dans ledger
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-26 Sun 15:53
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: banque
:END:
* DONE Clôture assurance-vie :succession:
:PROPERTIES:
:ARCHIVE_TIME: 2020-04-26 Sun 15:55
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Mail envoyé pour suivi (x2...)
CLOSED: [2019-05-09 Thu 19:23]
** DONE Appeler !
CLOSED: [2019-06-27 Thu 10:26]
** DONE Envoyer cte de décès
CLOSED: [2019-06-27 Thu 10:26]
** DONE Appeler banque populaire
CLOSED: [2019-07-01 Mon 14:44]
Compte fructis obsèque bien clôturé à l'époque, le courrier était une erreur...
** DONE Renvoyer à la bonne adresse mail les documents pour clôturer le compte
CLOSED: [2019-07-01 Mon 14:45]
Le notaire n'a pas fait les démarches. Était-ce à lui ?
** DONE Rappeler pour savoir comment toucher la deuxième assurance vie
Attendre retour d'AFER : ils vont voir avec le notaire pour le testament.
Ni thierry ni papa n'ont reçu de papiers.
** DONE Remplir documents
** DONE Papiers pour 2eme contrat
Envoyé
* DONE Assurance : demander pourquoi augmentation des prélèvements auto depuis décembre 2019
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-18 Mon 14:55
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
Mail envoyé le <2020-05-05 Tue>
* CANCELLED Mme Gartiser Catherine : expérience avec oiseaux, prête à payer et venir sur
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-18 Mon 14:55
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres/Vendre Shiku
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: misc
:END:
Metz. À recontacter après confinement
* CANCELLED 06 30 48 52 90 (enya 52 )
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-18 Mon 14:55
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres/Vendre Shiku
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: misc
:END:
* CANCELLED 06 30 71 74 04
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-18 Mon 14:55
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres/Vendre Shiku
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: misc
:END:
* CANCELLED 06 75 11 74 74
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-18 Mon 14:55
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres/Vendre Shiku
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: CANCELLED
:ARCHIVE_ITAGS: misc
:END:
* DONE Déclaration d'impôts 2020
DEADLINE: <2020-04-22 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-18 Mon 14:55
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
* DONE Se réengager auprès de Bouygues (fibre) pour payer 20€/mois
DEADLINE: <2020-04-27 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-18 Mon 14:55
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
* DONE Retard comptabilité
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-27 Wed 16:06
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: banque
:END:
* DONE Changer de CB (différé = trop gênant)
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-27 Wed 16:06
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: banque
:END:
- [X] virer 686€ pour y avoir droit
- [X] faire demande
* DONE Remboursement frais de déplacement janvier
:PROPERTIES:
:ARCHIVE_TIME: 2020-05-27 Wed 16:06
:ARCHIVE_FILE: ~/projects/tasks/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
Envoyé 2 mails, non payé...
Toujours pas payé en avril <2020-04-28 Tue>
* DONE Vendre Shiku
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-17 Wed 12:42
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE 2eme annonce
* DONE Retirer ECNI intesfi
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-17 Wed 12:43
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
** DONE Demande faite <2020-06-02 Tue>
* DONE Ouverture de stage en génétique été 2020
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-17 Wed 12:43
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
** DONE Vérifier que stage non ouvert
** DONE Accord chef de service
Mail envoyé <2020-04-28 Tue>
** DONE Accord de la fac (répartition)
* DONE Virement rente
:PROPERTIES:
:ARCHIVE_TIME: 2020-06-25 Thu 13:46
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Mail envoyé
** DONE Vérifier que la rente nous a été versé
** DONE Renvoyer vers le notaire pour demande de remboursement......
** DONE Reenvoyé à nouveau vers le notaire
Ne semblent pas avoir reçu le premier mail (ou font les idiots)
** DONE Relance par mail => on fait le mort
* DONE Demander remboursement oscaro :voiture:
:PROPERTIES:
:ARCHIVE_TIME: 2020-07-09 Thu 11:17
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE Mail
CLOSED: [2019-06-15 Sat 12:05]
** DONE Appel
CLOSED: [2019-06-20 Thu 13:55]
** DONE Devis butée à seb sport garage
CLOSED: [2019-06-27 Thu 10:26] DEADLINE: <2019-06-24 Mon>
** DONE Reparation
150€
** DONE Retourner anciennes (frais de transport remboursés)
** DONE Changer demande de remboursement : amortisseur -> butée
** DONE Envoyer les factures à frais.garantie@oscaro.com
** DONE Vérifier remboursement (1 mois, donc vers 15 août)
- Relancé par téléphone. Remboursement en attente mais a priori sera fait.
- Mail envoyé
- Remboursement mais seulement de la pièce (17€)
** KILL Demande le remboursement des frais de garagistes (150€)
- Relancé par téléphone au 24/09 pour les frais de garagistes (150€)
- Relancé par mail le [2020-06-18 Thu]
Pas de réponse, on abandonne
* DONE Script python pour ajouter les hiragan aux sous-titres
DEADLINE: <2020-07-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2020-07-12 Sun 23:32
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Japanese/Another
:ARCHIVE_CATEGORY: japanese
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japanese daily
:END:
* DONE Réinscription
:PROPERTIES:
:ARCHIVE_TIME: 2020-08-26 Wed 13:39
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
Rappel : http://medecine.univ-lorraine.fr/fr/formations-initiales/2e-cycle/fr
** DONE CVEC
** DONE Inscription administrative
Bien cocher "certificat master santé" pour avoir une convention SIR !
*** DONE Web
DEADLINE: <2020-07-15 Wed>
*** DONE Pièces justificatives
*** DONE Payer par chèque
Agent comptable de l'université de Loraine
** DONE Inscription pédagogique
* DONE Demande bourse 2020-2021
:PROPERTIES:
:ARCHIVE_TIME: 2020-09-19 Sat 13:39
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
** DONE Bourse normale
*** DONE Demande en ligne [2020-03-06 Fri 13:06]
*** DONE Envoi dossier papier
*** DONE Relancé par mail [2020-06-16 Tue]
*** DONE Attente contacte par l'assistante sociale
Cf mail du CROUS du [2020-06-18 Thu]
Relancé par mail le [2020-07-06 Mon 13:09] pour savoir si je peux prendre RV directement
*** KILL "Valider"le DSE pour pouvoir demander ASAA ?
Inutile
** DONE Allocation spécifique annuelle
*** DONE Prise RV avec assistante sociale
Propose le 2 septembre mais pas possible
Je propose de déposer le dossier d'ici fin juillet après réinscription
*** DONE Constituter dossier
Cf [[notmuch:id:1650725487.539607.1594208548737.JavaMail.zimbra@univ-lorraine.fr][mail]]
Cf [[~/personal/documents/medecine/demande_bourse_2020/Dossier ASAA 2020-2021.docx]]
Envoi par mail à Claire Jolivet
*** DONE RV téléphoniq ue Claire Jolivet <2020-09-02 Wed 10:15>
Pre-commission le 8 septembre, comission le 15 septembre avec résultats par mail
*** DONE Résultat
échelon 5: 4610€
* DONE Remettre la gouttière + vis foreuse
:PROPERTIES:
:ARCHIVE_TIME: 2020-09-19 Sat 13:41
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Maison/Toiture
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* KILL Demande de travaux ? => non
DEADLINE: <2020-09-22 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-09-22 Tue 10:24
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Maison/Toiture
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
** KILL Demande préalable de travaux
https://www.service-public.fr/particuliers/vosdroits/F17578
** KILL Plan de situation
https://www.cadastre.gouv.fr/scpc/rechercherPlan.do#
* DONE Demande remboursement ostéo du [2020-09-16 Wed]
:PROPERTIES:
:ARCHIVE_TIME: 2020-09-25 Fri 11:16
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE Envoyer
** DONE Vérifier remboursement
DEADLINE: <2020-09-29 Tue>
* DONE Chaîne
CLOSED: [2019-07-09 Tue 12:18]
:PROPERTIES:
:ARCHIVE_TIME: 2020-10-12 Mon 10:34
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Moto
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Retendre
CLOSED: [2019-07-01 Mon 13:53]
** DONE Commande clé dynamométrique pour vérifier
CLOSED: [2019-07-09 Tue 12:18]
* DONE Commande Minoxidil
DEADLINE: <2020-09-22 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 09:34
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Santé
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Mail envoyé
* DONE Vérifier rembourement consultation ostéo
DEADLINE: <2020-09-29 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 09:34
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Santé
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
20€ remboursé
* KILL Vérifier rembourement consultation Dr Abimelec
DEADLINE: <2020-10-06 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 09:34
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Santé
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
Non fait
* KILL Vérifier paiement gardes covid
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 09:54
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: fac
:END:
** KILL Mercy mars
Manque
** KILL Mercy avril
** DONE Nancy
* DONE Choix stage D4 semestre 1
DEADLINE: <2020-09-20 Sun> SCHEDULED: <2020-09-19 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 09:54
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
* DONE Vérifier remboursement CVEC
DEADLINE: <2020-10-13 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 09:54
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
* DONE Indemnité de transport 01/10-31/12/20
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 09:54
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
Demande faite le <2020-09-30 Wed>
* DONE Appel BU pour collège de médecine légale
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 09:54
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
* DONE Yami, Lukas, Franck
DEADLINE: <2020-09-19 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 21:16
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Mail
:ARCHIVE_CATEGORY: mail
:ARCHIVE_TODO: DONE
:END:
* DONE [#A] Repeindre balcon pour enlever rouille :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 21:16
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Yvain a fait la partie supérieure de la partie horizontale => refaire car rouille
Rustoléum pour anti-rouille puis 2 couches de peinture glycéro
* DONE [#A] Repeindre plafond chambre d'ami
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 21:16
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** Gratter
** Enduit
** Peindre
* KILL Notes cours médecine nucléaire
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 21:16
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Stage
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: stage
:END:
Jusque J2 inclus
* KILL Notes médecin généraliste
DEADLINE: <2019-07-09 Tue> SCHEDULED: <2019-07-08 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 21:16
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Stage
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: stage
:END:
* KILL Notes gynéco
:PROPERTIES:
:ARCHIVE_TIME: 2020-11-23 Mon 21:16
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Stage
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: stage
:END:
* DONE Emacs config from scratch : evil, org-mode
:PROPERTIES:
:ARCHIVE_TIME: 2020-12-15 Tue 12:20
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Blog/Post sur emacs
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: blog
:END:
* DONE Doom emacs
:PROPERTIES:
:ARCHIVE_TIME: 2020-12-15 Tue 12:20
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Blog/Post sur emacs
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: blog
:END:
* DONE Emacs config from scratch : evil, org-mode
:PROPERTIES:
:ARCHIVE_TIME: 2020-12-15 Tue 12:20
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Blog/Post sur emacs
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: blog
:END:
* DONE Doom emacs
:PROPERTIES:
:ARCHIVE_TIME: 2020-12-15 Tue 12:20
:ARCHIVE_FILE: ~/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Blog/Post sur emacs
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: blog
:END:
* DONE Présentation en psy
:PROPERTIES:
:ARCHIVE_TIME: 2021-01-31 Sun 15:44
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: fac
:END:
Utiliser cas 21 et 26 , puis 23 pour sa filled
[[file:/usr/home/alex/books/medecine/100 cas en psychiatrie.pdf][file:/usr/home/alex/books/medecine/100 cas en psychiatrie.pdf]]
* KILL Confirmation inscription ECN
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-18 Thu 15:10
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Fac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: fac
:END:
* DONE Romuald
DEADLINE: <2020-09-20 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-18 Thu 15:11
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Mail
:ARCHIVE_CATEGORY: mail
:ARCHIVE_TODO: DONE
:END:
* DONE Location hiver 2020
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-18 Thu 15:12
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Vacances
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Payer loyer
** DONE Envoyer caution par courrier
** DONE Signer et envoyer contrat
* DONE FFI cet été
:PROPERTIES:
:ARCHIVE_TIME: 2021-03-25 Thu 12:57
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Médecine
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** KILL Gériatrie Mercy
*** DONE Infos demandées à Timothée Bichet sur Facebook
*** DONE Candidater
Mail avec CV + paragraphe de motivation
n.blettner at chr-metz-thionville
** DONE Demander info à la DAM de metz
** DONE Candidater DAM
Pédiatrie, urgences, pneumo + autres si besoin
[[notmuch:id:OF53282FA9.5389ADDE-ONC1258699.004E97EB-C1258699.004E9EE0@chr-metz-thionville.fr][Email from Agnes Pianezzola: Tr : Recherche de postes FFI]]
Ok pour juillet-août
* DONE Ecn rang
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-02 Fri 14:31
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Projets
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Extraire les données avec haskell
*** DONE 1 année
*** DONE Toutes les années
** DONE Plot avec chart.js
* DONE PR: MAJ documentation pour partition linux à monter
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-19 Mon 21:07
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Contenu :
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=195209
** DONE Récupérer code source
https://www.freebsd.org/doc/handbook/updating-upgrading-documentation.html
** DONE Soumettre PR
Fait sur bug initial
* KILL Rendre patch sterm compatible
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-19 Mon 21:07
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
** KILL Mail au mainteneur
* DONE Renouvellement carte identité
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-21 Wed 09:51
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE Pre-demande
** DONE Payer timbre fiscal
** DONE PRendre RV
DEADLINE: <2020-10-21 Wed>
** DONE RV mairie
Pièces :
- [X] déclaration vol [[file:~/backups/hubic/Private/Personal/documents/admin/perte_carte_id/cerfa_14011-02.pdf][file:~/backups/hubic/Private/Personal/documents/admin/perte_carte_id/cerfa_14011-02.pdf]]
- [X] récapitulatif [[file:~/backups/hubic/Private/Personal/documents/admin/perte_carte_id/QTP37XYGZB-recapitulatif-cni.pdf][file:~/backups/hubic/Private/Personal/documents/admin/perte_carte_id/QTP37XYGZB-recapitulatif-cni.pdf]]
- [X] photo identité
- [X] justificatif de domicile
** DONE Récupérer carte
Atour du 31 octobre (SMS). Y aller en mairie sans RV mais avec récipissé
* DONE Cadeaux Noël 2020
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-21 Wed 09:52
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
- [X] Aurore : BD
- [X] Laure : jeux de plateau/switch/ps4
- [X] Yvain : BD picsou
- [ ] Robin
- [ ] Papa : abonnement planete linux
Envoyer paiement
Envoyer carte
- [X] Tina
* DONE Déclaration 2021
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-21 Wed 09:52
:ARCHIVE_FILE: /usr/home/alex/projects/blog/notes/todo.org
:ARCHIVE_OLPATH: Impôts
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Post sur config email :blog:
:PROPERTIES:
:ARCHIVE_TIME: 2021-04-23 Fri 12:01
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Blog
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Gnus vs notmuch
Notmuch : very fast, easy to search. But you need to have scripts to rename/move mails (so a bit of setup)
Gnus: very useful to read news and only show unread mails. Search with mairix is slow (not mairix itself) and slow at startup. Could not make notmuch work
I tried notmuch, then gnus, then notmuch
* KILL Port haskell-language-server
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-04 Tue 22:53
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
** KILL V1 Une seulle version de GHC
cabal new-configure
*** KILL Version avec dépendences manuelle : echec
#+begin_src shell
cabal new-configure
# $FreeBSD$
PORTNAME= haskell-language-server
DISTVERSION= 1.0.0
CATEGORIES= devel haskell
MAINTAINER= haskell@FreeBSD.org
COMMENT= Integration point for ghcide and haskell-ide-engine.
LICENSE= APACHE20
BUILD_DEPENDS= git:devel/git
USES= cabal
USE_CABAL= cabal-install-parsers-0.3.0.1_1 \
lukko-0.1.1.3_1 \
cryptohash-sha256-0.11.102.0 \
network-uri-2.6.4.1 \
tar-0.5.1.1_3
USE_GITHUB= yes
GH_ACCOUNT= haskell
post-patch:
${CP} ${WRKSRC}/install.hs ${WRKSRC}/install
. for package in ${USE_CABAL}
${MV} ${WRKSRC}/${package:C/_[0-9]+//} ${WRKSRC}/install
echo " ./"${package:C/_[0-9]+//} >> ${WRKSRC}/install/cabal.project
. endfor
do-build:
cd ${WRKSRC}/install && cabal v2-build
.include <bsd.port.mk>
#+end_src
*** DONE Génerer la list des dépendences
CABAL_HOME=$(pwd)/cabal-home
mkdir $CABAL_HOME
env HOME=${CABAL_HOME} cabal new-update
env HOME=${CABAL_HOME} cabal new-configure
env HOME=${CABAL_HOME} cabal new-build --dependencies-only
*** Conclusion
Port réécrit par arrowd :
- hs-hls-install est installé par un port séparé
- puis on l'utilise pour install hs-haskell-language-server
Toute la difficulté vient du fait qu'on ne peut pas laisser cabal gérer
* KILL Zsh (fresh install)
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-08 Sat 16:50
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Blog
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: blog
:END:
1. Install zsh
2. Install antibody (plugin manager). On archlinux, I like yay :
#+BEGIN_SRC shell
yay -Sy antibody
#+END_SRC
3. Create a list of plugins in ~/.zsh_plugins.txt yay :
#+BEGIN_SRC shell
echo '# Oh my zsh: fzf
robbyrussell/oh-my-zsh path:plugins/fzf' > ~/.zsh_plugins.txt
#+END_SRC
4. Load plugins statically (fastest)
#+BEGIN_SRC shell
antibody bundle < ~/.zsh_plugins.txt > ~/.zsh_plugins.sh
#+END_SRC
#+RESULTS:
5. Minimal .zshrc :
#+BEGIN_SRC shell
echo 'source ~/.zsh_plugins.sh' > ~/.zshrc
#+END_SRC
My config : FZF completion "everywhere"
My prompt
https://github.com/romkatv/powerlevel10k#antibody
I had to default to the ascii version. Even instaling the recommended font did not work in urxvt + source code pro.
(yay -S ttf-meslo-nerd-font-powerlevel10k)
* DONE Signaler incident avec NZBgeek
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-08 Sat 16:52
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: banque
:END:
Incident reçu le <2020-12-28 Tue>
Signalé à Boursorama le <2020-12-29 Tue>
* KILL Compléments alimentaires
:PROPERTIES:
:LOGGING: logrepeat
:LAST_REPEAT: [2021-05-08 Sat 16:53]
:ARCHIVE_TIME: 2021-05-08 Sat 16:54
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Loki
:ARCHIVE_CATEGORY: loki
:ARCHIVE_TODO: KILL
:END:
- State "DONE" from "TODO" [2021-04-30 Fri 22:13]
- State "DONE" from "TODO" [2021-04-19 Sat 10:37]
- State "DONE" from "TODO" [2021-04-15 Thu 10:37]
- State "DONE" from "TODO" [2021-04-11 Sun 10:37]
* Stage :stage:
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-08 Sat 16:54
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_CATEGORY: todo
:END:
:ARCHIVE:
* Vacances
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-08 Sat 16:54
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_CATEGORY: todo
:END:
* Loki
:PROPERTIES:
:CATEGORY: loki
:ARCHIVE_TIME: 2021-05-08 Sat 16:54
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_CATEGORY: loki
:END:
* Médecine
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-08 Sat 16:54
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_CATEGORY: todo
:END:
* Fac :fac:
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-08 Sat 16:54
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_CATEGORY: todo
:END:
* Impôts
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-08 Sat 16:54
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_CATEGORY: todo
:END:
* KILL Google chrome (linux binary)
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-08 Sat 16:54
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
On essaye
https://wiki.freebsd.org/LinuxJails
Plutôt que
https://forums.freebsd.org/threads/linuxulator-how-to-run-google-chrome-linux-binary-on-freebsd.77559/
** Tentative 1 : echec
#+begin_src shell
sudo pkg install linux-steam-utils debootstrap
#+end_src
(linux-stem-utils inutile ?)
#+begin_src shell
sudo debootstrap --no-check-gpg bionic /compat/ubuntu
#+end_src
Echec.
cp: '/etc/resolv.conf' and '/run/systemd/resolve/stub-resolv.conf' are the same file
** Tenttative 2
#+begin_src shell
pkg install linux-steam-utils debootstrap pulseaudio
debootstrap --arch=amd64 --no-check-gpg focal /compat/ubuntu
#+end_src
Ok pour install
#+begin_src
cd /compat/linux/lib64/ && rm ./ld-linux-x86-64.so.2 ; ln -s ../lib/x86_64-linux-gnu/ld-2.31.so ld-linux-x86-64.so.2
#+end_src
Ajouter à /etc/fstab
#+begin_src shell
# Ubuntu jail
devfs /compat/ubuntu/dev devfs rw,late 0 0
tmpfs /compat/ubuntu/dev/shm tmpfs rw,late,size=1g,mode=1777 0 0
fdescfs /compat/ubuntu/dev/fd fdescfs rw,late,linrdlnk 0 0
linprocfs /compat/ubuntu/proc linprocfs rw,late 0 0
linsysfs /compat/ubuntu/sys linsysfs rw,late 0 0
/tmp /compat/ubuntu/tmp nullfs rw,late 0 0
/home /compat/ubuntu/home nullfs rw,late 0 0
#+end_src
#+begin_src shell
mount -al
printf "APT::Cache-Start 251658240;" > /compat/ubuntu/etc/apt/apt.conf.d/00aptitude
printf "deb http://archive.ubuntu.com/ubuntu/ focal main restricted universe multiverse" > /compat/ubuntu/etc/apt/sources.list
# Add Chrome repository:
printf "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" > /compat/ubuntu/etc/apt/sources.list.d/google-chrome.list
fetch -o /compat/ubuntu/ https://dl.google.com/linux/linux_signing_key.pub
chroot /compat/ubuntu /bin/bash
#+end_src
Dans le chroot
#+begin_src shell
apt update
apt install gnupg
apt-key add linux_signing_key.pub
apt update
apt install -y google-chrome-stable
#+end_src
Then
#+begin_src shell
touch /compat/ubuntu/bin/chrome && chmod +x /compat/ubuntu/bin/chrome
#+end_src
Add it
#+begin_src shell
#!/compat/linux/bin/bash
export CHROME_PATH="/opt/google/chrome/chrome"
export CHROME_WRAPPER="`readlink -f "$0"`"
export LD_LIBRARY_PATH=/usr/local/steam-utils/lib64/fakeudev
export LD_PRELOAD=/usr/local/steam-utils/lib64/webfix/webfix.so
export LIBGL_DRI3_DISABLE=1
exec -a "$0" "$CHROME_PATH" --no-sandbox --no-zygote --test-type --v=0 "$@"
#+end_src
Echec : libtinfo.so.6 cannot openshared
=>
#+begin_src shell
sysctl compat.linux.emul_path=/compat/ubuntu
# Message d'erreur
chmod 1777 /dev/shm
#+end_src
Marche après reboot mais micro non reconnu par discord
Essai install discord
* DONE Le monde diplomatique octobre 2020
SCHEDULED: <2020-10-14 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-20 Thu 10:59
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Lecture
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
[[file:~/News/le_monde_diplomatique-2020-10.pdf][file:~/News/le_monde_diplomatique-2020-10.pdf]]
* DONE Le monde diplomatique novembre 2020
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-20 Thu 10:59
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Lecture
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
[[file:/media/books/Le Monde Diplomatique - 2020/Le Monde Diplomatique 2020-11.pdf][file:/media/books/Le Monde Diplomatique - 2020/Le Monde Diplomatique 2020-11.pdf]]
* KILL Demande carte solidaire Grand Est
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-31 Mon 23:25
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_ITAGS: misc
:END:
-80% tarif de train
Envoyé le [2021-02-13 Sat]
Jamais arrivée à la maison, refaire demande avec attestation sur l'honneur
* KILL Déclaration impots Laure
DEADLINE: <2019-05-16 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-05-31 Mon 23:25
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_ITAGS: misc
:END:
* DONE V0.1 Réduire les dépendences
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-12 Sat 13:22
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/Port Kitty
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
#+begin_src
diff --git a/x11/kitty/Makefile b/x11/kitty/Makefile
new file mode 100644
index 000000000..1c7fe338c
--- /dev/null
+++ b/x11/kitty/Makefile
@@ -0,0 +1,76 @@
+PORTNAME= kitty
+DISTVERSION= 0.20.2
+DISTVERSIONPREFIX= v
+CATEGORIES= x11
+
+USE_GITHUB= yes
+GH_ACCOUNT= kovidgoyal
+
+MAINTAINER= alexis.praga@free.fr
+COMMENT= Cross-platform, fast, featureful, GPU-based terminal emulator
+
+LICENSE= GPLv3
+LICENSE_FILE= ${WRKSRC}/LICENSE
+# # python3
+# # freetype2
+# # fontconfig
+# # wayland
+# # libx11
+# # libxkbcommon-x11
+# # libxi
+# hicolor-icon-theme
+# libgl
+# libcanberra
+# # dbus
+# # lcms2
+# # libxinerama
+# # libxcursor
+# # libxrandr
+# # wayland-protocols
+# python-sphinx
+
+LIB_DEPENDS= libdbus-1.so:devel/dbus \
+ libfontconfig.so:x11-fonts/fontconfig \
+ libfreetype.so:print/freetype2 \
+ libxkbcommon.so:x11/libxkbcommon \
+ liblcms2.so:graphics/lcms2 \
+ libharfbuzz.so:print/harfbuzz \
+ libpng.so:graphics/png \
+ libwayland-client.so:graphics/wayland \
+ libwayland-cursor.so:graphics/wayland
+
+# # + libglfw.so:graphics/glfw
+BUILD_DEPENDS= wayland-protocols>=0:graphics/wayland-protocols
+
+USES= gettext-runtime gl gmake pkgconfig python:3.5+ shebangfix xorg
+USE_GL= gl
+USE_XORG= x11 xcb xcursor xi xinerama xrandr
+
+SHEBANG_GLOB= *.py
+SHEBANG_FILES= update-on-ox build-terminfo update-on-ubuntu count-lines-of-code mypy-editor-integration
+
+BINARY_ALIAS= python=${PYTHON_CMD} python3=${PYTHON_CMD}
+
+OPTIONS_DEFINE= DOCS
+
+INSTALL_WRKSRC= ${WRKSRC}/linux-package
+
+_STRIP_TARGETS= lib/kitty/kitty/fast_data_types.so \
+ lib/kitty/kitty/glfw-x11.so \
+ lib/kitty/kittens/diff/diff_speedup.so \
+ lib/kitty/kittens/unicode_input/unicode_names.so \
+ lib/kitty/kitty/glfw-wayland.so \
+ lib/kitty/kittens/choose/subseq_matcher.so bin/kitty
+_EMPTY_DIRS= kittens/choose kittens/diff kittens/unicode_input kittens kitty
+
+do-build:
+ (cd ${WRKSRC} && \
+ ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py --update-check-interval=0 linux-package)
+
+ ${FIND} ${INSTALL_WRKSRC} -name __pycache__ -type d -exec ${RM} -r -- {} +
+
+do-install:
+ ${CP} -a ${INSTALL_WRKSRC}/ ${STAGEDIR}${PREFIX}
+ @${STRIP_CMD} ${_STRIP_TARGETS:S|^|${STAGEDIR}${PREFIX}/|}
+
+.include <bsd.port.mk>
diff --git a/x11/kitty/distinfo b/x11/kitty/distinfo
new file mode 100644
index 000000000..58b9010fc
--- /dev/null
+++ b/x11/kitty/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1619962289
+SHA256 (kovidgoyal-kitty-v0.20.2_GH0.tar.gz) = 531c4f5112c24189da9291ea7e2be4a60fdec63281866f4d17597d7e2ad3b293
+SIZE (kovidgoyal-kitty-v0.20.2_GH0.tar.gz) = 4237974
diff --git a/x11/kitty/pkg-descr b/x11/kitty/pkg-descr
new file mode 100644
index 000000000..6042101c1
--- /dev/null
+++ b/x11/kitty/pkg-descr
@@ -0,0 +1,18 @@
+Kitty is the fast, featureful, GPU based terminal emulator.
+
+kitty is designed for power keyboard users. To that end all its controls work
+with the keyboard (although it fully supports mouse interactions as well). Its
+configuration is a simple, human editable, single file for easy reproducibility
+(I like to store configuration in source control).
+
+The code in kitty is designed to be simple, modular and hackable. It is written
+in a mix of C (for performance sensitive parts) and Python (for easy hackability
+of the UI). It does not depend on any large and complex UI toolkit, using only
+OpenGL for rendering everything.
+
+Finally, kitty is designed from the ground up to support all modern terminal
+features, such as unicode, true color, bold/italic fonts, text formatting, etc.
+It even extends existing text formatting escape codes, to add support for
+features not available elsewhere, such as colored and styled (curly) underlines.
+One of the design goals of kitty is to be easily extensible so that new features
+can be added in the future with relatively less effort.
diff --git a/x11/kitty/pkg-message b/x11/kitty/pkg-message
new file mode 100644
index 000000000..f58f5922b
--- /dev/null
+++ b/x11/kitty/pkg-message
@@ -0,0 +1,258 @@
+bin/kitty
+lib/kitty/__main__.py
+lib/kitty/kittens/__init__.py
+lib/kitty/kittens/ask/__init__.py
+lib/kitty/kittens/ask/main.py
+lib/kitty/kittens/choose/__init__.py
+lib/kitty/kittens/choose/main.py
+lib/kitty/kittens/choose/subseq_matcher.so
+lib/kitty/kittens/clipboard/__init__.py
+lib/kitty/kittens/clipboard/main.py
+lib/kitty/kittens/diff/__init__.py
+lib/kitty/kittens/diff/collect.py
+lib/kitty/kittens/diff/config.py
+lib/kitty/kittens/diff/config_data.py
+lib/kitty/kittens/diff/diff_speedup.so
+lib/kitty/kittens/diff/highlight.py
+lib/kitty/kittens/diff/main.py
+lib/kitty/kittens/diff/patch.py
+lib/kitty/kittens/diff/render.py
+lib/kitty/kittens/diff/search.py
+lib/kitty/kittens/hints/__init__.py
+lib/kitty/kittens/hints/main.py
+lib/kitty/kittens/hints/url_regex.py
+lib/kitty/kittens/hyperlinked_grep/__init__.py
+lib/kitty/kittens/hyperlinked_grep/main.py
+lib/kitty/kittens/icat/__init__.py
+lib/kitty/kittens/icat/main.py
+lib/kitty/kittens/key_demo/__init__.py
+lib/kitty/kittens/key_demo/main.py
+lib/kitty/kittens/panel/__init__.py
+lib/kitty/kittens/panel/main.py
+lib/kitty/kittens/query_terminal/__init__.py
+lib/kitty/kittens/query_terminal/main.py
+lib/kitty/kittens/remote_file/__init__.py
+lib/kitty/kittens/remote_file/main.py
+lib/kitty/kittens/resize_window/__init__.py
+lib/kitty/kittens/resize_window/main.py
+lib/kitty/kittens/runner.py
+lib/kitty/kittens/show_error/__init__.py
+lib/kitty/kittens/show_error/main.py
+lib/kitty/kittens/ssh/__init__.py
+lib/kitty/kittens/ssh/main.py
+lib/kitty/kittens/tui/__init__.py
+lib/kitty/kittens/tui/dircolors.py
+lib/kitty/kittens/tui/handler.py
+lib/kitty/kittens/tui/images.py
+lib/kitty/kittens/tui/line_edit.py
+lib/kitty/kittens/tui/loop.py
+lib/kitty/kittens/tui/operations.py
+lib/kitty/kittens/tui/operations_stub.py
+lib/kitty/kittens/tui/path_completer.py
+lib/kitty/kittens/tui/utils.py
+lib/kitty/kittens/unicode_input/__init__.py
+lib/kitty/kittens/unicode_input/main.py
+lib/kitty/kittens/unicode_input/unicode_names.so
+lib/kitty/kitty/__init__.py
+lib/kitty/kitty/bgimage_fragment.glsl
+lib/kitty/kitty/bgimage_vertex.glsl
+lib/kitty/kitty/blit_fragment.glsl
+lib/kitty/kitty/blit_vertex.glsl
+lib/kitty/kitty/border_fragment.glsl
+lib/kitty/kitty/border_vertex.glsl
+lib/kitty/kitty/borders.py
+lib/kitty/kitty/boss.py
+lib/kitty/kitty/cell_fragment.glsl
+lib/kitty/kitty/cell_vertex.glsl
+lib/kitty/kitty/child.py
+lib/kitty/kitty/choose_entry.py
+lib/kitty/kitty/cli.py
+lib/kitty/kitty/cli_stub.py
+lib/kitty/kitty/client.py
+lib/kitty/kitty/complete.py
+lib/kitty/kitty/conf/__init__.py
+lib/kitty/kitty/conf/definition.py
+lib/kitty/kitty/conf/utils.py
+lib/kitty/kitty/config.py
+lib/kitty/kitty/config_data.py
+lib/kitty/kitty/constants.py
+lib/kitty/kitty/fast_data_types.so
+lib/kitty/kitty/fonts/__init__.py
+lib/kitty/kitty/fonts/box_drawing.py
+lib/kitty/kitty/fonts/core_text.py
+lib/kitty/kitty/fonts/fontconfig.py
+lib/kitty/kitty/fonts/list.py
+lib/kitty/kitty/fonts/render.py
+lib/kitty/kitty/glfw-wayland.so
+lib/kitty/kitty/glfw-x11.so
+lib/kitty/kitty/graphics_fragment.glsl
+lib/kitty/kitty/graphics_vertex.glsl
+lib/kitty/kitty/guess_mime_type.py
+lib/kitty/kitty/key_encoding.py
+lib/kitty/kitty/key_names.py
+lib/kitty/kitty/keys.py
+lib/kitty/kitty/launch.py
+lib/kitty/kitty/launcher/kitty
+lib/kitty/kitty/layout/__init__.py
+lib/kitty/kitty/layout/base.py
+lib/kitty/kitty/layout/grid.py
+lib/kitty/kitty/layout/interface.py
+lib/kitty/kitty/layout/splits.py
+lib/kitty/kitty/layout/stack.py
+lib/kitty/kitty/layout/tall.py
+lib/kitty/kitty/layout/vertical.py
+lib/kitty/kitty/main.py
+lib/kitty/kitty/marks.py
+lib/kitty/kitty/multiprocessing.py
+lib/kitty/kitty/notify.py
+lib/kitty/kitty/open_actions.py
+lib/kitty/kitty/options_stub.py
+lib/kitty/kitty/os_window_size.py
+lib/kitty/kitty/rc/__init__.py
+lib/kitty/kitty/rc/base.py
+lib/kitty/kitty/rc/close_tab.py
+lib/kitty/kitty/rc/close_window.py
+lib/kitty/kitty/rc/create_marker.py
+lib/kitty/kitty/rc/detach_tab.py
+lib/kitty/kitty/rc/detach_window.py
+lib/kitty/kitty/rc/disable_ligatures.py
+lib/kitty/kitty/rc/focus_tab.py
+lib/kitty/kitty/rc/focus_window.py
+lib/kitty/kitty/rc/get_colors.py
+lib/kitty/kitty/rc/get_text.py
+lib/kitty/kitty/rc/goto_layout.py
+lib/kitty/kitty/rc/kitten.py
+lib/kitty/kitty/rc/last_used_layout.py
+lib/kitty/kitty/rc/launch.py
+lib/kitty/kitty/rc/ls.py
+lib/kitty/kitty/rc/new_window.py
+lib/kitty/kitty/rc/remove_marker.py
+lib/kitty/kitty/rc/resize_window.py
+lib/kitty/kitty/rc/scroll_window.py
+lib/kitty/kitty/rc/send_text.py
+lib/kitty/kitty/rc/set_background_image.py
+lib/kitty/kitty/rc/set_background_opacity.py
+lib/kitty/kitty/rc/set_colors.py
+lib/kitty/kitty/rc/set_font_size.py
+lib/kitty/kitty/rc/set_spacing.py
+lib/kitty/kitty/rc/set_tab_title.py
+lib/kitty/kitty/rc/set_window_title.py
+lib/kitty/kitty/rc/signal_child.py
+lib/kitty/kitty/remote_control.py
+lib/kitty/kitty/rgb.py
+lib/kitty/kitty/session.py
+lib/kitty/kitty/shell.py
+lib/kitty/kitty/tab_bar.py
+lib/kitty/kitty/tabs.py
+lib/kitty/kitty/terminfo.py
+lib/kitty/kitty/tint_fragment.glsl
+lib/kitty/kitty/tint_vertex.glsl
+lib/kitty/kitty/typing.py
+lib/kitty/kitty/update_check.py
+lib/kitty/kitty/utils.py
+lib/kitty/kitty/window.py
+lib/kitty/kitty/window_list.py
+lib/kitty/logo/beam-cursor.png
+lib/kitty/logo/beam-cursor@2x.png
+lib/kitty/logo/kitty.png
+lib/kitty/logo/kitty.rgba
+share/applications/kitty.desktop
+%%PORTDOCS%%%%DOCSDIR%%/html/.buildinfo
+%%PORTDOCS%%%%DOCSDIR%%/html/.nojekyll
+%%PORTDOCS%%%%DOCSDIR%%/html/_downloads/433dadebd0bf504f8b008985378086ce/kitty.conf
+%%PORTDOCS%%%%DOCSDIR%%/html/_downloads/a489ebbb52d84eeb19a12b2fda7debda/diff.conf
+%%PORTDOCS%%%%DOCSDIR%%/html/_images/diff.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_images/hints_mode.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_images/panel.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_images/remote_file.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_images/screenshot.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_images/splits.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_images/unicode.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/binary.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/build.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/changelog.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/conf.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/faq.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/generated/launch.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/generated/rc.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/graphics-protocol.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/index.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/integrations.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/invocation.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/key-encoding.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/clipboard.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/custom.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/diff.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/hints.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/hyperlinked_grep.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/icat.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/panel.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/query_terminal.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/remote_file.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/kittens/unicode-input.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/launch.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/layouts.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/marks.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/open_actions.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/performance.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/pipe.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/protocol-extensions.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/rc_protocol.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/remote-control.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_sources/support.rst.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/alabaster.css
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/basic.css
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/custom.css
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/doctools.js
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/documentation_options.js
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/file.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/jquery-3.4.1.js
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/jquery-3.5.1.js
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/jquery.js
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/kitty.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/language_data.js
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/minus.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/plus.png
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/pygments.css
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/searchtools.js
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/underscore-1.3.1.js
+%%PORTDOCS%%%%DOCSDIR%%/html/_static/underscore.js
+%%PORTDOCS%%%%DOCSDIR%%/html/binary.html
+%%PORTDOCS%%%%DOCSDIR%%/html/build.html
+%%PORTDOCS%%%%DOCSDIR%%/html/changelog.html
+%%PORTDOCS%%%%DOCSDIR%%/html/conf.html
+%%PORTDOCS%%%%DOCSDIR%%/html/faq.html
+%%PORTDOCS%%%%DOCSDIR%%/html/generated/launch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/generated/rc.html
+%%PORTDOCS%%%%DOCSDIR%%/html/genindex.html
+%%PORTDOCS%%%%DOCSDIR%%/html/graphics-protocol.html
+%%PORTDOCS%%%%DOCSDIR%%/html/index.html
+%%PORTDOCS%%%%DOCSDIR%%/html/integrations.html
+%%PORTDOCS%%%%DOCSDIR%%/html/invocation.html
+%%PORTDOCS%%%%DOCSDIR%%/html/key-encoding.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/clipboard.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/custom.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/diff.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/hints.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/hyperlinked_grep.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/icat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/panel.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/query_terminal.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/remote_file.html
+%%PORTDOCS%%%%DOCSDIR%%/html/kittens/unicode-input.html
+%%PORTDOCS%%%%DOCSDIR%%/html/launch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/layouts.html
+%%PORTDOCS%%%%DOCSDIR%%/html/marks.html
+%%PORTDOCS%%%%DOCSDIR%%/html/objects.inv
+%%PORTDOCS%%%%DOCSDIR%%/html/open_actions.html
+%%PORTDOCS%%%%DOCSDIR%%/html/performance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/pipe.html
+%%PORTDOCS%%%%DOCSDIR%%/html/protocol-extensions.html
+%%PORTDOCS%%%%DOCSDIR%%/html/rc_protocol.html
+%%PORTDOCS%%%%DOCSDIR%%/html/remote-control.html
+%%PORTDOCS%%%%DOCSDIR%%/html/search.html
+%%PORTDOCS%%%%DOCSDIR%%/html/searchindex.js
+%%PORTDOCS%%%%DOCSDIR%%/html/support.html
+share/icons/hicolor/256x256/apps/kitty.png
+share/man/man1/kitty.1.gz
+share/misc/kitty.terminfo
#+end_src
* DONE Arriver à ulitiser linux-package
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-12 Sat 13:22
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/Port Kitty
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
N'installe pas correctement avec le Makefile suivant
#+begin_src
PORTNAME= kitty
DISTVERSION= 0.20.2
DISTVERSIONPREFIX= v
CATEGORIES= x11
USE_GITHUB= yes
GH_ACCOUNT= kovidgoyal
MAINTAINER= alexis.praga@free.fr
COMMENT= Cross-platform, fast, featureful, GPU-based terminal emulator
LICENSE= GPLv3
LICENSE_FILE= ${WRKSRC}/LICENSE
LIB_DEPENDS= libdbus-1.so:devel/dbus \
libfontconfig.so:x11-fonts/fontconfig \
libfreetype.so:print/freetype2 \
libxkbcommon.so:x11/libxkbcommon \
liblcms2.so:graphics/lcms2 \
libharfbuzz.so:print/harfbuzz \
libpng.so:graphics/png \
libwayland-client.so:graphics/wayland \
libwayland-cursor.so:graphics/wayland
BUILD_DEPENDS= wayland-protocols>=0:graphics/wayland-protocols
USES= gettext-runtime gl gmake pkgconfig python:3.5+ shebangfix xorg
USE_GL= gl
USE_XORG= x11 xcb xcursor xi xinerama xrandr
SHEBANG_GLOB= *.py
SHEBANG_FILES= update-on-ox build-terminfo update-on-ubuntu count-lines-of-code mypy-editor-integration
BINARY_ALIAS= python=${PYTHON_CMD} python3=${PYTHON_CMD}
OPTIONS_DEFINE= DOCS
INSTALL_WRKSRC= ${WRKSRC}/linux-package
_STRIP_TARGETS= lib/kitty/kitty/fast_data_types.so \
lib/kitty/kitty/glfw-x11.so \
lib/kitty/kittens/diff/diff_speedup.so \
lib/kitty/kittens/unicode_input/unicode_names.so \
lib/kitty/kitty/glfw-wayland.so \
lib/kitty/kittens/choose/subseq_matcher.so bin/kitty
_EMPTY_DIRS= kittens/choose kittens/diff kittens/unicode_input kittens kitty
do-build:
(cd ${WRKSRC} && \
${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py --update-check-interval=0 linux-package)
${FIND} ${INSTALL_WRKSRC} -name __pycache__ -type d -exec ${RM} -r -- {} +
do-install:
${CP} -a ${INSTALL_WRKSRC}/ ${STAGEDIR}${PREFIX}
@${STRIP_CMD} ${_STRIP_TARGETS:S|^|${STAGEDIR}${PREFIX}/|}
.include <bsd.port.mk>
#+end_src
* DONE Arriver à compiler la documentation
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-12 Sat 13:22
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/Port Kitty
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Sumbit
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-12 Sat 13:22
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/Port Kitty
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Accepté
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-12 Sat 13:22
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/Port Kitty
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* KILL Ajouter freebsd à la liste des packages sur github
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-12 Sat 13:22
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/Port Kitty
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
* Notes
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-12 Sat 13:22
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/Port Kitty
:ARCHIVE_CATEGORY: todo
:END:
1ere version disponible ici https://reviews.freebsd.org/file/data/4ppgweur3ew5zt7vctb7/PHID-FILE-d3rjxttzgkq55yxdm5d2/D27239.diff
Mais on peut l'installer simplement avec gmake
Pour la conversion en port :
python3 setup.py linux-package
mais les docs nécessite gmake
* DONE MAJ v0.21
:PROPERTIES:
:ARCHIVE_TIME: 2021-06-17 Thu 22:30
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/Port Kitty
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE 11.4-RELEASE-p11 amd64
** DONE 12.2-RELEASE-p8 amd64
** DONE 13.0-RELEASE-p2 amd64
** DONE 13.0-RELEASE-p2 arm64.aarch64
* DONE Inscription ECNi
DEADLINE: <2021-06-06 Sun> SCHEDULED: <2021-05-18 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Faculté
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Dossier FFI
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Stages
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
[[notmuch:id:OFC1062C15.55F475EB-ONC12586DC.003FB3AD-C12586DC.003FD4E0@chr-metz-thionville.fr][Email from Madison Andrez: Dossier administratif à produire pour la nomination en qualité de FFI durant la période estivale]]
* KILL Lasure :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
** TODO Tables/chaises
Tables OK, 3 chaises OK
** TODO Lasure RdC
* KILL Repeindre chaises :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
* DONE Bouygues : négocier pour baisse
DEADLINE: <2021-05-15 Sat> SCHEDULED: <2021-05-14 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Désherber (mousse + herbes) :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* KILL Repeindre radiateurs :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
Enlever la peinture (sabler avec compresseur + sable ? Pas de décapage)
Peinture pour métaux qui fasse antirouille, sur radiateur froid.
* KILL [#A] Enlever rouille radiateurs :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
* KILL [#A] Repeindre plafond cuisine
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
* KILL Renforcer porte garage :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
* KILL Vendre : porte-cd, table de couture :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
* KILL Backup photos de famille :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
** TODO Tri en cours
* KILL Souder la cloture à l'arrière du jardin :été2019:
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
* DONE Construire bac pour kalala
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:19
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Brosser les cosses
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Réparer injecteurs ?
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Devis Garage des Garennes
2200€
** DONE Devis Mazda
1720€ pour 3, 2200€ pour les 4
** DONE Avis Mazda
On change seulement le filtre à gasoil pour le moment (230€)
* KILL Changer les plaquettes
DEADLINE: <2020-10-11 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
Encore bonnes
* DONE Révisions : liquides
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:20
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
- direction assistée : OK
- freins : OK
- huile moteur : OK
- refroidissement : OK
* DONE Retour apdatateur sata-ide
DEADLINE: <2021-06-04 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:21
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
* DONE turkish airlines
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:21
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Autres/Échange voyage japon été 2020
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE Demande faite (open ticket) le [2020-06-17 Wed]
** DONE Relance le [2020-07-06 Mon]
Car laure a déjà reçu son échange
A priori ok, cf notmuch:id:817091247.13495.1594457372183.JavaMail.bea@crmcctr01
* DONE Ajouter disque dur externe 750G
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-02 Mon 12:21
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Pi
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE DVD
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-04 Wed 10:27
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Maison/Vente
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE 1er envoi demain
** DONE Récupérer carton pour second envoi (avec nouvelle annonce
* KILL Vidéos Chocolate cacao
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-10 Tue 12:01
:ARCHIVE_FILE: /usr/home/alex/projects/blog/todo.org
:ARCHIVE_OLPATH: Japanese
:ARCHIVE_CATEGORY: japanese
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: japanese
:END:
** KILL Tiramisu ice cream
* DONE [[https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=255233][Port ripgrep-all]]
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-18 Wed 10:04
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Soumettre
** DONE Vérifier syntaxe
** DONE Vérifier build sur 11.4 et 12.
*** DONE 13.0
*** DONE 12.2
*** DONE 11.4
* DONE Le monde diplomatique janvier 2021
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-19 Thu 11:25
:ARCHIVE_FILE: ~/projects/blog/todo.org
:ARCHIVE_OLPATH: Lecture
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* KILL Compiler du latex avec Hakyl
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-28 Sat 15:31
:ARCHIVE_FILE: /usr/home/alex/code/blog/todo.org
:ARCHIVE_OLPATH: Blog
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: blog
:END:
Problème : fonctionne en standalone mais pas en incluant un header (testé avec rubber)
* DONE [#A] Porter le site en org-mode
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-28 Sat 15:32
:ARCHIVE_FILE: /usr/home/alex/code/blog/todo.org
:ARCHIVE_OLPATH: Blog
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: blog
:END:
** DONE Régler le problème du footer
** DONE Gérer les fichiers statiques
** KILL Copie locale du CSS
* DONE v0.21.1
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-28 Sat 15:32
:ARCHIVE_FILE: /usr/home/alex/code/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/Port Kitty
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE MAJ nzbhydra à 3.9
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-29 Sun 12:15
:ARCHIVE_FILE: /usr/home/alex/code/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Mail au mainteneur
Devra être fait dans la semaine
* KILL Man page rclone
:PROPERTIES:
:ARCHIVE_TIME: 2021-08-29 Sun 12:15
:ARCHIVE_FILE: /usr/home/alex/code/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
Tuto
http://manpages.bsd.lv/mdoc.html
ET surtout man 7 mdoc
Éventuellement
https://forums.freebsd.org/threads/howto-create-a-manpage-from-scratch.13200/
** KILL Conversion depuis markdown avec pandoc => trop moche
** DONE Synposis
Completer avec
https://raw.githubusercontent.com/rclone/rclone/master/docs/content/_index.md
** KILL Commandes
*** DONE Résumé dans le man principal
https://github.com/rclone/rclone/blob/master/docs/content/commands/rclone.md
1 entrée pour chaque commande...
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/filtering.md][filtering.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/cache.md][cache.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/alias.md][alias.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/union.md][union.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/chunker.md][chunker.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/compress.md][compress.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/crypt.md][crypt.md]]
** KILL Backendds
1 entrée pour chaque
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/amazonclouddrive.md][amazonclouddrive.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/azureblob.md][azureblob.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/b2.md][b2.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/jottacloud.md][jottacloud.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/koofr.md][koofr.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/local.md][local.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/mailru.md][mailru.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/mega.md][mega.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/memory.md][memory.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/onedrive.md][onedrive.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/opendrive.md][opendrive.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/pcloud.md][pcloud.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/premiumizeme.md][premiumizeme.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/privacy.md][privacy.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/putio.md][putio.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/qingstor.md][qingstor.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/seafile.md][seafile.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/s3.md][s3.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/sftp.md][sftp.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/sharefile.md][sharefile.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/sugarsync.md][sugarsync.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/swift.md][swift.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/tardigrade.md][tardigrade.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/webdav.md][webdav.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/yandex.md][yandex.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/zoho.md][zoho.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/ftp.md][ftp.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/googlecloudstorage.md][googlecloudstorage.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/googlephotos.md][googlephotos.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/hdfs.md][hdfs.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/http.md][http.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/hubic.md][hubic.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/drive.md][drive.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/dropbox.md][dropbox.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/fichier.md][fichier.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/filefabric.md][filefabric.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/box.md][box.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/remote_setup.md][remote_setup.md]]
** KILL Options
*** DONE Résumé dans le man principal = [[~/projects/doc-freebsd/rclone/docs/content/flags.md][flags.md]]
*** KILL Version détaillée dans rclone-flags
** KILL Filters [[~/projects/doc-freebsd/rclone/docs/content/filtering.md][filtering.md]]
** KILL Remote control [[~/projects/doc-freebsd/rclone/docs/content/rc.md][rc.md]]
** Autres
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/gui.md][gui.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/authors.md][authors.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/bugs.md][bugs.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/docs.md][docs.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/faq.md][faq.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/install.md][install.md]]
*** KILL [[~/projects/doc-freebsd/rclone/docs/content/overview.md][overview.md]]
*** DONE [[~/projects/doc-freebsd/rclone/docs/content/_index.md][_index.md]]
* DONE Inscription CMU => Accepté à partir du 01/12
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:12
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE Notes
Simulation fite 10/2019 : seuil trop élevé : 18 000€ sur l'année (ou 13 000 si
2 personnes dans le foyer). À refaire dans 1 mois ou 2
** DONE Demande faite <2020-05-09 Sat>
[[file:~/backups/hubic/Private/Personal/documents/secu/DemandeComplementaireSanteSolidaire.pdf][file:~/backups/hubic/Private/Personal/documents/secu/DemandeComplementaireSanteSolidaire.pdf]]
** DONE Refusé le<2020-05-18 Mon> car ressources = 19201.22€
** DONE Nouvelle demande le<2020-10-05 Mon>
** DONE Résilier Unéo
*** DONE Lettre envoyée en recommandée le 15/11/2020
* DONE Remboursement Japan airlines
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:12
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Autres/Échange voyage japon été 2020
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE Demande faite
(Sans frais)
** DONE vérifier remboursement
* DONE ghc-events 0.15.1 -> 0.17.0
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:14
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/MAJ port haskell (no need for aarch64)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE git-annex 8.20210223 -> 8.20210803
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:14
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/MAJ port haskell (no need for aarch64)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Poudriere ok pour 11.4
Note: on a supprimé 2 options
* DONE git-brunch 1.5.0.0 -> 1.5.1.0
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:14
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/MAJ port haskell (no need for aarch64)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE hlint 3.2.7 -> 3.3.2
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:14
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/MAJ port haskell (no need for aarch64)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
test poudriere
* DONE hspec-discover 2.7.8 -> 2.8.3
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:14
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/MAJ port haskell (no need for aarch64)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE matterhorn 50200.12.0 -> 50200.13.0
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:14
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: FreeBSD/MAJ port haskell (no need for aarch64)
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* KILL Corriger problème d'adresse
DEADLINE: <2021-05-10 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:15
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: banque
:END:
CE metz. Mail aenvoyé à Paris (par erreur) et Mez le <2021-05-12 Wed>
* DONE Piano
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:16
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Maison/Vente
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE C5
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:16
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Maison/Vente
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Vendu, certificat de session signé
déclaration en ligne faite faite
* TODO Vérifier bruit de frottement
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:19
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Moto
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* TODO Révisions
* DONE Retendre la chaîne
DEADLINE: <2020-10-11 Sun>
* DONE Changer batterie
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:19
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Moto
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE TOD La chercher à Dafy le <2020-10-12 Mon> (attendre mail)
* DONE Changer clignotants
SCHEDULED: <2020-10-13 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:19
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Moto
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Prise male des nouveau clignotants ne correspond passage
Voir d'abord s'ils ont un modèle qui va bien => prise "universelle"
Donc on met une cosse male ronde de 4mm.
https://www.youtube.com/watch?v=wZOPN8jir48
Besoin d'arranger un peu la jonction...
* DONE Show currents tags
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:20
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Projets/tag-flac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Edit tags
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:20
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Projets/tag-flac
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* tag-flac
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:20
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Projets
:ARCHIVE_CATEGORY: todo
:END:
Edit tags like wdired, using this code https://www.emacswiki.org/emacs/tag.el adapted to metaflac
* Gymnastics :gym:
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:27
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_CATEGORY: todo
:END:
** HOLD Splits :daily:
:PROPERTIES:
:STYLE: habit
:LAST_REPEAT: [2020-06-01 Mon 14:28]
:END:
- State "DONE" from "TODO" [2020-06-01 Mon 14:28]
- State "DONE" from "TODO" [2020-05-29 Fri 00:00]
- State "DONE" from "TODO" [2020-05-28 Thu 00:35]
- State "DONE" from "TODO" [2020-05-26 Tue 00:28]
- State "DONE" from "TODO" [2020-05-22 Fri 00:28]
- State "DONE" from "TODO" [2020-05-20 Wed 00:56]
- State "DONE" from "TODO" [2020-05-17 Sun 22:15]
- State "DONE" from "TODO" [2020-05-16 Sat 22:15]
- State "DONE" from "TODO" [2020-05-13 Wed 22:15]
- State "DONE" from "TODO" [2020-05-12 Tue 22:15]
- State "DONE" from "TODO" [2020-05-10 Sun 22:38]
- State "DONE" from "TODO" [2020-05-09 Sat 22:38]
- State "DONE" from "TODO" [2020-05-08 Fri 00:25]
- State "DONE" from "TODO" [2020-05-04 Mon 00:22]
- State "DONE" from "TODO" [2020-05-03 Sun 00:22]
- State "DONE" from "TODO" [2020-05-02 Sat 00:22]
- State "DONE" from "TODO" [2020-04-27 Mon 00:22]
- State "DONE" from "TODO" [2020-04-26 Sun 00:22]
** TODO Handstand :daily:
SCHEDULED: <2021-04-14 Wed .+1d>
:PROPERTIES:
:STYLE: habit
:LAST_REPEAT: [2021-04-24 Sat 22:18]
:END:
- State "DONE" from "TODO" [2021-05-13 Thu 22:18]
- State "DONE" from "TODO" [2021-04-24 Sat 22:18]
- State "DONE" from "TODO" [2021-04-11 Sun 14:53]
- State "DONE" from "TODO" [2021-04-10 Sat 00:37]
- State "DONE" from "TODO" [2021-04-09 Fri 00:37]
- State "DONE" from "TODO" [2021-04-08 Thu 00:37]
- State "DONE" from "TODO" [2021-03-05 Fri 00:37]
- State "DONE" from "TODO" [2021-03-03 Wed 00:15]
- State "DONE" from "TODO" [2021-03-01 Mon 22:28]
- State "DONE" from "TODO" [2021-02-22 Mon 23:13]
- State "DONE" from "TODO" [2021-02-21 Sun 21:47]
- State "DONE" from "TODO" [2021-02-18 Thu 23:56]
- State "DONE" from "TODO" [2021-02-18 Thu 23:56]
- State "DONE" from "TODO" [2021-02-17 Wed 23:56]
- State "DONE" from "TODO" [2021-02-06 Sat 20:12]
- State "DONE" from "TODO" [2021-02-04 Thu 23:37]
- State "DONE" from "TODO" [2021-02-03 Wed 23:37]
- State "DONE" from "TODO" [2021-01-29 Fri 20:46]
- State "DONE" from "TODO" [2021-01-28 Thu 20:46]
- State "DONE" from "TODO" [2021-01-27 Wed 20:46]
- State "DONE" from "TODO" [2021-01-04 Mon 19:04]
- State "DONE" from "TODO" [2021-01-03 Sun 19:04]
- State "DONE" from "TODO" [2021-01-02 Sat 19:04]
- State "DONE" from "TODO" [2021-01-01 Fri 19:04]
- State "DONE" from "TODO" [2020-11-05 Thu 19:04]
- State "DONE" from "TODO" [2020-11-04 Mon 19:04]
- State "DONE" from "TODO" [2020-09-21 Mon 19:04]
- State "DONE" from "TODO" [2020-09-19 Sat 12:39]
- State "DONE" from "TODO" [2020-07-21 Tue 22:21]
- State "DONE" from "TODO" [2020-07-18 Sat 22:40]
- State "DONE" from "TODO" [2020-07-06 Mon 22:25]
- State "DONE" from "TODO" [2020-07-02 Thu 22:03]
- State "DONE" from "TODO" [2020-07-01 Wed 22:11]
- State "DONE" from "TODO" [2020-06-30 Tue 22:11]
- State "DONE" from "TODO" [2020-06-26 Fri 00:13]
- State "DONE" from "TODO" [2020-06-22 Mon 20:29]
- State "DONE" from "TODO" [2020-06-21 Sun 20:29]
- State "DONE" from "TODO" [2020-06-19 Fri 22:56]
- State "DONE" from "TODO" [2020-06-18 Thu 16:18]
- State "DONE" from "TODO" [2020-06-13 Sat 22:57]
- State "DONE" from "TODO" [2020-06-11 Thu 21:34]
- State "DONE" from "TODO" [2020-06-09 Tue 22:56]
- State "DONE" from "TODO" [2020-06-03 Wed 21:12]
- State "DONE" from "TODO" [2020-06-01 Mon 21:45]
- State "DONE" from "TODO" [2020-05-31 Sun 14:06]
- State "DONE" from "TODO" [2020-05-28 Thu 15:20]
- State "DONE" from "TODO" [2020-05-28 Thu 00:35]
- State "DONE" from "TODO" [2020-05-26 Tue 21:24]
- State "DONE" from "TODO" [2020-05-23 Sat 21:24]
- State "DONE" from "TODO" [2020-05-22 Fri 00:02]
- State "DONE" from "TODO" [2020-05-20 Wed 21:44]
- State "DONE" from "TODO" [2020-05-19 Tue 00:30]
- State "DONE" from "TODO" [2020-05-13 Wed 22:14]
- State "DONE" from "TODO" [2020-05-12 Tue 22:14]
- State "DONE" from "TODO" [2020-05-10 Sun 22:14]
- State "DONE" from "TODO" [2020-05-09 Sat 21:23]
- State "DONE" from "TODO" [2020-05-08 Fri 00:25]
- State "DONE" from "TODO" [2020-05-05 Tue 18:16]
- State "DONE" from "TODO" [2020-05-02 Sat 22:41]
- State "DONE" from "TODO" [2020-04-27 Mon 21:37]
- State "DONE" from "TODO" [2020-04-26 Sun 23:09]
- State "DONE" from "TODO" [2020-04-24 Fri 12:00]
- State "DONE" from "TODO" [2020-04-22 Wed 12:00]
- State "DONE" from "TODO" [2020-04-19 Sun 12:00]
- State "DONE" from "TODO" [2020-04-18 Sat 12:00]
- State "DONE" from "TODO" [2020-04-17 Fri 12:00]
- State "DONE" from "TODO" [2020-04-16 Thu 12:00]
- State "DONE" from "TODO" [2020-04-13 Mon 12:00]
- State "DONE" from "TODO" [2020-04-10 Fri 12:00]
- State "DONE" from "TODO" [2020-04-07 Tue 12:00]
- State "DONE" from "TODO" [2020-04-05 Sun 12:00]
- State "DONE" from "TODO" [2020-04-02 Thu 12:00]
- State "DONE" from "TODO" [2020-03-30 Mon 12:00]
- State "DONE" from "TODO" [2020-03-29 Sun 12:00]
- State "DONE" from "TODO" [2020-03-28 Sat 12:00]
- State "DONE" from "TODO" [2020-03-26 Thu 12:00]
- State "DONE" from "TODO" [2020-03-25 Wed 12:00]
- State "DONE" from "TODO" [2020-03-24 Tue 12:00]
- State "DONE" from "TODO" [2020-03-23 Mon 12:00]
- State "DONE" from "TODO" [2020-03-22 Sun 12:00]
- State "DONE" from "TODO" [2020-03-21 Sat 12:00]
- State "DONE" from "TODO" [2020-03-20 Fri 12:00]
- State "DONE" from "TODO" [2020-03-19 Thu 12:00]
- State "DONE" from "TODO" [2020-03-16 Mon 12:00]
- State "DONE" from "TODO" [2020-03-14 Sat 12:00]
- State "DONE" from "TODO" [2020-03-12 Thu 12:00]
- State "DONE" from "TODO" [2020-03-10 Tue 12:00]
- State "DONE" from "TODO" [2020-03-09 Mon 12:00]
- State "DONE" from "TODO" [2020-03-07 Sat 12:00]
- State "DONE" from "TODO" [2020-03-05 Thu 12:00]
- State "DONE" from "TODO" [2020-03-04 Wed 12:00]
- State "DONE" from "TODO" [2020-03-03 Tue 12:00]
- State "DONE" from "TODO" [2020-03-02 Mon 12:00]
- State "DONE" from "TODO" [2020-03-01 Sun 12:00]
- State "DONE" from "TODO" [2020-02-29 Sat 12:00]
- State "DONE" from "TODO" [2020-02-27 Thu 12:00]
- State "DONE" from "TODO" [2020-02-23 Sun 12:00]
- State "DONE" from "TODO" [2020-02-21 Fri 12:00]
- State "DONE" from "TODO" [2020-02-20 Thu 12:00]
- State "DONE" from "TODO" [2020-02-18 Tue 12:00]
- State "DONE" from "TODO" [2020-02-17 Mon 12:00]
- State "DONE" from "TODO" [2020-02-16 Sun 12:00]
- State "DONE" from "TODO" [2020-02-15 Sat 12:00]
- State "DONE" from "TODO" [2020-02-02 Sun 12:00]
- State "DONE" from "TODO" [2020-02-01 Sat 12:00]
- State "DONE" from "TODO" [2020-01-30 Thu 12:00]
- State "DONE" from "TODO" [2020-01-21 Tue 12:00]
- State "DONE" from "TODO" [2020-01-20 Mon 12:00]
- State "DONE" from "TODO" [2020-01-19 Sun 12:00]
- State "DONE" from "TODO" [2020-01-18 Sat 12:00]
- State "DONE" from "TODO" [2020-01-13 Mon 12:00]
- State "DONE" from "TODO" [2020-01-11 Sat 12:00]
- State "DONE" from "TODO" [2020-01-09 Thu 12:00]
- State "DONE" from "TODO" [2020-01-08 Wed 12:00]
- State "DONE" from "TODO" [2020-01-07 Tue 12:00]
- State "DONE" from "TODO" [2020-01-06 Mon 12:00]
- State "DONE" from "TODO" [2020-01-05 Sun 12:00]
- State "DONE" from "TODO" [2020-01-04 Sat 12:00]
- State "DONE" from "TODO" [2020-01-03 Fri 12:00]
- State "DONE" from "TODO" [2020-01-02 Thu 12:00]
** KILL Backflip on trampoline :daily:
:PROPERTIES:
:LAST_REPEAT: [2020-06-26 Fri 00:13]
:END:
- State "DONE" from "TODO" [2020-06-26 Fri 00:13]
- State "DONE" from "TODO" [2020-06-21 Sun 22:00]
- State "DONE" from "TODO" [2020-06-20 Sat 22:00]
- State "DONE" from "TODO" [2020-06-11 Thu 21:34]
- State "DONE" from "TODO" [2020-06-09 Tue 22:56]
- State "DONE" from "TODO" [2020-06-06 Sat 17:26]
- State "DONE" from "TODO" [2020-06-01 Mon 21:45]
- State "DONE" from "TODO" [2020-05-31 Sun 21:39]
- State "DONE" from "TODO" [2020-05-30 Sat 00:00]
- State "DONE" from "TODO" [2020-05-23 Sat 21:24]
- State "DONE" from "TODO" [2020-05-20 Wed 21:44]
- State "DONE" from "TODO" [2020-05-19 Tue 22:19]
- State "DONE" from "TODO" [2020-05-10 Sun 22:10]
- State "DONE" from "TODO" [2020-05-05 Tue 18:16]
- State "DONE" from "TODO" [2020-05-02 Sat 22:41]
- State "DONE" from "TODO" [2020-04-26 Sun 23:09]
- State "DONE" from "TODO" [2020-04-23 Thu 23:11]
- State "DONE" from "TODO" [2020-04-18 Sat 21:56]
- State "DONE" from "TODO" [2020-04-17 Fri 21:28]
- State "DONE" from "TODO" [2020-04-07 Tue 21:55]
- State "DONE" from "TODO" [2020-04-04 Sat 00:06]
- State "DONE" from "TODO" [2020-04-03 Fri 00:06]
- State "DONE" from "TODO" [2020-03-20 Fri 00:06]
- State "DONE" from "TODO" [2020-03-19 Thu 22:17]
- State "DONE" from "TODO" [2019-12-19 Thu 17:03]
- State "DONE" from "TODO" [2019-12-16 Mon 18:41]
- State "DONE" from "TODO" [2019-12-10 Tue 19:36]
- State "DONE" from "TODO" [2019-12-07 Sat 20:19]
- State "DONE" from "TODO" [2019-12-06 Fri 20:19]
- State "DONE" from "TODO" [2019-11-30 Sat 21:22]
- State "DONE" from "TODO" [2019-11-26 Tue 20:43]
- State "DONE" from "TODO" [2019-11-24 Sun 22:43]
- State "DONE" from "TODO" [2019-11-10 Sun 20:13]
- State "DONE" from "TODO" [2019-10-28 Mon 20:13]
- State "DONE" from "TODO" [2019-10-17 Thu 22:27]
- State "DONE" from "TODO" [2019-09-05 Thu 22:59]
- State "DONE" from "TODO" [2019-09-04 Wed 22:59]
- State "DONE" from "TODO" [2019-09-01 Sun 22:59]
- State "DONE" from "TODO" [2019-08-31 Sat 22:59]
- State "DONE" from "TODO" [2019-08-30 Fri 23:07]
- State "DONE" from "TODO" [2019-08-29 Thu 23:07]
- State "DONE" from "TODO" [2019-08-24 Sat 23:07]
- State "DONE" from "TODO" [2019-08-22 Thu 23:56]
- State "DONE" from "TODO" [2019-08-19 Mon 22:19]
- State "DONE" from "TODO" [2019-08-18 Sun 16:53]\\
On se rapproche de la verticale !
- State "DONE" from "TODO" [2019-08-15 Thu 23:04]
- State "DONE" from "TODO" [2019-08-09 Fri 22:15]
- State "DONE" from "TODO" [2019-08-08 Thu 22:20]
- State "DONE" from "TODO" [2019-08-07 Wed 22:20]
- State "DONE" from "TODO" [2019-08-06 Tue 21:52]
- State "DONE" from "TODO" [2019-07-13 Sat 23:02]
- State "DONE" from "TODO" [2019-07-12 Fri 22:34]
:LOGBOOK:
- State "DONE" from "TODO" [2019-07-10 Wed 22:26]
- State "DONE" from "TODO" [2019-07-09 Thu 13:10]
- State "DONE" from "TODO" [2019-07-04 Thu 13:10]
- State "DONE" from "TODO" [2019-07-03 Wed 13:10]
- State "DONE" from "TODO" [2019-06-16 Sun 13:10]
- State "DONE" from "TODO" [2019-06-15 Sat 13:10]
- State "DONE" from "TODO" [2019-06-12 Wed 22:41]
- State "DONE" from "TODO" [2019-06-07 Fri 00:53]
- State "DONE" from "TODO" [2019-05-30 Thu 00:53]
- State "DONE" from "TODO" [2019-05-28 Tue 00:53]
- State "DONE" from "TODO" [2019-05-27 Mon 00:53]
- State "DONE" from "TODO" [2019-05-25 Sat 22:05]
- State "DONE" from "TODO" [2019-05-01 Wed 16:39]
- State "DONE" from "TODO" [2019-05-25 Sat 13:11]
- State "DONE" from "TODO" [2019-05-24 Fri 13:11]
- State "DONE" from "TODO" [2019-05-23 Thu 13:11]
- State "DONE" from "TODO" [2019-05-21 Tue 13:11]
- State "DONE" from "TODO" [2019-05-20 Mon 13:11]
- State "DONE" from "TODO" [2019-05-16 Thu 13:11]
- State "DONE" from "TODO" [2019-05-15 Wed 13:11]
- State "DONE" from "TODO" [2019-04-23 Tue 16:17]
- State "DONE" from "TODO" [2019-02-03 Sun 18:01]
- State "DONE" from "TODO" [2018-11-13 Tue 14:54]
- State "DONE" from "TODO" [2018-11-11 Sun 12:17] \\
Backflips
- State "DONE" from "TODO" [2018-11-09 Fri 16:11] \\
Progression depuis le début avec vidéo. Pas trop mal. Front en bonne voie pour
la technique
- State "DONE" from "TODO" [2018-11-08 Thu 16:11] \\
Idem, juste 2min
- State "DONE" from "TODO" [2018-11-07 Wed 16:11] \\
:END:
2min, retour à la case 0
** KILL L-sit (grease the groove) :daily:
SCHEDULED: <2020-03-20 Fri .+1d>
:PROPERTIES:
:LAST_REPEAT: [2020-03-19 Thu 22:18]
:END:
* Moto
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 10:29
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_CATEGORY: todo
:END:
* DONE Porter wrapper poudriere avec Turtle
DEADLINE: <2021-09-06 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-06 Mon 19:08
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Haskell/Libraries/Shelly
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Branches distantes?
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-07 Tue 12:09
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Haskell/Darcs
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Darcs: push -f ?
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-07 Tue 12:09
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Haskell/Darcs
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* Darcs
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-07 Tue 12:09
:ARCHIVE_FILE: ~/code/blog/todo.org
:ARCHIVE_OLPATH: Haskell
:ARCHIVE_CATEGORY: todo
:END:
* DONE Completer [[file:posts/command-line-tips.org][file:/usr/home/alex/projects/blog/posts/command-line-tips.org]]
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-08 Wed 11:25
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Blog
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: blog
:END:
- ripgrep
- ripgrep-all
- fd : usable with emacs (fd-dired)
- fzf : usable with emacs (fd-dired) (less useful with doom as there is a recursive search)
** TODO Default application (archlinux)
Get the filetype with
xdg-mime query filetype ~/Books/test.pdf
Edit ~/.config/mimeapps.list
application/pdf=evince.deskop;
* KILL Repasser à hakyll
DEADLINE: <2021-09-06 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-08 Wed 11:25
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Blog
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: blog
:END:
Impossible d'avoir les metadata pour org
* DONE Porter avec Slick
DEADLINE: <2021-09-07 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-08 Wed 11:25
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Blog
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: blog
:END:
** DONE PR pour support org-mode
* DONE Shake 0.19.6
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-08 Wed 14:38
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Notes recherche médecine générale
DEADLINE: <2021-09-06 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-09 Thu 11:24
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Notes Dr Denomme-Pichon
DEADLINE: <2021-09-06 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-09 Thu 11:24
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE février 2021
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-09 Thu 12:11
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Lecture/Le monde diplomatique
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Envoyer procuration
DEADLINE: <2021-09-06 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-09 Thu 12:11
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Diagnostic
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-09 Thu 12:11
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Visite
** DONE Mail
DEADLINE: <2021-09-06 Mon>
** DONE Payer 350€
** DONE Rembourser le surplus à Aurélien, ELise
* DONE Envoyer colis de livres
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-09 Thu 12:11
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE git-annex 8.20210903
DEADLINE: <2021-09-06 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-12 Sun 22:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Mail Dr Denomme-Pichon
DEADLINE: <2021-09-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Mail référent génétique Nice
DEADLINE: <2021-09-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Mail référent biologie Montpellier
DEADLINE: <2021-09-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Mail référent biologie Marseille
DEADLINE: <2021-09-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Mail référent biologie Lyon
DEADLINE: <2021-09-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* KILL Mail référent biologie Nice
DEADLINE: <2021-09-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
* DONE Mail Dr Plutino (Nice)
DEADLINE: <2021-09-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Mail Luke Mansard (interne de bio + génétique à Montpellier)
DEADLINE: <2021-09-10 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Réunion Dr Plutino
DEADLINE: <2021-09-10 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Notes entretiens
DEADLINE: <2021-09-11 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-13 Mon 10:47
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* KILL Uploader canada avec casse corrigé à relire
DEADLINE: <2021-09-14 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-15 Wed 19:04
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: misc
:END:
* DONE Pourquoi ssh ne fonctionne pas sur le pi ?
DEADLINE: <2021-09-17 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-17 Fri 14:59
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
* HOLD Japanesepod101
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-30 Thu 13:18
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Japanese
:ARCHIVE_CATEGORY: japanese
:ARCHIVE_TODO: HOLD
:ARCHIVE_ITAGS: japanese
:END:
** DONE Beglnner S1 (170)
** DONE Beglnner S4
** TODO Upper beglnner S1
*** TODO Lire leçon
*** DONE Audio
** TODO Lower intermediate S1
*** TODO Audio [41/]
*** TODO PDF [8/]
* HOLD Another :daily:
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-30 Thu 13:18
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Japanese
:ARCHIVE_CATEGORY: japanese
:ARCHIVE_TODO: HOLD
:ARCHIVE_ITAGS: japanese
:END:
* DONE STRT Totono
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-30 Thu 13:18
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Japanese/Visual Novel
:ARCHIVE_CATEGORY: japanese
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japanese
:END:
Miyuki route, ~15h
* Ormolu
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-30 Thu 17:57
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:END:
* DONE Ormolu 0.3.0.0
DEADLINE: <2021-09-14 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-30 Thu 17:57
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE haskell-language-server 1.3.0.0
DEADLINE: <2021-09-18 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2021-09-30 Thu 17:57
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
- [X] build
- [X] update hls-install
- [X] poudre hls-install
- [ ] poudre hls
* DONE Remboursement turkish airlines
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-04 Mon 12:26
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres/Échange voyage japon été 2020
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE Demande fait pour 2 tickets le <2021-08-02 Mon>
Réponse reçue <2021-08-10 Tue> : demande de remboursement faite en ligne avec IBAN mais échec
** DONE Mail boursorama pour rembourement sur autre CB
DEADLINE: <2021-09-09 Thu>
** DONE Confirmer que le remboursement est possible à TK
DEADLINE: <2021-09-10 Fri>
* DONE Remboursement turkish airlines
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-04 Mon 12:26
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres/Échange voyage japon été 2020
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
** DONE Demande fait pour 2 tickets le <2021-08-02 Mon>
Réponse reçue <2021-08-10 Tue> : demande de remboursement faite en ligne avec IBAN mais échec
** DONE Mail boursorama pour rembourement sur autre CB
DEADLINE: <2021-09-09 Thu>
** DONE Confirmer que le remboursement est possible à TK
DEADLINE: <2021-09-10 Fri>
** DONE Mail envoyé pour demande remboursement
** DONE Envoyer procuration le <2021-09-08 Wed>
* DONE Reproduire erreur avec eglot et jump to definition
DEADLINE: <2021-09-14 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-04 Mon 12:26
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
* Visual Novel
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-04 Mon 15:37
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Japanese
:ARCHIVE_CATEGORY: japanese
:ARCHIVE_ITAGS: japanese
:END:
* DONE mars 2021
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-04 Mon 15:38
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Lecture/Le monde diplomatique
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Envoi chèque de caution par courrier
DEADLINE: <2021-10-04 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-12 Tue 11:43
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Logement
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Envoyer garant
DEADLINE: <2021-10-04 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-12 Tue 11:43
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Logement
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Envoyer bail
DEADLINE: <2021-10-04 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-12 Tue 11:43
:ARCHIVE_FILE: ~/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Logement
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Échange voyage japon été 2020
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-14 Thu 11:17
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Autres
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: misc
:END:
* DONE Tester hledger
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-14 Thu 11:17
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Banques
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Rules for csv
#+begin_src
sort sor
skip 1
separator ;
fields date,date2,description,category_, _, amount, _, _,account1, balance
comment category:%category_
account1 compte:boursorama
if Complémentaires santé
account2 dépenses:santé:mutuelle
if Carburant
account2 dépenses:voiture
if Alimentation
account2 dépenses:alimentation
#+end_src
* DONE PR pour push dans darcsum
DEADLINE: <2021-09-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-14 Thu 11:17
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Emacs
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Tester ebdb
DEADLINE: <2021-09-09 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-14 Thu 11:17
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Emacs
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* Emacs
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-14 Thu 11:17
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/todo.org
:ARCHIVE_CATEGORY: todo
:END:
* KILL Diagnostic électronique
:PROPERTIES:
:ARCHIVE_TIME: 2021-10-14 Thu 11:19
:ARCHIVE_FILE: /usr/home/alex/code/blog/notes/todo.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
Contexte: iphone branché sur prise jack avant de démarrer. Au moment de mettre le contact, aucun voyant d'allumé, impossible de démarrer.
5min après, de nouveau du courant et on peut redémarrer.
Plus de son via la prise jack.
Appel garage des Garennes => voir avec Mazda ou spécialiste en électronique
Mazda fermé jusque 23 août
** DONE RV le [2020-09-10 Thu]
Pas de souci électronique hormis la "plaque électrique" (GPS, radio). Demande de devis à Marseille
** KILL Attendre devis
DEADLINE: <2020-09-28 Mon>
# -*- mode: org -*-
Archived entries from file /home/alex/roam/personal/inbox.org
* DONE Scraper Lonely Planet
CLOSED: [2023-11-19 Sun 00:01] SCHEDULED: <2023-11-18 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-20 Mon 21:39
:ARCHIVE_FILE: ~/roam/personal/inbox.org
:ARCHIVE_CATEGORY: inbox
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: inbox
:END:
:LOGBOOK:
CLOCK: [2023-11-18 Sat 21:58]
:END:
/Entered on/ [2023-11-18 Sat 21:57]
# -*- mode: org -*-
Archived entries from file /home/alex/org/projects/bisonex.org
:PROPERTIES:
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: DONE
:END:
:PROPERTIES:
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: KILL
:END:
#+end_src
#+begin_src
#+end_src
#+begin_src
#+end_src
#+end_src
#+end_src
#+end_src
#+end_src
#+end_src
#+end_src
#+end_src
:PROPERTIES:
:END:
on est inférieur à Kumaran et al 2019
** KILL Regarder les FN (SNP)
CLOSED: [2023-03-13 lun. 15:55] SCHEDULED: <2023-03-04 Sat >
*** Manuel:
NC_000001.11:1385919 pas de read 1/1:FN:.:i1_5:INDEL:homalt:.
NC_000001.11:1623412 1 read 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1668449 33 read sur 160 voient l'allèle alternative 1/1:FN:am:ti:SNP:homalt:.
NC_000001.11:1676135 67 reads, non vu 0/1:FN:.:ti:SNP:het:.
NC_000001.11:1734812 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745808 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745814 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1953616 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:2512975 0/1:FN:.:ti:SNP:het:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
* KILL Comprendre/améliorer Recall SNP 0.855
CLOSED: [2023-03-13 lun. 15:55] SCHEDULED: <2023-03-04 Sat>
#+RESULTS:
: NC_000001.11: 448
: NC_000002.12: 307
: NC_000003.12: 228
: NC_000004.12: 175
: NC_000005.10: 237
: NC_000006.12: 1223
: NC_000007.14: 274
: NC_000008.11: 414
: NC_000009.12: 161
: NC_000010.11: 194
: NC_000011.10: 304
: NC_000012.12: 254
: NC_000013.11: 168
: NC_000014.9: 184
: NC_000015.10: 250
: NC_000016.10: 239
: NC_000017.11: 373
: NC_000018.10: 85
: NC_000019.10: 576
: NC_000020.11: 83
: NC_000021.9: 67
: NC_000022.11: 117
* KILL Awk
CLOSED: [2023-03-12 Sun 22:12]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
NB: awk car bcftools query ne semble pas prendre en compte les nouvelles colonnes
On confirnme le nombre de SNP:
❯ awk '!/^#/ && $10~/:FN:/ && $10~/SNP/' test-allchr.vcf | wc -l
6665
Une minorité concerne des problème d'haploides
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/' test-allchr.vcf
304
avec 1/3 où l'exome manque une allèles
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/ && $10~/homalt/' test-allchr.vcf | wc -l
101
et 2/3 où il y a une allèle "en trop"
La majorité ne sont pas vu
❯ awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/' test-allchr.vcf | wc -l
6361
Nombre de reads pour chaque position en bash (!)
#+begin_src bash
awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf | xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b
am {} | wc -l' > count.csv
function cleanCount(fname)
f = DataFrame(CSV.File(fname, header=false))
transform!(f, :Column1 => ByRow(x -> string.(split(x, ":"))[1]) => :chrom)
transform!(f, :Column1 => ByRow(x -> string.(split(x, "-"))[2]) => :pos)
select!(f, Not([:Column1]))
rename!(f, :Column2 => :nb)
end
f = cleanCount("count.csv")
grouped = groupby(f, :chrom)
for (k, g) in pairs(grouped)
println("$(k.chrom): $(size(g, 1))")
end
(4430, 2)
#+begin_src julia
using CSV, DataFrames
* KILL Répartition par chromosome: variable mais seul le 6 = hotspot
CLOSED: [2023-03-07 Tue 22:44]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
#+begin_src julia
using CSV, DataFrames
f = DataFrame(CSV.File("count.csv", header=false))
size(f[f.Column2 .< 10,:])
1: 448 reads, 64 not in exons
2: 307 reads, 47 not in exons
3: 228 reads, 37 not in exons
4: 175 reads, 28 not in exons
5: 237 reads, 38 not in exons
6: 1223 reads, 304 not in exons
7: 274 reads, 52 not in exons
8: 414 reads, 41 not in exons
9: 161 reads, 47 not in exons
10: 194 reads, 37 not in exons
11: 304 reads, 39 not in exons
12: 254 reads, 32 not in exons
13: 168 reads, 120 not in exons
14: 184 reads, 26 not in exons
15: 250 reads, 90 not in exons
16: 239 reads, 29 not in exons
17: 373 reads, 35 not in exons
18: 85 reads, 17 not in exons
19: 576 reads, 46 not in exons
20: 83 reads, 22 not in exons
21: 67 reads, 14 not in exons
22: 117 reads, 24 not in exons
reads = groupedCount("../NA12878/happy/count.csv")
exons = groupedExons("exons.csv")
for g in range(1, size(reads)[1])
local found
found = transform(reads[g], :pos => ByRow(x -> isExon(x, exons, g)) => :exon)
readsMissing = found[ismissing.(found.exon), :]
# print("$(k.chrom):")
print(g)
print(": $(size(reads[g])[1]) reads, ")
println("$(size(readsMissing)[1]) not in exons")
end
function groupedExons(fname)
f = DataFrame(CSV.File(fname, header=["chrom", "start", "end"], delim="\t"))
transform!(f, [:start, :end] => ByRow((x,y) -> Interval(x, y)) => :interval)
select!(f, Not([:start, :end]))
groupby(f, :chrom)
end
# Check is position x is in exons for chromosome chr
function isExon(x, exons, chr)
# Remove duplicates
exonsU = unique(exons[chr])
res = transform(exonsU, :interval => ByRow(z -> x in z) => :check)
# Result only found interval
found = res[res.check,:].interval
isempty(found) ? missing : first(found)
end
function groupedCount(fname)
f = DataFrame(CSV.File(fname, header=false))
transform!(f, :Column1 => ByRow(x -> string.(split(x, ":"))[1]) => :chrom)
transform!(f, :Column1 => ByRow(x -> parse(Int64, string.(split(x, "-"))[2])) => :pos)
select!(f, Not([:Column1]))
rename!(f, :Column2 => :nb)
groupby(f, :chrom)
end
# Check the number of reads for each false negative (stored in count.csv)
# from hap.py output:
# awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf | xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b am {} | wc -l' > count.csv
#+begin_src julia
using CSV, DataFrames, Intervals
SNP: false negative 6665
SNP: not seen 6361
SNP: missing allel 101
SNP: surnumeraries allel 203
1. On confirme le nombre de SNP.
2. Une minorité concerne des problème d'haploides avec
- 1/3 où l'exome manque une allèles
- 2/3 où il y a une allèle "en trop"
3. La majorité ne sont pas vu (6361)
Nombre de reads pour chaque position en bash (!)
#+begin_src bash
awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf | xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b
am {} | wc -l' > count.csv
* KILL Reads en dehors des exons
CLOSED: [2023-03-09 Thu 22:43]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
Ça a l'air sur des exemples simples ...
#+begin_src sh
wget https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz
awk '/BestRefSeq\texon/ && /transcript_id=NM/ {print $1"\t"$4"\t"$5;}' GRCh38_latest_genomic.gff | grep ^NC | save exons.csv
* KILL Julia
CLOSED: [2023-03-13 lun. 11:11]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:52
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
Conflict BAM et vcf
#+begin_src julia
using GeneticVariation
reader = VCF.Reader(open("../out/test-bed/test-allchr.vcf", "r"))
fn = 0
notSeen = 0
missingAllel = 0
surnumAllel = 0
for record in reader
global fn, notSeen
global missingAllel, surnumAllel
if VCF.genotype(record)[1][2] == "FN" && VCF.genotype(record)[1][5] == "SNP"
# println(record)
# println("$(VCF.chrom(record)) $(VCF.pos(record))")
fn = fn +1
if VCF.genotype(record)[2][5] == "NOCALL"
notSeen = notSeen + 1
else
if VCF.genotype(record)[1][6] == "homalt"
missingAllel = missingAllel + 1
elseif VCF.genotype(record)[2][6] == "homalt"
surnumAllel = surnumAllel + 1
end
end
end
end
close(reader)
println("SNP: false negative $fn")
println("SNP: not seen $notSeen")
println("SNP: missing allel $missingAllel")
println("SNP: surnumeraries allel $surnumAllel")
Nombre de reads pour chaque position en bash (!)
#+begin_src bash
awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf | xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b
am {} | wc -l' > count.csv
La majorité ne sont pas vu
❯ awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/' test-allchr.vcf | wc -l
6361
On confirnme le nombre de SNP:
❯ awk '!/^#/ && $10~/:FN:/ && $10~/SNP/' test-allchr.vcf | wc -l
6665
Une minorité concerne des problème d'haploides
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/' test-allchr.vcf
304
avec 1/3 où l'exome manque une allèles
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/ && $10~/homalt/' test-allchr.vcf | wc -l
101
et 2/3 où il y a une allèle "en trop"
* DONE Awk
CLOSED: [2023-03-12 Sun 22:12]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-12 Sun 22:19
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: DONE
:END:
NB: awk car bcftools query ne semble pas prendre en compte les nouvelles colonnes
Écheck sur
$ HCDIR=build/bin bash src/sh/run_hapenum_test.sh
Traceback (most recent call last):
File "build/bin/hap.py", line 26, in <module>
import pysam
File "/nix/store/3w2v5cl4x6ddq4281awcab9412r5gkaw-python3-3.10.9-env/lib/python3.10/site-packages/pysam/__init__.py", line 4, in <module>
from pysam.libchtslib import *
ImportError: No module named libchtslib
IL faut commenter detect var
# OK !
HCDIR=build/bin build/bin/test_haplotypes
# OK !
bash src/sh/make_hg19.sh
HCDIR=build/bin HG19=hg19.fa bash src/sh/run_multimer
ge_test.sh
On lance donc les tests à la main (trop d'erreurs sur les chemins)
nix develop .#hap-py
$ genericBuild
Mais problème de proxy
*** KILL Dérivation nix pour modules python
CLOSED: [2022-12-11 Sun 11:09]
*** KILL Lancer sarek en mode test
CLOSED: [2022-12-11 Sun 11:09]
#+begin_src sh
nix-shell -p python310Packages.pyyaml --run "nextflow run nf-core/sarek -profile test --executor slurm --queue smp --outdir test -resume"
#+end_src
*** KILL Lancer sarek sur données allégées
CLOSED: [2022-12-11 Sun 11:09]
* DONE Essai 1
CLOSED: [2023-02-13 Mon 11:50]
:PROPERTIES:
:ARCHIVE_TIME: 2023-02-14 Tue 10:42
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_OLPATH: Nouveau workflow/Dépendences avec Nix/hap.py/Faire fonctionner Tests
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: DONE
:END:
Problème avec chemin python pour pysam : Tools/__init__.py échoue mais on peut utilise build/bin/hap.py
If you feel that permissions on this path are set incorrectly, you can manually
change them by executing
$ sudo chown 1696:513 /Home/Users/apraga/.conda/pkgs/urls.txt
#+end_quote
Corrigé avec
#+begin_src sh
chown 1696:513 /Home/Users/apraga/.conda/pkgs/urls.txt
Voir https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04407-x
** KILL GATK
CLOSED: [2022 -11-11 Fri 20:01]
https://broadinstitute.github.io/warp/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README
A priori, respecte les bonnes pratiques
** KILL Essayer snmake avec bonne pratiques
https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/main/.github/workflows/main.yml
Installer Mamba (micromamba ne fonctionne pas sous nix)
Ne fonctionne pas sous WSL2... MultiQC n’est pas assez à jour
Problèmes de versions...
** KILL Sarek
CLOSED: [2022-12-11 Sun 11:09]
*** Dépendences
**** Nix
#+begin_src sh
nix profile install nixpkgs#mosdepth nixpkgs#python3
nix-shell -p python310Packages.pyyaml --run "nextflow run nf-core/sarek -profile test --executor slurm --queue smp --outdir test -resume"
#+end_src
***** KILL derivation nix pour profile complet
CLOSED: [2022-12-11 Sun 11:09]
**** KILL Sans nix
CLOSED: [2022-09-24 Sat 10:20]
On utilise conda
#+begin_src sh
module unload nix
module load anaconda3@2021.05/gcc-12.1.0
module load nextflow@22.04.0/gcc-12.1.0
module load openjdk@11.0.14.1_1/gcc-12.1.0
nextflow run nf-core/sarek -profile conda,test --executor slurm --queue smp --outdir test -resume
#+end_src
Essai 1: erreurs de permissions, corrigé en relancant le programme
#+begin_quote
Failed to create Conda environment
command: conda create --mkdir --yes --quiet --prefix /Work/Users/apraga/test-sarek/work/conda/env-2d53b1db50de676670cf1a91ef0cf6db bioconda::tabix=1.11
status : 1
message:
NotWritableError: The current user does not have write permissions to a required path.
path: /Home/Users/apraga/.conda/pkgs/urls.txt
uid: 1696
gid: 513
:ARCHIVE_TIME: 2023-01-15 Sun 12:03
:ARCHIVE_FILE: ~/org/projects/bisonex.org
* KILL Implémenter d’autres pipeline
CLOSED: [2023-01-15 Sun 12:03]
** DONE BAM
CLOSED: [2023-01-12 Thu 15:47]
picard ValidateSamFile
On regarde juste le code d'erreur (0 = pas d'erreur)
** DONE Fastq
CLOSED: [2023-01-12 Thu 15:48]
fastqc
Il faut ensuite extraire les zip and chercher les erreur dedans
:ARCHIVE_OLPATH: Données
:ARCHIVE_TIME: 2023-01-12 Thu 15:48
* DONE Vérifier qualité données sur mesocentre
CLOSED: [2023-01-12 Thu 15:48]
* Internat
:PROPERTIES:
:CATEGORY: internat
:END:
* Recherche
:PROPERTIES:
:CATEGORY: recherche
:END:
** WDR45
:PROPERTIES:
:CATEGORY: wdr45
:END:
Envoyé <2022-07-22 Fri>
Pas de réponse
*** DONE Donner la réponse à Chloé + Patricia Fergelot
*** TODO appel à collaboration avec Chloé
**** WAIT Questionnaire
***** DONE v0.1
CLOSED: [2022-12-03 Sat 12:35] SCHEDULED: <2022-10-01 Sat>
SCHEDULED: <2022-08-06 Sat>
*** DONE Mail Dr Adang pour détails collaboration
*** DONE Visio Julien Theveno
CLOSED: [2023-07-21 Fri 17:54] DEADLINE: <2023-07-21 Fri>
- pas en clinique mais soit Auragen, soit labo de cyto (Pr Coutton) pour avoir un stage de labo
- Ok pour accueillir mai 2024
- thématique
- bioinformatique avec projet à définir sur des améliorations non urgentes +/- publi
- soit appel de variants difficile
- soit bionano (en cours)
- diagnostic : 2-3 génomes à lire par semaine
- préciser le sujet avec bioinformaticienne (Virgine ??)
- nombreuses demandes d'interCHU au semestre dernier mais personne pour les 2 prochains (interprétation ailleurs)
- se déroulera au CHU de grenoble (pôle mère-enfant) dans tous les cas
*Julien Thevenon non disponible en août*
2 stages à Lyon pour Auragen =
- interprétation onco
Grenoble = la partie bioinfo
*** DONE Mail coordonateur DES biologie médicale Grenoble pour préciser
CLOSED: [2023-07-21 Fri 17:54] SCHEDULED: <2023-07-21 Fri>
**** DONE Lettre de recommandation Paul
CLOSED: [2023-09-10 Sun 22:38]
*** TODO Vision Julien Thevenon Virginie ?? (bionfo)
/Entered on/ [2023-09-20 Wed 22:15]
Confirmé <2023-10-04 Wed>
**** DONE Informations complémentaires Julien Thevenon
CLOSED: [2023-10-01 Sun 14:49] SCHEDULED: <2023-09-26 Tue>
*** DONE Envoyer dossier Anais et Luna
CLOSED: [2023-10-04 Wed 19:35] SCHEDULED: <2023-10-04 Wed>
*** DONE Envoyer dossier à Mme Lucet à Grenoble
CLOSED: [2023-10-04 Wed 19:35] SCHEDULED: <2023-10-05 Thu>
Confirmé <2023-10-04 Wed>
/Entered on/ [2023-11-05 Sun 11:41]
** Logement trevenans :trevenans:
Attente décision
*** DONE Envoyer état des lieux
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
*** DONE Envoyer papiers : clé, wifi, autorisation accès
CLOSED: [2023-11-05 Sun 15:10] SCHEDULED: <2023-11-05 Sun>
/Entered on/ [2023-11-05 Sun 14:55]
/Entered on/ [2023-11-05 Sun 14:56]
Appel 2023-11-03: ouverture nouvelle ligne dans 9 jours
RV demain
/Entered on/ [2023-11-19 Sun 22:40]
** DONE Inscription fac 2023
SCHEDULED: <2023-11-23 Thu>
*** TODO Réparer frigo
Mail envoyé 2023-12-04
/Entered on/ [2023-12-04 Mon 20:40]
SCHEDULED: <2023-12-21 Thu>
*** DONE Mail Mme Ossajedi poubelles
CLOSED: [2023-11-21 Tue 22:53] SCHEDULED: <2023-11-27 Mon>
**** DONE Attestation box ?
CLOSED: [2023-11-30 Thu 19:15] SCHEDULED: <2023-11-28 Tue>
*** DONE Résilier ancien contrat :internet:
CLOSED: [2023-11-30 Thu 19:15] SCHEDULED: <2023-11-27 Mon>
*** DONE Demander pour ouverture de ligne
CLOSED: [2023-11-20 Mon 18:28] SCHEDULED: <2023-11-20 Mon>
*** DONE Assurance habitation: envoyé
CLOSED: [2023-11-08 Wed 19:19] SCHEDULED: <2023-11-12 Sun>
*** DONE Mail rapporteur
CLOSED: [2023-11-08 Wed 19:03] SCHEDULED: <2023-11-06 Mon>
*** DONE Envoyer mail syndicat des internes
CLOSED: [2023-11-08 Wed 19:03] SCHEDULED: <2023-11-03 Fri>
*** DONE Envoyer dossier complet avec signature à Besançon
CLOSED: [2023-10-01 Sun 21:10]
**** DONE Faire signer la feuille par Quentin
CLOSED: [2023-09-11 Mon 19:14] SCHEDULED: <2023-09-10 Sun>
**** DONE Faire signer la feuille par Julien
CLOSED: [2023-09-13 Wed 22:57] SCHEDULED: <2023-09-10 Sun>
**** KILL Faire signer la feuille par la fac
CLOSED: [2023-09-20 Wed 22:15] SCHEDULED: <2023-09-18 Mon>
**** DONE Lettre de motivation
CLOSED: [2023-10-01 Sun 20:54] SCHEDULED: <2023-09-24 Sun>
**** DONE Projet "~/documents/interchu-grenoble-projet.tex"
CLOSED: [2023-10-01 Sun 20:54] SCHEDULED: <2023-09-24 Sun>
/Entered on/ [2023-11-10 Fri 16:58]
*** DONE CVEC
CLOSED: [2023-11-18 Sat 11:43]
* Japonais
:PROPERTIES:
:CATEGORY: japonais
:END:
** TODO Intermediate japanase (Kluemper)
:PROPERTIES:
:STYLE: habit
:END:
- State "DONE" from "TODO" [2023-11-20 Mon 21:45]
- State "DONE" from "TODO" [2023-11-19 Sun 22:39]
* Maison
:PROPERTIES:
:CATEGORY: maison
:END:
** Serveur
:PROPERTIES:
:CATEGORY: serveur
:END:
*** Seedbox
:PROPERTIES:
:CATEGORY: seedbox
:END:
**** TODO Re-partager musique :red:
**** TODO Re-partager livres :mam:
* Moto
:PROPERTIES:
:CATEGORY: moto
:END:
* Programmation :cs:
** Gentoo :gentoo:
*** GURU :guru:
**** DONE Ebuild pour adapteur wifi TBW-108B
CLOSED: [2023-05-22 Mon 22:50]
Sur branche dev
**** DONE net-wireless/rtl8723bu: migration to linux-mod-r1.eclass
CLOSED: [2023-07-02 Sun 11:13] SCHEDULED: <2023-07-02 Sun>
**** DONE Ebuild hut
CLOSED: [2023-07-02 Sun 10:57]
sur dev
*** TODO Article nzbget sur wiki
/Entered on/ [2022-10-22 Sat 17:31]
** Learning Haskell :haskell:
*** [#A] [[https://www.reddit.com/r/haskell/comments/npxfba/comment/h084wwa/?utm_source=share&utm_medium=web2x&context=3][Reddit suggestion]]]
**** Learn Foundational building blocks
- [X] [[https://mmhaskell.com/monads/functors][Functor]]
- [X] [[https://mmhaskell.com/monads/applicatives][Applicatives]]
- [X] [[https://mmhaskell.com/monads/tutorial][Monads]]
- [X] [[https://mmhaskell.com/monads/reader-writer][Reader, writer]]
- [X] [[https://mmhaskell.com/monads/state][State]]
- [X] [[https://mmhaskell.com/monads/transformers][Transformers]]
- [ ] [[https://mmhaskell.com/monads/laws][Laws]]
**** Real-world example
***** STRT Look at the example
- [X] Database
- [ ] API
***** Relax for a few days and watch how interactive programs are being composed
***** Get back to the real-world example and make it a complete Cabal project.
***** [[https://mmhaskell.com/testing/test-driven-development][Testing]]
**** [#A] Best resource : [[https://downloads.haskell.org/~ghc/8.10.4/docs/html/users_guide/glasgow_exts.html#language-options][Language Reference]]
whenever you see an unknown language extension or a compilation flag, look it up in Language Reference and try to understand it. You don't have to fully understand them though, just read about them and keep them on your mind. One day they will begin to automatically click into a sound set of concepts.
Language Reference is one of the most underappreciated sources of information (it's almost universally overlooked in language communities - it was the case for Python, and I find it to be true for Haskell as well). You mentioned that you don't like REPL examples, and neither do I. Luckily, the User Guide/Reference has introductory sections for people like us. Once I knew how to compile a single file and to run it, the rest was just a matter of getting to know things by their name in a new ecosystem.
**** DONE Learn to compose things
When you already know how to compile and run single-module interactive console programs, it takes about a day to understand basics of Cabal, and about a week to learn about input parsing and output formatting. Do you need CLI args? Use optparse-applicative. Env vars? Use envy. JSON? Use aeson and a cheatsheet. Don't think about performance and/or API conventions, that's not what you should be concerned of at this point, as you are just learning to compose things together from individual parts.
**** Experiment with various libraires, read haskell planetarium
At this point you have enough knowledge to begin experimenting with various libraries and APIs. Learn how to use Hoogle, and read as much as you can/want on Haskell Planetarium.
*** KILL Learn Haskell for your greater good
:PROPERTIES:
:CUSTOM_ID: kill-learn-haskell-for-your-greater-good
:END:
50%
*** HOLD [[books.org::Haskell%20Programming%20From%20First%20Principles][Haskell programming from first principles]]
*** TODO 24 days of haskell
**** TODO <[Hackage 2015]> - "https://conscientiousprogrammer.com/blog/2015/11/30/haskell-tidbits-24-days-of-hackage-2015-day-1-introduction-and-stack/"
**** TODO <[GHC extensions]> - "https://blog.ocharles.org.uk/pages/2014-12-01-24-days-of-ghc-extensions.html"
*** STRT <[Hackage 2012]> - https://blog.ocharles.org.uk/pages/2012-12-01-24-days-of-hackage.html
-> postgresql
*** TODO <[Hackage 2013]> - https://blog.ocharles.org.uk/pages/2013-12-01-24-days-of-hackage.html
*** GHC
**** GHC commentary
Notamment Ollie Charles's 24 days of GHC Extensions,
**** Lire [[https://www.aosabook.org/en/ghc.html]]
*** Vidéos
**** STRT https://www.youtube.com/watch?v=re96UgMk6GQ
*** Articles historiques
1. [[https://watermark.silverchair.com/320098.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAsYwggLCBgkqhkiG9w0BBwagggKzMIICrwIBADCCAqgGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMHXfjdjwhGI2t4bLLAgEQgIICeQjZ-I8gmuaFqBktP4IOifHODtMAHcNF_LwRYyq7NswQ7vT6LJho9P_junCAORLGMV9dgq9JMePH2PFKNxXxrEP1VY7rIDG0gzoeObSkgMDn4MXalrIxD3ejY8vsGYy6vce8Kh70J_UJ8RamO1l3BNNUzy2W6VRaa_cMQr_ekdwcz0oihz0BVKn_bgm_8DjiiPhzj8uU9flVhi13t_oIFA6b3At2QMmPe7Z9OyfLkXivKkmKKNoHwSS7AnTIYAKCO383e4kG6NzZ_elai-XMAJs2Nk0vcgaltld1KeaW3269104DdIlFGevJUVNgwE_4LIheSYRZr9Gr0yRR6TROxdsyxrmgQ22Pzxxpnl8-KdjkW6aRSCKNk_yb5hYcPoRa3ldc5yPV15j8i4t9Mv4U_mBwmIRtMIKPdEHeMvcRx6c8_8uT4RV2esuOPfZlA05bzBgJhMS87M8myxisH-exkTMkm58o6nzHf1lGxzn_JS1VSHbhJCUl82ubzzOWjvl3QJM_vv805XTbn_G-fcRi0d9EQIRTqoObWVFyXW-pz16bWoZPZnBQ1gOmc3hPTGBMZjFR6p9VEAO7bKcK8o0yQDjVWEELNwfAAHc-oF_wLiEjXDNBoUttghgQzzvymKY_jSZhcU8TraVu2i551fpuDNEjSJd0qY5Rg3J6eWU550nJmnoWmX6o7KGiYp0vVMfOoFYXJ1trZWSGoRhDQP2LOLIOt3t2idlj6kV_MoCY3BRnkbxf4XIH7gLJf6Dky6hXFbTU8Fjsn8XHBeKSmaAYJ-sbmGB_BdZO8hHyvHvPv0lTtGcSuKywoJhMbblXRzyuacj_6mZQl5j3tAWhy][Why functional programming matters]]
Très lisible
2. [[https://dl.acm.org/doi/pdf/10.1145/91556.91592][Comprehending monads]]
Introduction du concept
3. [[https://dl.acm.org/doi/pdf/10.1145/158511.158524][Imperative functional programming]]
Application des monads poru résoudre le problème IO
** Julia
:PROPERTIES:
:CATEGORY: julia
:END:
*** TODO Juliacon 2023
:PROPERTIES:
:ID: 42f6a7bf-ac90-4737-884e-c35187776a4c
:END:
- [ ] <[Graphs, matrices]> - <yt-play "X2JEWdCFf70">
- [ ] <[Alan, julia and climate]> - <yt-play "SclkiqCn4Cs">
- [ ] <[Sherlocks Homes, mathematics and julia]> - <yt-play "zX-U6-6Prso">
- [ ] <[Sound synthesis]> - <yt-play "SvnDr9nnOZs">
- [ ] <[JuMP by example]> - <yt-play "rIan_XbYyaM">
- [ ] <[neurophysiological symbolic modeling]> - <yt-play "qC6tzsn8Uxc">
- [ ] <yt-play "ipDCx174Qkw">
- [ ] <yt-play "hKa2eTeb_lo">
- [ ] <yt-play "4omFGfcvvOY">
- [ ] <yt-play "d7SA36kVaq0">
- [ ] <yt-play "5uF3VqgjiVE">
- [ ] <yt-play "jIuRXzo4m38">
- [ ] <yt-play "iUarLpmZmco">
- [ ] <yt-play "WVT9wJegC6Q">
- [ ] <yt-play "ZVvP7rAIvkE">
- [ ] <yt-play "RXjjTQffen0">
- [ ] <yt-play "TpyHGaCB8P4">
- [ ] <yt-play "ksh-CNM2YJU">
- [ ] <yt-play "_sZdWVZeKqI">
- [ ] <yt-play "_Y6mNrN7eWA">
- [ ] <yt-play "tnw_BI2tRaA">
- [ ] <yt-play "qgmgg_Bzgyg">
- [ ] <yt-play "Nlq3J7PCB_Q">
- [ ] <yt-play "ruxYAY5_bfE">
- [X] <[Biomakie.jl]> - <yt-play "-C7Zbh6UTgk">
- [X] <[machine learing for biological data]> - <yt-play "Q9eYgwvJfWE">
- [X] <[Genomic analysis]> - <yt-play "egWrDz6RDRs">
- [ ] <[MRI denoising]> - <yt-play "dOsuIBUUDc4">
- [ ] <[modeling neural control circuit]> - <yt-play "f2XVrDoF35A">
- [ ] <[earth system software]> - <yt-play "O2rANteGTTY">
- [ ] <[fracture]> - <yt-play "6zt-TEUuMu8">
- [ ] <[fluid dynamic]> - <yt-play "R9b1xiqQtC8">
- [ ] <[Parquet]> - <yt-play "-QRacAGsxOI">
- [ ] <[pipeline]> - <yt-play "ECERq8BHvn4">
**** TODO Convertir FLAC en mp3 V0 et 320
#+begin_src sh
perl ~/softwares/flac2mp3/flac2mp3.pl --preset=320 test test320
#+end_src
***** DONE Jacques Amade
CLOSED: [2023-11-26 Sun 19:13]
/Entered on/ [2023-12-02 Sat 11:58]
** DONE Renvoyer équipements box
CLOSED: [2023-12-03 Sun 23:19] SCHEDULED: <2023-12-02 Sat>
SCHEDULED: <2023-12-24 Sun>
**** DONE Tester 1 album RED
CLOSED: [2023-12-17 Sun 22:52] SCHEDULED: <2023-12-17 Sun>
SCHEDULED: <2023-12-24 Sun>
- State "DONE" from "TODO" [2023-11-24 Fri 22:13]
- State "DONE" from "TODO" [2023-11-26 Sun 22:13]
- State "DONE" from "TODO" [2023-12-05 Tue 23:16]
- State "DONE" from "TODO" [2023-12-11 Mon 23:16]
- State "DONE" from "TODO" [2023-12-10 Sun 23:16]
- State "DONE" from "TODO" [2023-12-08 Fri 23:16]
- State "DONE" from "TODO" [2023-11-25 Sat 22:13]
- State "DONE" from "TODO" [2023-12-07 Thu 23:16]
- State "DONE" from "TODO" [2023-12-06 Wed 23:16]
- State "DONE" from "TODO" [2023-11-29 Wed 23:16]
- State "DONE" from "TODO" [2023-12-03 Sun 23:16]
- State "DONE" from "TODO" [2023-12-02 Sat 23:16]
- State "DONE" from "TODO" [2023-11-23 Thu 22:13]
- State "DONE" from "TODO" [2023-11-22 Wed 21:33]
- State "DONE" from "TODO" [2023-11-21 Tue 21:45]
- State "DONE" from "TODO" [2023-11-28 Tue 22:31]
- State "DONE" from "TODO" [2023-11-27 Mon 22:31]
- State "DONE" from "TODO" [2023-12-01 Fri 23:16]
:LAST_REPEAT: [2023-12-07 Thu 23:47]
SCHEDULED: [2023-12-12 Tue .+1d]
*** DONE UFR santé: mail envoyé car inscription impossible
CLOSED: [2023-11-22 Wed 20:41] SCHEDULED: <2023-11-22 Wed>
** DONE Demande remboursement essence formation IH
CLOSED: [2023-11-25 Sat 11:26] SCHEDULED: <2023-11-24 Fri>
/Entered on/ [2023-11-23 Thu 22:56]
- EFS: non
- CHU : renvoie vers trevenans
** Hémato
:PROPERTIES:
:CATEGORY: hemato
:END:
*** TODO Cours UNESS
**** DONE Examens d'hémostase
CLOSED: [2023-11-26 Sun 20:50] SCHEDULED: <2023-11-25 Sat 19:00>
/Entered on/ [2023-12-17 Sun 22:04]
**** DONE Cours myélome
CLOSED: [2023-12-17 Sun 22:34] SCHEDULED: <2023-12-17 Sun>
*** DONE Dossier à compléter
CLOSED: [2023-10-01 Sun 20:54]
- extraction ADN séquencage
:END:
** InterCHU Grenoble mai 2024
:PROPERTIES:
:CATEGORY: interchu
* Voiture :voiture:
** Mazda 5
*** Notes
- Plaquettes : arrière gauche ok (50%) le <2022-09-03 Sat>
- besoin d'une clé 14 pour changer les plaquettes
* Gentoo
:PROPERTIES:
:CATEGORY: gentoo
:END:
/Entered on/ [2023-12-13 Wed 23:25]
** DONE Page nushell
CLOSED: [2023-12-15 Fri 18:34] SCHEDULED: <2023-12-15 Fri>
/Entered on/ [2023-12-15 Fri 17:19]
** DONE Ebuild julia 1.9.4
CLOSED: [2023-12-16 Sat 22:16] SCHEDULED: <2023-12-15 Fri>
/Entered on/ [2023-12-15 Fri 18:40]
1. Ne peut pas installer une version "custom" LLVM pour problème de droit
(voir /var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/deps/scratch/llvm-julia-14.0.6-3/build_Release/cmake_install.cmake)
bindings/ocaml/cmake_install.cmake:47 (include)
cmake_install.cmake:76 (include)
* ACCESS DENIED: unlink: /usr/lib64/ocaml/llvm/llvm.mli
* ACCESS DENIED: open_wr: /usr/lib64/ocaml/llvm/llvm.mli
* ACCESS DENIED: unlink: /usr/lib64/ocaml/llvm/llvm.mli
* ACCESS DENIED: fopen_wr: /usr/lib64/ocaml/llvm/llvm.mli
CMake Error at bindings/ocaml/llvm/cmake_install.cmake:54 (file):
file INSTALL cannot copy file
"/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/deps/scratch/llvm-julia-14.0.6-3/build_Release/bindings/ocaml/llvm/llvm.mli"
to "/usr/lib64/ocaml/llvm/llvm.mli": Permission denied.
Call Stack (most recent call first):
bindings/ocaml/cmake_install.cmake:47 (include)
cmake_install.cmake:76 (include)
make[1]: *** [/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/deps/llvm.mk:279: /var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr-staging/llvm-julia-14.0.6-3/build_Release.tar] Error 1
make[1]: Leaving directory '/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/deps'
make: *** [Makefile:62: julia-deps] Error 2
* ERROR: dev-lang/julia-1.9.4::gentoo failed (compile phase):
* emake failed
*
* If you need support, post the output of `emerge --info '=dev-lang/julia-1.9.4::gentoo'`,
* the complete build log and the output of `emerge -pqv '=dev-lang/julia-1.9.4::gentoo'`.
* The complete build log is located at '/var/tmp/portage/dev-lang/julia-1.9.4/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/dev-lang/julia-1.9.4/temp/environment'.
* Working directory: '/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4'
* S: '/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4'
* ----------------------- SANDBOX ACCESS VIOLATION SUMMARY -----------------------
* LOG FILE: "/var/tmp/portage/dev-lang/julia-1.9.4/temp/sandbox.log"
*
#+begin_quote
VERSION 1.0
FORMAT: F - Function called
FORMAT: S - Access Status
FORMAT: P - Path as passed to function
FORMAT: A - Absolute Path (not canonical)
FORMAT: R - Canonical Path
FORMAT: C - Command Line
F: unlink
S: deny
P: /usr/lib64/ocaml/llvm/llvm.mli
A: /usr/lib64/ocaml/llvm/llvm.mli
R: /usr/lib64/ocaml/llvm/llvm.mli
C: cmake -DCMAKE_INSTALL_PREFIX=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr-staging/llvm-julia-14.0.6-3/build_Release/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr -P cmake_install.cmake
F: open_wr
S: deny
P: /usr/lib64/ocaml/llvm/llvm.mli
A: /usr/lib64/ocaml/llvm/llvm.mli
R: /usr/lib64/ocaml/llvm/llvm.mli
C: cmake -DCMAKE_INSTALL_PREFIX=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr-staging/llvm-julia-14.0.6-3/build_Release/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr -P cmake_install.cmake
F: unlink
S: deny
P: /usr/lib64/ocaml/llvm/llvm.mli
A: /usr/lib64/ocaml/llvm/llvm.mli
R: /usr/lib64/ocaml/llvm/llvm.mli
C: cmake -DCMAKE_INSTALL_PREFIX=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr-staging/llvm-julia-14.0.6-3/build_Release/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr -P cmake_install.cmake
F: fopen_wr
S: deny
P: /usr/lib64/ocaml/llvm/llvm.mli
A: /usr/lib64/ocaml/llvm/llvm.mli
R: /usr/lib64/ocaml/llvm/llvm.mli
C: cmake -DCMAKE_INSTALL_PREFIX=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr-staging/llvm-julia-14.0.6-3/build_Release/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr -P cmake_install.cmake
#+end_quote
2. Hack: faire "make" dans /var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4
Installation openblas
make clean
Problème avec cette approche, ne trouve pas la librairie dans usr/lib64 (car elle est dans usr/lib)
#+begin_quote
Warning: git information unavailable; versioning information limited
cd /var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/base && if ! JULIA_BINDIR=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/bin WINEPATH="/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/bin;$WINEPATH" JULIA_NUM_THREADS=1 /var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/bin/julia -O3 -C "native" --output-o /var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/lib/julia/sys-o.a.tmp --startup-file=no --warn-overwrite=yes --sysimage /var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/lib/julia/sys.ji /var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/contrib/generate_precompile.jl 1; then echo '*** This error is usually fixed by running `make clean`. If the error persists, try `make cleanall`. ***'; false; fi
lld: error: unable to find library -ljulia
lld: error: unable to find library -ljulia-internal
ERROR: failed process: Process(setenv(`/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/tools/lld -flavor gnu '' -shared -o /tmp/jl_EWdHAb/compiled/v1.9/jl_qcZsaH --whole-archive /tmp/jl_EWdHAb/compiled/v1.9/jl_nU44gE --no-whole-archive -L/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/lib64 -L/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/lib64/julia -L/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/lib64 -ljulia -ljulia-internal`,["MFLAGS=", "PATH=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/tools:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin", "MAKELEVEL=2", "PWD=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/base", "DISPLAY=:0", "BUILDROOT=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4", "PKG_CONFIG_LIBDIR=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/lib/pkgconfig", "MAKEFLAGS=", "SHELL=/bin/bash", "LC_ALL=C" … "_=/var/tmp/portage/dev-lang/julia-1.9.4/work/julia-1.9.4/usr/bin/julia", "OPENBLAS_DEFAULT_NUM_THREADS=1", "MAKE_TERMERR=/dev/pts/5", "MAKE_TERMOUT=/dev/pts/5", "USER=root", "HOME=/root", "TERM=tmux-256color", "JULIA_NUM_THREADS=1", "LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:ca=00:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.avif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.cfg=00;32:*.conf=00;32:*.diff=00;32:*.doc=00;32:*.ini=00;32:*.log=00;32:*.patch=00;32:*.pdf=00;32:*.ps=00;32:*.tex=00;32:*.txt=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:*~=00;90:*#=00;90:*.bak=00;90:*.old=00;90:*.orig=00;90:*.part=00;90:*.rej=00;90:*.swp=00;90:*.tmp=00;90:*.dpkg-dist=00;90:*.dpkg-old=00;90:*.ucf-dist=00;90:*.ucf-new=00;90:*.ucf-old=00;90:*.rpmnew=00;90:*.rpmorig=00;90:*.rpmsave=00;90:", "OPENBLAS_MAIN_FREE=1"]), ProcessExited(1)) [1]
#+end_quote
On fait donc un symlink
cd usr && ln -s lib lib64
** DONE Package tectonic
CLOSED: [2023-12-13 Wed 23:40] SCHEDULED: <2023-12-13 Wed>
:PROPERTIES:
:CATEGORY: mazda5
:END:
** Apprendre le machine learning
:PROPERTIES:
:CATEGORY: machine learning
:END:
[[https://www.reddit.com/r/MachineLearning/comments/5z8110/d_a_super_harsh_guide_to_machine_learning/][Source: reddit]]
Plus facile, à faire avant Elements... ?
*** [[https://www.coursera.org/learn/machine-learning/home/info][Andrew NG coursera]]
*** The Deep Learning Book: https://www.deeplearningbook.org/front_matter.pdf
*** Put tensor flow or torch on a linux box and run examples: http://cs231n.github.io/aws-tutorial/
*** Autres cours en lignes
**** https://mlcourse.ai/book/index.html
**** https://www.fast.ai/
** Article thèse :bisonex:
https://reviewer-feedback.springernature.com/feedback/11227/1405df9319bf5fb0dbbd4bacc8fe53b7/guidance
Journal of supercomputing
/Entered on/ [2023-11-21 Tue 22:56]
* Santé
https://reviewer-feedback.springernature.com/feedback/11227/1405df9319bf5fb0dbbd4bacc8fe53b7/guidance
Apport: formule "clé-en-main" pour valider de l'exome portable et reproductible
*** Principe
- valider appel de variant sur patients de références
- GIAB: FASTQ (HG001 ...)
- CHM13
- gènes "medically relevant"
- valider pipeline complet sur
- patient "de synthèse" avec insertion de variants connus
- données simulées (simuscop) avec liste de variants
- outils pour
- télécharger et préparer les données
- comparer le résultat d'un pipeline aux données de références
*** Méthode
- environnement : - package avec Nix (reproductible, portable)
- données récupérées avec nextflow
- pipeline nextflow pour BAM -> FASTQ et lifter les VCF de référénce en hg38 si besoin
*** KILL DataToolkit
CLOSED: [2023-11-25 Sat 13:58]
Le modèle est assez souple pour gérer les données et les transformations.
- principalement: pour des transformations complexes comme un liftover sur un .BED -> nextflow est plus adapté
- moins adapté pour gérer une liste de données ? not. pour conversion bam -> fastq sur plusieurs fichiers (on ne peut pas réutiliser la function)
Le dossier peut être changé avec https://tecosaur.github.io/DataToolkitDocs/common/stable/plugins/store/
Pour simplement télécharger les données
Utiliser driver = "passthrough"
#+begin_src julia
data_config_version = 0
uuid = "5619f8bc-50b2-4899-832e-541ac9f66226"
name = "exomevalidator"
plugins = ["store", "defaults", "memorise"]
[config.defaults.storage._]
checksum = "auto"
[[syndipCram]]
uuid = "2546eb32-496d-4809-9561-676914813b00"
description = "Raw data in CRAM for syndip using exome sequencing (Broad institute)"
[[syndipCram.storage]]
driver = "web"
checksum = "crc32c:975bd69f"
url = "https://storage.googleapis.com/broad-public-datasets/CHM1_CHM13_WES/CHMI_CHMI3_Nex1.cram"
[[syndipCram.loader]]
driver = "passthrough"
# For writing to a given file
#driver = "io->file"
#path = "lol.cram"
[[syndipKit]]
uuid = "fdaa3cea-903a-4430-99b6-aa117373e011"
description = "Syndip kit with truth set, regions and executables for comparison"
[[syndipKit.storage]]
driver = "web"
checksum = "crc32c:1bfdadf7"
url = "https://github.com/lh3/CHM-eval/releases/download/v0.5/CHM-evalkit-20180222.tar"
[[syndipKit.loader]]
driver = "tar"
#+end_src
*** Questions
- choix de l'outil global : nextflow ou julia ?
- nextflow :
- avantages: plus facile de traiter les données, permet de lancer des calculs long sur supercalculateur (bam -> fastq et happy), meilleure communauté
- inconvénients: gérer à la main les checksum, en théorie, pas besoin d'un supercalculateur, nettoyage de données à la main du WORK, pas vraiment un pipeline car 2 étapes
- julia:
- avantages: datatoolkit plus élégant, plus facile de publier, éviter le framework nextfolw (un peu lourd)
- inconvénient: peu adapté pour lancer sur un supercalculeur les transformation
- Peut-on avoir un seul environnement (Julia ou nix) ?
- besoin de certains packages -> julia seul ne suffit pas nix
- packager julia avec nix ? pour le moment, on garde les 2
- attente de la PR
- https://github.com/JuliaCN/Julia2Nix.jl
- téléchargement avec nextflow seul ? Attente de cette PR pour le checksum dans nextflow
https://github.com/nextflow-io/nextflow/pull/4415/commits/30163c7f8bdc071ba6698e41ec64064d4fa7109f
- choix de l'outil d'insertion de variants
- safesim ? https://github.com/genetronhealth/safesim Plus récent
https://www.sciencedirect.com/science/article/pii/S2352914823001533
Meilleure distribution VAF que varben mais seulement tumoral ?
Semble gérer indel
- varben : 2021, python2, à tester/packager https://www.sciencedirect.com/science/article/pii/S1525157820305857
- bamsurgeon : plante pour des données
- xamscissors : non fonctionnel pour indel
- pipeline nf-core pour simulation en cours d'intégration : on se greffe dessus ?
- tester tout clinvar avec simuscop et xamscissors ?
** DONE Review "Parallelization with Load Balancing of the Weather Model WSM7 for Heterogeneous CPU-GPU Platforms"
CLOSED: [2023-12-04 Mon 20:39] SCHEDULED: <2023-11-25 Sat 15:00> DEADLINE: <2023-12-04 Mon>
- en beta (plus de support pour nextflow)
Inconvénient :
*** STRT [[file:books.org::*The elements of statistical learning (217)][The elements of statistical learning (217)]] :
**** STRT Chap 1-4
**** Chap 7-8
*** Introduction to statistical learning
CLOSED: [2023-11-21 Tue 22:53] SCHEDULED: <2023-11-21 Tue>
**** DONE Correction v2 + envoi co-auteurs
CLOSED: [2023-11-26 Sun 18:54] SCHEDULED: <2023-11-26 Sun>
**** DONE Resoumettre
CLOSED: [2023-12-01 Fri 20:21] SCHEDULED: <2023-12-03 Sun>
envoyé le <2022-10-11 Tue>
/Entered on/ [2023-11-28 Tue 22:32]
*** TODO Envoyer mémoire à Hakim
/Entered on/ [2023-11-28 Tue 22:33]
*** TODO Envoyer tableau + courriers à Hakim
SCHEDULED: <2023-12-20 Wed>
SCHEDULED: <2023-12-20 Wed>
** NF1
:PROPERTIES:
:CATEGORY: nf1
:END:
*** DONE Récupérer clinique : courriers + IRM
CLOSED: [2023-12-01 Fri 20:17] DEADLINE: <2023-12-01 Fri 11:00>
*** Notes
Rare ?
- non présent gnomAD
- rapportée 1x clinvar VOUS
- au même endroit mais autres fauxsense
- G>A (p.Arg1000His) = clinvar VOUS x2
- G>T (p.Arg1000Leu) = clinvar VOUS x2 dont 1 callisé comme "prédisposition au cancer héréditaire" sans plus de précisions
- le faux sens à côté est bien connu c.2998C>T (p.R1000C) : 3 soumission clinvar et plusieurs article
PMID: 33563663, 27838393, 25074460, 31645765, 29636988, 30476936, 21520333, 29489754
- synonyme T>C est clinvar bénin
- frameshift c.2998_2999del (p.Arg1000fs) prenant cette base est rapporté 2x clinvar classe 4
Onco ? non rapporté dans cosmic *mais* c.2998C>T (p.R1000C) est rapportée
- dans le foie : homme de 48A
- sur la peau : Desmoplastic melanoma (publié dans PMID 26343386,
cosmic : 498 mutations somatique foie + NF1
- [[https://pubmed.ncbi.nlm.nih.gov/26343386/][PMID 26343386]]
- [[https://pubmed.ncbi.nlm.nih.gov/28481359/][PMID 28481359]] -> touche [[https://www.wikipathways.org/index.php/Pathway:WP382][voie MAPK]]
- interaction possible avec autres mutation ? pas sur le même chromosome...
- NM_001042492.3(NF1):c.350T>G (p.Ile117Ser) retrouvée 2x chez un patient
- non rapporté dans cosmic
- NM_001042492.3(NF1):c.5991G>A (p.Trp1997Ter)
- cosmic : rapporté dans pheochromocytome x1 et pheochromocytome x1 (patho)
*** Tâches
[cite:@dubbink2018]: 1 patient NF1 + mutation somatique /CNNTB1/
[cite:@seminog2012] étude épidémio : surrisque de cancer du foie chez patient NF1 (cf note)
[cite:@ucar2007] 1 cas de NF1 avec hépatoblastome sans confirmation moléculaire
[cite:@landry2021]: épidémio récente : pas de cas rapporté NF1 + foie
[cite:@varan2015]: épidémio plus ancienne : idem
[cite:@kappler2010]: rien ne correspond
Voie RAS impliquée dans hépatoblastome ?
Possible selon https://pubmed.ncbi.nlm.nih.gov/19665249/
https://www.nature.com/articles/labinvest2016142
CLOSED: [2022-10-22 Sat 23:33] DEADLINE: <2022-09-17 Sat>
***** Notes
List journaux acceptant case reports
https://static1.squarespace.com/static/5db7b349364ff063a6c58ab8/t/6071fb065173800a11ccd0a2/1618082566620/Case+Report+Journals+2020.pdf
- Acad Pediatr : non, scope inadéquat
- BMC Pediatrics ? trop cher (2 290€) Impact factor 2.1
- Curr Opin Pediatr : il faut être invité
- Front Pediatr : 2000$ case report
https://www.frontiersin.org/journals/pediatrics/for-authors/publishing-fees
- Ital J Pediatr : trop cher (cf bmc)
- J Pediatr Health Care : out of scope
- J Pediatr Hematol Oncol Nurs : out of scope
- Minerva Pediatr : gratuit si soumission pas en open access
https://www.minervamedica.it/en/journals/minerva-pediatrics/notice-to-authors.php
#+begin_quote
hybrid journal which publishes scientific papers on pediatrics, neonatology, adolescent medicine, child and adolescent psychiatry and pediatric surgery
#+end_quote
case report pour la forme de lettres à l’éditeur apparement
https://www.minervamedica.it/en/journals/minerva-pediatrics/article.php?cod=R15Y2021N05A0467
#+begin_quote
Subscription-based model
Page charges. Publication of the manuscript is free of charge. Language revision and excessive alterations to proofs will be charged to the authors.
#+end_quote
- Pediatr Clin North Am : out of scope
- Pediatr Dev Pathol : gratuit
Case report ok :
#+begin_quote
The Journal covers the spectrum of disorders of early development (including embryology, placentology, and teratology), gestational and perinatal diseases, and all diseases of childhood. Studies may be in any field of experimental, anatomic, or clinical pathology, including molecular pathology. Case reports are published only if they provide new insights into disease mechanisms or new information.
#+end_quote
https://journals.sagepub.com/author-instructions/PDP
#+begin_quote
There are no fees payable to submit to or publish in this journal.
#+end_quote
- Pediatr Hematol Oncol : gratuit
scope limite :
#+begin_quote
aim to define optimal therapeutic strategies for children and young adults with cancer and blood disorders.
#+end_quote
Case report ok :
#+begin_quote
PHO will consider exceptional case studies and case series. These submissions must illuminate novel biological or clinical understanding of cancer or blood diseases must be submitted in the identical format as a letter to the editorial
#+end_quote
#+begin_quote
Authors of accepted peer-reviewed articles have the choice to pay a fee to allow perpetual unrestricted online access to their published article to readers globally, immediately upon publication. Authors may take advantage of the open access option at the point of submission. Please note that this choice has no influence on the peer review and acceptance process. These articles are subject to the journal's standard peer-review process and will be accepted or rejected based on their own merit.
The article processing charge (APC) is charged on acceptance of the article and should be paid within 30 days by the author, funding agency or institution. Payment must be processed for the article to be published
#+end_quote
https://www.tandfonline.com/action/authorSubmission?show=instructions&journalCode=ipho20#oa
#+begin_quote
There are no submission fees, publication fees or page charges for this journal.
#+end_quote
https://www.springer.com/gp/authors-editors/authorandreviewertutorials/submitting-to-a-journal-and-peer-review/cover-letters/10285574
# If known, address the editor who will be assessing your manuscript by their name. Include the date of submission and the journal you are submitting to.
Dear Editor,
# First paragraph: include the title of your manuscript and the type of manuscript it is (e.g. review, research, case study). Then briefly explain the background to your study, the question you sought out to answer and why.
We would like submit to American Journal of Medical Genetics (part A) a novel
case report entitled "Hepatoblastoma in a patient with Neurofibromatosis type 1:
a case report" to the for consideration of publication. Even though a large
variety of tumours have been reported in neurofibromatosis type 1, this is, to
our knowledge, only the third case in medical litterature linked with
hepatoblastoma and the first with germline and somatic molecular analysis.
Following-up the discovery of a liver mass in a 11-year old girl, epithelial
hepatoblastoma with pulmonary metastasis was diagnosed. Germline and somatic
molecular analysis showed classical driver variant for hepatoblastoma and a
germline class 4 /NF1/ variant also found in the tumour. We discuss potential
causal link between the two.
# Third paragraph: here you should indicate why the readers of the journal #would be interested in the work.
# biological and medical aspects of genetic disorders and birth defects, as well as in-depth documentation of phenotype analysis within the current context of genotype/phenotype correlations.
To facilitate early detection of rare cancers like hepatoblastoma, reporting
such associations is important to increase clinical awareness and improve
follow-up of /NF1/ patients. It also highlights the difficulty of genetic
counseling with aggressive tumours and genetic diseases in the same family.
Thank you for considering our case report for publication.
Sincerely,
****** DONE Soumission initiale
CLOSED: [2023-07-27 Thu 23:31]
CLOSED: [2023-11-19 Sun 22:33] SCHEDULED: <2023-11-19 Sun>
**** DONE Mail paul
**** DONE Correction réponse reviewer +/ article (gain)
CLOSED: [2023-11-23 Thu 22:57] SCHEDULED: <2023-11-23 Thu>
**** DONE Implémenter corrections article
****** DONE Figures > 2 en Supplementary
CLOSED: [2023-07-27 Thu 23:31] DEADLINE: <2023-07-24 Mon>
****** DONE Vérifier citation format APA
CLOSED: [2023-07-27 Thu 23:31] DEADLINE: <2023-07-24 Mon>
****** DONE Ajouter le consentement dans les méthodes
CLOSED: [2023-07-27 Thu 23:31] DEADLINE: <2023-07-24 Mon>
****** DONE Rajouter la machine avec séquencage
CLOSED: [2023-07-27 Thu 23:31] DEADLINE: <2023-07-24 Mon>
****** DONE Cover letter
CLOSED: [2023-07-27 Thu 23:31] DEADLINE: <2023-07-26 Wed>
***** DONE Soumission AJMG
CLOSED: [2023-07-30 Sun 14:50] SCHEDULED: <2023-07-26 Wed>
CLOSED: [2022-11-27 Sun 11:28]
**** DONE v0.1
CLOSED: [2022-12-04 Sun 22:13]
CLOSED: [2023-03-20 lun. 14:29]
CLOSED: [2023-03-20 lun. 14:30]
CLOSED: [2023-06-11 Sun 18:39] SCHEDULED: <2023-05-28 Sun>
CLOSED: [2023-07-02 Sun 10:52] SCHEDULED: <2023-06-11 Sun>
CLOSED: [2023-07-21 Fri 17:46] SCHEDULED: <2023-07-16 Sun>
**** DONE Soumission
CLOSED: [2023-10-07 Sat 18:00]
**** DONE Relancer avant soumission
**** DONE Dernières correction JP
**** DONE Correction Hirsch + Vidau
**** DONE Version validée par paul v0.2.7
**** DONE Corrections v0.2
*** TODO Article
*** DONE Poster v0.1
CLOSED: [2022-12-04 Sun 22:13]
CLOSED: [2022-12-04 Sun 22:13]
CLOSED: [2022-12-04 Sun 22:13]
*** DONE Plan de l’article
**** KILL Appel ITACA
**** KILL Appel ANDDI rares
*** KILL Trouver autres cas ?
Wnt/β-cateninng : impliqué dans NF1
activation Ras/MAPk -> augemantation niveau de βcatenine
[rappel : entraine des neurofibromes qui sont bénin mais qui peuvent se transformer en tumeur maligne]. Modèle murin + étude de l'expression murine model : activation -> (activation)
- [cite:@luscan2014] : idem, le plus convaincant, activation de la voie dans MPNSTS
- In Neurofibromatosis type 1, GTPase function is ablated leading to unsuppressed activation of
the Ras/MAPK signaling pathway[19], which can lead to enhanced Wnt/β-catenin signaling through
quenching GSK-3β’s inhibitory effect on Wnt/β-catenin signaling[20]
- lien avec ossification
- sourics avec défaut /NF1/ : augmentation niveau de βcatenine sur phase précoce de consolidation fracture osseuse
- néfopam (inhibe βcatenin) : améliore ossification [cite:@baht2017] sur de courtes période de temps
- idem mais sur souris agếes et dans Nature (mais sans NF1, juste confirme le lien) [cite:@kwak2019]
- [cite:@watson2013] : activation de la voie -> développement + progression des tumeurs nerveues périphériques
https://www.sciencedirect.com/science/article/pii/S8756328217300571?casa_token=hXS_Cmtozt8AAAAA:enMW1d09t-ms-mlCC6eMIX-C2XyvxuastFwmLi8wkYVO3zZlDdEtSY1eU-7s27xcHLoNe3hrXCM
(cf leur biblio)
mini review phttps://www.ijpmonline.org/article.asp?issn=0377-4929;year=2020;volume=63;issue=1;spage=112;epage=115;aulast=Ghose#ref9
- hépatoblastome selon [cite:@dubbink2018] (perte de fonction -> excès β-catening par absence de dégradation)
NF2
- [cite:@kim2016] activation
- schwannomees NF2 via hyperactivation https://www.nature.com/articles/cdd201654
et vestibular schwanoma
https://www.nature.com/articles/s41401-022-00908-4
**** Autres
[cite:@skoczen2019] hépatoblastome + neuroblastome avec plusieurs variants dont NF1
CLOSED: [2022-11-27 Sun 11:28]
CLOSED: [2022-11-27 Sun 11:28]
**** DONE Pathway
**** DONE NF1 + autres cancers
CLOSED: [2022-11-27 Sun 11:28]
CLOSED: [2022-11-27 Sun 11:28]
**** DONE Autre case report NF1 + hépatoblastome ?
*** DONE Biblio
CLOSED: [2023-11-23 Thu 21:46]
**** DONE article T. Hirsch
**** Autres cancers atypiques avec NF1 ? (hotspot, voie MAPK impliquée)
Voir notes de [cite:@landry2021]
monoallélique -> inactivation partielle pourrait jouer un rôle
NF1 driver possible selon leur critère : \ge 2 patients
et p<-value < 0.05 avec MutSigCV et Oncodrive
**** 2 autres mutation NF1 somatique chez Hirsch
**** notre patiente
- mutations drivers : CTNNB1, TERT et gain de méthylation 11p15 retrouvé dans [cite:@hirsch2021]
- 1 mutation NF1 constit retrouvée en somatique (tumeur + métastase)
- [[https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr17%3A31230268%2D31230268&hgsid=1418628939_u4ASAyqv2xSI3YwznwQRfOaGJo4t][NM_001042492.3(NF1):c.2999G>C (p.Arg1000Pro)]] probablement patho
- mais pas de double hit (une seule allèle)
- + variant intronique mais sans anomalie RNAseq et classe 2 clinvar
NM_001042492.3(NF1):c.6147+8 ?>?
**** Mutation NF1
**** Cancers sans double hits ?
***** Double hit
" the majority of NF1-associated tumours exhibit biallelic inactivation of NF1 [9, 10]."
[10] = knudson
[9] = brehms2009:
| Non nervous | Gastrointestinal stromal tumour | Second hit NF1 and some copy number alterations [15] |
| | Somatostatinoma | ? |
| | Phaeochromocytoma | Second hit NF1 [16-18] |
| | Breast cancer | ? |
| | Rhabdomyosarcoma | ? |
|-----------------------+------------------------------------------+---------------------------------------------------------------------------------------------------|
| Nervous system tumour | Astrocytoma | Second hit NF1, mutation in TP53, deletion of CDKN2A |
| | Malignant peripheral nerve-sheath tumour | Second hit NF1, multiple copy number alterations, mutation in TP53, deletion of CDKN2A [24,25-27] |
| | Neuroblastoma | Second hit NF1, amplification of MYCN, deletion of 1p36 [28,29] |
Loss of heterozygosity of the NF1 region has been identified in phaeochromocytomas from patients with NF1.16,17 Bausch and colleagues18 noted somatic loss of the non-mutated NF1 allele in 67% of phaeochromocytomas in patients with NF1 with an identified germline mutation.
- Pour les gliomes, double hit :https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6857804/ -> "As expected, we found that multiple clones for each tumor contained only the germline or somatic mutation, indicating that the two mutations reside on different alleles"
***** Single hit
La référence pointe vers Wong2019 93:1-3. doi:10.1212/WNL.0000000000008623 avec autopsy + philogeny pour ordre des variations
#+begin_quote
This molecular ontology analysis provides a proof-of-concept demonstration that some gliomagenesis-associated events (i.e., KMT2B mutation/amplification) occur before NF1 biallelic inactivation and may be sufficient to drive gliomagenesis in an NF1 heterozygous backgroun
#+end_quote
Gliome : Fischer2021 https://doi.org/10.1007/s00401-021-02276:
majorité ont du double hit mais
#+begin_quote
a somatic abnormality in the second NF1 allele was not found in 3 samples (two with FGFR1 + PIK3CA mutations, one with a MYB:QKI alteration). This suggests that in rare cases, glioma pathogenesis in the context of NF1 may not dependent on loss of the second NF1 allele, as reported for a young adult with NF1 and a malignant glioma [30]
#+end_quote
- Eoli et al 2019: revue cancer neuro : biallelic inactivation is "critical"
- Dunnett-Kane et al 2020: contre-exemple : mutation somatique /NF1/ dans mélanome et adénocarcinome pulmonaire mais pas de prédisposition !
- Fisher et al 2021: gliome (voir single-hit)
Liste des tumeurs somatiques : pas d’hépatoblastome (Philpot2017 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5480124/)
Genereviews: /NF1/ somatiques sans clinique NF1
- D'Angelo et al 2019: gliome https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6857804/
#+begin_quote
As expected, we found that multiple clones for each tumor contained only the germline or somatic mutation, indicating that the two mutations reside on different alleles
#+end_quote
* Backups
:PROPERTIES:
:CATEGORY: backup
:END:
** TODO Git-annex en local
*** DONE vers /annex
CLOSED: [2023-10-01 Sun 15:34] SCHEDULED: <2023-09-30 Sat>
- [X] public
- [X] private
- [X] data
*** DONE vers raspberry:/media/annex
CLOSED: [2023-10-01 Sun 15:34] SCHEDULED: <2023-10-01 Sun>
- [X] public
- [X] private
- [X] data
*** TODO vers laptop:~/annex
- [ ] public
- [X] private
- [ ] data
*** DONE depuis /annex
CLOSED: [2023-10-01 Sun 16:15] SCHEDULED: <2023-09-30 Sat>
- [X] public
- [X] private
- [ ] data
*** DONE mega avec restic
CLOSED: [2023-10-01 Sun 16:08] SCHEDULED: <2023-10-01 Sun>
- [X] public
- [X] private
*** DONE google drive avec restic
CLOSED: [2023-10-01 Sun 15:33] SCHEDULED: <2023-10-01 Sun>
- [X] public
- [X] private
*** DONE Tester backup avec restic
CLOSED: [2023-10-01 Sun 16:15] SCHEDULED: <2023-10-01 Sun>
- [X] private sur gdrive
- [ ] public sur gdrive
** DONE papers : git lfs (non encrypté)
CLOSED: [2023-09-30 Sat 19:19] SCHEDULED: <2023-09-30 Sat>
* Banque
:PROPERTIES:
:CATEGORY: banque
:END:
* Blog
:PROPERTIES:
:CATEGORY: blog
:END:
* Divers
** TODO Photos famille
On utilise le drive commun qu'a fait Elise. Pour éviter les soucis de connexion, on modifie juste le dossier partagé:
https://drive.google.com/drive/folders/11wJ0E_KZv7I88wdv_ULHqd5KvWFfF0DF?usp=sharing_eip_m&invite=CPX0rho&ts=63ea1879
Autres drives :
alexis: https://drive.proton.me/urls/PQ5M6TKVRM#q8yulEV8T5WG
papa : https://www.mailo.com/mailo/docs/docs.php?s=IaK9Ajz8kwQJXNPnhJofRuDwyrNSZVy4&dir=mqn0f3%2bozZXc%2bwh4DeXwhVTY1Zz4zci5rZ4XcNHRmX7wPT0d9WG%2b0g%3d%3d&ea_encode=0
*** DONE Copier photos famille drive papa -> drive proton, drive yvain sur drive famille
CLOSED: [2023-02-12 Sun 23:17]
*** TODO Copier photos famille depuis drive yvain sur drive famille
*** TODO Trier photos sur drive yvain
** DONE certificat de baptême
CLOSED: [2023-11-22 Wed 20:28] SCHEDULED: <2023-11-21 Tue>
/Entered on/ [2023-10-11 Wed 23:13]
Message envoyé sur le site 2023-10-11 Wed
*** DONE Appeler
CLOSED: [2023-11-21 Tue 22:52] SCHEDULED: <2023-11-21 Tue>
*** DONE Demander à Aurélien
CLOSED: [2023-11-21 Tue 22:52] SCHEDULED: <2023-11-21 Tue>
** DONE Payer inscription gymnastique
CLOSED: [2023-11-21 Tue 22:52] SCHEDULED: <2023-11-21 Tue>
/Entered on/ [2023-11-19 Sun 22:41]
** DONE Réserver location ski
CLOSED: [2023-11-23 Thu 21:45] SCHEDULED: <2023-11-22 Wed>
/Entered on/ [2023-11-22 Wed 22:04]
/Entered on/ [2023-11-25 Sat 11:30]
/Entered on/ [2023-12-16 Sat 19:05]
/Entered on/ [2023-12-16 Sat 19:15]
** DONE Commander cadeau Élise
CLOSED: [2023-12-17 Sun 18:03] SCHEDULED: <2023-12-16 Sat>
* Génétique
** Collège [0/32]
*** 1. Architecture du génome
*** 2. Structure et fonction du génome humains: chromosomes sexuels
*** 3. Structure et fonction du génome humains
*** 4. Hérédité mendélienne
*** 5. Génétique des populations
*** 6. Cytogénétique conventionnelle
*** 7. Cytogénétique moléculaire
*** 8. Anomalies hémopathies et tumeurs solides
*** STRT 9.Anomalies génétiques à l’échelle du gène
*** STRT 10. Principales techniques d’analyses des anomalies génétiques à l’échelle du gène
*** 11. Séquencage haut débit
*** 12. Conseil génétique
*** 13. Examen de l’enfant
*** 14. Hétérogénéite des maladies génétiques
*** 15. DPN, DPI
*** 16. Dépistage néonatal
*** 17. DPS
*** 18. Dispositions législatives
*** 19. Enjeux éthiques
*** 20. Maladies mitochondriales
*** 21. Empreinte parentale
*** 22. Mutations dynamiques
*** 23. Oncogénétique
*** 24. Bases de données
*** 25. Perspectives thérapeutiques
*** 26. Pharmacogénétique
*** 27. Génétique des maladies complexes
*** 28. T21
*** 29. Mucoviscidose
*** 30. Xfragile
*** 31. Maladies rares
*** 32. Médecine génomique
** TODO Biologie cellulaire et moléculaire Dunod [22/209]
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*** Fiche 203
*** Fiche 204
*** Fiche 205
*** Fiche 206
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*** Fiche 209
** TODO Biologie chimie Dunod
** DONE Transférer Harry Potter 1 + thriller pour Yvain
CLOSED: [2023-12-17 Sun 23:28] SCHEDULED: <2023-12-17 Sun>
** DONE Command minoxidil
CLOSED: [2023-11-26 Sun 21:56] SCHEDULED: <2023-11-26 Sun>
# -*- mode: org -*-
Archived entries from file /home/alex/org/recherche.org
* DONE Biblio ophn1
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-23 Sat 22:57
:ARCHIVE_FILE: ~/org/recherche.org
:ARCHIVE_OLPATH: WDR45
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: DONE
:END:
uement dans dbsnp
#+begin_src sh :dir ~/code/bisonex/test_isec
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20.vcf.gz
bcftools isec -n=2 -i - -i 'INFO/CLNSIG="Pathogenic"' $snp $clinvar -p tmp
# grep '^[^#]' tmp/0000.vcf | wc -l
#+end_src
#+RESULTS:
Soit tout dbsnp donc rien
Note : on ne peut pas exclure les clinvar patho directement
#+begin_src sh :dir ~/code/bisonex/test_isec
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20.vcf.gz
bcftools isec -i - -e 'INFO/CLNSIG="Pathogenic"' $snp $clinvar -p tmp
for i in tmp/*.vcf ; do echo $i; grep '^[^#]' $i | wc -l; done
#+end_src
Car on ne peut plus faire la différence !
Si on utilise la version d'Alexis
#+begin_src sh :dir ~/code/bisonex/test_isec
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20_notremapped.vcf.gz
python ../script/pythonScript/clinvar_sbSNP.py \
--clinvar $clinvar \
--chrm_name_table ../database/RefSeq/refseq_to_number_only_consensual.txt \
--dbSNP $snp --output tmp.txt
sort tmp.txt > common-notpatho-alexis.txt
wc -l common-notpatho-alexis.txt
#+end_src
#+RESULTS:
: 518832 common-notpatho-alexis.txt
Si on cherche les clinvar patho (donc non présent dans la sortie)
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f '%ID\n' dbSNP_common_chr20.vcf.gz | sort > all.txt
sort common-notpatho-alexis.txt > alexis.txt
comm -23 all.txt alexis.txt > patho.txt
#+end_src
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f '%POS\n' -i 'ID=@patho.txt' dbSNP_common_chr20.vcf.gz -o pos.txt
for pos in $(cat pos.txt); do
bcftools query -f '%CHROM %POS %ID %REF %ALT\n' -i 'POS='$pos dbSNP_common_chr20.vcf.gz
bcftools query -f '%CHROM %POS %ID %REF %ALT %INFO/CLNSIG\n' -i 'POS='$pos clinvar_chr20.vcf.gz
echo "------"
done
#+end_src
#+RESULTS:
| NC_000020.11 | 3234173 | rs3827075 | T | A,C,G | |
| NC_000020.11 | 3234173 | 262001 | T | G | Conflicting_interpretations_of_pathogenicity |
| NC_000020.11 | 3234173 | 1072511 | T | TGGCGAAGC | Pathogenic |
| NC_000020.11 | 3234173 | 208613 | TGGCGAAGC | G | Pathogenic |
| NC_000020.11 | 3234173 | 1312 | TGGCGAAGC | T | Pathogenic |
| ------ | | | | | |
| NC_000020.11 | 4699605 | rs1799990 | A | G | |
| NC_000020.11 | 4699605 | 13397 | A | G | Benign/Likely_benign |
| ------ | | | | | |
| NC_000020.11 | 10652589 | rs1131695 | G | A,C,T | |
| NC_000020.11 | 10652589 | 163705 | G | . | Benign |
| NC_000020.11 | 10652589 | 143063 | G | A | Benign |
| NC_000020.11 | 10652589 | 234555 | G | C | Pathogenic |
| ------ | | | | | |
| NC_000020.11 | 10658574 | rs1801138 | G | A,T | |
| NC_000020.11 | 10658574 | 42481 | G | A | Benign |
| NC_000020.11 | 10658574 | 992651 | G | T | Likely_pathogenic |
| NC_000020.11 | 10658574 | 213550 | GC | A | Pathogenic |
| ------ | | | | | |
| NC_000020.11 | 10672794 | rs79338570 | G | A,C | |
| NC_000020.11 | 10672794 | 255557 | G | A | Benign/Likely_benign |
| NC_000020.11 | 10672794 | 594067 | G | C | Conflicting_interpretations_of_pathogenicity |
| NC_000020.11 | 10672794 | 1324603 | G | GGA | Likely_pathogenic |
| ------ | | | | | |
| NC_000020.11 | 18525868 | rs146917730 | C | T | |
| NC_000020.11 | 18525868 | 811603 | C | T | Conflicting_interpretations_of_pathogenicity |
| ------ | | | | | |
| NC_000020.11 | 25390747 | rs373200654 | G | C | |
| NC_000020.11 | 25390747 | 338000 | G | C | Conflicting_interpretations_of_pathogenicity |
| ------ | | | | | |
| NC_000020.11 | 32800145 | rs2424926 | C | G,T | |
| NC_000020.11 | 32800145 | 338173 | C | G | Benign |
| NC_000020.11 | 32800145 | 338174 | C | T | Conflicting_interpretations_of_pathogenici
tPM:Miseq\tCN:CHU_Minjoz\tLB:definition_to_add' \
-t 24 \
$INDEX \
63003856_S135_R1_001.fastq.gz 63003856_S135_R2_001.fastq.gz \
| samtools sort --threads 24 -o 63003856_S135.bam -
#+end_src
#+begin_src
bwa mem -R "@RG\tID:$sample\tSM:$sample\tPL:ILLUMINA\tPM:Miseq\tCN:CHU_Minjoz\tLB:definition_to_add" -v 2 -t `nproc` $genomeRef ${fastq[0]} ${fastq[1]} | $samtools sort -@ `nproc` -O BAM -o $tmpDir/$post_bwa
#+end_src
****** DONE Avec gatk 4.2 (version alexis) : idem
$ samtools view -c mapped/63003856_S135.bam
128077211
****** DONE Nettoyé
CLOSED: [2022-12-26 Mon 22:08]
[57/4b5b4c] Cached process > preprocess:GATK4_CLEANSAM (63003856_S135)
$ samtools view -c work/57/4b5b4c647b98bb7099c4d1ba24bd75/63003856_S135.bam
128077211
Et la sortie
$ samtools view -c out/63003856_S135/preprocessing/clean-sam/sorted.bam
128077211
contre
$ samtools view -c /Work/Groups/bisonex/ref_63003856_S135/63003856_S135_cleaned.bam
128077207
On regarde les stats en détails (de la version nettoyée)
$ samtools flagstat work/57/4b5b4c647b98bb7099c4d1ba24bd75/63003856_S135.bam
128077211 + 0 in total (QC-passed reads + QC-failed reads)
126905130 + 0 primary
0 + 0 secondary
1172081 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
127941054 + 0 mapped (99.89% : N/A)
126768973 + 0 primary mapped (99.89% : N/A)
126905130 + 0 paired in sequencing
63452565 + 0 read1
63452565 + 0 read2
125263664 + 0 properly paired (98.71% : N/A)
126676024 + 0 with itself and mate mapped
92949 + 0 singletons (0.07% : N/A)
979608 + 0 with mate mapped to a different chr
675398 + 0 with mate mapped to a different chr (mapQ>=5)
$ samtools flagstat /Work/Groups/bisonex/ref_63003856_S135/63003856_S135_cleaned.bam
128077207 + 0 in total (QC-passed reads + QC-failed reads)
126905130 + 0 primary
0 + 0 secondary
1172077 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
127941051 + 0 mapped (99.89% : N/A)
126768974 + 0 primary mapped (99.89% : N/A)
126905130 + 0 paired in sequencing
63452565 + 0 read1
63452565 + 0 read2
125263790 + 0 properly paired (98.71% : N/A)
126676026 + 0 with itself and mate mapped
92948 + 0 singletons (0.07% : N/A)
979618 + 0 with mate mapped to a different chr
675412 + 0 with mate mapped to a different chr (mapQ>=5)
****** DONE mark duplicate
CLOSED: [2022-12-26 Mon 22:27]
Alexis
$ samtools view -c /Work/Groups/bisonex/ref_63003856_S135/63003856_S135_marked_dup.bam
128077207
Nous (pas de sortie dans out/)
$ samtools view -c work/46/bd75b4547452af36ee2c6b45362922/63003856_S135
128077211
logique car on ne supprime pas de donné...
******* Arguments ok
#+begin_src
gatk --java-options "-Xmx3g" MarkDuplicates \
--INPUT sorted.bam \
--OUTPUT marked_dups.bam \
--METRICS_FILE marked_dups.bam.metrics \
--TMP_DIR . \
--REFERENCE_SEQUENCE genomeRef.fna \
#+end_src
#+begin_src
$gatk MarkDuplicates \
-I $tmpDir/$post_cleanSam \
-O $tmpDir/$post_markDuplicate \
-M $tmpDir/"$sample"_marked_dup.metrix \
--CREATE_INDEX true \
--VERBOSITY WARNING
#+end_src
****** KILL baserecalibrator
CLOSED: [2023-01-04 Wed 19:15]
#+begin_src
$gatk BaseRecalibrator \
-I $tmpDir/$post_markDuplicate \
-R $genomeRef \
--known-sites $dbsnpDir/dbSNP_common.vcf.gz \
-O $tmpDir/$post_BaseRecalibrator
#+end_src
$ cd /Work/Users/apraga/bisonex/out/63003856_S135/preprocessing/baserecalibrator
$ sed 's/sample/63003856_S135/' 63003856_S135.table > 63003856_S135.table2
Les fichiers n'ont pas le même nombre d'erreurs mais assez proches. Sur le premier table, 3 score
#:GATKTable:3:94:%d:%d:%d:;
#:GATKTable:Quantized:Quality quantization map
QualityScore Count QuantizedScore
11 298878631 11
25 542282996 25
34 12846268833 34
vs (référence0)
11 298877785 11
25 542282089 25
34 12846264839 34
******* options ok
#+begin_src
gatk --java-options "-Xmx3g" BaseRecalibrator \
--input marked_dups.bam \
--output 63003856_S135.table \
--reference genomeRef.fna \
\
--known-sites dbSNP_common.vcf.gz \
--tmp-dir . \
#+end_src
****** KILL applybqsr
CLOSED: [2023-01-04 Wed 19:15]
options ok
#+begin_src
gatk --java-options "-Xmx3g" ApplyBQSR \
--input marked_dups.bam \
--output 63003856_S135.bam \
--reference genomeRef.fna \
--bqsr-recal-file 63003856_S135.table \
\
--tmp-dir . \
#+end_src
#+begin_src
$gatk ApplyBQSR -R $genomeRef \
-I $tmpDir/$post_markDuplicate \
--bqsr-recal-file $tmpDir/$post_BaseRecalibrator \
-O $bamDir/$post_ApplyBQSR \
--verbosity WARNING
#+end_src
missing file
***** KILL Variant caling
CLOSED: [2023-01-04 Wed 19:16]
****** KILL haplotypecaller
CLOSED: [2023-01-04 Wed 19:15]
******** options ok
#+begin_src
gatk --java-options "-Xmx3g" HaplotypeCaller \
--input 63003856_S135.bam \
--output 63003856_S135.vcf.gz \
--reference genomeRef.fna \
--dbsnp dbSNP.gz \
\
\
--tmp-dir . \
--max-mnp-distance 2
#+end_src
#+begin_src
$gatk --java-options "-Xmx32g" HaplotypeCaller \
-R $genomeRef \
-I $bamDir/$post_ApplyBQSR \
-O $vcfDir/$post_haplotypecaller \
-D "$dbsnpDir"/GCF_000001405.39.gz \
--max-mnp-distance 2 \
--verbosity WARNING
#+end_src
******** DONE Nombres lignes gatk 4.3.0 : trop différent
CLOSED: [2023-01-04 Wed 19:11]
$ grep '^NC' out/63003856_S135/variantCalling/haplotypecaller/63003856_S135.vcf | wc -l
1631935
$ grep '^NC' /Work/Groups/bisonex/ref-vcf/63003856_S135 .vcf | wc -l
1506894
******** DONE Regarder les flags d'haplotypecaller : nombreuses différences...
CLOSED: [2023-01-04 Wed 19:02]
| --dbsnp /Work/Users/apraga/bisonex/work/08/fca52ac598f21a2812f866bd590792/dbSNP.gz | --dbsnp /mnt/j/bases_de_donnees/dbSNP/GCF_000001405.39.gz |
| --max-mnp-distance 2 | --max-mnp-distance 2 |
| --output 63003856_S135.vcf.gz | --output /mnt/j/working_directory_pipeline_analyse_exome/vcf/63003856_S135.vcf |
| --input 63003856_S135.bam | --input /mnt/j/working_directory_pipeline_analyse_exome/bam/63003856_S135_recalibrated_hg38.bam |
| --reference genomeRef.fna | --reference /mnt/j/bases_de_donnees/genome/GRCh38_latest_genomic.fna |
| --tmp-dir . | --verbosity WARNING |
| --use-posteriors-to-calculate-qual false | --use-posteriors-to-calculate-qual false |
| --dont-use-dragstr-priors false | --dont-use-dragstr-priors false |
| --use-new-qual-calculator true | --use-new-qual-calculator true |
| --annotate-with-num-discovered-alleles false | --annotate-with-num-discovered-alleles false |
| --heterozygosity 0.001 | --heterozygosity 0.001 |
| --indel-heterozygosity 1.25E-4 | --indel-heterozygosity 1.25E-4 |
| --heterozygosity-stdev 0.01 | --heterozygosity-stdev 0.01 |
| --standard-min-confidence-threshold-for-calling 30.0 | --standard-min-confidence-threshold-for-calling 30.0 |
| --max-alternate-alleles 6 | --max-alternate-alleles 6 |
| --max-genotype-count 1024 | --max-genotype-count 1024 |
| --sample-ploidy 2 | --sample-ploidy 2 |
| --num-reference-samples-if-no-call 0 | --num-reference-samples-if-no-call 0 |
| --genotype-assignment-method USE_PLS_TO_ASSIGN | --genotype-assignment-method USE_PLS_TO_ASSIGN |
| --contamination-fraction-to-filter 0.0 | --contamination-fraction-to-filter 0.0 |
| --output-mode EMIT_VARIANTS_ONLY | --output-mode EMIT_VARIANTS_ONLY |
| --all-site-pls false | --all-site-pls false |
| --flow-likelihood-parallel-threads 0 | --gvcf-gq-bands 1 |
| --flow-likelihood-optimized-comp false | --gvcf-gq-bands 2 |
| --flow-use-t0-tag false | --gvcf-gq-bands 3 |
| --flow-probability-threshold 0.003 | --gvcf-gq-bands 4 |
| --flow-remove-non-single-base-pair-indels false | --gvcf-gq-bands 5 |
| --flow-remove-one-zero-probs false | --gvcf-gq-bands 6 |
| --flow-quantization-bins 121 | --gvcf-gq-bands 7 |
| --flow-fill-empty-bins-value 0.001 | --gvcf-gq-bands 8 |
| --flow-symmetric-indel-probs false | --gvcf-gq-bands 9 |
| --flow-report-insertion-or-deletion false | --gvcf-gq-bands 10 |
| --flow-disallow-probs-larger-than-call false | --gvcf-gq-bands 11 |
| --flow-lump-probs false | --gvcf-gq-bands 12 |
| --flow-retain-max-n-probs-base-format false | --gvcf-gq-bands 13 |
| --flow-probability-scaling-factor 10 | --gvcf-gq-bands 14 |
| --flow-order-cycle-length 4 | --gvcf-gq-bands 15 |
| --flow-number-of-uncertain-flows-to-clip 0 | --gvcf-gq-bands 16 |
| --flow-nucleotide-of-first-uncertain-flow T | --gvcf-gq-bands 17 |
| --keep-boundary-flows false | --gvcf-gq-bands 18 |
| --gvcf-gq-bands 1 | --gvcf-gq-bands 19 |
| --gvcf-gq-bands 2 | --gvcf-gq-bands 20 |
| --gvcf-gq-bands 3 | --gvcf-gq-bands 21 |
| --gvcf-gq-bands 4 | --gvcf-gq-bands 22 |
| --gvcf-gq-bands 5 | --gvcf-gq-bands 23 |
| --gvcf-gq-bands 6 | --gvcf-gq-bands 24 |
| --gvcf-gq-bands 7 | --gvcf-gq-bands 25 |
| --gvcf-gq-bands 8 | --gvcf-gq-bands 26 |
| --gvcf-gq-bands 9 | --gvcf-gq-bands 27 |
| --gvcf-gq-bands 10 | --gvcf-gq-bands 28 |
| --gvcf-gq-bands 11 | --gvcf-gq-bands 29 |
| --gvcf-gq-bands 12 | --gvcf-gq-bands 30 |
| --gvcf-gq-bands 13 | --gvcf-gq-bands 31 |
| --gvcf-gq-bands 14 | --gvcf-gq-bands 32 |
| --gvcf-gq-bands 15 | --gvcf-gq-bands 33 |
| --gvcf-gq-bands 16 | --gvcf-gq-bands 34 |
| --gvcf-gq-bands 17 | --gvcf-gq-bands 35 |
| --gvcf-gq-bands 18 | --gvcf-gq-bands 36 |
| --gvcf-gq-bands 19 | --gvcf-gq-bands 37 |
| --gvcf-gq-bands 20 | --gvcf-gq-bands 38 |
| --gvcf-gq-bands 21 | --gvcf-gq-bands 39 |
| --gvcf-gq-bands 22 | --gvcf-gq-bands 40 |
| --gvcf-gq-bands 23 | --gvcf-gq-bands 41 |
| --gvcf-gq-bands 24 | --gvcf-gq-bands 42 |
| --gvcf-gq-bands 25 | --gvcf-gq-bands 43 |
| --gvcf-gq-bands 26 | --gvcf-gq-bands 44 |
| --gvcf-gq-bands 27 | --gvcf-gq-bands 45 |
| --gvcf-gq-bands 28 | --gvcf-gq-bands 46 |
| --gvcf-gq-bands 29 | --gvcf-gq-bands 47 |
| --gvcf-gq-bands 30 | --gvcf-gq-bands 48 |
| --gvcf-gq-bands 31 | --gvcf-gq-bands 49 |
| --gvcf-gq-bands 32 | --gvcf-gq-bands 50 |
| --gvcf-gq-bands 33 | --gvcf-gq-bands 51 |
| --gvcf-gq-bands 34 | --gvcf-gq-bands 52 |
| --gvcf-gq-bands 35 | --gvcf-gq-bands 53 |
| --gvcf-gq-bands 36 | --gvcf-gq-bands 54 |
| --gvcf-gq-bands 37 | --gvcf-gq-bands 55 |
| --gvcf-gq-bands 38 | --gvcf-gq-bands 56 |
| --gvcf-gq-bands 39 | --gvcf-gq-bands 57 |
| --gvcf-gq-bands 40 | --gvcf-gq-bands 58 |
| --gvcf-gq-bands 41 | --gvcf-gq-bands 59 |
| --gvcf-gq-bands 42 | --gvcf-gq-bands 60 |
| --gvcf-gq-bands 43 | --gvcf-gq-bands 70 |
| --gvcf-gq-bands 44 | --gvcf-gq-bands 80 |
| --gvcf-gq-bands 45 | --gvcf-gq-bands 90 |
| --gvcf-gq-bands 46 | --gvcf-gq-bands 99 |
| --gvcf-gq-bands 47 | --floor-blocks false |
| --gvcf-gq-bands 48 | --indel-size-to-eliminate-in-ref-model 10 |
| --gvcf-gq-bands 49 | --disable-optimizations false |
| --gvcf-gq-bands 50 | --dragen-mode false |
| --gvcf-gq-bands 51 | --apply-bqd false |
| --gvcf-gq-bands 52 | --apply-frd false |
| --gvcf-gq-bands 53 | --disable-spanning-event-genotyping false |
| --gvcf-gq-bands 54 | --transform-dragen-mapping-quality false |
| --gvcf-gq-bands 55 | --mapping-quality-threshold-for-genotyping 20 |
| --gvcf-gq-bands 56 | --max-effective-depth-adjustment-for-frd 0 |
| --gvcf-gq-bands 57 | --just-determine-active-regions false |
| --gvcf-gq-bands 58 | --dont-genotype false |
| --gvcf-gq-bands 59 | --do-not-run-physical-phasing false |
| --gvcf-gq-bands 60 | --do-not-correct-overlapping-quality false |
| --gvcf-gq-bands 70 | --use-filtered-reads-for-annotations false |
| --gvcf-gq-bands 80 | --adaptive-pruning false |
| --gvcf-gq-bands 90 | --do-not-recover-dangling-branches false |
| --gvcf-gq-bands 99 | --recover-dangling-heads false |
| --floor-blocks false | --kmer-size 10 |
| --indel-size-to-eliminate-in-ref-model 10 | --kmer-size 25 |
| --disable-optimizations false | --dont-increase-kmer-sizes-for-cycles false |
| --dragen-mode false | --allow-non-unique-kmers-in-ref false |
| --flow-mode NONE | --num-pruning-samples 1 |
| --apply-bqd false | --min-dangling-branch-length 4 |
| --apply-frd false | --recover-all-dangling-branches false |
| --disable-spanning-event-genotyping false | --max-num-haplotypes-in-population 128 |
| --transform-dragen-mapping-quality false | --min-pruning 2 |
| --mapping-quality-threshold-for-genotyping 20 | --adaptive-pruning-initial-error-rate 0.001 |
| --max-effective-depth-adjustment-for-frd 0 | --pruning-lod-threshold 2.302585092994046 |
| --just-determine-active-regions false | --pruning-seeding-lod-threshold 9.210340371976184 |
| --dont-genotype false | --max-unpruned-variants 100 |
| --do-not-run-physical-phasing false | --linked-de-bruijn-graph false |
| --do-not-correct-overlapping-quality false | --disable-artificial-haplotype-recovery false |
| --use-filtered-reads-for-annotations false | --enable-legacy-graph-cycle-detection false |
| --use-flow-aligner-for-stepwise-hc-filtering false | --debug-assembly false |
| --adaptive-pruning false | --debug-graph-transformations false |
| --do-not-recover-dangling-branches false | --capture-assembly-failure-bam false |
| --recover-dangling-heads false | --num-matching-bases-in-dangling-end-to-recover -1 |
| --kmer-size 10 | --error-correction-log-odds -Infinity |
| --kmer-size 25 | --error-correct-reads false |
| --dont-increase-kmer-sizes-for-cycles false | --kmer-length-for-read-error-correction 25 |
| --allow-non-unique-kmers-in-ref false | --min-observations-for-kmer-to-be-solid 20 |
| --num-pruning-samples 1 | --base-quality-score-threshold 18 |
| --min-dangling-branch-length 4 | --dragstr-het-hom-ratio 2 |
| --recover-all-dangling-branches false | --dont-use-dragstr-pair-hmm-scores false |
| --max-num-haplotypes-in-population 128 | --pair-hmm-gap-continuation-penalty 10 |
| --min-pruning 2 | --expected-mismatch-rate-for-read-disqualification 0.02 |
| --adaptive-pruning-initial-error-rate 0.001 | --pair-hmm-implementation FASTEST_AVAILABLE |
| --pruning-lod-threshold 2.302585092994046 | --pcr-indel-model CONSERVATIVE |
| --pruning-seeding-lod-threshold 9.210340371976184 | --phred-scaled-global-read-mismapping-rate 45 |
| --max-unpruned-variants 100 | --disable-symmetric-hmm-normalizing false |
| --linked-de-bruijn-graph false | --disable-cap-base-qualities-to-map-quality false |
| --disable-artificial-haplotype-recovery false | --enable-dynamic-read-disqualification-for-genotyping false |
| --enable-legacy-graph-cycle-detection false | --dynamic-read-disqualification-threshold 1.0 |
| --debug-assembly false | --native-pair-hmm-threads 4 |
| --debug-graph-transformations false | --native-pair-hmm-use-double-precision false |
| --capture-assembly-failure-bam false | --bam-writer-type CALLED_HAPLOTYPES |
| --num-matching-bases-in-dangling-end-to-recover -1 | --dont-use-soft-clipped-bases false |
| --error-correction-log-odds -Infinity | --min-base-quality-score 10 |
| --error-correct-reads false | --smith-waterman JAVA |
| --kmer-length-for-read-error-correction 25 | --emit-ref-confidence NONE |
| --min-observations-for-kmer-to-be-solid 20 | --force-call-filtered-alleles false |
| --likelihood-calculation-engine PairHMM | --soft-clip-low-quality-ends false |
| --base-quality-score-threshold 18 | --allele-informative-reads-overlap-margin 2 |
| --dragstr-het-hom-ratio 2 | --smith-waterman-dangling-end-match-value 25 |
| --dont-use-dragstr-pair-hmm-scores false | --smith-waterman-dangling-end-mismatch-penalty -50 |
| --pair-hmm-gap-continuation-penalty 10 | --smith-waterman-dangling-end-gap-open-penalty -110 |
| --expected-mismatch-rate-for-read-disqualification 0.02 | --smith-waterman-dangling-end-gap-extend-penalty -6 |
| --pair-hmm-implementation FASTEST_AVAILABLE | --smith-waterman-haplotype-to-reference-match-value 200 |
| --pcr-indel-model CONSERVATIVE | --smith-waterman-haplotype-to-reference-mismatch-penalty -150 |
| --phred-scaled-global-read-mismapping-rate 45 | --smith-waterman-haplotype-to-reference-gap-open-penalty -260 |
| --disable-symmetric-hmm-normalizing false | --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 |
| --disable-cap-base-qualities-to-map-quality false | --smith-waterman-read-to-haplotype-match-value 10 |
| --enable-dynamic-read-disqualification-for-genotyping false | --smith-waterman-read-to-haplotype-mismatch-penalty -15 |
| --dynamic-read-disqualification-threshold 1.0 | --smith-waterman-read-to-haplotype-gap-open-penalty -30 |
| --native-pair-hmm-threads 4 | --smith-waterman-read-to-haplotype-gap-extend-penalty -5 |
| --native-pair-hmm-use-double-precision false | --min-assembly-region-size 50 |
| --flow-hmm-engine-min-indel-adjust 6 | --max-assembly-region-size 300 |
| --flow-hmm-engine-flat-insertion-penatly 45 | --active-probability-threshold 0.002 |
| --flow-hmm-engine-flat-deletion-penatly 45 | --max-prob-propagation-distance 50 |
| --pileup-detection false | --force-active false |
| --pileup-detection-enable-indel-pileup-calling false | --assembly-region-padding 100 |
| --num-artificial-haplotypes-to-add-per-allele 5 | --padding-around-indels 75 |
| --artifical-haplotype-filtering-kmer-size 10 | --padding-around-snps 20 |
| --pileup-detection-snp-alt-threshold 0.1 | --padding-around-strs 75 |
| --pileup-detection-indel-alt-threshold 0.5 | --max-extension-into-assembly-region-padding-legacy 25 |
| --pileup-detection-absolute-alt-depth 0.0 | --max-reads-per-alignment-start 50 |
| --pileup-detection-snp-adjacent-to-assembled-indel-range 5 | --enable-legacy-assembly-region-trimming false |
| --pileup-detection-bad-read-tolerance 0.0 | --interval-set-rule UNION |
| --pileup-detection-proper-pair-read-badness true | --interval-padding 0 |
| --pileup-detection-edit-distance-read-badness-threshold 0.08 | --interval-exclusion-padding 0 |
| --pileup-detection-chimeric-read-badness true | --interval-merging-rule ALL |
| --pileup-detection-template-mean-badness-threshold 0.0 | --read-validation-stringency SILENT |
| --pileup-detection-template-std-badness-threshold 0.0 | --seconds-between-progress-updates 10.0 |
| --bam-writer-type CALLED_HAPLOTYPES | --disable-sequence-dictionary-validation false |
| --dont-use-soft-clipped-bases false | --create-output-bam-index true |
| --override-fragment-softclip-check false | --create-output-bam-md5 false |
| --min-base-quality-score 10 | --create-output-variant-index true |
| --smith-waterman JAVA | --create-output-variant-md5 false |
| --emit-ref-confidence NONE | --max-variants-per-shard 0 |
| --force-call-filtered-alleles false | --lenient false |
| --reference-model-deletion-quality 30 | --add-output-sam-program-record true |
| --soft-clip-low-quality-ends false | --add-output-vcf-command-line true |
| --allele-informative-reads-overlap-margin 2 | --cloud-prefetch-buffer 40 |
| --smith-waterman-dangling-end-match-value 25 | --cloud-index-prefetch-buffer -1 |
| --smith-waterman-dangling-end-mismatch-penalty -50 | --disable-bam-index-caching false |
| --smith-waterman-dangling-end-gap-open-penalty -110 | --sites-only-vcf-output false |
| --smith-waterman-dangling-end-gap-extend-penalty -6 | --help false |
| --smith-waterman-haplotype-to-reference-match-value 200 | --version false |
| --smith-waterman-haplotype-to-reference-mismatch-penalty -150 | --showHidden false |
| --smith-waterman-haplotype-to-reference-gap-open-penalty -260 | --QUIET false |
| --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 | --use-jdk-deflater false |
| --smith-waterman-read-to-haplotype-match-value 10 | --use-jdk-inflater false |
| --smith-waterman-read-to-haplotype-mismatch-penalty -15 | --gcs-max-retries 20 |
| --smith-waterman-read-to-haplotype-gap-open-penalty -30 | --gcs-project-for-requester-pays |
| --smith-waterman-read-to-haplotype-gap-extend-penalty -5 | --disable-tool-default-read-filters false |
| --flow-assembly-collapse-hmer-size 0 | --minimum-mapping-quality 20 |
| --flow-assembly-collapse-partial-mode false | --disable-tool-default-annotations false |
| --flow-filter-alleles false | --enable-all-annotations false |
| --flow-filter-alleles-qual-threshold 30.0 | --allow-old-rms-mapping-quality-annotation-data false |
| --flow-filter-alleles-sor-threshold 3.0 | Version="4.2.4.1",Date="December 3, 2022 at 1:20:38 AM CET"> |
| --flow-filter-lone-alleles false |
| --flow-filter-alleles-debug-graphs false |
| --min-assembly-region-size 50 |
| --max-assembly-region-size 300 |
| --active-probability-threshold 0.002 |
| --max-prob-propagation-distance 50 |
| --force-active false |
| --assembly-region-padding 100 |
| --padding-around-indels 75 |
| --padding-around-snps 20 |
| --padding-around-strs 75 |
| --max-extension-into-assembly-region-padding-legacy 25 |
| --max-reads-per-alignment-start 50 |
| --enable-legacy-assembly-region-trimming false |
| --interval-set-rule UNION |
| --interval-padding 0 |
| --interval-exclusion-padding 0 |
| --interval-merging-rule ALL |
| --read-validation-stringency SILENT |
| --seconds-between-progress-updates 10.0 |
| --disable-sequence-dictionary-validation false |
| --create-output-bam-index true |
| --create-output-bam-md5 false |
| --create-output-variant-index true |
| --create-output-variant-md5 false |
| --max-variants-per-shard 0 |
| --lenient false |
| --add-output-sam-program-record true |
| --add-output-vcf-command-line true |
| --cloud-prefetch-buffer 40 |
| --cloud-index-prefetch-buffer -1 |
| --disable-bam-index-caching false |
| --sites-only-vcf-output false |
| --help false |
| --version false |
| --showHidden false |
| --verbosity INFO |
| --QUIET false |
| --use-jdk-deflater false |
| --use-jdk-inflater false |
| --gcs-max-retries 20 |
| --gcs-project-for-requester-pays |
| --disable-tool-default-read-filters false |
| --minimum-mapping-quality 20 |
| --disable-tool-default-annotations false |
| --enable-all-annotations false |
| --allow-old-rms-mapping-quality-annotation-data false" |
| Version="4.3.0.0",Date="December 16, 2022 at 12:51:03 AM CET"> |
****** KILL [#B] filterDepth : 21 en trop
CLOSED: [2023-01-04 Wed 19:16]
Nouvelle version (correcton bug markdupicates)
#+begin_src sh
grep '^NC' out/63003856_S135/variantCalling/filter-depth.vcf |wc -l
82054
#+end_src
Alexis
#+begin_src sh
zgrep '^NC' /Work/Groups/bisonex/ref_63003856_S135/63003856_S135_DP_over_30.vcf | wc -l
82033
#+end_src
Ne vient pas du filtre sur la profondeur:
bcftools filter -i 'FORMAT/AD[0:1]<=10' 63003856_S135_DP_over_30.vcf
bcftools filter -i 'FORMAT/DP<=30' 63003856_S135_DP_over_30.vcf
Idem pour notre version. Rien ne sort.
On compare le nombre de lignes
#+begin_src sh
bgzip out/63003856_S135/variantCalling/filter-depth.vcf
tabix /Work/Groups/bisonex/ref_63003856_S135/63003856_S135_DP_over_30.vcf.gz
tabix out/63003856_S135/variantCalling/filter-depth.vcf.gz
bcftools isec out/63003856_S135/variantCalling/filter-depth.vcf.gz /Work/Groups/bisonex/ref_63003856_S135/63003856_S135_DP_over_30.vcf.gz -p compare-filter-depth
find compare-filter-depth/ -type f -exec wc -l {} \;
84763 compare-filter-depth/sites.txt
710 compare-filter-depth/0001.vcf
8 compare-filter-depth/README.txt
85339 compare-filter-depth/0002.vcf
85340 compare-filter-depth/0003.vcf
725 compare-filter-depth/0000.vcf
#+end_src
****** KILL exclude SNP + consensual : 34 en trop !!
CLOSED: [2023-01-04 Wed 19:16]
$ grep '^NC' out/63003856_S135/variantCalling/filter-polymorphisms.vcf | wc -l
8898
vs
$ grep '^NC' /Work/Groups/bisonex/ref_63003856_S135/63003856_S135_DP_over_30_not_SNP_consensual_sequence.vcf | wc -l
8864
****** KILL Filter technical variants
CLOSED: [2023-01-04 Wed 19:16]
**** DONE Gatk 4.2.4 : idem
CLOSED: [2023-01-07 Sat 00:05]
***** DONE Variant calling
CLOSED: [2023-01-07 Sat 00:05]
****** DONE haplotypecaller: mieux mais non identique !
CLOSED: [2023-01-07 Sat 00:05]
******* DONE Nombres lignes gatk 4.2.2 : faible différence
CLOSED: [2023-01-04 Wed 19:18]
$ zgrep '^NC' 63003856_S135.vcf.gz | wc -l
1506931
$ grep '^NC' /Work/Groups/bisonex/ref-vcf/63003856_S135 .vcf | wc -l
1506894
******* DONE Flags la même version de gatk 4.2.2 : ok identique
CLOSED: [2023-01-04 Wed 19:09]
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller
| ",Version="4.2.4.1",Date="January 4, 2023 at 1:46:41 AM CET"> | Version="4.2.4.1",Date="December 3, 2022 at 1:20:38 AM CET"> |
| --dbsnp /Work/Users/apraga/bisonex/work/5d/feb81028d262d7701bed0a759ff6f6/dbSNP.gz | --dbsnp /mnt/j/bases_de_donnees/dbSNP/GCF_000001405.39.gz |
| --max-mnp-distance 2 | --max-mnp-distance 2 |
| --output 63003856_S135.vcf.gz | --output /mnt/j/working_directory_pipeline_analyse_exome/vcf/63003856_S135.vcf |
| --input 63003856_S135.bam | --input /mnt/j/working_directory_pipeline_analyse_exome/bam/63003856_S135_recalibrated_hg38.bam |
| --reference genomeRef.fna | --reference /mnt/j/bases_de_donnees/genome/GRCh38_latest_genomic.fna |
| --tmp-dir . | --verbosity WARNING |
| --use-posteriors-to-calculate-qual false | --use-posteriors-to-calculate-qual false |
| --dont-use-dragstr-priors false | --dont-use-dragstr-priors false |
| --use-new-qual-calculator true | --use-new-qual-calculator true |
| --annotate-with-num-discovered-alleles false | --annotate-with-num-discovered-alleles false |
| --heterozygosity 0.001 | --heterozygosity 0.001 |
| --indel-heterozygosity 1.25E-4 | --indel-heterozygosity 1.25E-4 |
| --heterozygosity-stdev 0.01 | --heterozygosity-stdev 0.01 |
| --standard-min-confidence-threshold-for-calling 30.0 | --standard-min-confidence-threshold-for-calling 30.0 |
| --max-alternate-alleles 6 | --max-alternate-alleles 6 |
| --max-genotype-count 1024 | --max-genotype-count 1024 |
| --sample-ploidy 2 | --sample-ploidy 2 |
| --num-reference-samples-if-no-call 0 | --num-reference-samples-if-no-call 0 |
| --genotype-assignment-method USE_PLS_TO_ASSIGN | --genotype-assignment-method USE_PLS_TO_ASSIGN |
| --contamination-fraction-to-filter 0.0 | --contamination-fraction-to-filter 0.0 |
| --output-mode EMIT_VARIANTS_ONLY | --output-mode EMIT_VARIANTS_ONLY |
| --all-site-pls false | --all-site-pls false |
| --gvcf-gq-bands 1 | --gvcf-gq-bands 1 |
| --gvcf-gq-bands 2 | --gvcf-gq-bands 2 |
| --gvcf-gq-bands 3 | --gvcf-gq-bands 3 |
| --gvcf-gq-bands 4 | --gvcf-gq-bands 4 |
| --gvcf-gq-bands 5 | --gvcf-gq-bands 5 |
| --gvcf-gq-bands 6 | --gvcf-gq-bands 6 |
| --gvcf-gq-bands 7 | --gvcf-gq-bands 7 |
| --gvcf-gq-bands 8 | --gvcf-gq-bands 8 |
| --gvcf-gq-bands 9 | --gvcf-gq-bands 9 |
| --gvcf-gq-bands 10 | --gvcf-gq-bands 10 |
| --gvcf-gq-bands 11 | --gvcf-gq-bands 11 |
| --gvcf-gq-bands 12 | --gvcf-gq-bands 12 |
| --gvcf-gq-bands 13 | --gvcf-gq-bands 13 |
| --gvcf-gq-bands 14 | --gvcf-gq-bands 14 |
| --gvcf-gq-bands 15 | --gvcf-gq-bands 15 |
| --gvcf-gq-bands 16 | --gvcf-gq-bands 16 |
| --gvcf-gq-bands 17 | --gvcf-gq-bands 17 |
| --gvcf-gq-bands 18 | --gvcf-gq-bands 18 |
| --gvcf-gq-bands 19 | --gvcf-gq-bands 19 |
| --gvcf-gq-bands 20 | --gvcf-gq-bands 20 |
| --gvcf-gq-bands 21 | --gvcf-gq-bands 21 |
| --gvcf-gq-bands 22 | --gvcf-gq-bands 22 |
| --gvcf-gq-bands 23 | --gvcf-gq-bands 23 |
| --gvcf-gq-bands 24 | --gvcf-gq-bands 24 |
| --gvcf-gq-bands 25 | --gvcf-gq-bands 25 |
| --gvcf-gq-bands 26 | --gvcf-gq-bands 26 |
| --gvcf-gq-bands 27 | --gvcf-gq-bands 27 |
| --gvcf-gq-bands 28 | --gvcf-gq-bands 28 |
| --gvcf-gq-bands 29 | --gvcf-gq-bands 29 |
| --gvcf-gq-bands 30 | --gvcf-gq-bands 30 |
| --gvcf-gq-bands 31 | --gvcf-gq-bands 31 |
| --gvcf-gq-bands 32 | --gvcf-gq-bands 32 |
| --gvcf-gq-bands 33 | --gvcf-gq-bands 33 |
| --gvcf-gq-bands 34 | --gvcf-gq-bands 34 |
| --gvcf-gq-bands 35 | --gvcf-gq-bands 35 |
| --gvcf-gq-bands 36 | --gvcf-gq-bands 36 |
| --gvcf-gq-bands 37 | --gvcf-gq-bands 37 |
| --gvcf-gq-bands 38 | --gvcf-gq-bands 38 |
| --gvcf-gq-bands 39 | --gvcf-gq-bands 39 |
| --gvcf-gq-bands 40 | --gvcf-gq-bands 40 |
| --gvcf-gq-bands 41 | --gvcf-gq-bands 41 |
| --gvcf-gq-bands 42 | --gvcf-gq-bands 42 |
| --gvcf-gq-bands 43 | --gvcf-gq-bands 43 |
| --gvcf-gq-bands 44 | --gvcf-gq-bands 44 |
| --gvcf-gq-bands 45 | --gvcf-gq-bands 45 |
| --gvcf-gq-bands 46 | --gvcf-gq-bands 46 |
| --gvcf-gq-bands 47 | --gvcf-gq-bands 47 |
| --gvcf-gq-bands 48 | --gvcf-gq-bands 48 |
| --gvcf-gq-bands 49 | --gvcf-gq-bands 49 |
| --gvcf-gq-bands 50 | --gvcf-gq-bands 50 |
| --gvcf-gq-bands 51 | --gvcf-gq-bands 51 |
| --gvcf-gq-bands 52 | --gvcf-gq-bands 52 |
| --gvcf-gq-bands 53 | --gvcf-gq-bands 53 |
| --gvcf-gq-bands 54 | --gvcf-gq-bands 54 |
| --gvcf-gq-bands 55 | --gvcf-gq-bands 55 |
| --gvcf-gq-bands 56 | --gvcf-gq-bands 56 |
| --gvcf-gq-bands 57 | --gvcf-gq-bands 57 |
| --gvcf-gq-bands 58 | --gvcf-gq-bands 58 |
| --gvcf-gq-bands 59 | --gvcf-gq-bands 59 |
| --gvcf-gq-bands 60 | --gvcf-gq-bands 60 |
| --gvcf-gq-bands 70 | --gvcf-gq-bands 70 |
| --gvcf-gq-bands 80 | --gvcf-gq-bands 80 |
| --gvcf-gq-bands 90 | --gvcf-gq-bands 90 |
| --gvcf-gq-bands 99 | --gvcf-gq-bands 99 |
| --floor-blocks false | --floor-blocks false |
| --indel-size-to-eliminate-in-ref-model 10 | --indel-size-to-eliminate-in-ref-model 10 |
| --disable-optimizations false | --disable-optimizations false |
| --dragen-mode false | --dragen-mode false |
| --apply-bqd false | --apply-bqd false |
| --apply-frd false | --apply-frd false |
| --disable-spanning-event-genotyping false | --disable-spanning-event-genotyping false |
| --transform-dragen-mapping-quality false | --transform-dragen-mapping-quality false |
| --mapping-quality-threshold-for-genotyping 20 | --mapping-quality-threshold-for-genotyping 20 |
| --max-effective-depth-adjustment-for-frd 0 | --max-effective-depth-adjustment-for-frd 0 |
| --just-determine-active-regions false | --just-determine-active-regions false |
| --dont-genotype false | --dont-genotype false |
| --do-not-run-physical-phasing false | --do-not-run-physical-phasing false |
| --do-not-correct-overlapping-quality false | --do-not-correct-overlapping-quality false |
| --use-filtered-reads-for-annotations false | --use-filtered-reads-for-annotations false |
| --adaptive-pruning false | --adaptive-pruning false |
| --do-not-recover-dangling-branches false | --do-not-recover-dangling-branches false |
| --recover-dangling-heads false | --recover-dangling-heads false |
| --kmer-size 10 | --kmer-size 10 |
| --kmer-size 25 | --kmer-size 25 |
| --dont-increase-kmer-sizes-for-cycles false | --dont-increase-kmer-sizes-for-cycles false |
| --allow-non-unique-kmers-in-ref false | --allow-non-unique-kmers-in-ref false |
| --num-pruning-samples 1 | --num-pruning-samples 1 |
| --min-dangling-branch-length 4 | --min-dangling-branch-length 4 |
| --recover-all-dangling-branches false | --recover-all-dangling-branches false |
| --max-num-haplotypes-in-population 128 | --max-num-haplotypes-in-population 128 |
| --min-pruning 2 | --min-pruning 2 |
| --adaptive-pruning-initial-error-rate 0.001 | --adaptive-pruning-initial-error-rate 0.001 |
| --pruning-lod-threshold 2.302585092994046 | --pruning-lod-threshold 2.302585092994046 |
| --pruning-seeding-lod-threshold 9.210340371976184 | --pruning-seeding-lod-threshold 9.210340371976184 |
| --max-unpruned-variants 100 | --max-unpruned-variants 100 |
| --linked-de-bruijn-graph false | --linked-de-bruijn-graph false |
| --disable-artificial-haplotype-recovery false | --disable-artificial-haplotype-recovery false |
| --enable-legacy-graph-cycle-detection false | --enable-legacy-graph-cycle-detection false |
| --debug-assembly false | --debug-assembly false |
| --debug-graph-transformations false | --debug-graph-transformations false |
| --capture-assembly-failure-bam false | --capture-assembly-failure-bam false |
| --num-matching-bases-in-dangling-end-to-recover -1 | --num-matching-bases-in-dangling-end-to-recover -1 |
| --error-correction-log-odds -Infinity | --error-correction-log-odds -Infinity |
| --error-correct-reads false | --error-correct-reads false |
| --kmer-length-for-read-error-correction 25 | --kmer-length-for-read-error-correction 25 |
| --min-observations-for-kmer-to-be-solid 20 | --min-observations-for-kmer-to-be-solid 20 |
| --base-quality-score-threshold 18 | --base-quality-score-threshold 18 |
| --dragstr-het-hom-ratio 2 | --dragstr-het-hom-ratio 2 |
| --dont-use-dragstr-pair-hmm-scores false | --dont-use-dragstr-pair-hmm-scores false |
| --pair-hmm-gap-continuation-penalty 10 | --pair-hmm-gap-continuation-penalty 10 |
| --expected-mismatch-rate-for-read-disqualification 0.02 | --expected-mismatch-rate-for-read-disqualification 0.02 |
| --pair-hmm-implementation FASTEST_AVAILABLE | --pair-hmm-implementation FASTEST_AVAILABLE |
| --pcr-indel-model CONSERVATIVE | --pcr-indel-model CONSERVATIVE |
| --phred-scaled-global-read-mismapping-rate 45 | --phred-scaled-global-read-mismapping-rate 45 |
| --disable-symmetric-hmm-normalizing false | --disable-symmetric-hmm-normalizing false |
| --disable-cap-base-qualities-to-map-quality false | --disable-cap-base-qualities-to-map-quality false |
| --enable-dynamic-read-disqualification-for-genotyping false | --enable-dynamic-read-disqualification-for-genotyping false |
| --dynamic-read-disqualification-threshold 1.0 | --dynamic-read-disqualification-threshold 1.0 |
| --native-pair-hmm-threads 4 | --native-pair-hmm-threads 4 |
| --native-pair-hmm-use-double-precision false | --native-pair-hmm-use-double-precision false |
| --bam-writer-type CALLED_HAPLOTYPES | --bam-writer-type CALLED_HAPLOTYPES |
| --dont-use-soft-clipped-bases false | --dont-use-soft-clipped-bases false |
| --min-base-quality-score 10 | --min-base-quality-score 10 |
| --smith-waterman JAVA | --smith-waterman JAVA |
| --emit-ref-confidence NONE | --emit-ref-confidence NONE |
| --force-call-filtered-alleles false | --force-call-filtered-alleles false |
| --soft-clip-low-quality-ends false | --soft-clip-low-quality-ends false |
| --allele-informative-reads-overlap-margin 2 | --allele-informative-reads-overlap-margin 2 |
| --smith-waterman-dangling-end-match-value 25 | --smith-waterman-dangling-end-match-value 25 |
| --smith-waterman-dangling-end-mismatch-penalty -50 | --smith-waterman-dangling-end-mismatch-penalty -50 |
| --smith-waterman-dangling-end-gap-open-penalty -110 | --smith-waterman-dangling-end-gap-open-penalty -110 |
| --smith-waterman-dangling-end-gap-extend-penalty -6 | --smith-waterman-dangling-end-gap-extend-penalty -6 |
| --smith-waterman-haplotype-to-reference-match-value 200 | --smith-waterman-haplotype-to-reference-match-value 200 |
| --smith-waterman-haplotype-to-reference-gap-open-penalty -260 | --smith-waterman-haplotype-to-reference-gap-open-penalty -260 |
| --smith-waterman-haplotype-to-reference-mismatch-penalty -150 | --smith-waterman-haplotype-to-reference-mismatch-penalty -150 |
| --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 | --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 |
| --smith-waterman-read-to-haplotype-match-value 10 | --smith-waterman-read-to-haplotype-match-value 10 |
| --smith-waterman-read-to-haplotype-mismatch-penalty -15 | --smith-waterman-read-to-haplotype-mismatch-penalty -15 |
| --smith-waterman-read-to-haplotype-gap-open-penalty -30 | --smith-waterman-read-to-haplotype-gap-open-penalty -30 |
| --smith-waterman-read-to-haplotype-gap-extend-penalty -5 | --smith-waterman-read-to-haplotype-gap-extend-penalty -5 |
| --min-assembly-region-size 50 | --min-assembly-region-size 50 |
| --max-assembly-region-size 300 | --max-assembly-region-size 300 |
| --active-probability-threshold 0.002 | --active-probability-threshold 0.002 |
| --max-prob-propagation-distance 50 | --max-prob-propagation-distance 50 |
| --force-active false | --force-active false |
| --assembly-region-padding 100 | --assembly-region-padding 100 |
| --padding-around-indels 75 | --padding-around-indels 75 |
| --padding-around-snps 20 | --padding-around-snps 20 |
| --padding-around-strs 75 | --padding-around-strs 75 |
| --max-extension-into-assembly-region-padding-legacy 25 | --max-extension-into-assembly-region-padding-legacy 25 |
| --max-reads-per-alignment-start 50 | --max-reads-per-alignment-start 50 |
| --enable-legacy-assembly-region-trimming false | --enable-legacy-assembly-region-trimming false |
| --interval-set-rule UNION | --interval-set-rule UNION |
| --interval-padding 0 | --interval-padding 0 |
| --interval-exclusion-padding 0 | --interval-exclusion-padding 0 |
| --interval-merging-rule ALL | --interval-merging-rule ALL |
| --read-validation-stringency SILENT | --read-validation-stringency SILENT |
| --seconds-between-progress-updates 10.0 | --seconds-between-progress-updates 10.0 |
| --disable-sequence-dictionary-validation false | --disable-sequence-dictionary-validation false |
| --create-output-bam-index true | --create-output-bam-index true |
| --create-output-bam-md5 false | --create-output-bam-md5 false |
| --create-output-variant-index true | --create-output-variant-index true |
| --create-output-variant-md5 false | --create-output-variant-md5 false |
| --max-variants-per-shard 0 | --max-variants-per-shard 0 |
| --lenient false | --lenient false |
| --add-output-sam-program-record true | --add-output-sam-program-record true |
| --add-output-vcf-command-line true | --add-output-vcf-command-line true |
| --cloud-prefetch-buffer 40 | --cloud-prefetch-buffer 40 |
| --cloud-index-prefetch-buffer -1 | --cloud-index-prefetch-buffer -1 |
| --disable-bam-index-caching false | --disable-bam-index-caching false |
| --sites-only-vcf-output false | --sites-only-vcf-output false |
| --help false | --help false |
| --version false | --version false |
| --showHidden false | --showHidden false |
| --verbosity INFO | --QUIET false |
| --QUIET false | --use-jdk-deflater false |
| --use-jdk-deflater false | --use-jdk-inflater false |
| --use-jdk-inflater false | --gcs-max-retries 20 |
| --gcs-max-retries 20 | --gcs-project-for-requester-pays |
| --gcs-project-for-requester-pays | --disable-tool-default-read-filters false |
| --disable-tool-default-read-filters false | --minimum-mapping-quality 20 |
| --minimum-mapping-quality 20 | --disable-tool-default-annotations false |
| --disable-tool-default-annotations false | --enable-all-annotations false |
| --enable-all-annotations false | --allow-old-rms-mapping-quality-annotation-data false |
| --allow-old-rms-mapping-quality-annotation-data false | |
****** DONE filter depth : Toujours la même différence...
CLOSED: [2023-01-07 Sat 00:05]
$ grep '^NC' filter-depth.vcf | wc -l
82054
$ zgrep '^NC' /Work/Groups/bisonex/ref_63003856_S135/63003856_S135_DP_over_30.vcf.gz | wc -l
82033
Non lié à la profondeur : on teste avec
bcftools filter -i 'FORMAT/DP<=30' filter-depth.vcf
bcftools filter -i 'FORMAT/AD[0:1]<=10' filter-depth.vcf
****** DONE Vérifier qu'en utilsant 2 filtres différents on a bien la même chose : oui
CLOSED: [2023-01-07 Sat 00:05]
$ bcftools filter -e 'FORMAT
| --heterozygosity-stdev 0.01 |
| --standard-min-confidence-threshold-for-calling 30.0 | --standard-min-confidence-threshold-for-calling 30.0 |
| --max-alternate-alleles 6 | --max-alternate-alleles 6 |
| --max-genotype-count 1024 | --max-genotype-count 1024 |
| --sample-ploidy 2 | --sample-ploidy 2 |
| --num-reference-samples-if-no-call 0 | --num-reference-samples-if-no-call 0 |
| --genotype-assignment-method USE_PLS_TO_ASSIGN | --genotype-assignment-method USE_PLS_TO_ASSIGN |
| --contamination-fraction-to-filter 0.0 | --contamination-fraction-to-filter 0.0 |
| --output-mode EMIT_VARIANTS_ONLY | --output-mode EMIT_VARIANTS_ONLY |
| --all-site-pls false | --all-site-pls false |
| --gvcf-gq-bands 1 | --gvcf-gq-bands 1 |
| --gvcf-gq-bands 2 | --gvcf-gq-bands 2 |
| --gvcf-gq-bands 3 | --gvcf-gq-bands 3 |
| --gvcf-gq-bands 4 | --gvcf-gq-bands 4 |
| --gvcf-gq-bands 5 | --gvcf-gq-bands 5 |
| --gvcf-gq-bands 6 | --gvcf-gq-bands 6 |
| --gvcf-gq-bands 7 | --gvcf-gq-bands 7 |
| --gvcf-gq-bands 8 | --gvcf-gq-bands 8 |
| --gvcf-gq-bands 9 | --gvcf-gq-bands 9 |
| --gvcf-gq-bands 10 | --gvcf-gq-bands 10 |
| --gvcf-gq-bands 11 | --gvcf-gq-bands 11 |
| --gvcf-gq-bands 12 | --gvcf-gq-bands 12 |
| --gvcf-gq-bands 13 | --gvcf-gq-bands 13 |
| --gvcf-gq-bands 14 | --gvcf-gq-bands 14 |
| --gvcf-gq-bands 15 | --gvcf-gq-bands 15 |
| --gvcf-gq-bands 16 | --gvcf-gq-bands 16 |
| --gvcf-gq-bands 17 | --gvcf-gq-bands 17 |
| --gvcf-gq-bands 18 | --gvcf-gq-bands 18 |
| --gvcf-gq-bands 19 | --gvcf-gq-bands 19 |
| --gvcf-gq-bands 20 | --gvcf-gq-bands 20 |
| --gvcf-gq-bands 21 | --gvcf-gq-bands 21 |
| --gvcf-gq-bands 22 | --gvcf-gq-bands 22 |
| --gvcf-gq-bands 23 | --gvcf-gq-bands 23 |
| --gvcf-gq-bands 24 | --gvcf-gq-bands 24 |
| --gvcf-gq-bands 25 | --gvcf-gq-bands 25 |
| --gvcf-gq-bands 26 | --gvcf-gq-bands 26 |
| --gvcf-gq-bands 27 | --gvcf-gq-bands 27 |
| --gvcf-gq-bands 28 | --gvcf-gq-bands 28 |
| --gvcf-gq-bands 29 | --gvcf-gq-bands 29 |
| --gvcf-gq-bands 30 | --gvcf-gq-bands 30 |
| --gvcf-gq-bands 31 | --gvcf-gq-bands 31 |
| --gvcf-gq-bands 32 | --gvcf-gq-bands 32 |
| --gvcf-gq-bands 33 | --gvcf-gq-bands 33 |
| --gvcf-gq-bands 34 | --gvcf-gq-bands 34 |
| --gvcf-gq-bands 35 | --gvcf-gq-bands 35 |
| --gvcf-gq-bands 36 | --gvcf-gq-bands 36 |
| --gvcf-gq-bands 37 | --gvcf-gq-bands 37 |
| --gvcf-gq-bands 38 | --gvcf-gq-bands 38 |
| --gvcf-gq-bands 39 | --gvcf-gq-bands 39 |
| --gvcf-gq-bands 40 | --gvcf-gq-bands 40 |
| --gvcf-gq-bands 41 | --gvcf-gq-bands 41 |
| --gvcf-gq-bands 42 | --gvcf-gq-bands 42 |
| --gvcf-gq-bands 43 | --gvcf-gq-bands 43 |
| --gvcf-gq-bands 44 | --gvcf-gq-bands 44 |
| --gvcf-gq-bands 45 | --gvcf-gq-bands 45 |
| --gvcf-gq-bands 46 | --gvcf-gq-bands 46 |
| --gvcf-gq-bands 47 | --gvcf-gq-bands 47 |
| --gvcf-gq-bands 48 | --gvcf-gq-bands 48 |
| --gvcf-gq-bands 49 | --gvcf-gq-bands 49 |
| --gvcf-gq-bands 50 | --gvcf-gq-bands 50 |
| --gvcf-gq-bands 51 | --gvcf-gq-bands 51 |
| --gvcf-gq-bands 52 | --gvcf-gq-bands 52 |
| --gvcf-gq-bands 53 | --gvcf-gq-bands 53 |
| --gvcf-gq-bands 54 | --gvcf-gq-bands 54 |
| --gvcf-gq-bands 55 | --gvcf-gq-bands 55 |
| --gvcf-gq-bands 56 | --gvcf-gq-bands 56 |
| --gvcf-gq-bands 57 | --gvcf-gq-bands 57 |
| --gvcf-gq-bands 58 | --gvcf-gq-bands 58 |
| --gvcf-gq-bands 59 | --gvcf-gq-bands 59 |
| --gvcf-gq-bands 60 | --gvcf-gq-bands 60 |
| --gvcf-gq-bands 70 | --gvcf-gq-bands 70 |
| --gvcf-gq-bands 80 | --gvcf-gq-bands 80 |
| --gvcf-gq-bands 90 | --gvcf-gq-bands 90 |
| --gvcf-gq-bands 99 | --gvcf-gq-bands 99 |
| --floor-blocks false | --floor-blocks false |
| --indel-size-to-eliminate-in-ref-model 10 | --indel-size-to-eliminate-in-ref-model 10 |
| --disable-optimizations false | --disable-optimizations false |
| --dragen-mode false | --dragen-mode false |
| --apply-bqd false | --apply-bqd false |
| --apply-frd false | --apply-frd false |
| --disable-spanning-event-genotyping false | --disable-spanning-event-genotyping false |
| --transform-dragen-mapping-quality false | --transform-dragen-mapping-quality false |
| --mapping-quality-threshold-for-genotyping 20 | --mapping-quality-threshold-for-genotyping 20 |
| --max-effective-depth-adjustment-for-frd 0 | --max-effective-depth-adjustment-for-frd 0 |
| --just-determine-active-regions false | --just-determine-active-regions false |
| --dont-genotype false | --dont-genotype false |
| --do-not-run-physical-phasing false | --do-not-run-physical-phasing false |
| --do-not-correct-overlapping-quality false | --do-not-correct-overlapping-quality false |
| --use-filtered-reads-for-annotations false | --use-filtered-reads-for-annotations false |
| --adaptive-pruning false | --adaptive-pruning false |
| --do-not-recover-dangling-branches false | --do-not-recover-dangling-branches false |
| --recover-dangling-heads false | --recover-dangling-heads false |
| --kmer-size 10 | --kmer-size 10 |
| --kmer-size 25 | --kmer-size 25 |
| --dont-increase-kmer-sizes-for-cycles false | --dont-increase-kmer-sizes-for-cycles false |
| --allow-non-unique-kmers-in-ref false | --allow-non-unique-kmers-in-ref false |
| --num-pruning-samples 1 | --num-pruning-samples 1 |
| --min-dangling-branch-length 4 | --min-dangling-branch-length 4 |
| --recover-all-dangling-branches false | --recover-all-dangling-branches false |
| --max-num-haplotypes-in-population 128 | --max-num-haplotypes-in-population 128 |
| --min-pruning 2 | --min-pruning 2 |
| --adaptive-pruning-initial-error-rate 0.001 | --adaptive-pruning-initial-error-rate 0.001 |
| --pruning-lod-threshold 2.302585092994046 | --pruning-lod-threshold 2.302585092994046 |
| --pruning-seeding-lod-threshold 9.210340371976184 | --pruning-seeding-lod-threshold 9.210340371976184 |
| --max-unpruned-variants 100 | --max-unpruned-variants 100 |
| --linked-de-bruijn-graph false | --linked-de-bruijn-graph false |
| --disable-artificial-haplotype-recovery false | --disable-artificial-haplotype-recovery false |
| --enable-legacy-graph-cycle-detection false | --enable-legacy-graph-cycle-detection false |
| --debug-assembly false | --debug-assembly false |
| --debug-graph-transformations false | --debug-graph-transformations false |
| --capture-assembly-failure-bam false | --capture-assembly-failure-bam false |
| --num-matching-bases-in-dangling-end-to-recover -1 | --num-matching-bases-in-dangling-end-to-recover -1 |
| --error-correction-log-odds -Infinity | --error-correction-log-odds -Infinity |
| --error-correct-reads false | --error-correct-reads false |
| --kmer-length-for-read-error-correction 25 | --kmer-length-for-read-error-correction 25 |
| --min-observations-for-kmer-to-be-solid 20 | --min-observations-for-kmer-to-be-solid 20 |
| --base-quality-score-threshold 18 | --base-quality-score-threshold 18 |
| --dragstr-het-hom-ratio 2 | --dragstr-het-hom-ratio 2 |
| --dont-use-dragstr-pair-hmm-scores false | --dont-use-dragstr-pair-hmm-scores false |
| --pair-hmm-gap-continuation-penalty 10 | --pair-hmm-gap-continuation-penalty 10 |
| --expected-mismatch-rate-for-read-disqualification 0.02 | --expected-mismatch-rate-for-read-disqualification 0.02 |
| --pair-hmm-implementation FASTEST_AVAILABLE | --pair-hmm-implementation FASTEST_AVAILABLE |
| --pcr-indel-model CONSERVATIVE | --pcr-indel-model CONSERVATIVE |
| --phred-scaled-global-read-mismapping-rate 45 | --phred-scaled-global-read-mismapping-rate 45 |
| --disable-symmetric-hmm-normalizing false | --disable-symmetric-hmm-normalizing false |
| --disable-cap-base-qualities-to-map-quality false | --disable-cap-base-qualities-to-map-quality false |
| --enable-dynamic-read-disqualification-for-genotyping false | --enable-dynamic-read-disqualification-for-genotyping false |
| --dynamic-read-disqualification-threshold 1.0 | --dynamic-read-disqualification-threshold 1.0 |
| --native-pair-hmm-threads 4 | --native-pair-hmm-threads 4 |
| --native-pair-hmm-use-double-precision false | --native-pair-hmm-use-double-precision false |
| --bam-writer-type CALLED_HAPLOTYPES | --bam-writer-type CALLED_HAPLOTYPES |
| --dont-use-soft-clipped-bases false | --dont-use-soft-clipped-bases false |
| --min-base-quality-score 10 | --min-base-quality-score 10 |
| --smith-waterman JAVA | --smith-waterman JAVA |
| --emit-ref-confidence NONE | --emit-ref-confidence NONE |
| --force-call-filtered-alleles false | --force-call-filtered-alleles false |
| --soft-clip-low-quality-ends false | --soft-clip-low-quality-ends false |
| --allele-informative-reads-overlap-margin 2 | --allele-informative-reads-overlap-margin 2 |
| --smith-waterman-dangling-end-match-value 25 | --smith-waterman-dangling-end-match-value 25 |
| --smith-waterman-dangling-end-mismatch-penalty -50 | --smith-waterman-dangling-end-mismatch-penalty -50 |
| --smith-waterman-dangling-end-gap-open-penalty -110 | --smith-waterman-dangling-end-gap-open-penalty -110 |
| --smith-waterman-dangling-end-gap-extend-penalty -6 | --smith-waterman-dangling-end-gap-extend-penalty -6 |
| --smith-waterman-haplotype-to-reference-match-value 200 | --smith-waterman-haplotype-to-reference-match-value 200 |
| --smith-waterman-haplotype-to-reference-mismatch-penalty -150 | --smith-waterman-haplotype-to-reference-mismatch-penalty -150 |
| --smith-waterman-haplotype-to-reference-gap-open-penalty -260 | --smith-waterman-haplotype-to-reference-gap-open-penalty -260 |
| --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 | --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 |
| --smith-waterman-read-to-haplotype-match-value 10 | --smith-waterman-read-to-haplotype-match-value 10 |
| --smith-waterman-read-to-haplotype-mismatch-penalty -15 | --smith-waterman-read-to-haplotype-mismatch-penalty -15 |
| --smith-waterman-read-to-haplotype-gap-open-penalty -30 | --smith-waterman-read-to-haplotype-gap-open-penalty -30 |
| --smith-waterman-read-to-haplotype-gap-extend-penalty -5 | --smith-waterman-read-to-haplotype-gap-extend-penalty -5 |
| --min-assembly-region-size 50 | --min-assembly-region-size 50 |
| --max-assembly-region-size 300 | --max-assembly-region-size 300 |
| --active-probability-threshold 0.002 | --active-probability-threshold 0.002 |
| --max-prob-propagation-distance 50 | --max-prob-propagation-distance 50 |
| --force-active false | --force-active false |
| --assembly-region-padding 100 | --assembly-region-padding 100 |
| --padding-around-indels 75 | --padding-around-indels 75 |
| --padding-around-snps 20 | --padding-around-snps 20 |
| --padding-around-strs 75 | --padding-around-strs 75 |
| --max-extension-into-assembly-region-padding-legacy 25 | --max-extension-into-assembly-region-padding-legacy 25 |
| --max-reads-per-alignment-start 50 | --max-reads-per-alignment-start 50 |
| --enable-legacy-assembly-region-trimming false | --enable-legacy-assembly-region-trimming false |
| --interval-set-rule UNION | --interval-set-rule UNION |
| --interval-padding 0 | --interval-padding 0 |
| --interval-exclusion-padding 0 | --interval-exclusion-padding 0 |
| --interval-merging-rule ALL | --interval-merging-rule ALL |
| --read-validation-stringency SILENT | --read-validation-stringency SILENT |
| --seconds-between-progress-updates 10.0 | --seconds-between-progress-updates 10.0 |
| --disable-sequence-dictionary-validation false | --disable-sequence-dictionary-validation false |
| --create-output-bam-index true | --create-output-bam-index true |
| --create-output-bam-md5 false | --create-output-bam-md5 false |
| --create-output-variant-index true | --create-output-variant-index true
m
post_BaseRecalibrator = _recal.table
post_ApplyBQSR = _recalibrated_hg38.bam
post_haplotypecaller = .vcf
post_depth_filter = _DP_over_30.vcf
post_exclude_SNP = _DP_over_30_not_SNP
post_consensual = _DP_over_30_not_SNP_consensual_sequence.vcf
post_technical = _DP_over_30_not_SNP_consensual_sequence_not_technical.vcf.gz
******* DONE Clean sam
CLOSED: [2023-01-20 Fri 23:44]
ref
$ samtools view -H 63003856_S135_cleaned.bam | grep PN
@PG ID:samtools PN:samtools PP:bwa VN:1.10 CL:/mnt/h/tools/samtools sort -@ 4 -O BAM -o /mnt/j/working_directory_pipeline_analyse_exome/tmp_63003856_S135/63003856_S135.bam
@PG ID:samtools PN:samtools PP:bwa VN:1.13 CL:samtools sort -@ 4 -O BAM -o files/tmp_63003856_S135/63003856_S135.bam
******* DONE Markduplicates
CLOSED: [2023-01-20 Fri 23:44]
ref
| @PG ID:MarkDuplicates VN:Version:4.2.4.1 CL:MarkDuplicates | @PG ID:MarkDuplicates VN:Version:4.2.4.1 CL:MarkDuplicates | |
| --INPUT /mnt/j/working_directory_pipeline_analyse_exome/tmp_63003856_S135/63003856_S135_cleaned.bam | --INPUT files/tmp_63003856_S135/63003856_S135_cleaned.bam | |
| --OUTPUT /mnt/j/working_directory_pipeline_analyse_exome/tmp_63003856_S135/63003856_S135_marked_dup.bam | --OUTPUT files/tmp_63003856_S135/63003856_S135_marked_dup.bam | |
| --METRICS_FILE /mnt/j/working_directory_pipeline_analyse_exome/tmp_63003856_S135/63003856_S135_marked_dup.metrix | --METRICS_FILE files/tmp_63003856_S135/63003856_S135_marked_dup.metrix | |
| --VERBOSITY WARNING | --VERBOSITY WARNING | |
| --CREATE_INDEX true | --CREATE_INDEX true | |
| --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 | --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 | |
| --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 | --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 | |
| --SORTING_COLLECTION_SIZE_RATIO 0.25 | --SORTING_COLLECTION_SIZE_RATIO 0.25 | |
| --TAG_DUPLICATE_SET_MEMBERS false | --TAG_DUPLICATE_SET_MEMBERS false | |
| --REMOVE_SEQUENCING_DUPLICATES false | --REMOVE_SEQUENCING_DUPLICATES false | |
| --TAGGING_POLICY DontTag | --TAGGING_POLICY DontTag | |
| --CLEAR_DT true | --CLEAR_DT true | |
| --DUPLEX_UMI false | --DUPLEX_UMI false | |
| --ADD_PG_TAG_TO_READS true | --ADD_PG_TAG_TO_READS true | |
| --REMOVE_DUPLICATES false | --REMOVE_DUPLICATES false | |
| --ASSUME_SORTED false | --ASSUME_SORTED false | |
| --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES | --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES | |
| --PROGRAM_RECORD_ID MarkDuplicates | --PROGRAM_RECORD_ID MarkDuplicates | |
| --PROGRAM_GROUP_NAME MarkDuplicates | --PROGRAM_GROUP_NAME MarkDuplicates | |
| --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> | --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> | |
| --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 | --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 | |
| --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 | --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 | |
| --QUIET false | --QUIET false | |
| --VALIDATION_STRINGENCY STRICT | --VALIDATION_STRINGENCY STRICT | |
| --COMPRESSION_LEVEL 2 | --COMPRESSION_LEVEL 2 | |
| --MAX_RECORDS_IN_RAM 500000 | --MAX_RECORDS_IN_RAM 500000 | |
| --CREATE_MD5_FILE false | --CREATE_MD5_FILE false | |
| --GA4GH_CLIENT_SECRETS client_secrets.json | --GA4GH_CLIENT_SECRETS client_secrets.json | |
| --help false | --help false | |
| --version false | --version false | |
| --showHidden false | --showHidden false | |
| --USE_JDK_DEFLATER false | --USE_JDK_DEFLATER false | |
| --USE_JDK_INFLATER false | --USE_JDK_INFLATER false | |
| @PG ID:samtools.1 PN:samtools PP:samtools VN:1.13 CL:samtools view -H 63003856_S135_marked_dup.bam |
******* DONE ApplyBQSR
CLOSED: [2023-01-20 Fri 23:48]
Ref
@PG ID:GATK ApplyBQSR VN:4.2.4.1 CL:ApplyBQSR
| --output /mnt/j/working_directory_pipeline_analyse_exome/bam/63003856_S135_recalibrated_hg38.bam | --output files/bam/63003856_S135_recalibrated_hg38.bam |
| --bqsr-recal-file /mnt/j/working_directory_pipeline_analyse_exome/tmp_63003856_S135/63003856_S135_recal.table | --bqsr-recal-file files/tmp_63003856_S135/63003856_S135_recal.table |
| --input /mnt/j/working_directory_pipeline_analyse_exome/tmp_63003856_S135/63003856_S135_marked_dup.bam | --input files/tmp_63003856_S135/63003856_S135_marked_dup.bam |
| --reference /mnt/j/bases_de_donnees/genome/GRCh38_latest_genomic.fna | --reference /Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna |
| --verbosity WARNING | --verbosity WARNING |
| --preserve-qscores-less-than 6 | --preserve-qscores-less-than 6 |
| --use-original-qualities false | --use-original-qualities false |
| --quantize-quals 0 | --quantize-quals 0 |
| --round-down-quantized false | --round-down-quantized false |
| --emit-original-quals false | --emit-original-quals false |
| --global-qscore-prior -1.0 | --global-qscore-prior -1.0 |
| --interval-set-rule UNION | --interval-set-rule UNION |
| --interval-padding 0 | --interval-padding 0 |
| --interval-exclusion-padding 0 | --interval-exclusion-padding 0 |
| --interval-merging-rule ALL | --interval-merging-rule ALL |
| --read-validation-stringency SILENT | --read-validation-stringency SILENT |
| --seconds-between-progress-updates 10.0 | --seconds-between-progress-updates 10.0 |
| --disable-sequence-dictionary-validation false | --disable-sequence-dictionary-validation false |
| --create-output-bam-index true
e-exome-kit/downloads.html
***** DONE D'où vient la différence ?
CLOSED: [2023-04-02 Sun 17:11] SCHEDULED: <2023-03-09 Thu>
****** DONE Statistiques
CLOSED: [2023-03-15 mer. 13:41] SCHEDULED: <2023-03-04 Sat>
On confirnme le nombre de SNP 6665
- 304 ont un problème d’haploide/allèle différente
- 28 avec une différence de génotype
- La majorité ne sont pas vu 6361
[1] "ALl FN 6665"
[1] "Genotype mismatch 28"
[1] "haplotype mismatch 304"
[1] "Missing 6333"
****** DONE Majorité des FN pour SPN sont peu couverts
CLOSED: [2023-03-16 Thu 16:54]
Chromosome 1 : majorité des FN ne sont pas vus...
cf figure
#+attr_html: :width 500px
[[file:reads.png]]
1623412 : 5’UTR
1953616 : intronique mais dans bed...
2589991
3488573
3488732
3780326
3884683
3914055
4711993
4712657
****** DONE Alignement
CLOSED: [2023-03-15 mer. 13:41]
******* DONE Impact de la version mineure du genome: non
CLOSED: [2023-03-09 Thu 23:13]
******** DONE GHC38 + version alexis + exons refseq
CLOSED: [2023-03-22 Wed 00:02]
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision
INDEL ALL 7226 3417 3809 6979 1599 1919 228 353 0.472876 0.683992
SNP ALL 59052 37827 21225 43483 1913 3741 676 35 0.640571 0.951865
METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
0.274968 0.559171 NaN NaN 1.547733 2.756698
0.086034 0.765792 2.433271 2.350254 1.575230 1.492375
******** DONE GHC38.p13 + notre version alexis + exons refseq
CLOSED: [2023-03-22 Wed 00:02]
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision
INDEL ALL 7226 3417 3809 6978 1599 1918 228 353 0.472876 0.683992
SNP ALL 59052 37825 21227 43480 1913 3740 675 35 0.640537 0.951862
METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
0.274864 0.559171 NaN NaN 1.547733 2.756151
0.086017 0.765767 2.433271 2.350281 1.575230 1.492346
****** DONE Vérifier si coordonnées génomiques (vcf)
CLOSED: [2023-03-09 Thu 23:05]
****** DONE Variant calling
CLOSED: [2023-03-22 Wed 23:11]
******* DONE Désactiver dbSNP : idem
CLOSED: [2023-03-22 Wed 15:00]
Après haplotycaller
$ sha256sum work/94/d4ae5999ca59a25469b1ed221b7b1b/NA12878_NIST.vcf.gz
193fb37e2a581bb2855ae6fd11638f3b97958515def0e4295005e6a60c9dc650 work/94/d4ae5999ca59a25469b1ed221b7b1b/NA12878_NIST.vcf.gz
Fichier utilisé par hap.py
$ sha256sum work/5b/199360963641524a076d06b621e7e0/NA12878_NIST.vcf.gz
193fb37e2a581bb2855ae6fd11638f3b97958515def0e4295005e6a60c9dc650 work/5b/199360963641524a076d06b621e7e0/NA12878_NIST.vcf.gz
On a bien le même que [[*Bed donnés par GIAB (en hg19) : résultats corrects][Bed donnés par GIAB (en hg19) : résultats corrects]]
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision
INDEL ALL 4871 3461 1410 7048 1554 1987 193 346 0.710532 0.692946
SNP ALL 46032 39367 6665 44599 1186 4042 304 30 0.855209 0.970757
METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
0.281924 0.701629 NaN NaN 1.617499 3.067409
0.090630 0.909327 2.529552 2.402151 1.620686 1.627342
****** DONE Définition des exons
CLOSED: [2023-03-22 Wed 23:16]
******* KILL Vérifier qu'il ne manque pas des exons (avec bam ?)
CLOSED: [2023-03-16 Thu 16:54] SCHEDULED: <2023-03-05 Sun>
******* KILL Vérifier la couverture des variants introniques
CLOSED: [2023-03-22 Wed 15:01]
NC_000001.11 23344310 : intronique mais la région dans le bed couvre en partie l'exon
Profondeur sur le variant : 14 reads sur l'alt
******* Notes: UTR = exon - CDS
intron dans le gene = mRNA - exon
On le vérifie avec
25 │ NC_000001.11 BestRefSeq exon 65520 65573
27 │ NC_000001.11 BestRefSeq CDS 65565 65573
https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A65520%2D65573&hgsid=295007972_J1rAQiur4dC2KLadnaOCw27WUihG
mRNA :
https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A65419%2D71585&hgsid=295007972_J1rAQiur4dC2KLadnaOCw27WUihG
******* DONE Statistiques : reads par type (introns, UTR, exons)
CLOSED: [2023-03-22 Wed 23:16]
- la répartition par chromosome est relativement homogène, sauf sur le 6 ()
- la majorité est en 5' et 3'UTR (selon Best refseq)
#+begin_src julia
using CSV
using DataFrames, DataFramesMeta
using XAM, GenomicFeatures
function exonFromBestRefSeq(f)
println("Reading exons from $(f)")
cols = ["seqname", "source", "feature", "start", "end", "score", "strand", "frame", "attribute"]
d = DataFrame(CSV.File(f ,header=cols, delim="\t",comment="#"))
@chain d begin
@rsubset :feature in ["exon", "CDS", "mRNA"] :source .== "BestRefSeq"
@select :seqname :source :feature :start :end
@distinct
end
end
# Get exons from refseq (Bestrefeq, gnomon or just refseq)
function getExon(f)
if isfile(f)
println("Reading exons from preprocessed $(f)")
d = DataFrame(CSV.File(f))
else
d = exonFromBestRefSeq("GRCh38_latest_genomic.gff.gz")
CSV.write(f, d)
end
return d
end
# Return false negative and TRUTH annotation (genotype, type...)
# Read vcf manually: it's a tab-separated file and we extract the TRUTH column manually
#BD = Decision for call (TP/FP/FN/N)
#BK = tSub-type for decision (match/mismatch type)
#BI = Additional comparison information
#QQ = Variant quality for ROC creation.
#BV = High-level variant type (SNP|INDEL).
#BL = High-level location type (het|homref|hetalt|homalt|nocall).
function getFN(f)
cols = ["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO", "FORMAT", "TRUTH", "QUERY"]
vcf = DataFrame(CSV.File(f,comment="#", delim="\t",
header = cols))
# Extract genothype and other subcolumn fronm FORMAT
format = split(vcf[1,:FORMAT], ":")
@chain vcf begin
@rtransform $format=split(:TRUTH, ':')
@subset :BD .== "FN"
@select :type=:BVT :CHROM :POS :REF :ALT :GT :BK :BLT
end
end
# Search a variant in refseq exons
# Return the smallest interval (CDS)
function searchVariant(chrom, pos, exons)
res = @subset exons :seqname .== chrom :start .<= pos :end .>= pos
if isempty(res)
return "intronicOutsideGene"
elseif "CDS" in res.feature
return "CDS"
elseif "exon" in res.feature
# UTR = exon - CDS
return "UTR"
elseif "mRNA" in res.feature
# intron = mRNA - exon
return "intronicGene"
else
return "intronicOutsideGene"
end
end
# Once the bam file has been opened, count the reads for a single variant
function countReadsVariant(reader, chrom, pos)
n = 0
for record in eachoverlap(reader, chrom,pos:pos)
n += 1
end
return n
end
# For all variants, get the number of reads from the bam file
function countReads(d)
bamDir = "../script/files/bam"
bam = bamDir * "/NA12878_NIST7035_recalibrated_hg38.bam"
bai = bam * ".bai"
reader = open(BAM.Reader, bam, index=bai)
d2 = @transform(d, @byrow :reads = countReadsVariant(reader, :CHROM, :POS))
close(reader)
return d2
end
function exonicStatus(d, exons)
# Check variants are in exon: for each variant, search in all exons
@transform(d, @byrow :match = searchVariant(:CHROM, :POS, exons))
end
exons = getExon("GRCh38_latest_genomic_exon.csv")
d = getFN("../out/test-bed/test-allchr.vcf") |>
x -> exonicStatus(x, exons) |>
countReads
# # bed = DataFrame(CSV.File("../out/test-bed/exons_illumina_hg38.bed",comment="#", delim="\t", header=false))
CSV.write("falseNegatives.csv", d)
#+end_src
Discordance nombre de reads avec igv mais cohérent avec samtools : vu avec Alexis : probablement du à IVG, on reste sur samtools
$ samtools view NA12878_NIST7035_recalibrated_hg38.bam NC_000001.11:1734812-1734812 -F "0x200" | wc -l
164
****** KILL Comprendre pourquoi le chromosome 6 a plus de FN
CLOSED: [2023-03-29 Wed 22:39]
Vérifier le graphe fait en julia
$ grep "FN.*SNP" test-allchr.vcf | grep NC_000006 -c
1264
@subset d :type .== "SNP" :CHROM .== "NC_000006.12"
1264×10 DataFrame
Région HLA: difficile car nombreux allèles alternatifs.
Mais dans nos données, sont principalement non vus.
La répartition des reads est similaire aux autres régions...
#+begin_src julia
vcf = vcfHappy("test-allchr.vcf")
d = DataFrame(CSV.File("data/falseNegatives.csv"))
d2 = @subset d :POS .>= 29600000 :POS .<= 32000000 :type .== "SNP" :CHROM .=="NC_000006.12"
#+end_src
#+RESULTS:
: julia> nrow(@subset d2 :BK .== ".")
: 612
: julia> nrow(@subset d2 :BK .!= ".")
: 6
: julia> nrow(@subset d2 :BK .!= "am")
: 612
****** KILL comparer avec Kumaran 2021
CLOSED: [2023-03-22 Wed 23:16]
Bed probablement différent, on a presque un facteur 2 sur le nombre de variant (TP..)
****** KILL Comparer avec stats de NA12878 dans example/happy sur chr21 (exons fournis)
CLOSED: [2023-03-04 Sat 11:01]
******* DONE DP_over_30_not_SNP_consensual_sequence.vcf: horrible
CLOSED: [2023-02-25 Sat 19:47]
déplorable
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 519 16 503 1579 1032 531 2 2 0.030829 0.015267 0.336289 0.020421 NaN NaN 1.775956 4.768382
INDEL PASS 519 16 503 1579 1032 531 2 2 0.030829 0.015267 0.336289 0.020421 NaN NaN 1.775956 4.768382
SNP ALL 22131 1191 20940 4346 2342 813 4 1 0.053816 0.337107 0.187069 0.092815 2.971834 1.967235 1.579776 1.492828
SNP PASS 22131 1191 20940 4346 2342 813 4 1 0.053816 0.337107 0.187069 0.092815 2.971834 1.967235 1.579776 1.492828
******* DONE DP _over_30 : mieux
CLOSED: [2023-03-04 Sat 11:01]
/Work/Users/apraga/bisonex/work/69/cc1391f5a0fbf4db958a370ec17a19
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision
INDEL ALL 76 20 56 36 6 10 1 3 0.263158 0.769231
INDEL PASS 76 20 56 36 6 10 1 3 0.263158 0.769231
SNP ALL 582 312 270 370 9 49 0 0 0.536082 0.971963
SNP PASS 582 312 270 370 9 49 0 0 0.536082 0.971963
******** DONE NC_000021.9:45515163 TA -> T : référence non normalisée ??
CLOSED: [2023-03-04 Sat 11:01]
NC_000021.9 45515163 . TA T 50 PASS BS=45515163;Regions=CONF,TS_contained GT:BD:BK:BI:BVT:BLT:QQ 0/1:FN:lm:d1_5:INDEL:het:. ./.:.:.:.:NOCALL:nocall:0
NC_000021.9 45515163 . TAA T 694.02 PASS BS=45515163;Regions=CONF,TS_contained GT:BD:BK:BI:BVT:BLT:QQ ./.:.:.:.:NOCALL:nocall:. 0/1:FP:lm:d1_5:INDEL:het:694.02
Mais dans notre vcf
NC_000021.9 45515163 rs11284347 TAA T,TA
La séqu
ence est TAAAA donc notre TAA -> TA aurait du être reconnu comme identique. Faut-il utiliser un autre fasta ?
La décomposition de xcmp est
45515163 TAA -> T
45515164 AA -> A
NB: testée avec pre.py
#+begin_src
grep '^#' NA12878_NIST7035_DP_over_30.vcf > NA12878_NIST7035_DP_over_30_chr21.vcf
grep '^NC_000021' NA12878_NIST7035_DP_over_30.vcf >> NA12878_NIST7035_DP_over_30_chr21.vcf
pre.py NA12878_NIST7035_DP_over_30_chr21.vcf out.vcf.gz -r GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta
#+end_src
Selon l'algorithm, on devrait avoir TA -> T et non AA -> A (non left-align)
Si on débug:
#+begin_src
grep "^#" NA12878_NIST7035_DP_over_30_chr21.vcf > test_align.vcf
grep 45515163 NA12878_NIST7035_DP_over_30_chr21.vcf >> test_align.vcf.gz
bgzip test_align.vcf.gz
bcftools index test_align.vcf.gz
multimerge test_align.vcf.gz -o out.vcf.gz -r GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta
#+end_src
Idem... Si on utile un genome de référence plus récent ?
#+begin_src
multimerge test_align.vcf.gz -o out.vcf.gz -r /Work/Groups/bisonex/data/genome/GRCh38.p13/genomeRef.fna --process-full=1
#+end_src
Idem. Et vcfeval ?
#+begin_src
tabix HG001_GRCh38_1_22_v4.2.1_benchmark_chr21.vcf.gz
tabix test_align.vcf.gz
rtg vcfeval -b HG001_GRCh38_1_22_v4.2.1_benchmark_chr21.vcf.gz -c test_align.vcf.gz -t /Work/Groups/bisonex/data/genome/GRCh38.p13/genomeRef.sdf -o vcfeval-test
#+end_src
Selected score threshold using: maximized F-measure
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
99.000 0 0 1 54828 0.0000 0.0000 0.0000
None 0 0 1 54828 0.0000 0.0000 0.0000
On essaie les différentes étapes
#+begin_src
multimerge test_align.vcf.gz -o out.vcf.gz -r /Work/Groups/bisonex/data/genome/GRCh38.p13/genomeRef.fna --homref-split 1 --homref-vcf-out 1 --trimalleles 1 --splitalleles 1
#+end_src
1er changement
TAA T
TAA TA
Après réflexion, c'est la référence qui n'est pas normalisée ! (left-trimmed)
******** DONE NC_000021.9 14108836 T -> C
CLOSED: [2023-03-04 Sat 11:01]
Dans le bam mais filtré par DP
******* DONE variant calling seul : meilleur score pour l'instant (77% recall, 95% precision)
CLOSED: [2023-03-04 Sat 11:01]
tests/chr21-alexis
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision
INDEL ALL 76 43 33 82 18 20 3 5 0.565789 0.709677
SNP ALL 582 448 134 530 25 57 6 1 0.769759 0.947146
METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
0.243902 0.629617 NaN NaN 1.181818 1.612903
0.107547 0.849289 3.098592 2.925926 1.530435 1.774869
******** NC_000021.9:14144627 : FN, dans le bam mais pas dans le vcf (2 reads/9)
On récupére tout le vcf: pas dedans
Dans le bam : 9/2
Idem pour le bam dans notre pipeline
- base qualité 33 sur les 2 reads
https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant
https://gatk.broadinstitute.org/hc/en-us/articles/360035891111-Expected-variant-at-a-specific-site-was-not-called
On debug
#+begin_src
cd /Work/Users/apraga/bisonex/out/NA12878_NIST7035/preprocessing/applybqsr
samtools view -b NA12878_NIST7035.bam NC_000021.9 -o NA12878_NIST7035_chr21.bam
samtools index NA12878_NIST7035_chr21.bam
#+end_src
********* --debug
#+begin_src
gatk --java-options "-Xmx3g" HaplotypeCaller --input NA12878_NIST7035_chr21.bam \
--output debug_chr1.vcf.gz \
--reference /Work/Groups/bisonex/data/genome/GRCh38.p13/genomeRef.fna \
--dbsnp /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz \
--tmp-dir . \
--max-mnp-distance 2 --debug &> lol.txt
#+end_src
Les allèles sont bien retrouvées
#+begin_quote
14:41:05.530 INFO EventMap - === Best Haplotypes ===
14:41:05.530 INFO EventMap - AATTTAATTTTCTTACCTTTCTGGGTATGTAAGTGATTTTA
14:41:05.530 INFO EventMap - > Cigar = 41M
14:41:05.530 INFO EventMap - >> Events = EventMap{}
14:41:05.530 INFO EventMap - AATTTAATTTTCTTACCTTTTTGGGTATGT
exons.fa | sed 's/:/,/;s/-/,/;s/^>//' > exons.csv
#+end_src
****** DONE Sur 200 premiers exons du chr1
CLOSED: [2023-04-30 Sun 19:17]
#+begin_src sh :dir ~/code/bisonex/test-reseq :results silent
head -n200 exons.fna > exons-200.fna
bwa index exons-200.fna
#+end_src
Simulation avec 30x
#+begin_src sh :dir ~/code/bisonex/test-reseq :results silent
../ReSeq/bin/reseq illuminaPE -R exons-200.fna -s Ec-Hi2000-TruSeq.reseq --ipfIterations 0 -1 reseq1.fq -2 reseq2.fq -c 30
#+end_src
Attention, pour l'alignement, il faut le nfa complet ! Sinon erreur du type
Erreurs:::sam_hdr_create] Duplicated sequence "NC_000001.10:762970-763155" in file "-"
Et pas de bam avec
samtools sort: failed to change sort order header to 'coordinate'
#+begin_src
bwa mem ../test-simuscop/bwa/genomeRef.fna reseq1.fq reseq2.fq | samtools sort -o reseq.bam
#+end_src
Manque des exons et l'allure ne correspond pas...
****** DONE Utiliser le fichier de capture : exons trop petits
CLOSED: [2023-04-30 Sun 19:25]
Comme pour ART
Trop court avec
echo -e "NC_000001.11\t153817371\t153817542" > gatad2b-exon6.bed
Donc on ajoute 1000 de chaque côté
#+begin_src sh :dir ~/code/bisonex/test-reseq :results silent
echo -e "NC_000001.11\t153816371\t153818542" > gatad2b-exon6.bed
bedtools getfasta -fi ../test-simuscop/genomeRef.fna -bed gatad2b-exon6.bed -fo gatad2b-exon6.fna
bwa index gatad2b-exon6.bed
../ReSeq/bin/reseq illuminaPE -R gatad2b-exon6.fna -s Ec-Hi2000-TruSeq.reseq --ipfIterations 0 -1 reseq1.fq -2 reseq2.fq -c 30
bwa mem ../test-simuscop/bwa/genomeRef.fna reseq1.fq reseq2.fq | samtools sort -o reseq.bam
samtools index reseq.bam
#+end_src
***** KILL Sur le chromosome 15 puis trier à la main sur les zones de capture ?
CLOSED: [2023-04-30 Sun 19:44]
#+begin_src sh :dir ~/code/bisonex/test-reseq :results silent
samtools faidx ../test-simuscop/genomeRef.fna NC_000015.10 > chr15.fna
../ReSeq/bin/reseq illuminaPE -R chr15.fna -s Ec-Hi2000-TruSeq.reseq --ipfIterations 0 -1 reseq1.fq -2 reseq2.fq -c 30
#+end_src
**** DONE ART : fonctionne très mal en targeted
CLOSED: [2023-04-30 Sun 11:49]
***** DONE Génération de reads
CLOSED: [2023-04-30 Sun 11:49]
****** DONE Avec seulement les exons en séquence
CLOSED: [2023-04-30 Sun 10:24]
head -n6 exons.fa | save three-exons.fna
../art_bin_MountRainier/art_illumina -ss HS25 -i three-exons.fna -o ./paired_end_com -l 150 -f 10 -p -m 500 -s 10 -sam
Le sam n'est pas visible sur igv mais si on aligne avec bwa mem, on a quelques reads
****** DONE Extraire une zone de capture dans le fasta
CLOSED: [2023-04-30 Sun 11:49]
NC_000001.11 g.153817496 A>T
******* DONE Essai 1: ne dépasse pas la zone
CLOSED: [2023-04-30 Sun 10:49]
#+begin_src sh :dir ~/code/bisonex/test-art :results silent
echo -e "NC_000001.11\t153817371\t153817542" > gatad2b-exon6.bed
bedtools getfasta -fi ../test-simuscop/genomeRef.fna -bed gatad2b-exon6.bed -fo gatad2b-exon6.fa
#+end_src
-ss HS25 : nom du profile illumina
-l 150 : reads de 150
-f 10 : coverage de 10
-p : paired end
-m 500 : longueur moyenne des fragment d'ADN
-s 10 : déviation standard
#+begin_src sh :dir ~/code/bisonex/test-art :results silent
../art_bin_MountRainier/art_illumina -ss HS25 -i gatad2b-exon6.fa -o ./gatad2b -l 150 -f 100 -p -m 500 -s 10
#+end_src
#+begin_src sh :dir ~/code/bisonex/test-art :results silent
bwa mem ../test-simuscop/bwa/genomeRef gatad2b1.fq gatad2b2.fq | samtools sort -o gatad2b.b
am
samtools index gatad2b.bam
#+end_src
#+attr_html: :width 800px
[[./art-capture-1.png]]
******* Avec offset
50bp idem
NC_000001.11 153817371 153817542 -> NC_000001.11 153817321 153817592
On essaie 1000
NC_000001.11 153817371 153817542 -> NC_000001.11 153816371 153818542 ->
#+begin_src sh :dir ~/code/bisonex/test-art :results silent
echo -e "NC_000001.11\t153816371\t153818542" > gatad2b-exon6-offset.bed
bedtools getfasta -fi ../test-simuscop/genomeRef.fna -bed gatad2b-exon6-offset.bed -fo gatad2b-exon6-offset.fa
../art_bin_MountRainier/art_illumina -ss HS25 -i gatad2b-exon6-offset.fa -o ./gatad2b -l 150 -f 100 -p -m 500 -s 10
bwa mem ../test-simuscop/bwa/genomeRef gatad2b1.fq gatad2b2.fq | samtools sort -o gatad2b.bam
samtools index gatad2b.bam
#+end_src
mieux mais trop large
#+attr_html: :width 800px
[[./art-exon6-offset1000.png]]
Sur les vraies données, on a une large de 500bp environ
#+attr_html: :width 800px
[[./illumina-ref-exon6.png]]
Ici l'exon fait 250bp donc on rajouter 125bp de chaque côté
NC_000001.11 153817371 153817542
NC_000001.11 153817246 153817667
Résulats incohérents :on a 2 colonnes séparées !
Essai avec +200bp de chaque côt
NC_000001.11 153817371 153817542
NC_000001.11 153817171 153817742
#+begin_src sh :dir ~/code/bisonex/test-art :results silent
echo -e "NC_000001.11\t153817171\t153817742"> gatad2b-exon6-offset.bed
bedtools getfasta -fi ../test-simuscop/genomeRef.fna -bed gatad2b-exon6-offset.bed -fo gatad2b-exon6-offset.fa
../art_bin_MountRainier/art_illumina -ss HS25 -i gatad2b-exon6-offset.fa -o ./gatad2b -l 150 -f 100 -p -m 500 -s 50
bwa mem ../test-simuscop/bwa/genomeRef gatad2b1.fq gatad2b2.fq | samtools sort -o gatad2b.bam
samtools index gatad2b.bam
#+end_src
En changeant la longueur des reads
#+begin_src sh :dir ~/code/bisonex/test-art :results silent
echo -e "NC_000001.11\t153817171\t153817742"> gatad2b-exon6-offset.bed
bedtools getfasta -fi ../test-simuscop/genomeRef.fna -bed gatad2b-exon6-offset.bed -fo gatad2b-exon6-offset.fa
../art_bin_MountRainier/art_illumina -ss HS25 -i gatad2b-exon6-offset.fa -o ./gatad2b -l 126 -f 100 -p -m 500 -s 50
bwa mem ../test-simuscop/bwa/genomeRef gatad2b1.fq gatad2b2.fq | samtools sort -o gatad2b.bam
samtools index gatad2b.bam
#+end_src
Idem, fait 2 "tas" séparés de chaque côté de l'exon
+/- 100
#+begin_src sh :dir ~/code/bisonex/test-art :results silent
echo -e "NC_000001.11\t153817271\t153817642" > gatad2b-exon6-offset.bed
bedtools getfasta -fi ../test-simuscop/genomeRef.fna -bed gatad2b-exon6-offset.bed -fo gatad2b-exon6-offset.fa
../art_bin_MountRainier/art_illumina -ss HS25 -i gatad2b-exon6-offset.fa -o ./gatad2b -l 125 -f 100 -p -m 500 -s 30
bwa mem ../test-simuscop/bwa/genomeRef gatad2b1.fq gatad2b2.fq | samtools sort -o gatad2b.bam
samtools index gatad2b.bam
#+end_src
**** KILL NGSNG : plante
CLOSED: [2023-05-01 Mon 09:27]
https://github.com/RAHenriksen/NGSNGS
***** KILL Essai avec fasta
CLOSED: [2023-05-01 Mon 09:27]
#+begin_src sh :dir ~/code/bisonex/test-ngsngs :results silent
echo -e "NC_000001.11\t153817371\t153817542" > gatad2b-exon6.bed
bedtools getfasta -fi ../test-simuscop/genomeRef.fna -bed gatad2b-exon6.bed -fo gatad2b-exon6.fa
#+end_src
-ss HS25 : nom du profile illumina
-l 150 : reads de 150
-f 10 : coverage de 10
-p : paired end
-m 500 : longueur moyenne des fragment d'ADN
-s 10 : déviation standard
#+begin_src sh :dir ~/code/bisonex/test-art :results silent
../art_bin_MountRainier/art_illumina -ss HS25 -i gatad2b-exon6.fa -o ./gatad2b -l 150 -f 100 -p -m 500 -s 10
#+end_src
#+begin_src sh :dir ~/code/bisonex/test-art :results silent
bwa mem ../test-simuscop/bwa/genomeRef gatad2b1.fq gatad2b2.fq | samtools sort -o gatad2b.b
am
samtools index gatad2b.bam
#+end_src
**** KILL Script maison :generate:
CLOSED: [2023-05-13 Sat 18:29] SCHEDULED: <2023-05-01 Mon>
***** KILL SNV
CLOSED: [2023-05-13 Sat 18:29] SCHEDULED: <2023-05-01 Mon>
****** DONE Script python: ok seulement pour reads corrigé, trop long sinon
CLOSED: [2023-05-01 Mon 13:32]
Même sur un seul chromosome (15)...
****** DONE Couper les données avec bedtools intersect ?
CLOSED: [2023-05-01 Mon 20:33]
-wa pour avoir les reads qui corresponds
-v pour ceux qui n'intersecte pass
ok sur un exemple
******* DONE Test simple : ok
CLOSED: [2023-05-01 Mon 13:43]
#+attr_html: :width 500px
[[./test-intersect-chr15.png]]
#+attr_html: :width 500px
[[./test-nointersect-chr15.png]]
******* DONE Chromosome 15 : vérifier BAM
CLOSED: [2023-05-01 Mon 20:33] SCHEDULED: <2023-05-01 Mon>
#+begin_src
samtools view -b `63003856_S135.bam` NC_000015.10 > `63003856_S135_chr15.bam`
#+end_src
On génère un python avec les dépendances
#+begin_src
nix-build
#+end_src
Puis on lance un script julia qui va couper le bam en 2, lancer le script python sur l'intersection et fusionner le résultat
#+begin_src
julia -Jbisonex.so --project=. insertVariants.jl `63003856_S135_chr15.bam` test_new.bam
#+end_src
NB: pour accélerer l'exécution, générer une sysimage :
#+begin_src julia
(1.7) pkg> activate .
julia> create_sysimage(; sysimage_path="bisonex.so")
#+end_src
3 variants: Ok sur le nombre de reads et les variants
Ok pour homozygote
#+attr_html: :width 500px
[[./check-snv-chr15.png]]
******* DONE Chromosome 15 Vérifier VAF avec checkBam.jl: ok
julia> @subset snv :chrom .== "NC_000015.10"
26×10 DataFrame
Row │ chrom pos variant variantType zygosity ref alt refCount altCount readsCount
│ SubStrin…? Int64 SubStrin…? String? String15 SubStrin… SubStrin… Int64 Int64 Int64
─────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ NC_000015.10 74343027 g.74343027C>T snv heterozygous C T 61 58 120
2 │ NC_000015.10 75400778 g.75400778C>G snv heterozygous C G 108 79 187
3 │ NC_000015.10 89327201 g.89327201C>T snv heterozygous C T 243 241 486
4 │ NC_000015.10 48767448 g.48767448A>C snv heterozygous A C 72 70 142
5 │ NC_000015.10 75411685 g.75411685T>C snv heterozygous T C 79 81 160
6 │ NC_000015.10 66703292 g.66703292C>T snv heterozygous C T 70 60 130
7 │ NC_000015.10 89325639 g.89325639G>A snv heterozygous G A 257 267 524
8 │ NC_000015.10 89330184 g.89330184G>A snv heterozygous G A 258 287 548
9 │ NC_000015.10 89330184 g.89330184G>A snv heterozygous G A 258 287 548
10 │ NC_000015.10 89325639 g.89325639G>A snv heterozygous G A 257 267 524
11 │ NC_000015.10 42401752 g.42401752G>A snv homozygous G A 61 212 273
12 │ NC_000015.10 89327201 g.89327201C>T snv heterozygous C T 243 241 486
13 │ NC_000015.10 38339896 g.38339896G>A snv heterozygous G A 56 86 144
14 │ NC_000015.10 26869324 g.26869324A>T snv heterozygous A T 62 49 113
15 │ NC_000015.10 66435145 g.66435145G>A snv heterozygous G A 98 95 193
16 │ NC_000015.10 60514655 g.60514655G>A snv heterozygous G A 94 99 194
17 │ NC_000015.10 42410947 g.42410947A>G snv heterozygous A G 153 123 276
18 │ NC_000015.10 75430368 g.75430368C>T snv heterozygous C T 80 62 142
19 │ NC_000015.10 25375494 g.25375494T>C snv heterozygous T C 103 104 207
20 │ NC_000015.10 60497497 g.60497497C>A snv heterozygous C A 61 65 126
21 │ NC_000015.10 74891539 g.74891539C>T snv heterozygous C T 118 124 242
22 │ NC_000015.10 48488433 g.48488433A>G snv heterozygous A G 367 122 492
23 │ NC_000015.10 89318565 g.89318565A>G snv heterozygous A G 303 98 404
24 │ NC_000015.10 89323426 g.89323426C>G snv heterozygous C G 93 109 202
25 │ NC_000015.10 89318595 g.89318595T>C snv heterozygous T C 321 128 453
26 │ NC_000015.10 48488437 g.48488437T>C snv heterozygous T C 356 132 488
CLOSED: [2023-05-01 Mon 17:18]
****** KILL Chromosome1 15 :Test haplotype caller : échec car CIGARE non mis à jour
CLOSED: [2023-05-13 Sat 18:29] SCHEDULED: <2023-05-01 Mon>
#+begin_src
julia -Jbisonex.so --project=. insertVariants.jl `63003856_S135_chr15.bam` 63003856_S135_chr15_inserted.bam
scp 63003856_S135_chr15_inserted.bam* meso:/Work/Users/apraga/bisonex/tests/synthetic/
#+end_src
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/synthetic :results silent
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz .
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz.tbi
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.dict .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna.fai .
#+end_src
puis
#+begin_src
gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam --output testchr15.vcf.
a/genome/GRCh38.p13/genomeRef* .
bwa mem -t 24 genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
********* DONE Test picard : idem
CLOSED: [2023-05-23 Tue 01:16]
Dans bisonex/code/BamScissors.jl
❯ picard SamToFastq -I 63003856_chr22_sorted.bam -F testpicard1.fastq -F2 testpicard2.fastq
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef testpicard1.fastq.gz testpicard2.fastq.gz | samtools sort -@24 -o testpicard.bam -
********* DONE Il ne manque pas des reads dans les fastq :
CLOSED: [2023-05-23 Tue 01:26]
bisonex/code/BamScissors.jl on bamscissors [!?] via ஃ v1.9.0
❯ samtools flagstat aligned/output.bam
1306273 + 0 in total (QC-passed reads + QC-failed reads)
1296055 + 0 primary
0 + 0 secondary
10218 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
1304871 + 0 mapped (99.89% : N/A)
1294653 + 0 primary mapped (99.89% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
bisonex/code/BamScissors.jl on bamscissors [!?] via ஃ v1.9.0
❯ samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
❯ echo $(zcat 63003856_chr22_init2.fq.gz | wc -l)/4 | bc
1296055
bisonex/code/BamScissors.jl on bamscissors [!?] via ஃ v1.9.0 took 2s
❯ echo $(zcat 63003856_chr22_init1.fq.gz | wc -l)/4 | bc
1296055
❯ samtools flagstat 63003856_chr22_sorted.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
********* DONE Avec sort -O BAM idem
CLOSED: [2023-05-23 Tue 01:21]
********* DONE Singleton ou non mapped ? nonVirtPosition
CLOSED: [2023-05-23 Tue 01:22]
❯ samtools bam2fq -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz -0 both -s single.fq.gz -n 63003856_chr22_sorted.bam
bisonex/code/BamScissors.jl on bamscissors [!?] via ஃ v1.9.0
❯ wc -l 63003856_chr22_init* both single.fq.gz
403540 63003856_chr22_init1.fq.gz
404788 63003856_chr22_init2.fq.gz
0 both
0 single.fq.gz
808328 total
********* Problème d'aligner car les reads sont bien dans le .fastq ?
Ex:
zgrep "A00853:477:HMLWYDSX3:2:2624:2826:18630" 63003856_chr22_{1,2}.fq.gz
63003856_chr22_1.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
63003856_chr22_2.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
******** DONE Refaire la manip sur bam chr22 non modifié + mail Alexis
CLOSED: [2023-05-23 Tue 23:27]
[1]_samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11 -f 0x2 -o 63003856_chr22.bam
Les reads sont bien tous mappé
samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
[2] samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
flagstat idem
[3] samtools fastq -1 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -n 63003856_chr22_sorted.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2592110 reads
Nombre de reads ok (= la moitié) et les séquences ne sont pas identiques pour le premier read (= on n'a pas 2x la même chose)
echo $(zcat 63003856_chr22_1.fq.gz | wc -l)/4 | bc
1296055
echo $(zcat 63003856_chr22_2.fq.gz | wc -l)/4 | bc
1296055
[4]
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz -o wtf.bam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1752492 sequences (240000014 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 702821, 0, 18)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (54, 197, 268)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 696)
[M::mem_pestat] mean and std.dev: (163.92, 129.71)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 910)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (129, 175, 233)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 441)
[M::mem_pestat] mean and std.dev: (185.56, 75.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 545)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (56, 192, 239)
[M::mem_pestat] low and
00022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573 163 NC_000022.11 42212845 0 151M = 42212883 189 CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:151 MC:Z:151M AS:i:151 XS:i:151 RG:Z:sample
A00853:477:HMLWYDSX3:1:1413:4390:28573 83 NC_000022.11 42212883 0 151M = 42212845 -189 ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:151 MC:Z:151M AS:i:151 XS:i:151 RG:Z:sample
samtools view applybqsr/63003856_S135_R.bam NC_000022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573 163 NC_000022.11 42212845 0 151M = 42212883 189 CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT ACC+FBCDCBBBAEAEDEEBBCCCECACBAEBEBDCCBCBFDCCCCFACEBEBCEEDCCCCFDCAEDCACBCEBBCFEACCFBDCACDCBCEBDBBCFEEDCCCFAFEACECCCECAEEDCADCBEDC7BEBCCCFBAFDCECCFBEAACA MC:Z:151M MD:Z:151 PG:Z:MarkDuplicates RG:Z:sample NM:i:0 AS:i:151 XS:i:151
A00853:477:HMLWYDSX3:1:1413:4390:28573 83 NC_000022.11 42212883 0 151M = 42212845 -189 ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT AADECCCBDCBFCE<?CDEEEEBDEACDEAC;:BFBCBCDCCBEAEACAEFCCEAFBCBCCDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE:CECBABBEBEE;DBFCCCDBCDBCCBBC?@BEEDA MC:Z:151M MD:Z:151 PG:Z:MarkDuplicates RG:Z:sample NM:i:0 AS:i:151 XS:i:151
********* DONE Réaligner à partir de la sortie de bwa mem
CLOSED: [2023-05-24 Wed 22:32]
#+begin_src sh
cd out/63003856_S135_R/preprocessing/mapped/
samtools view 63003856_S135_R.bam NC_000022.11 -f 0x2 -o 63003856_chr22.bam
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq -1 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -n 63003856_chr22_sorted.bam
#+end_src
ON vérifie la qualité
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" 63003856_chr22_1.fq.gz
#+end_src
#+RESULTS:
: @A00853:477:HMLWYDSX3:1:1413:4390:28573
: AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
#+begin_src
NXF_OPTS=-D"user.name=apraga" nextflow run main.nf -c nextflow.config -profile standard,helios -resume --input="out/63003856_S135_R/preprocessing/mapped/63003856_chr22_{1,2}.fq.gz" --outdir=out/63003856_chr22-from-mapped
#+end_src
Puis ::
#+begin_src
cd /Work/Users/apraga/bisonex/out/63003856_chr22-from-mapped/63003856_chr22/preprocessing/mapped
samtools view 63003856_chr22.bam | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
#+end_src
#+RESULTS:
: A00853:477:HMLWYDSX3:1:1413:4390:28573 163 NW_014040930.1 115017 0 151M = 115055 189 CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:151 MC:Z:151M AS:i:151 XS:i:151 RG:Z:sample
: A00853:477:HMLWYDSX3:1:1413:4390:28573 83 NW_014040930.1 115055 0 151M = 115017 -189 ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:151 MC:Z:151M AS:i:151 XS:i:151 RG:Z:sample
******** DONE Aligner sur génome de référence limité au chromosome 22
CLOSED: [2023-05-24 Wed 23:18]
********* KILL Test données non modifiées
CLOSED: [2023-05-24 Wed 23:18]
/Work/Users/apraga/bisonex/tests/bamscissors
#+begin_src
cd /Work/Groups/bisonex/data/genome/GRCh38.p13/
mkdir chr22/
samtools faidx genomeRef.fna NC_000022.11 > chr22/chr22.fna
cd chr22
samtools faidx chr22.fna
bwa index chr22.fna
#+end_src
#+begin_src
cd /Work/Users/apraga/bisonex/tests/bamscissors
ln -s ../ ../out/63003856_S135_R/preprocessing/applybqsr/63003856_chr22_{1,2}.fq.gz .
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz -o smallref.sam
#+end_src
********* DONE Test données modifiées: ok
CLOSED: [2023-05-24 Wed 23:18]
Données dans data/init
#+begin_src sh
time julia insertVariant.jl
rsync -avz data/init/*.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
#+begin_src
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz | samtools sort -@24 - -o smallref.bam
#+end_src
#+begin_src
rsync -avz meso:/Work/Users/apraga/bisonex/tests/bamscissors/smallref.bam mapped/
#+end_src
******* DONE Test haplotypecaller 1 variant
CLOSED: [2023-05-29 Mon 15:38]
******* DONE Test haplotypecaller tous les variants
******* DONE Comprendre pourquoi la répartiton ne suit pas la loi normale
CLOSED: [2023-06-01 Thu 21:44]
Certains hétérozygote soint à 0.01 ou 1...
******** DONE augmenter le nombre d'échantillions: idem
CLOSED: [2023-05-31 Wed 22:24]
******** DONE Vérifier le nombre de reads marqué vs édité
CLOSED: [2023-06-01 Thu 21:44]
******** DONE vérifier que 100 appel à rand(d, 1)[1] est semblable à un appel de rand(d, 100)
CLOSED: [2023-05-31 Wed 22:24]
julia> df = vcat(DataFrame(:y => z, :type => "z"), DataFrame(:y => y, :type => "y"));
julia> y = [rand(d, 1)[1] for x in 1:1000];
julia> z = rand(d,1000);
julia> df = vcat(DataFrame(:y => z, :type => "z"), DataFrame(:y => y, :type => "y"));
draw(data(df)*histogram(bins=100)*mapping(:y, color=:type,dodge=:type))
******* DONE Améliorer les performances
CLOSED: [2023-06-02 Fri 23:39]
#+begin_src julia
@time include("xamscissors.jl")
#+end_src
430s pour chromosome 22. Majorité dans l'édition de reads:
******** DONE Inserér tous les variants d'un reads d'un coup
CLOSED: [2023-06-01 Thu 23:09]
Ne change rien
******** DONE Test avec -t4: idem
CLOSED: [2023-06-01 Thu 23:17]
******** DONE Test mésocentre : idem
CLOSED: [2023-06-01 Thu 23:40]
348s
******** Changer la structure de données des
Dataframe -> dict = les performances horribles ont disparuse
******* KILL Refaire le test avec la nouvelle version
CLOSED: [2023-06-12 Mon 23:27]
******** DONE Génération des données
CLOSED: [2023-06-02 Fri 23:40]
Mésocentre
#+begin_src sh
cd /Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing/mapped
samtools view 63003856_S135_R.bam NC_000022.11 -o 63003856_S135_R_chr22.bam
samtools index 63003856_S135_R_chr22.bam
cp 63003856_S135_R_chr22.bam* /Work/Users/apraga/bisonex/tests/xamscissors/
cd /Work/Users/apraga/bisonex/tests/xamscissors
#+end_src
On génère les données
#+begin_src julia
using XAMScissors
insertSNV("./63003856_S135_R_chr22.bam", "snvs_chr22.csv", "out")
#+end_src
Puis
#+begin_src sh
julia xamscissors.jl
#+end_src
******** DONE Run
CLOSED: [2023-06-03 Sat 18:26]
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/runInserted.nf -profile standard,helios --input="tests/xamscissors/out/inserted_{1,2}.fq.gz"
******** DONE Après haplotypecaller : ok
CLOSED: [2023-06-03 Sat 18:27] SCHEDULED: <2023-06-03 Sat>
******** KILL Après filtre vep
CLOSED: [2023-06-12 Mon 23:27] SCHEDULED: <2023-06-03 Sat>
****** KILL PHase 3 : tous les SNV
CLOSED: [2023-06-12 Mon 23:28] SCHEDULED: <2023-06-03 Sat>
******* DONE Générer les données
CLOSED: [2023-06-03 Sat 20:16] SCHEDULED: <2023-06-03 Sat>
#+begin_src julia
using XAMScissors
insertSNV("../../out/63003856_S135_R/preprocessing/mapped/63003856_S135_R.bam", "snvs.csv", "out")
#+end_src
temps d'exécution 73min
#+begin_src sh
nohup bash -c 'time julia xamscissors.jl' &
xamscissors-63003856/*.fq.gz /Work/Groups/bisonex/data/xamscissors/
#+end_src
******* DONE Regénérer avec @time pour avoir les performaces
CLOSED: [2023-06-03 Sat 21:45]
markReads 6.265202 seconds (1.36 M allocations: 137.090 MiB, 1.00% gc time, 9.79% compilation time)
editReads 1327.701623 seconds (1.03 G allocations: 81.996 GiB, 0.59% gc time, 0.03% compilation time)
samtools index 117.743727 seconds (53 allocations: 1.883 KiB)
samtools sort 2820.074930 seconds (66 allocations: 2.789 KiB)
bam2fastq 134.148952 seconds (794 allocations: 40.539 KiB, 0.01% compilation time)
real 73m33.273s
user 77m38.194s
sys 1m26.684s
[bam_sort_core] merging from 60 files and 1 in-memory blocks...
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 126905130 reads
real 73m6.934s
user 77m25.397s
sys 1m21.339s
******* KILL Après haplotypecaller 556/590, majorité = échec alignement
CLOSED: [2023-06-12 Mon 23:27] SCHEDULED: <2023-06-04 Sun>
Haplotypecaller 556 found over 590
Amongst 34 missed variant, 2 have a mapping quality > 0
2×7 DataFrame
Row │ chrom pos ref alt zygosity meanQual stdQual
│ String15 Int64 String1 String1 String7 Float64 Float64
─────┼─────────────────────────────────────────────────────────────────────────
1 │ NC_000017.11 39672244 G A het 60.0 0.0
2 │ NC_000001.11 155235252 A G het 0.258065 2.48868
NC_000017.11 39672244 G A het => ok, problème de représentation car 2 variant côte à cote
NC_000001.11 155235252 A G het => peu de reads alternatifs (9/93 donc ok)
Position: chromoe
1 et 6 surtout
34×7 DataFrame
Row │ chrom pos ref alt zygosity
│ String15 Int64 String1 String
1 String7
─────┼──────────────────────────────────────────────────────
1 │ NC_000001.11 153817496 A T het
2 │ NC_000001.11 155235252 A G het
3 │ NC_000001.11 155236268 G A het
4 │ NC_000001.11 155290591 C T het
5 │ NC_000001.11 155291918 G A het
6 │ NC_000001.11 155294358 G T het
7 │ NC_000002.12 149010343 C T het
8 │ NC_000006.12 32039426 T A het
9 │ NC_000006.12 32040110 G T het
10 │ NC_000006.12 32040723 G A het
11 │ NC_000006.12 32041006 C T het
12 │ NC_000006.12 32041147 G A het
13 │ NC_000006.12 33443054 G T het
14 │ NC_000006.12 33451815 C T het
15 │ NC_000006.12 170283230 C A het
16 │ NC_000006.12 170283754 G A het
17 │ NC_000006.12 170285637 T C het
18 │ NC_000006.12 170289678 A C het
19 │ NC_000010.11 87961118 G A het
20 │ NC_000012.12 2449086 C G het
21 │ NC_000015.10 74343027 C T het
22 │ NC_000016.10 16163078 G A het
23 │ NC_000016.10 21262032 C G het
24 │ NC_000016.10 21962506 C T homo
25 │ NC_000017.11 7513122 C T
het
26 │ NC_000017.11 7513752 C T het
27 │ NC_000017.11 39672244 G A het
28 │ NC_000017.11 46018710 C T het
29 │ NC_000019.10 54144058 G A het
30 │ NC_000021.9 43063074 A G het
31 │ NC_000021.9 43426167 C T het
32 │ NC_000022.11 18918421 A G het
33 │ NC_000022.11 42087168 T A homo
34 │ NC_000022.11 42213078 T G het
******* DONE Voir où est l'alignement alternatif: sur NW_ (zone supprimée)
CLOSED: [2023-06-04 Sun 22:15] SCHEDULED: <2023-06-04 Sun>
ex chr15 74343027
A00853:477:HMLWYDSX3:2:2444:22354:28870
#+begin_src
cd /Work/Groups/bisonex/data/xamscissors
zgrep -A4 "A00853:477:HMLWYDSX3:2:2444:22354:28870" *.fq.gz
#+end_src
63003856_xamscissors_1.fq.gz:@A00853:477:HMLWYDSX3:2:2444:22354:28870
63003856_xamscissors_1.fq.gz:CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC
63003856_xamscissors_1.fq.gz:+
63003856_xamscissors_1.fq.gz:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF
63003856_xamscissors_2.fq.gz:@A00853:477:HMLWYDSX3:2:2444:22354:28870
63003856_xamscissors_2.fq.gz:GACAGAAAGGAAGTGTTCACCACGATTACCGTGGCATCCTCTACAGACTCCTGGGAGACAGCAAGATGTCCTTCGAGGACATCAAGGCCAACGTCACAGAGATGCCGGCAGGAGGGGTGGACACGGTG
63003856_xamscissors_2.fq.gz:+
63003856_xamscissors_2.fq.gz:FF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:F:FF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,:FFF,FFFFFF:FFFFFFFFFFFFF
******** DONE Avec BLAT: sur _fix
CLOSED: [2023-06-04 Sun 21:07]
1er =
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN
--------------------------------------------------------------------------------------------------------------
browser details YourSeq 124 1 128 128 98.5% chr15_ML143370v1_fix + 172243 172370 128 What is chrom_fix?
browser details YourSeq 124 1 128 128 98.5% chr15 + 74342974 74343101 128
browser details YourSeq 23 1 25 128 96.0% chr19 - 33396097 33396121 25
Second
--------------------------------------------------------------------------------------------------------------
browser details YourSeq 126 1 128 128 99.3% chr15_ML143370v1_fix - 172243 172370 128 What is chrom_fix?
browser details YourSeq 126 1 128 128 99.3% chr15 - 74342974 74343101 128
browser details YourSeq 23 104 128 128 96.0% chr19 + 33396097 33396121 25
******** DONE Bwa mem à la main GRCh38.p13 : on est dans une zone NW
CLOSED: [2023-06-04 Sun 21:51]
On met les 2 reads dans des fichiers séparés puis
#+begin_src sh
cd /Work/Users/apraga/bisonex/tests/xamscissors/align
bwa mem /Work/Groups/bisonex/data/genome/GRCh38.p13/bwa/genomeRef test1.fq test2.fq
#+end_src
A00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;
******** DONE GRCh38.p14: idem
CLOSED: [2023-06-04 Sun 21:51]
A00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGG
AGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;
******** DONE GRCh38 : ok
CLOSED: [2023-06-04 Sun 22:15]
bwa mem /Work/Projects/bisonex/data/genome/GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna test1.fq test2.fq
******* DONE Vérifier que les reads ont la même qualité sur les fichiers d'origine: oui
CLOSED: [2023-06-04 Sun 21:07]
******* DONE Supprimer les NW_ ?
CLOSED: [2023-06-10 Sat 10:40] SCHEDULED: <2023-06-04 Sun>
@A00853:477:HMLWYDSX3:3:2114:14742:8860
CAGGCCAGCCGCTCAGCCCGCTCCTTTCACCCTCTGCAGGAGAGCCTCGTGGCAGGCCAGTGGAGGGACATGATGGACTACATGCTCCAAGGGGTGGCGCAGCCGAGCATGGAAGAGGGCTCTGGACAGCTCCTGGAAGGGCACTTGCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00853:477:HMLWYDSX3:3:2114:14742:8860
CTTTTGCTTGTCCCCAGGACGCACCTCAGGGTGGTGAAGCAAAAAAACCACGGCCCAGGAGAGGGTGGGTGCTGTGGTCTCAGTGCCACCGATCAGGAGGTCCACTGCAGCCATGTGCAAGTGCCCTTCCAGGAGCTGTCCAGAGCCCTCT
+
FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFF,FFFFFFFFFFFF:F:FFFF:FFFFF,,FFF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFFFFF:FFFF,F:FFFFF:FFFFFFFFF:FFFF,FFFFFFFFF
******* DONE Supprimer NW_ et NT_
****** KILL Phase 2 : chr22, vaf variable :T2T:
CLOSED: [2023-08-12 Sat 15:59]
****** KILL Phase 3 : tous SNV, vaf variable :T2T:
CLOSED: [2023-08-12 Sat 15:59]
***** KILL Test Indel
CLOSED: [2023-08-12 Sat 15:59]
**** Divers
***** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]
*** KILL Liste varants "clinically relevent" (Clinge - CT-R d)
CLOSED: [2023-06-25 Sun 15:53] SCHEDULED: <2023-06-25 Sun>
[cite:@wilcox2021]
Vu avec alexis: pas notre cas d'usage
*** TODO Variant cento confirmé en Sanger :xamscissors:
**** DONE Générer la liste
CLOSED: [2023-08-13 Sun 22:26] SCHEDULED: <2023-08-13 Sun 12:00>
**** DONE 2 variants chr20 dans HG002 avec XAMscissors: homozygote
CLOSED: [2023-08-15 Tue 00:13] SCHEDULED: <2023-08-13 Sun 13:00>
***** DONE Insertion
CLOSED: [2023-08-13 Sun 23:31] SCHEDULED: <2023-08-13 Sun>
On récupère le BAM
#+begin_src sh :dir /home/alex/code/bisonex/out
scp /Work/Users/apraga/bisonex/out/HG002-151002_7001448_0359_AC7F6GANXX-GRCh38/preprocessing/mapped/HG002-151002_7001448_0359_AC7F6GANXX-GRCh38.bam
#+end_src
On formate les données et on génère les fastq
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
julia --project=.. xamscissors.jl
#+end_src
On upload
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
cd out
mv inserted_1.fq.gz HG002-sanger-inserted-chr20_1.fq.gz
mv inserted_2.fq.gz HG002-sanger-inserted-chr20_2.fq.gz
#+end_src
On upload
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
scp HG002-sanger-inserted-chr20_*.fq.gz meso:/Work/Users/apraga/bisonex/data/
#+end_src
Fichier de configuration
patient,sample,fastq1,fastq2
HG002,sanger-chr20,data/HG002-sanger-inserted-chr20_1.fq.gz,data/HG002-sanger-inserted-chr20_2.fq.gz
On lance la simulation
#+begin_src
nextflow run main.nf -profile standard,helios --input=samples-synthetic.csv --genome=GRCh38 -bg
#+end_src
***** DONE Vérifier post alignement
CLOSED: [2023-08-13 Sun 23:44] SCHEDULED: <2023-08-13 Sun>
***** DONE Vérifier haplotypecaller
CLOSED: [2023-08-15 Tue 00:13] SCHEDULED: <2023-08-13 Sun>
***** DONE Vérifier post-filtre
CLOSED: [2023-08-15 Tue 00:13]
**** DONE 2 variant chr20 dans HG002 heterozygote
CLOSED: [2023-08-15 Tue 13:45] SCHEDULED: <2023-08-15 Tue>
La zygosité n'était pas correcte...
**** DONE chr20 hétérozygote 2 variants avec XAMscissors à jour
CLOSED: [2023-08-19 Sat 20:45] SCHEDULED: <2023-08-19 Sat>
***** DONE Insertion
CLOSED: [2023-08-19 Sat 20:08]
XAMscissors avec dépendence git
NA12878 après bwa mem
Sur le mésocentre, dans code/sanger/
#+begin_src
ln -s /Work/Users/apraga/bisonex/out/2300346867_NA12878-63118093_S260-full-GRCh38/preprocessing/mapped/2300346867_NA12878-63118093_S260-GRCh38.bam
julia --project=.
include("xamscissors.jl")
#+end_src
Renommer out-chr20/inserted -> data/data/NA12878-sanger-inserted-chr20
On lance le calcul avec samples-synthetic.csv
NA12878,sanger-chr20,data/NA12878-sanger-inserted-chr20_1.fq.gz,data/NA12878-sanger-inserted-chr20_2.fq.gz
#+begin_src
nextflow run main.nf -profile standard,helios --input=samples-synthetic.csv --genome=GRCh38 -bg
#+end_src
***** DONE Vérifier après appel de variant
CLOSED: [2023-08-19 Sat 20:42] SCHEDULED: <2023-08-19 Sat>
#+begin_src
cd /Work/Users/apraga/bisonex/out/NA12878-sanger-chr20-GRCh38/callVariant/haplotypecaller
zgrep "46043645\|62334188" NA12878-sanger-chr20-GRCh38.vcf.gz
#+end_src
#+RESULTS:
: chr20 46043645 rs1332625463 G A 933.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.624;DB;DP=96;ExcessHet=0.0000;FS=1.654;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.83;ReadPosRankSum=1.833;SOR=0.516 GT:AD:DP:GQ:PL 0/1:49,46:95:99:941,0,1103
: chr20 62334188 . G A 910.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.975;DP=87;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.59;ReadPosRankSum=-1.566;SOR=0.685 GT:AD:DP:GQ:PL0/1:39,47:86:99:918,0,757
***** DONE Vérifier après filtre depth
CLOSED: [2023-08-19 Sat 20:44] SCHEDULED: <2023-08-19 Sat>
#+begin_src sh
cd /Work/Users/apraga/bisonex/out/NA12878-sanger-chr20-GRCh38/callVariant
zgrep "46043645\|62334188" filter-depth.vcf
#+end_src
#+RESULTS:
: chr20 46043645 rs1332625463 G A 933.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.624;DB;DP=96;ExcessHet=0;FS=1.654;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=9.83;ReadPosRankSum=1.833;SOR=0.516 GT:AD:DP:GQ:PL 0/1:49,46:95:99:941,0,1103
: chr20 62334188 . G A 910.64 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.975;DP=87;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;Q
***** DONE Vérifier après filtre polymorphisme
CLOSED: [2023-08-19 Sat 20:44] SCHEDULED: <2023-08-19 Sat>
zgrep "46043645\|62334188" filter-polymorphisms.vcf
chr20 46043645 rs1332625463 G A 933.64 PASS . GT:AD:DP:GQ:PL 0/1:49,46:95:99:941,0,1103
chr20 62334188 . G A 910.64 PASS . GT:AD:DP:GQ:PL 0/1:39,47:86:99:918,0,757
***** DONE vérifier après filter vep
CLOSED: [2023-08-19 Sat 20:45]
#+begin_src sh
cd /Work/Users/apraga/bisonex/out/NA12878-sanger-chr20-GRCh38/annotate
zgrep "46043645\|62334188" postvep-filter.tsv
#+end_src
#+RESULTS:
: rs1332625463 chr20:46043645 A ENSG00000124140 ENST00000243964 Transcript missense_variant 1380 1250 417 G/D gGt/gAt rs1332625463 G MODERATE - 1 - YES - Ensembl- 1 probably_damaging(0.981) ENST00000243964.7:c.1250G>A ENSP00000243964.4:p.Gly417Asp - chr20:g.46043645G>A 0 0 0 0 0 0 0 0 0 - - - -- - - rs1332625463 NTR 6.8 [03.77%-11.14%]
: chr20_62334188_G/A chr20:62334188 A ENSG00000130702 ENST00000252999 Transcript stop_gained,splice_region_variant 2804 2737 913 Q/* Cag/Tag COSV99440955 G HIGH - -1 - YES -Ensembl - 1 - ENST00000252999.7:c.2737C>T ENSP00000252999.3:p.Gln913Ter - chr20:g.62334188G>A - - - - - - - - - - 1 1 - - -- chr20:62334188-62334188 Alter by SPiCE + Alter ESR 69.33 [61.29%-76.59%]
**** KILL [#B] Tout insérer dans HG002 avec XAMscissors: erreur patient..
CLOSED: [2023-08-16 Wed 20:21] SCHEDULED: <2023-08-14 Mon>
***** DONE Insertion
CLOSED: [2023-08-16 Wed 20:21]
On récupère le BAM
#+begin_src sh :dir /home/alex/code/bisonex/out
scp /Work/Users/apraga/bisonex/out/HG002-151002_7001448_0359_AC7F6GANXX-GRCh38/preprocessing/mapped/HG002-151002_7001448_0359_AC7F6GANXX-GRCh38.bam
#+end_src
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
julia --project=.. xamscissors.jl
cd out-all
mv inserted_1.fq.gz HG002-sanger-inserted-_1.fq.gz
mv inserted_2.fq.gz HG002-sanger-inserted-_2.fq.gz
scp HG002-sanger-inserted-all_*.fq.gz meso:/Work/Users/apraga/bisonex/data/
#+end_src
Fichier de configuration
patient,sample,fastq1,fastq2
HG002,sanger-all,data/HG002-sanger-inserted-all_1.fq.gz,data/HG002-sanger-inserted-all_2.fq.gz
On lance la simulation
#+begin_src
nextflow run main.nf -profile standard,helios --input=samples-synthetic.csv --genome=GRCh38 -bg
#+end_src
***** DONE Résultat après haplopecaller: 3 reads manquants mais logique
CLOSED: [2023-08-16 Wed 19:13]
Comparaison naive: Haplotypecaller 146 found over 149
Manquant:
Row │ chrom pos ref alt zygosity meanQual stdQual depth
│ String7 Int64 String1 String1 String7 Float64 Float64 Int64
─────┼─────────────────────────────────────────────────────────────────────────
1 │ chr12 13720138 C T het 60.0 NaN 1
2 │ chr17 10296150 T A het 60.0 0.0 3
3 │ chr21 43426167 C T het 0.0 0.0 88
Donc pas assez de reads pour les 2 premiers et le dernier a des reads de mauvaise qualité (mais bien inséré).
On est limité par le système d'un patient....
***** DONE Résultat après filter depth: 30 variants perdu mais logique
CLOSED: [2023-08-16 Wed 20:18] SCHEDULED: <2023-08-16 Wed>
On perd 30 variant
13×8 DataFrame
Row │ chrom pos ref alt variant meanQual stdQual depth
│ String7 Int64 String1 String1 String Float64 Float64 Int64
─────┼───────────────────────────────────────────────────────────────────────────────────────
1 │ chr3 71112628 C T chr3:g.71112628C>T 60.0 0.0 62
2 │ chr12 13720138 C T chr12:g.13720138C>T 60.0 NaN 1
3 │ chr12 40367710 A G chr12:g.40367710A>G 59.3333 3.30289 45
4 │ chr14 58458545 G A chr14:g.58458545G>A 60.0 0.0 9
5 │ chr15 66703292 C T chr15:g.66703292C>T 60.0 0.0 33
6 │ chr16 30965737 C A chr16:g.30965737C>A 60.
] 2300104572_63076232
- [X] 2300109602_63076765
- [X] 2300109665_63076770
- [X] 2300119721_63078732
- [X] 2300137773_63078133
- [X] 2300137834_63078123
- [X] 2300167821_63086183
- [X] 2300172698_63113453
- [X] 2300188216_63090609
- [X] 2300188281_63090632
- [ ] 2300188800_63090616
- [ ] 2300193193645_63090623
- [ ] 2300193668_63090611
- [ ] 2300195426_63090608
- [ ] 2300201017_63089636
- [ ] 2300227479_63098330
- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [ ] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 23003
34609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
** TODO Variants manqués :checkpipeline:
*** DONE 63012582: chr10:g.102230760 filtré par AD :63012582:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
Il est en sortie d'haplotypecaller !
Attention à la position : POS=102230753 noté CG->C
GT:AD:DP:GQ:PL 0/1:26,8:34:99:146,0,671
Filtré par la condition AD <= 10 (porté par 8 reads seulement)
Non confirméen sanger, rendu vous
**** KILL image BAM cento
CLOSED: [2023-10-08 Sun 23:13]
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 23:23] SCHEDULED: <2023-10-08 Sun>
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE 63060439: chr15:g.26869324 = Problème de profondeur DP=15 :63060439:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
GABRA5
Rendu VOUS avec un variant patho MDB5 pour même patient (VOUS- même)
Non confirmé en Sanger
GT:AD:DP:GQ:PL 0/1:9,6:15:99:103,0,213
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 22:56]
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE Un seul exécutable pour toutes les étapes
CLOSED: [2023-11-04 Sat 19:00] SCHEDULED: <2023-10-21 Sat>
Un utilitaire en ligne de commande qui appel les différentes étapes.
On utilise une structure unique pour toutes les étapes mais qui sera remplie au fur et à mesure. En stockant dans un csv à chaque étape
**** DONE parse variants
CLOSED: [2023-10-21 Sat 23:29] SCHEDULED: <2023-10-21 Sat>
**** DONE Ajouter négatifs dans la liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
**** DONE Mettre à jour liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
- [X] Régéner la liste des variants
- [ ] Retrouver les variants modifié à la main avec diff
On ne garde que les ajouts
#+begin_src sh
awk -F ',' '{print $1","$2":"$3$4$5}' extracted.csv | ^sort | save -f extracted_concat.csv
xsv select 1-2 ~/annex/data/centogene/variants/variant_genomic.csv | ^sort | save variant_genomic_corr.csv -f
diff extracted_concat.csv variant_genomic_corr.csv | grep '^>' | save -f update.diff
#+end_src
- [X] Ajouter négatifs
345 variants non trouvés avant modification
141 après modification
- [X] Ajouter différence
- [X] Corriger erreurs de parsing
**** KILL Lifter coordonées variants cento génomique en GRCh38
CLOSED: [2023-10-21 Sat 22:47]
**** DONE Parser coordonnée patient
CLOSED: [2023-11-04 Sat 18:59] SCHEDULED: <2023-10-31 Tue>
**** DONE Un seul type de données
CLOSED: [2023-11-01 Wed 00:55] SCHEDULED: <2023-10-31 Tue>
***** DONE Vérifier avec derniere version sauvegardé
CLOSED: [2023-11-01 Wed 00:55] SCHEDULED: <2023-10-31 Tue>
file,transcript,coding,codingPos,codingChange,proteinChange,classification,zygosity
->
patient,transcript (cento),transcript (canonical),coding,genomic (hg38),classification (cento),zygosity,gene,Confirmed in sanger,Found by bisonex,chrom,pos,ref,alt
- [ ] Fusionner coding,codingPos,codingChange
- [ ] Ne pas écrire proteinchange
- [ ] Fichier de référence : insérer champs vides avec awk : transcript (canonical), genomic puis gene, etc
- [ ] Fichier de référence : renommer header
- [ ] vérifier que fichier toujours identique
#+begin_src julia
using DataFramesMeta, CSV
# - [ ] Fichier de référence : insérer champs vides avec awk : transcript (canonical), genomic puis gene, etc
# - [ ] Fichier de référence : renommer header
# - [ ] vérifier que fichier toujours identique
#file,transcript,coding,codingPos,codingChange,proteinChange,classification,zygosity
#->
#patient,transcript (cento),transcript (canonical),coding,genomic (hg38),classification (cento),zygosity,gene,Confirmed in sanger,Found by bisonex,chrom,pos,ref,alt
function mergeCoding(c, p, ch)
"negatif" in [c, p, ch] ? "negatif" : c * p * ch
end
function negative(t, pos)
t == "negatif" ? -1 : pos
end
cols = [:patient,:"transcript (cento)",:"transcript (canonical)",:coding,:"genomic (hg38)",
:"classification (cento)",:zygosity,:gene,:"Confirmed in sanger",:"Found by bisonex",
:chrom,:pos,:ref,:alt]
d = @chain CSV.read("variant_extracted.csv", DataFrame) begin
# Fusionner coding,codingPos,codingChange
@transform :coding = mergeCoding.(:coding, :codingPos, :codingChange)
# Ne pas écrire proteinchange
@select $(Not([:codingPos, :codingChange, :proteinChange]))
# Add missing mcolumns
@rename :"transcript (cento)" = :transcript :patient = :file :"classification (cento)" = :classification
@transform :"transcript (canonical)" = missing :"genomic (hg38)" = missing :gene = missing
@transform :"Confirmed in sanger" = missing :"Found by bisonex" = missing
@transform :chrom = missing :pos = missing :ref = missing :alt = missing
# Rorder
@select :patient :"transcript (cento)" :"transcript (canonical)" :coding :"genomic (hg38)" :"classification (cento)" :zygosity :gene :"Confirmed in sanger" :"Found by bisonex" :chrom :pos :ref :alt
# Set -1 for negative variant
@rtransform :pos = :"transcript (cento)" == "negatif" ? -1 : :pos
@rtransform :"transcript (canonical)"= :"transcript (cento)" == "negatif" ? "negatif" : :"transcript (canonical)"
@rtransform :"genomic (hg38)" = :"transcript (cento)" == "negatif" ? "negatif" : :"genomic (hg38)"
@rtransform :coding = :"transcript (cento)" == "negatif" ? "negatif" : :coding
@rtransform :gene = :"transcript (cento)" == "negatif" ? "negatif" : :gene
@rtransform :pos = ismissing(:pos) ? -1 : :pos
end
CSV.write("variant_extracted_remap.csv", d)
d2 = @chain CSV.read("extracted.csv", DataFrame) begin
@orderby :patient
end
CSV.write("extracted_sorted.csv", d2)
#+end_src
ON trie les fichiers pour bien avoir le bon order (sinon diff ne fonctionne pas ??)
diff extracted_sorted.csv variant_extracted_remap.csv -u | save extracted.diff
patch -p1 extracted_sorted.csv extracted.diff
patching file extracted_sorted.csv
diff extracted_sorted.csv variant_extracted_remap.csv -u
**** KILL variant_recoder pour avoir les coordonnées VCF
CLOSED: [2023-10-25 Wed 09:13] SCHEDULED: <2023-10-21 Sat>
mobidetails n e trouve pas les ieux transcrits
**** DONE Annotation mobidetails (gen
e + données gonémique)
CLOSED: [2023-10-25 Wed 09:14]
**** DONE Envoyer liste à Paul
SCHEDULED: <2023-10-26 Thu>
**** DONE compare chaque variant avec la sortie du pipeline
CLOSED: [2023-10-31 Tue 00:18] SCHEDULED: <2023-10-21 Sat>
Avec la fonction "test" dans Search.hs
1126 extracted
654 annotated
253 raw data
102 raw and annotated
236 raw and extracted
17 raw NOT extracted
890 extract WITHOUT raw
#+begin_src sh
❯ open diff.txt | from csv | get id | into string | each {|e| "~/annex/data/centogene/reports/" ++ $e ++ "*.pdf"} | each {|e| firefox $e }
#+end_src
Les 17 manquants sont
- 62913191 : CNV
- 62959388 : MT-ATP6
- 62999572 : MT-ATP6
- 62999627 : CNV
- 62999630 : CNV
- 63004218: CNV
- 63006466 : CNV
- 63009152 : manqué à extraire -> bien présent
- 63015289: CNV
- 63024910 : MT-ATP6
- 63040251 : CNV
- 63043050 : CNV
- 63118093 : NA12878
- NA12878 x4
*** DONE
Comparer variants cento à sortie bisonex: 50/121 confirmé en sanger, 71/121 non testé, 0 confirmés manqué par pipeline, 5 manqué mais non confirmés
CLOSED: [2023-11-08 Wed 00:19] SCHEDULED: <2023-11-04 Sat>
*** Comparger sanger : variant seul
Compliqué de reconstituer l'arbre familial. L'information est là mais demande du travail.
ON suppose que le variant n'est que dans la famille....
Résultats
❯ open sangerized.csv | where "Found by bisonex" == "found" | where "Confirmed in sanger" == "true" | length
50
❯ open sangerized.csv | where "Found by bisonex" == "found" | where "Confirmed in sanger" == "" | length
71
❯ open sangerized.csv | where "Found by bisonex" == "missed" | where "Confirmed in sanger" == "" | length
5
❯ open sangerized.csv | where "Found by bisonex" == "missed" | where "Confirmed in sanger" == "true" | length
0
[[id:cd79a77c-a0b6-4bb1-9e08-fe08dc89e3aa][Résultats finaux]]
*** DONE Regarder 5 variants manqués: 3 explicables, 2 non
CLOSED: [2023-11-09 Thu 00:22] SCHEDULED: <2023-11-05 Sun>
open searched.csv | where "Found by bisonex" == "missed"
62982193 7884996 : haplotypecaller ok... -> filtré car AD=5 <= 10
63012582 102230760 : non présent haplotypcellar mais une délétion en 755 (en 754 CG -> C). Vérifié mobidetails
63019340 50721335 : non présent haplotypecaller (vérifié igv). vérifié mobidetails
63060439 26869324 : filtré car 15 reads
63109239 14358800 : présent haplotypecaller : filtré car DP=29 <= 30
Non présent haplotypecaller avec bcftools mais zgrep ok
zgrep 7884996 call_variant/haplotypecaller/*62982193*/*
zgrep 102230760 call_variant/haplotypecaller/*63012582*/*
zgrep 50721335 call_variant/haplotypecaller/*63019340*/*
zgrep 26869324 call_variant/haplotypecaller/*63060439*/*
zgrep 14358800 call_variant/haplotypecaller/*63109239*/*
*** DONE Flowchart
CLOSED: [2023-11-09 Thu 00:22]
*** DONE Refaire extraction
CLOSED: [2023-11-04 Sat 19:02] SCHEDULED: <2023-11-04 Sat>
*** DONE Refaire annotation avec mobidetails
CLOSED: [2023-11-04 Sat 19:02] SCHEDULED: <2023-11-04 Sat>
*** DONE Refaire annotation avec transcrit non reconnus
CLOSED: [2023-11-04 Sat 20:42] SCHEDULED: <2023-11-04 Sat>
5 transcrits, donnés égalemen tpar
#+begin_src nu
open annotated.csv | where coding != "negatif" | where chrom == ""
#+end_src
| 62676048 | NM_001080420.1 | SHANK3 | référénce non valide |
| 62690893 | NM_001080420.1 | KDM6B | idem |
| 62690893 | NM_001080420.1 | KDM6B | même variant |
| 62795429 | NM_016381.3 | TREX1 | NM_033629.5 |
| 63019340 | NM_001080420.1 | SHANK3 | NM_001372044.2 |
SCHEDULED: <2023-11-01 Wed>
*** DONE Rajouter variant pour 63009152
CLOSED: [2023-11-04 Sat 20:47] SCHEDULED: <2023-11-01 Wed>
*** DONE Regénérer annotation avec NC_
CLOSED: [2023-11-04 Sat 18:59] SCHEDULED: <2023-10-31 Tue>
*** DONE Comparer variants manqué avec sanger: 0 confirmés
CLOSED: [2023-11-06 Mon 23:48] SCHEDULED: <2023-11-04 Sat>
*** DONE Annoter variants avec sanger
CLOSED: [2023-11-08 Wed 23:17] SCHEDULED: <2023-11-07 Tue>
*** DONE Mail paul avec résultats
CLOSED: [2023-11-09 Thu 00:22] SCHEDULED: <2023-11-05 Sun>
*** DONE Vérifier coordonnées des 2 variants manquants
CLOSED: [2023-11-12 Sun 16:53] SCHEDULED: <2023-11-11 Sat>
Les 2 sont des homopolymer
- 1er = même variant mais représenté différement
- SHANK3 ?
**** PITX3: filtrée car AD=8
NB: représentation synonyme
Même séquence
>hg38_dna range=chr10:102230742-102230777 5'pad=2 3'pad=2 strand=+ repeatMasking=none
GGAGCCAGCCCGGGGGGGCCCCCGCCCAGGCCCTG
>hg19_dna range=chr10:103990500-103990534 5'pad=0 3'pad=0 strand=+ repeatMasking=none
GGAGCCAGCCCGGGGGGGCCCCCGCCCAGGCCCTG
Selon IGV:
GGAGCCAGCCC(G)GGGGGGCCCCCGCCCAGGCCCTG
Selon cento
GGAGCCAGCCCGGGGGG(G)CCCCCGCCCAGGCCCTG
#+begin_src sh :dir ~/annex/data/bisonex/
bcftools filter -i 'POS=102230760' call_variant/haplotypecaller/*63012582*/*.vcf.gz
#+end_src
DP ok mais AD trop faible
GT:AD:DP:GQ:PL 0/1:26,8:34:99:146,0,671
**** SHANK3: transcrit supprimé depuis: ok
Retrouvé par ERic: 50721504dup
On vérifie
#+begin_src sh :dir ~/annex/data/bisonex/
bcftools filter -i 'POS=50721504' call_variant/haplotypecaller/*63019340*/*.vcf.gz
#+end_src
#+begin_src sh :dir ~/annex/data/bisonex/
zgrep '50721504' annotate/full/*63019340*.tsv
#+end_src
*** TODO Sanger pour 4 VOUS manqués
SCHEDULED: <2023-12-20 Wed>
/Entered on/ [2023-11-13 Mon 22:40]
** TODO Chercher nouveaux gènes
SCHEDULED: <2023-12-20 Wed>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-12-21 Thu>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-12-21 Thu>
* Communication
** DONE Mail NGS-diag
CLOSED: [2023-10-06 Fri 08:04] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]
* Presentations
** DONE Abstract FOSDEM 2024
CLOSED: [2023-12-06 Wed 22:37] DEADLINE: <2023-12-07 Thu> SCHEDULED: <2023-12-04 Mon>
/Entered on/ [2023-12-03 Sun 23:17]
https://pretalx.fosdem.org/fosdem-2024/me/submissions/FSQC3U/
Diagnosing genetic diseases presents significant challenges. Modern sequencers produce vast amounts of data, requiring intensive processing and filtering before analysis. The intricate mechanisms inherent in rare diseases necessitate a high level of expertise from biologists to identify potential causes. This is why it is crucial to demonstrate these results come from accurate, efficient, and reproducible bioinformatics pipelines. Indeed, accuracy is vital for patient diagnosis, efficiency is needed to handle the growing data volume and patient backlog, and reproducibility is essential to ensure the quality of the results.
This talk is aimed at a diverse audience and will give feedback on Nix integration in our workflow.
It will focus on how Nix significantly improved reproducibility and discuss some challenges we encountered, especially with large databases and running on high-performance computing architectures.
0 0.0 18
7 │ chr17 10296150 T A chr17:g.10296150T>A 60.0 0.0 3
8 │ chr17 61968202 A C chr17:g.61968202A>C 60.0 0.0 46
9 │ chr21 43426167 C T chr21:g.43426167C>T 0.0 0.0 88
10 │ chrX 124056226 T G chrX:g.124056226T>G 60.0 0.0 40
11 │ chrX 24737739 G T chrX:g.24737739G>T 60.0 0.0 16
12 │ chrX 40591349 C T chrX:g.40591349C>T 60.0 0.0 37
13 │ chrX 53193275 G A chrX:g.53193275G>A 60.0 0.0 32
Le filtre est sur DP (read depth) et non la profondeur. Sur 1 et 3, DP=29 et 28...
Si on est hétérozygote, le DP est la moitié de la profondeur donc c'est logique...
***** DONE Résultat après filter polymorphism : idem
CLOSED: [2023-08-16 Wed 20:18]
***** Résultat après filtre VEP
**** KILL [#B] Tout insérer dans NA12878 avec XAMscissors: reads manquants
CLOSED: [2023-08-19 Sat 20:04] SCHEDULED: <2023-08-14 Mon>
***** KILL Insertion
CLOSED: [2023-08-19 Sat 20:03]
On récupère le BAM
#+begin_src sh :dir /home/alex/code/bisonex/out
rsync -avz meso:/Work/Users/apraga/bisonex/out/2300346867_NA12878-63118093_S260-GRCh38/preprocessing/mapped 2300346867_NA12878-63118093_S260-GRCh38/preprocessing/
#+end_src
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
julia --project=.. xamscissors.jl
cd out-all
mv inserted_1.fq.gz NA12878-sanger-inserted-all_1.fq.gz
mv inserted_2.fq.gz NA12878-sanger-inserted-all_2.fq.gz
rsync -avz NA12878-sanger-inserted_* meso:/Work/Users/apraga/bisonex/data/
#+end_src
Fichier de configuration
patient,sample,fastq1,fastq2
NA12878,sanger-all,data/NA12878-sanger-inserted-all_1.fq.gz,data/NA12878-sanger-inserted-all_2.fq.gz
On lance la simulation
#+begin_src
nextflow run main.nf -profile standard,helios --input=samples-synthetic.csv --genome=GRCh38 -bg
#+end_src
***** DONE Résultat après haplotyecaller: 3 varinat perdus => ok
CLOSED: [2023-08-17 Thu 19:13]
Haplotypecaller 143 found over 146
3×3 DataFrame
| variant | meanQual | depth |
|---------------------+----------+-------|
| chr12:g.13720138C>T | 60.0 | 1 |
| chr17:g.10296150T>A | 60.0 | 3 |
| chr21:g.43426167C>T | 0.0 | 88 |
Pas assez de read (1,2) et problème d'alignement (3)
***** KILL Résultat après filtre depth : +10 variants perduis
CLOSED: [2023-08-19 Sat 20:04] SCHEDULED: <2023-08-18 Fri>
filter depth : another 10 missed variants
10×3 DataFrame
| variant | meanQual | depth |
|---------------------+----------+-------|
| chr3:g.71112628C>T | 60.0 | 62 |
| chr12:g.40367710A>G | 58.0435 | 46 |
| chr14:g.58458545G>A | 60.0 | 9 |
| chr15:g.66703292C>T | 60.0 | 33 |
| chr16:g.30965737C>A | 60.0 | 18 |
| chr17:g.61968202A>C | 60.0 | 46 |
| chrX:g.124056226T>G | 60.0 | 40 |
| chrX:g.24737739G>T | 60.0 | 16 |
| chrX:g.40591349C>T | 60.0 | 37 |
| chrX:g.53193275G>A | 60.0 | 32 |
| | | |
S'ils sont hétérozygotes, 0.5*depth est effectivement < 30 (notre filtre...)
****** KILL Problème d'inserstion des reads: on en perd de nombreux ! -> regénérer données
CLOSED: [2023-08-19 Sat 20:04] SCHEDULED: <2023-08-18 Fri>
Ex: chrX:g.124056226T>G : on passe de 65 reads à 1
***** DONE Résultat après filtre common variant: +0 ok
CLOSED: [2023-08-17 Thu 19:32]
***** KILL Résultat après filtre VEP : +23 perdus ??
CLOSED: [2023-08-19 Sat 20:04] SCHEDULED: <2023-08-18 Fri>
filter vep : another 23 missed variants
23×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼───────────────────────────────────────
1 │ chr1:g.183222115C>T 60.0 168
2 │ chr1:g.39388062C>T 60.0 285
3 │ chr2:g.240719197G>C 60.0 77
4 │ chr3:g.41227353G>C 60.0 105
5 │ chr4:g.15536991T>G 60.0 41
6 │ chr5:g.14474096G>A 60.0 191
7 │ chr8:g.43122149C>T 60.0 237
8 │ chr9:g.128603589A>C 60.0 304
9 │ chr9:g.137452819G>C 60.0 107
10 │ chr10:g.129957338T>C 60.0 116
11 │ chr10:g.247389T>G 60.0 56
12 │ chr11:g.61313668G>A 60.0 83
13 │ chr12:g.45850467C>T 60.0 291
14 │ chr14:g.64216315C>G 60.0 263
15 │ chr15:g.60514655G>A 60.0 259
16 │ chr17:g.61966475G>T 60.0 144
17 │ chr17:g.7852503T>C 60.0 190
18 │ chr19:g.13230158G>A 60.0 172
19 │ chr19:g.38523211C>G 60.0 93
20 │ chr19:g.4110557G>C 59.9929 425
21 │ chr20:g.62334188G>A 60.0 62
22 │ chrX:g.47575255G>A 60.0 244
23 │ chrX:g.53409112G>A 60.0 136
**** DONE [#A] Tout insérer dans NA12878 avec XAMscissors (XAMScissors à jour)
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-19 Sat>
***** DONE Insertion
CLOSED: [2023-08-20 Sun 09:15]
***** DONE Vérifier après haplotypecaller: 3 variants manquant mais ok
CLOSED: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
3×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼──────────────────────────────────────
1 │ chr12:g.13720138C>T 60.0 1
2 │ chr17:g.10296150T>A 60.0 1
3 │ chr21:g.43426167C>T 0.0 59
Manque de profondeur sur 2 et mauvaise qualité sur 3
***** DONE Vérifier après filterdepth: 0 perdus en plus
CLOSED: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
***** DONE Vérifier après filterpolymorphis : 0 perdus en plus
CLOSED: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
***** DONE Vérifier après filter vep: 2 perdus en plus
CLOSED: [2023-08-20 Sun 12:37] SCHEDULED: <2023-08-20 Sun>
2×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼─────────────────────────────────────
1 │ chr17:g.7852503T>C 60.0 96
2 │ chrX:g.47575255G>A 60.0 145
***** DONE 1ere correction spip: meilleur nombre de variants en sortie mais manque toujours ces 2
CLOSED: [2023-08-20 Sun 11:38]
***** DONE --pick : résout le problème
CLOSED: [2023-08-2
0 Sun 12:37]
chrX:g.47575255G>A est rendu downstream_gene_variant avec l'option --pick
Or il n'est pas en5' dans les transcrits refseq...
https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chrX%3A47575242%2D47575268&hgsid=301211823_xpelPqPJije7wSIhg070JeGH5ZwV
https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/238296/browser/
Idem pour l'autre
chr17:g.7852503T>C
https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/182993/browser/
Note:
VEP chooses one block of annotation per variant, using an ordered set of criteria. This order may be customised using --pick_order.
MANE Select transcript status
MANE Plus Clinical
061871
- [X] 2300055440_63061880
- [X] 230006894_63064950
- [X] 2300071111_63070356
- [X] 2300083434_63071675
- [X] 2300103609_63076239
- [X
transcript status
canonical status of transcript
APPRIS isoform annotation
transcript support level
biotype of transcript ("protein_coding" preferred)
CCDS status of transcript
consequence rank according to this table
translated, transcript or feature length (longer preferred)
"Wherever possible we would discourage you from summarising data in this way. "
**** DONE Mail alexis
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-20 Sun>
**** TODO Données simuscop 200x
SCHEDULED: <2023-12-21 Thu>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] SCHEDULED: <2023-09-17 Sun>
1. Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
2. Liftover avec UCSC (en ligne)
NB: vérifié sur le premier résultat en cherche le read contenant le variant (samtools view -r puis samtools view | grep en T2T) et avec l'aide d'IGV, on a un variant qui correspond en
chr1:10757746
3. En supposant que l'ordre des variants n'a pas changé, on ajoute simplement REF et ALT avec annotateLifted.jl
Annotation spip *très lente* : 1h13 !
Résultat:
2×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼──────────────────────────────────────
1 │ chr12:g.13594572 60.0 1
2 │ chr17:g.10204026 60.0 1
144 found over 146
filter depth : another 0 missed variants
filter poly : another 0 missed variants
filter vep : another 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** TODO Medically relevant genes
SCHEDULED: <2023-12-26 Tue>
/Entered on/ [2023-10-18 Wed 22:37]
** TODO HG002 en T2T
/Entered on/ [2023-11-25 Sat 17:58]
https://github.com/marbl/HG002
*** TODO Tester les benchmark préliminaires
SCHEDULED: <2023-12-26 Tue>
https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/analysis/NIST_HG002_DraftBenchmark_defrabbV0.011-20230725/
* Ré-interprétation :reanalysis:
** DONE Lancer tests sur données brutes [225/250] <(samples.csv)> <(runs.waiting)>
CLOSED: [2023-10-14 Sat 11:58] SCHEDULED: <2023-10-08 Sun>
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high boundaries for computing mean and std.dev: (1, 605)
[M::mem_pestat] mean and std.dev: (158.00, 110.30)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 788)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RR
[M::process] read 839618 sequences (114952336 bp)...
[M::mem_process_seqs] Processed 1752492 reads in 375.714 CPU sec, 17.645 real sec
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 336379, 0, 5)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (128, 174, 232)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 440)
[M::mem_pestat] mean and std.dev: (184.73, 74.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 544)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 839618 reads in 183.039 CPU sec, 7.961 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 24 -o wtf.bam /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz
[main] Real time: 38.278 sec; CPU: 565.821 sec
Bon nombre de reads pourtant
samtools flagstat wtf.bam
2611059 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
18949 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2611058 + 0 mapped (100.00% : N/A)
2592109 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2590970 + 0 properly paired (99.96% : N/A)
2592108 + 0 with itself and mate mapped
1 + 0 singletons (0.00% : N/A)
458 + 0 with mate mapped to a different chr
63 + 0 with mate mapped to a different chr (mapQ>=5)
$ samtools sort -@24 -o wtf_sorted.bam wtf.sam
[bam_sort_core] merging from 0 files and 24 in-memory blocks...
samtools flagstat wtf.bam
2611059 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
18949 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2611058 + 0 mapped (100.00% : N/A)
2592109 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2590970 + 0 properly paired (99.96% : N/A)
2592108 + 0 with itself and mate mapped
1 + 0 singletons (0.00% : N/A)
458 + 0 with mate mapped to a different chr
63 + 0 with mate mapped to a different chr (mapQ>=5)
Effectivement, ce n'est pas un problème d'IGV
❯ samtools mpileup 63003856_chr22.bam -r NC_000022.11:42213078-42213078
[mpileup] 1 samples in 1 input files
NC_000022.11 42213078 N 19 TTtTTtTTTtTTtTtTttt kkk_kkkkFkFF_FkFkQk
bisonex/code/BamScissors.jl on bamscissors [!?] via ஃ v1.9.0
❯ samtools mpileup aligned/wtf_sorted.bam -r NC_000022.11:42213078-42213078
[mpileup] 1 samples in 1 input files
NC_000022.11 42213078 N 5 TTtTT _FkFF
******** DONE Regarder où ont été aligné les reads (nouveau run)
CLOSED: [2023-05-24 Wed 23:18]
********* DONE Préparation
CLOSED: [2023-05-24 Wed 21:59]
On relance le pipeline pour avoir un BAM propre
On garde les reads non mappé à partsir de la sortie d'applybqsr
#+begin_src sh
NXF_OPTS=-D"user.name=apraga" nextflow run main.nf -c nextflow.config -profile standard,helios --input="/Work/Projects/bisonex/cento/fastq/2200467051_63003856/63003856_S135_R{1,2}_001.fastq.gz" --outdir=out -bg
cd out/63003856_S135_R/preprocessing/applybqsr/
samtools view 63003856_S135_R.bam NC_000022.11 -f 0x2 -o 63003856_chr22.bam
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq -1 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -n 63003856_chr22_sorted.bam
make run BG= READS="out/63003856_S135_R/preprocessing/applybqsr/63003856_chr22_{1,2}.fq.gz"
cd out/63003856_chr22/preprocessing/mapped/
samtools index 63003856_chr22.bam
samtools mpileup 63003856_chr22.bam -r NC_000022.11:42213078-42213078
#+end_src
On récupère les 2 bam dans
#+begin_src
cd /home/alex/recherche/bisonex/code/BamScissors.jl/
rsync -avz meso:/Work/Users/apraga/bisonex/out/63003856_chr22/preprocessing/mapped data
rsync -avz meso:/Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing/applybqsr/ data/init/
#+end_src
********* Vérification que le reads est ailleurs
On cherche un read manquant dans le second alignement
#+begin_src sh
samtools view data/init/63003856_chr22.bam | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
#+end_src
#+RESULTS:
: A00853:477:HMLWYDSX3:1:1413:4390:28573 163 NC_000022.11 42212845 0 151M = 42212883 189 CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT ACC+FBCDCBBBAEAEDEEBBCCCECACBAEBEBDCCBCBFDCCCCFACEBEBCEEDCCCCFDCAEDCACBCEBBCFEACCFBDCACDCBCEBDBBCFEEDCCCFAFEACECCCECAEEDCADCBEDC7BEBCCCFBAFDCECCFBEAACA MC:Z:151M MD:Z:151 PG:Z:MarkDuplicates RG:Z:sample NM:i:0 AS:i:151 XS:i:151
: A00853:477:HMLWYDSX3:1:1413:4390:28573 83 NC_000022.11 42212883 0 151M = 42212845 -189 ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT AADECCCBDCBFCE<?CDEEEEBDEACDEAC;:BFBCBCDCCBEAEACAEFCCEAFBCBCCDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE:CECBABBEBEE;DBFCCCDBCDBCCBBC?@BEEDA MC:Z:151M MD:Z:151 PG:Z:MarkDuplicates RG:Z:sample NM:i:0 AS:i:151 XS:i:151
#+begin_src sh
samtools view data/mapped/63003856_chr22.bam | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
#+end_src
#+RESULTS:
: A00853:477:HMLWYDSX3:1:1413:4390:28573 163 NW_014040930.1 115017 0 151M = 115055 189 CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT ACC+FBCDCBBBAEAEDEEBBCCCECACBAEBEBDCCBCBFDCCCCFACEBEBCEEDCCCCFDCAEDCACBCEBBCFEACCFBDCACDCBCEBDBBCFEEDCCCFAFEACECCCECAEEDCADCBEDC7BEBCCCFBAFDCECCFBEAACA NM:i:0 MD:Z:151 MC:Z:151M AS:i:151 XS:i:151 RG:Z:sample
: A00853:477:HMLWYDSX3:1:1413:4390:28573 83 NW_014040930.1 115055 0 151M = 115017 -189 ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT AADECCCBDCBFCE<?CDEEEEBDEACDEAC;:BFBCBCDCCBEAEACAEFCCEAFBCBCCDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE:CECBABBEBEE;DBFCCCDBCDBCCBBC?@BEEDA NM:i:0 MD:Z:151 MC:Z:151M AS:i:151 XS:i:151 RG:Z:sample
Effectivement, on aligne sur une zonne supprimée !
******** DONE Corriger la qualité: non
CLOSED: [2023-05-24 Wed 22:19]
********* DONE Comparaison avec le fastq de référénce : qualité !!
CLOSED: [2023-05-24 Wed 22:17]
#+begin_src sh
cd /Work/Users/apraga/bisonex/work/6e/8548fc90263830bf677f36585f11dc
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" 63003856_chr22_1.fq.gz
#+end_src
@A00853:477:HMLWYDSX3:1:1413:4390:28573
AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
+
ADEEB@?CBBCCBDCBDCCCFBD;EEBEBBABCEC:EEBEAADCFCDFBFECCFCFFFFCCGFEDGFBBEEDCAECCEEBCECBDBCEEDCCBCBFAECCFEACAEAEBCCDCBCBFB:;CAEDCAEDBEEEEDC?<ECFBCDBCCCEDAA
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" /Work/Projects/bisonex/cento/fastq/2200467051_63003856/63003856_S135_R1_001.fastq.gz
#+end_src
AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
********* DONE Regarder la qualité après bwa mem vs applybqsr: différente
CLOSED: [2023-05-24 Wed 22:18]
Sur le mésocentre, dans /Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing
$ samtools view mapped/63003856_S135_R.bam NC_0
gz --reference genomeRef.fna --tmp-dir . -L NC_000015.10
#+end_src
scp meso:/Work/Users/apraga/bisonex/tests/synthetic/testchr15.vcf.gz haplotypecaller-chr15.vcf.gz
Aucun variant inséré
- base quality ok
-
******* DONE bam out : non appelé
CLOSED: [2023-05-01 Mon 21:57]
gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam --output haplotypecaller-chr15.vcf.gz --reference genomeRef.f
na --tmp-dir . -L NC_000015.10 --bam-output debug.bam
******* DONE --linked-de-bruijn-graph : idem
CLOSED: [2023-05-01 Mon 21:57]
readlink testchr15.vcf.gz -f^C
[apraga@mesointeractive synthetic]$ gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam --output haplotypecaller-chr15.vcf.gz --reference genomeRef.fna --tmp-dir . -L NC_000015.10 --linked-de-bruijn-graph
******* KILL regénérer fastq
CLOSED: [2023-05-13 Sat 18:29]
Non
****** KILL Générer bam données pour tous les chromosomes
CLOSED: [2023-05-13 Sat 18:29]
timeit julia -Jbisonex.so --project=. insertVariants.jl ~/code/bisonex/out/63003856/preprocessing/63003856_S135.bam 63003856_S135_inserted.bam
40min 516ms 835µs 405ns
Avertissement:
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
Inserted.bam et excluded.bam (fichier avant le merge) ont l'air ok...
On réessaie à la main : ça passe
#+begin_src
samtools merge test-all.bam inserted.bam excluded.bam
❯ mv test-all.bam `63003856_S135_inserted.bam` -f
❯ mv test-all.bam.bai `63003856_S135_chr15_inserted.bam.bai` -f
#+end_src
****** DONE BAm2fastq pour avoir CIGAR à jour : échec (variants "cachés")
CLOSED: [2023-05-04 Thu 20:30] SCHEDULED: <2023-05-01 Mon>
On lance la génération de bam depuis le mesocentro (la copie plante via le VPN)
#+begin_src sh
cd /Work/Users/apraga/recherche/bisonex/generate
julia --project=. insertVariants.jl ../../../bisonex/out/63003856_S135/preprocessing/applybqsr/63003856_S135.bam 63003856_S135_inserted.bam
#+end_src
Workflow après avec désactivé storeDir pour SAMTOOLS_BAM2FQ dans nextflow.config (pourquoi ??)
#+begin_src nextflow
include { SAMTOOLS_BAM2FQ } from "${params.modulesDir}/samtools/bam2fq/main"
include { SAMTOOLS_SORT as sortBamByName } from "${params.modulesDir}/samtools/sort/main"
workflow {
f = Channel.fromPath("${params.da
taDir}/synthetic/63003856_S135_inserted.bam",
checkIfExists: true).map{it -> [["id": "synthetic_63003856"], it]}
// Important: use "-n" option !!
sortBamByName(f)
SAMTOOLS_BAM2FQ(sortBamByName.out.bam, true)
}
#+end_src
Puis
#+begin_src
cp work/34/fb2fc136f6f6d7f42d0960512f06de/*.fq.gz /Work/Groups/bisonex/data/synthetic/
#+end_src
****** KILL Lancer pipeline
CLOSED: [2023-05-04 Thu 20:30] SCHEDULED: <2023-05-01 Mon>
NXF_OPTS=-D"user.name=apraga" nextflow run main.nf -c nextflow.config -profile standard,helios -bg --input="/Work/Groups/bisonex/data/synthetic/synthetic_63003856_{1,2}.fq.gz" --outdir out/synthetic_63003856
**** HOLD Bamsurgeon :bamsurgeon:
***** HOLD Package nix
1. Patcher la recherche du génome de référence pour bien trouver les index (en utilisant une regexp comme nf-core)
2. Rajouter le chemin de picard dans les arguments
3. Option -O3 pour performance
****** DONE Erreur ValueError: quality and sequence mismatch
CLOSED: [2023-05-19 Fri 18:44]
******* DONE Idem avec dernière version sur github
CLOSED: [2023-05-18 Thu 14:36]
******* DONE Version 1.3: ok mais
CLOSED: [2023-05-19 Fri 18:44]
Test sur chr22: variants ok mais VAF=1...
S'exécute "normalement" (échec selon nextflow) mais le bam de sorstie quasiment vide
La fusion du bam avec les variants et du fichier de référence n'a fonctionné correctement.
******** DONE Lancer replacereads.py à la main
CLOSED: [2023-05-18 Thu 21:41]
Dans /Work/Users/apraga/bisonex/work/f3/ce044f80ca91016d68d1bc4f4f5301
#+begin_src sh
/nix/store/xw277la6w4sjqlsvw9h32cvrlacrfkgm-python3-3.10.9-env/bin/python3.10 /nix/store/abzangf0q8k37053p776cfkw181dzjn3-bamsurgeon-1.3/bin/bamsurgeon/replacereads.py -b cento.bam -r addsnv.e14561be-4fdd-45cc-9989-048ab6da6cc6.muts.bam -o snv-manual.bam
#+end_src
Puis
#+begin_src
samtools sort snv-manual.bam -o snv-manual-sorted.bam
#+end_src
A l'air de fonctionne
****** HOLD Corriger run nextflow pour éviter les erreurs
Trop de message d'erreur en sortie ?
****** DONE Test sur mini-bam: échec
CLOSED: [2023-05-14 Sun 21:12]
❯ samtools view -h ~/code/bisonex/simuscop-cento-200x/cento/preprocessing/mapped/cento.bam | head -n1000 | samtools view -Sb - > mini.bam
❯ samtools index mini.bam
Sans spécfier le variant:
#+begin_quote
NC_000001.11 17651 17651
#+end_quote
./result/bin/addsnv -v snv.txt -f mini.bam -r ../data/genomeRef.fna -o test.bam
****** DONE Test chr22
CLOSED: [2023-05-15 Mon 23:24]
Pas assez de reads, on prend le chromosome 22
#+begin_src sh
samtools view ../simuscop-cento-200x/cento/preprocessing/mapped/cento.bam NC_000022.11 -b -o chr22.bam
samtools index chr22.bam
#+end_src
Mésocentre
dans tests/bamsurgeno
#+begin_src
addsnv -v snv.txt -f chr22.bam -r ../genomeRef.fna -o test.bam --aligner mem
#+end_src
******* DONE SNV aléatoire:
CLOSED: [2023-05-15 Mon 23:13]
NC_000022.11 17499704 17499704 0.2
On retrouve bien un variant à cette position A > T
******* DONE SNV avec ALT prédéfini : retrouvée dans IGV (mais pas dans pileup)
CLOSED: [2023-05-15 Mon 23:13]
NC_000022.11 17499704 17499704 0.2 G
******* DONE Variants patients chr22: ok IGV
CLOSED: [2023-05-15 Mon 23:23]
Fichier non trié donc
samtools sort test.bam -o test-sorted.bam
samtools index test-sorted.bam
******* DONE Vérifier qu'il faut POS et POS+1: non
CLOSED: [2023-05-14 Sun 21:21]
***** HOLD Variants cento
****** STRT SNV
Attention à la mémoire: 32G ne semble pas suffire avec 12 threads
#+begin_src sh
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/bamsurgeon.nf -profile standard,helios --input=tests/bamsurgeon/snv-cento.tsv -bg
#+end_src
ET
#+begin_src nextflow
workflow {
f = Channel.fromPath(params.input, checkIfExists: true)
bam = Channel.fromPath("simuscop-cento-200x/cento/preprocessing/mapped/cento.bam",
checkIfExists: true)
bamIndex = bam.map { it -> it + ".bai" }
downloadGenome | indexGenome
indexGenome.out.index | view
addSNV(f, bam, bamIndex, downloadGenome.out, indexGenome.out.index, indexGenome.out.dict, indexGenome.out.fai)
}
#+end_src
******* DONE v1.3: Lancer le pipeline pour vérifier qu'on retrouve les variants
CLOSED: [2023-05-19 Fri 18:41] SCHEDULED: <2023-05-18 Thu>
******* HOLD Corrigier position pour avoir une bonne VAF
POS POS+1 VAF ALT
Attention, la base corrigée est à POS+1...
******* DONE Comparaison manuelle avec julia (VAF = 1...)
CLOSED: [2023-05-19 Fri 21:58]
552 found over 585
****** TODO del
****** TODO ins
**** KILL [[id:966a298c-948a-4694-a6f5-c326b1046a05][XAMscissors.jl]] :xamscissors:
CLOSED: [2023-08-12 Sat 15:59]
***** KILL Test SNV
CLOSED: [2023-08-12 Sat 15:59]
****** DONE Phase 1 : chr22, VAF=1
CLOSED: [2023-05-29 Mon 15:36]
******* DONE 1 SNV : ok !
CLOSED: [2023-05-20 Sat 19:35] SCHEDULED: <2023-05-20 Sat>
#+begin_src
make run READS="tests/bamscissors/corrected_{1,2}.fq.gz"
Puis on lance le pipeline sur correct_1
- [X] Variant visible dans IGV
- [X] Variant visible après alignement
- [X] Variant visible après appel de variant
******* KILL Tester SNV chromosome 22
CLOSED: [2023-05-29 Mon 15:36] SCHEDULED: <2023-05-20 Sat>
****** KILL PHase 2 : chr22, VAF variable
CLOSED: [2023-06-12 Mon 23:27] SCHEDULED: <2023-06-03 Sat>
******* DONE de nombreux reads sont perdus -> ok sur un SNV en alignant sur chromosome 22
CLOSED: [2023-05-29 Mon 15:38]
Problème dansr le BAM car sans les insertion
******** DONE Filtrer les reads sans pair : idem
CLOSED: [2023-05-23 Tue 00:01]
FOUND:Found 16662 unpaired mates
at htsjdk.samtools.SAMUtils.processValidationError(SAMUtils.java:470)
at picard.sam.SamToFastq.doWork(SamToFastq.java:224)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
ex: chr22:42213078
On essaie
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11 -hf 0x2 -o 63003856_chr22.bam
Ne rale pas...
SCHEDULED: <2023-05-22 Mon>
******** DONE Problème de la conversion BAM -> fastq ?
CLOSED: [2023-05-24 Wed 23:19]
********* DONE Test bamtofastq sur le BAM originel: idem
CLOSED: [2023-05-23 Tue 01:16]
Dans ~/recherche/code/bisonex/Bamscissors.jl
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11 -hf 0x2 -o 63003856_chr22.bam
On trie bien par nom de read
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
Conversion en fastq. Attention à bien prendre le *fichier trié* !
samtools bam2fq -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz -n 63003856_chr22_sorted.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2592110 reads
On envoie sur le mésocentre
scp 63003856_chr22_init{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors
On démarre un job avec 24 coeurs pour aller vite
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_init1.fq.gz 63003856_chr22_init2.fq.gz | samtools sort -@24 -o output.bam -
Dans /home/alex/recherche/bisonex/code/BamScissors.jl/aligned
❯ scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam*
********* DONE Avec samtools fastq
CLOSED: [2023-05-23 Tue 01:16]
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -o 63003856_chr22_sorted.bam
scp 63003856_chr22_{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
mesocentre
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam\* aligned/
********* DONE En rajoutant .fna dans le doserrie (+samtools fastq): idem
CLOSED: [2023-05-23 Tue 01:16]
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef* .
ln -s /Work/Projects/bisonex/dat
AAGTGATTTTA
14:41:05.530 INFO EventMap - > Cigar = 41M
14:41:05.530 INFO EventMap - >> Events = EventMap{NC_000021.9:14144627-14144627 [C*, T],}
14:41:05.530 INFO HaplotypeCallerGenotypingEngine - Genotyping event at 14144627 with alleles = [C*, T]
#+end_quote
NB: même en filtranrt sur le chromosome 21 avec julia, haplotypecaller parcourt tous les chromosomes
********* DONE --linked-de-bruijn-graph : idem
CLOSED: [2023-02-26 Sun 17:26]
********* DONE examine sortie --bamout : non présent
CLOSED: [2023-02-26 Sun 19:53]
#+begin_src
cd test/chr21-alexis
gatk --java-options "-Xmx3g" HaplotypeCaller \
--input /Work/Users/apraga/bisonex/script/files/bam/NA12878_chr21.bam \
--output debug_chr1.vcf.gz \
--reference /Work/Groups/bisonex/data/genome/GRCh38.p13/genomeRef.fna \
--dbsnp /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz \
--tmp-dir . \
--max-mnp-distance 2 -bamout debug.bam
#+end_src
Pas de reads
#+begin_quote
If you see nothing overlapping your region, then it might not have been flagged as active, or could have failed to assemble.
#+end_quote
********* 14582339: FN mais pas de reads...
********* 14583327 idem
********* 17512551 idem
********* 17567111: difference d'haplotype
********* 17567621 pas de reads
****** DONE Comparer avec sortie du variant calling vcf donné par GIAB
CLOSED: [2023-04-02 Sun 17:11]
******* DONE vcfeval
CLOSED: [2023-04-01 Sat 11:59] SCHEDULED: <2023-04-01 Sat>
#+begin_src sh
nextflow run workflows/test.nf -profile standard,helios -resume --test.vcfeval --test.giabVCF --outdir=test-giabVCF
cat test-giabVCF/vcfeval/output/summary.txt
#+end_src
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
1.000 44818 44818 2892 6087 0.9394 0.8804 0.9089
None 44819 44819 2896 6086 0.9393 0.8804 0.9089
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
1.000 44818 44818 2892 6087 0.9394 0.8804 0.9089
None 44819 44819 2896 6086 0.9393 0.8804 0.9089
******* DONE happy
CLOSED: [2023-04-01 Sat 11:56]
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.PrecisioN
INDEL PASS 4871 3678 1193 7036 1299 2011 208 217 0.755081 0.741493
SNP PASS 46032 41138 4894 47694 1622 4930 362 31 0.893683 0.962071
METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
0.285816 0.748225 NaN NaN 1.617499 2.524051
0.103367 0.926617 2.529552 2.412446 1.620686 1.688868
****** DONE Statistiques avec vcfeval
CLOSED: [2023-04-02 Sun 17:10] SCHEDULED: <2023-04-01 Sat>
***** DONE Résultats finaux
CLOSED: [2023-04-14 Fri 09:53]
:PROPERTIES:
:ID: cd79a77c-a0b6-4bb1-9e08-fe08dc89e3aa
:END:
Version GIAB avec hap.py + vcfeval:
#+begin_src sh
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareNA12878-giab --test.compare=happy,vcfeval --test.query=giab --test.id=HG001
#+end_src
Notre version avec hap.py + vcfeval
#+begin_src sh
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareNA12878 --test.vcfeval --test.query="out/NA12878_NIST/variantCalling/haplotypecaller/NA12878_NIST.vcf.gz" --test.happy
#+end_src
On concatene les csv avec une colonne indicant le type
# awk '{if (NR==1) {print "Data,Algorithm" $0} else {print "bisonx,happy,"$0}}' compareNA12878/happy/NA12878.summary.csv
compareNA12878/happy/NA12878.summary.csv
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUER
Y.TOTAL.het_hom_ratio |
| INDEL | ALL | 4871 | 3461 | 1410 | 7048 | 1554 | 1987 | 193 | 346 | 0.710532 | 0.692946 | 0.281924 | 0.701629 | | | 1.6174985978687606 | 3.0674091441969518 |
| INDEL | PASS | 4871 | 3461 | 1410 | 7048 | 1554 | 1987 | 193 | 346 | 0.710532 | 0.692946 | 0.281924 | 0.701629 | | | 1.6174985978687606 | 3.0674091441969518 |
| SNP | ALL | 46032 | 39367 | 6665 | 44599 | 1186 | 4042 | 304 | 30 | 0.855209 | 0.970757 | 0.09063 | 0.909327 | 2.529551552318896 | 2.402150701647346 | 1.6206857273037931 | 1.6273423688862698 |
| SNP | PASS | 46032 | 39367 | 6665 | 44599 | 1186 | 4042 | 304 | 30 | 0.855209 | 0.970757 | 0.09063 | 0.909327 | 2.529551552318896 | 2.402150701647346 | 1.6206857273037931 | 1.6273423688862698 |
compareNA12878/vcfeval/NA12878.summary.txt
ntent.com/qasimyu/simuscop/master/testData/Illumina_HiSeq2000.profile
#+end_src
#+RESULTS:
#+begin_src sh :dir ~/code/bisonex/test-simuscop
cat > config_wes.txt << EOL
ref = genomeRef.fna
profile = ./Illumina_HiSeq2000.profile
variation = ./variant.txt
target = ./gatad2b-exon6.bed
layout = PE
threads = 1
name = single
output = test-gatad2b-hiseq2000
coverage = 20
EOL
simuReads config_wes.txt
bwa mem -R '@RG\tID:sample\tSM:sample\tPL:ILLUMINA\tPM:Miseq\tCN:lol\tLB:definition_to_add' bwa/genomeRef test-gatad2b-hiseq2000/single_1.fq test-gatad2b-hiseq2000/single_2.fq | samtools sort -o single-hiseq2000.bam
samtools index single-hiseq2000.bam
#+end_src
#+RESULTS:
******* KILL Tester exemple sur github
CLOSED: [2023-04-29 Sat 19:56]
#+begin_src sh
git clone https://github.com/qasimyu/simuscop/
cd simuscop
simuReads configFiles/config_test_wes.txt
#+end_src
******* KILL Centrer la fenêtre sur les zones de capture
CLOSED: [2023-04-30 Sun 13:28] SCHEDULED: <2023-04-29 Sat>
1000bp par défaut, ce qui est plus grand que les zones de captures...
Changer fragzip ne fonctionne pas
Si on rajoute un offset sur l'exon: 200bp, est encore plus allongé
NC_000001.11 153817371 153817542 ->
NC_000001.11 153817171 153817742
Si on désactive les target ?
Regarder les target sur le chromosome 1
#+begin_src sh :dir ~/code/bisonex/test-simuscop :results silent
scp meso:/Work/Projects/bisonex/data/simuscop/VCGS_Exome_Covered_Targets_hg38_40.1MB_renamed.bed .
#+end_src
#+begin_src sh :dir ~/code/bisonex/test-simuscop :results silent
head -n 100 VCGS_Exome_Covered_Targets_hg38_40.1MB_renamed.bed > 100exons.bed
echo -e "s\tsingle\tNC_000001.11\t153817496\tA\tT\thet"> variant.txt
cat > config_wes.txt << EOL
ref = genomeRef.fna
profile = ./63003856.profile
variation = ./variant.txt
layout = PE
threads = 4
target = 100exons.bed
name = single
output = test-gatad2b
coverage = 200
EOL
./simuscop/bin/simuReads config_wes.txt
bwa mem bwa/genomeRef test-gatad2b/single_1.fq test-gatad2b/single_2.fq | samtools sort -o single.bam
samtools index single.bam
#+end_src
***** KILL Vérifier tous les variants sont retrouvés en 200x: hg38
CLOSED: [2023-06-12 Mon 23:25]
****** DONE Après alignement
CLOSED: [2023-04-29 Sat 18:27] SCHEDULED: <2023-04-28 Fri>
******* DONE SNV: avec doublons
CLOSED: [2023-04-28 Fri 18:12]
On utilise [[file:~/recherche/bisonex/simuscop/checkBam.jl][checkBam.jl]]
#+begin_src julia
d = prepareVariant("../parsevariants/variant_genomic.csv")
root = "/home/alex/code/bisonex/simuscop-cento/cento"
bam = root * "/preprocessing/applybqsr/cento.bam"
bai = root * "/preprocessing/recalibrated/cento.bam.bai"
snv = getSNV(d, bam, bai)
#+end_src
Nombreux faux homozygouteS
Vérification avec checkFalseHemizygous(snv) : nombreux doublons dans le fichier pour simuscop...
******* DONE SNV sans doublons
CLOSED: [2023-04-29 Sat 18:27]
******** DONE 18 faux homozygote mais avec peu de reads
CLOSED: [2023-04-29 Sat 18:27]
julia> @subset snv :refCount .== 0 :altCount .> 0 :zygosity .== "heterozygous"
18×10 DataFrame
Row │ chrom pos variant variantType zygosity ref alt refCount altCount readsCount
│ SubStrin…? Int64 SubStrin…? String? String15 SubStrin… SubStrin… Int64 Int64 Int64
─────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ NC_000022.11 42213078 g.42213078T>G snv heterozygous T G 0 1 1
2 │ NC_000012.12 101680427 g.101680427C>A snv heterozygous C A 0 3 3
3 │ NC_000014.9 105385684 g.105385684G>C snv heterozygous G C 0 4 4
4 │ NC_000011.10 125978299 g.125978299C>T snv heterozygous C T 0 3 3
5 │ NC_000023.11 77998618 g.77998618C>T snv heterozygous C T 0 2 2
6 │ NC_000015.10 66703292 g.66703292C>T snv heterozygous C T 0 3 3
7 │ NC_000010.11 87961118 g.87961118G>A snv heterozygous G A 0 3 3
8 │ NC_000012.12 112477719 g.112477719A>G snv heterozygous A G 0 2 2
9 │ NC_000020.11 6778406 g.6778406C>T snv heterozygous C T 0 3 3
10 │ NC_000023.11 68192943 g.68192943G>A snv heterozygous G A 0 2 2
11 │ NC_000004.12 987858 g.987858C>T snv heterozygous C T 0 3 4
12 │ NC_000015.10 66435145 g.66435145G>A snv heterozygous G A 0 1 2
13 │ NC_000002.12 47809595 g.47809595C>T snv heterozygous C T 0 2 2
14 │ NC_000003.12 136477305 g.136477305C>G snv heterozygous C G 0 4 4
15 │ NC_000005.10 157285458 g.157285458C>T snv heterozygous C T 0 3 3
16 │ NC_000012.12 23604413 g.23604413T>G snv heterozygous T G 0 5 5
17 │ NC_000019.10 52219703 g.52219703C>T snv heterozygous C T 0 1 1
18 │ NC_000016.10 88856757 g.88856757C>T snv heterozygous C T 0 8 8
******** DONE 8 non retrouvé => probablement hors de la zjone de capture
CLOSED: [2023-04-28 Fri 19:49]
julia> @subset snv :refCount .== 0 :altCount .== 0
8×10 DataFrame
Row │ chrom pos variant variantType zygosity ref alt refCount altCount readsCount
│ SubStrin…? Int64 SubStrin…? String? String15 SubStrin… SubStrin… Int64 Int64 Int64
─────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ NC_000015.10 74343027 g.74343027C>T snv heterozygous C T 0 0 0
2 │ NC_000011.10 20638345 g.20638345A>G snv heterozygous A G 0 0 0
3 │ NC_000004.12 139370252 g.139370252C>T snv heterozygous C T 0 0 2
4 │ NC_000017.11 61966475 g.61966475G>T snv heterozygous G T 0 0 0
5 │ NC_000019.10 54144058 g.54144058G>A snv heterozygous G A 0 0 0
6 │ NC_000023.11 77635947 g.77635947A>G snv hemizygous A G 0 0 0
7 │ NC_000005.10 1258495 g.1258495G>A snv heterozygous G A 0 0 0
8 │ NC_000012.12 2449086 g.2449086C>G snv heterozygous C G 0 0 0
****** KILL Après haplotypecaller
CLOSED: [2023-06-12 Mon 23:24]
******* KILL 20x
CLOSED: [2023-04-29 Sat 15:39]
Manque 183 sur 766
[[file:~/recherche/bisonex/simuscop/checkVCF.jl][checkVCF.jl]]
#+begin_src julia
@subset leftjoin(d2, dHaplo2, on=:genomic) ismissing.(:Column1)
#+end_src
Problème de profondeur ?
Ex: chr13 nombre de 101081606
NC_000011.10 16014966 g.16014966G>A
1 read sur 11 pour allèle alternative
Sur le patient de référence, 202 reads!
Celui-ci n'est pas le fichier de capture (ni dans le bam !)
ex: NC_000015.10 74343027 g.74343027C>T
Pour les autres, on devrait les retrouver...
Vérifier le nombre de reads sur 63003856
Vérifier la paramétrisation du modèle également
******* DONE [#B] 200x
CLOSED: [2023-05-18 Thu 11:04] SCHEDULED: <2023-04-30 Sun>
120 manquants (99 sans doublon)!
On vérifie dans IGV (vcf + bam après alignement) :
******** snv NC_000015.10 74343027
- rien d'appelé
- pas une région répétée
- base quality (voir [[*Phred score][Phred score]] ) à 37 donc ok
- variant retrouvé à 26/42
- Bam après aplybqsr: base qualità 35 donc ok
chr15 également à 89318565, variant retrouvé à 25/33 avec basequal de 37
Sans oublier de charger les instructions avx
#+begin_src sh
module load gcc@11.3.0/gcc-12.1.0
#+end_src
On coupe le .bam par chromosome pour débugger (sur le mesocentre)
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/simuscop-cento-200x/cento/testing :results silent
ln -s ../preprocessing/applybqsr/cento.bam .
ln -s ../preprocessing/recalibrated/cento.bam.bai .
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz .
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz.tbi .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.dict .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna.fai .
#+end_src
On doit lancer à la main (org-mode ne connait pas le chemin de samtools)
samtools view -b cento.bam NC_000015.10 > cento_chr15.bam
samtools index cento_chr15.bam
Puis on se restreint au chronmosome 15
samtools faidx genomeRef.fna NC_000015.10 > genomeRef_chr15.fa
samtools faidx genomeRef_chr15.fa
gatk CreateSequenceDictionary -R genomeRef_chr15.fa -O genomeRef_chr15.dict
On restreint au chromosome 15 avec l'option -L (dure = 1min)
gatk --java-options "-Xmx3072M" HaplotypeCaller --input cento_chr15.bam \
--output test.vcf.gz --reference genomeRef.fna --dbsnp dbSNP.gz --tmp-dir . --max-mnp-distance 2 -L NC_000015.10
******** DONE Tutorial haplotycaller
CLOSED: [2023-05-01 Mon 19:58]
Procédure : https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant
********* DONE Supprimer --max-mnp-distance = 2: idem
CLOSED: [2023-04-30 Sun 15:42]
********* DONE --debug &> run.log : Non appelé...
CLOSED: [2023-04-30 Sun 15:52]
********* DONE --linked-de-bruijn-graph: idem
CLOSED: [2023-04-30 Sun 15:55]
********* DONE --recover-all-dangling-branches
CLOSED: [2023-04-30 Sun 16:01]
********* DONE --min-pruning 0 : plus mais pas celui là
CLOSED: [2023-04-30 Sun 15:59]
********* DONE --bam-output
CLOSED: [2023-04-30 Sun 16:50]
********** DONE : rien !
CLOSED: [2023-04-30 Sun 16:08]
********** DONE + --recover-all-dangling-branches : rien !
CLOSED: [2023-04-30 Sun 16:08]
********* DONE Données filtrées ? apparement non
CLOSED: [2023-04-30 Sun 16:41]
183122 read(s) filtered by: MappingQualityReadFilter
3674 read(s) filtered by: NotDuplicateReadFilter
********** DONE --disable-read-filter MappingQualityReadFilter: idem
CLOSED: [2023-04-30 Sun 16:34]
On a bien - 0 read(s) filtered by: MappingQualityAvailableReadFilter
********** DONE --disable-read-filter NotDuplicateReadFilter: idem
CLOSED: [2023-04-30 Sun 16:40]
********* DONE Essayer freebayes : idem
CLOSED: [2023-04-30 Sun 16:22]
freebayes -f genomeRef.fna -r NC_000015.10 cento_chr15.bam > freebayes-test-chr15.vcf
********* DONE Avec toutes les options : idem
--linked-de-bruijn-graph --recover-all-dangling-branches --min-pruning 0 --bam-output debug.bam
CLOSED: [2023-04-30 Sun 16:50]
********* DONE Vérifier qu'on regarde le même bam : oui
CLOSED: [2023-04-30 Sun 16:50]
********* DONE Désactiver dbSNP : idem
CLOSED: [2023-04-30 Sun 16:52]
********* DONE Changer kmer size : idem
CLOSED: [2023-04-30 Sun 16:56]
par exemple[[https://gatk.broadinstitute.org/hc/en-us/community/posts/360075653152-REAL-Variant-not-called-by-HaplotypeCaller][forum gatk]] --kmer-size 18 --kmer-size 22
********* DONE --adaptive-pruning true
CLOSED: [2023-05-01 Mon 19:57]
******** DONE Mapping quality : est à 0 !!!!
CLOSED: [2023-05-01 Mon 19:58]
******* KILL Comparer VCF avec vcfeval :haplotypecaller:
CLOSED: [2023-06-12 Mon 23:24]
On prépare les données en julia
#+begin_src ~/recherche/bisonex/simuscop
julia --project=. toVCF.jl
#+end_src
Puis on export sur le mésocentre
#+begin_src
scp variants_for_vcfeval.tsv.gz* meso:cento_variants/
#+end_src
#+begin_src
z bis
cd simuscop-200x
rtg vcfeval -b ~/cento_variants/variants_for_vcfeval.tsv.gz -c cento/variantCalling/haplotypecaller/cento.vcf.gz -o compare-haplotypecaller -t /Work/Groups/bisonex/data/giab/GRCh38/genomeRef.sdf
#+end_src
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
82.000 540 540 60 45 0.9000 0.9231 0.9114
None 546 546 329 39 0.6240 0.9333 0.7479
******* KILL Comparer avec hap.py :haplotypecaller:
CLOSED: [2023-06-12 Mon 23:24]
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/checkInserted.nf -profile standard,helios --outdir=compare-simuscop-200x --query=out/simuscop-cento-200x/cento/callVariant/haplotypecaller/cento.vcf.gz --truth=cento_variants/variants_for_vcfeval.tsv.gz --id=simuscop-200x-check
******* DONE Méthode naïve 549/585
CLOSED: [2023-05-04 Thu 21:57]
Haplotypecaller: Nb reference SNV 692 vs found 585
Variant calling, filter technical: reference SNV 692 vs found 521
****** KILL Avant annotation
CLOSED: [2023-06-12 Mon 23:25] SCHEDULED: <2023-04-28 Fri>
#+begin_src
cd cento/variantCalling
bgzip filter-technical.vcf
tabix -p vcf filter-technical.vcf.gz -f
#+end_src
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
12.000 519 519 55 66 0.9042 0.8872 0.8956
None 519 519 55 66 0.9042 0.8872 0.8956
******* DONE Méthode naïve 521/585
CLOSED: [2023-05-04 Thu 21:57]
Haplotypecaller: Nb reference SNV 692 vs found 585
Variant calling, filter technical: reference SNV 692 vs found 521
******* KILL Comparer avec hap.py
CLOSED: [2023-06-12 Mon 23:24]
****** KILL Après filtre annotation
CLOSED: [2023-06-12 Mon 23:25]
******* DONE Méthode naïve : 493/585
CLOSED: [2023-05-04 Thu 22:09]
******* KILL Comparer avec hap.py
CLOSED: [2023-06-12 Mon 23:25]
******* KILL VCf eval
CLOSED: [2023-06-12 Mon 23:25]
cd cento/annotation/
bgzip postvep-filter.vcf
tabix postvep-filter.vcf.gz
cd ../..
rtg vcfeval -b ~/cento_variants/variants_for_vcfeval.tsv.gz -c cento/annotation/postvep-filter.vcf.gz -o compare-vepfilter -t /Work/Groups/bisonex/data/giab/GRCh38/genomeRef.sdf
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
12.000 491 491 50 94 0.9076 0.8393 0.8721
None
491 491 50 94 0.9076 0.8393 0.8721
***** KILL Vérifier tous les variants sont retrouvés en 200x: hg38 :T2T:
CLOSED: [2023-08-12 Sat 15:54]
****** DONE Après alignement
CLOSED: [2023-04-29 Sat 18:27] SCHEDULED: <2023-04-28 Fri>
******* DONE SNV: avec doublons
CLOSED: [2023-04-28 Fri 18:12]
On utilise [[file:~/recherche/bisonex/simuscop/checkBam.jl][checkBam.jl]]
#+begin_src julia
d = prepareVariant("../parsevariants/variant_genomic.csv")
root = "/home/alex/code/bisonex/simuscop-cento/cento"
bam = root * "/preprocessing/applybqsr/cento.bam"
bai = root * "/preprocessing/recalibrated/cento.bam.bai"
snv = getSNV(d, bam, bai)
#+end_src
Nombreux faux homozygouteS
Vérification avec checkFalseHemizygous(snv) : nombreux doublons dans le fichier pour simuscop...
******* DONE SNV sans doublons
CLOSED: [2023-04-29 Sat 18:27]
******** DONE 18 faux homozygote mais avec peu de reads
CLOSED: [2023-04-29 Sat 18:27]
julia> @subset snv :refCount .== 0 :altCount .> 0 :zygosity .== "heterozygous"
18×10 DataFrame
Row │ chrom pos variant variantType zygosity ref alt refCount altCount readsCount
│ SubStrin…? Int64 SubStrin…? String? String15 SubStrin… SubStrin… Int64 Int64 Int64
─────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ NC_000022.11 42213078 g.42213078T>G snv heterozygous T G 0 1 1
2 │ NC_000012.12 101680427 g.101680427C>A snv heterozygous C A 0 3 3
3 │ NC_000014.9 105385684 g.105385684G>C snv heterozygous G C 0 4 4
4 │ NC_000011.10 125978299 g.125978299C>T snv heterozygous C T 0 3 3
5 │ NC_000023.11 77998618 g.77998618C>T snv heterozygous C T 0 2 2
6 │ NC_000015.10 66703292 g.66703292C>T snv heterozygous C T 0 3 3
7 │ NC_000010.11 87961118 g.87961118G>A snv heterozygous G A 0 3 3
8 │ NC_000012.12 112477719 g.112477719A>G snv heterozygous A G 0 2 2
9 │ NC_000020.11 6778406 g.6778406C>T snv heterozygous C T 0 3 3
10 │ NC_000023.11 68192943 g.68192943G>A snv heterozygous G A 0 2 2
11 │ NC_000004.12 987858 g.987858C>T snv heterozygous C T 0 3 4
12 │ NC_000015.10 66435145 g.66435145G>A snv heterozygous G A 0 1 2
13 │ NC_000002.12 47809595 g.47809595C>T snv heterozygous C T 0 2 2
14 │ NC_000003.12 136477305 g.136477305C>G snv heterozygous C G 0 4 4
15 │ NC_000005.10 157285458 g.157285458C>T snv heterozygous C T 0 3 3
16 │ NC_000012.12 23604413 g.23604413T>G snv heterozygous T G 0 5 5
17 │ NC_000019.10 52219703 g.52219703C>T snv heterozygous C T 0 1 1
18 │ NC_000016.10 88856757 g.88856757C>T snv heterozygous C T 0 8 8
******** DONE 8 non retrouvé => probablement hors de la zjone de capture
CLOSED: [2023-04-28 Fri 19:49]
julia> @subset snv :refCount .== 0 :altCount .== 0
8×10 DataFrame
Row │ chrom pos variant variantType zygosity ref alt refCount altCount readsCount
│ SubStrin…? Int64 SubStrin…? String? String15 SubStrin… SubStrin… Int64 Int64 Int64
─────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ NC_000015.10 74343027 g.74343027C>T snv heterozygous C T 0 0 0
2 │ NC_000011.10 20638345 g.20638345A>G snv heterozygous A G 0 0 0
3 │ NC_000004.12 139370252 g.139370252C>T snv heterozygous C T 0 0 2
4 │ NC_000017.11 61966475 g.61966475G>T snv heterozygous G T 0 0 0
5 │ NC_000019.10 54144058 g.54144058G>A snv heterozygous G A 0 0 0
6 │ NC_000023.11 77635947 g.77635947A>G snv hemizygous A G 0 0 0
7 │ NC_000005.10 1258495 g.1258495G>A snv heterozygous G A 0 0 0
8 │ NC_000012.12 2449086 g.2449086C>G snv heterozygous C G 0 0 0
****** KILL Après haplotypecaller
CLOSED: [2023-06-12 Mon 23:24]
******* KILL 20x
CLOSED: [2023-04-29 Sat 15:39]
Manque 183 sur 766
[[file:~/recherche/bisonex/simuscop/checkVCF.jl][checkVCF.jl]]
#+begin_src julia
@subset leftjoin(d2, dHaplo2, on=:genomic) ismissing.(:Column1)
#+end_src
Problème de profondeur ?
Ex: chr13 nombre de 101081606
NC_000011.10 16014966 g.16014966G>A
1 read sur 11 pour allèle alternative
Sur le patient de référence, 202 reads!
Celui-ci n'est pas le fichier de capture (ni dans le bam !)
ex: NC_000015.10 74343027 g.74343027C>T
Pour les autres, on devrait les retrouver...
Vérifier le nombre de reads sur 63003856
Vérifier la paramétrisation du modèle également
******* DONE [#B] 200x
CLOSED: [2023-05-18 Thu 11:04] SCHEDULED: <2023-04-30 Sun>
120 manquants (99 sans doublon)!
On vérifie dans IGV (vcf + bam après alignement) :
******** snv NC_000015.10 74343027
- rien d'appelé
- pas une région répétée
- base quality (voir [[*Phred score][Phred score]] ) à 37 donc ok
- variant retrouvé à 26/42
- Bam après aplybqsr: base qualità 35 donc ok
chr15 également à 89318565, variant retrouvé à 25/33 avec basequal de 37
Sans oublier de charger les instructions avx
#+begin_src sh
module load gcc@11.3.0/gcc-12.1.0
#+end_src
On coupe le .bam par chromosome pour débugger (sur le mesocentre)
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/simuscop-cento-200x/cento/testing :results silent
ln -s ../preprocessing/applybqsr/cento.bam .
ln -s ../preprocessing/recalibrated/cento.bam.bai .
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz .
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz.tbi .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.dict .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna.fai .
#+end_src
On doit lancer à la main (org-mode ne connait pas le chemin de samtools)
samtools view -b cento.bam NC_000015.10 > cento_chr15.bam
samtools index cento_chr15.bam
Puis on se restreint au chronmosome 15
samtools faidx genomeRef.fna NC_000015.10 > genomeRef_chr15.fa
samtools faidx genomeRef_chr15.fa
gatk CreateSequenceDictionary -R genomeRef_chr15.fa -O genomeRef_chr15.dict
On restreint au chromosome 15 avec l'option -L (dure = 1min)
gatk --java-options "-Xmx3072M" HaplotypeCaller --input cento_chr15.bam \
--output test.vcf.gz --reference genomeRef.fna --dbsnp dbSNP.gz --tmp-dir . --max-mnp-distance 2 -L NC_000015.10
******** DONE Tutorial haplotycaller
CLOSED: [2023-05-01 Mon 19:58]
Procédure : https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant
********* DONE Supprimer --max-mnp-distance = 2: idem
CLOSED: [2023-04-30 Sun 15:42]
********* DONE --debug &> run.log : Non appelé...
CLOSED: [2023-04-30 Sun 15:52]
********* DONE --linked-de-bruijn-graph: idem
CLOSED: [2023-04-30 Sun 15:55]
********* DONE --recover-all-dangling-branches
CLOSED: [2023-04-30 Sun 16:01]
********* DONE --min-pruning 0 : plus mais pas celui là
CLOSED: [2023-04-30 Sun 15:59]
********* DONE --bam-output
CLOSED: [2023-04-30 Sun 16:50]
********** DONE : rien !
CLOSED: [2023-04-30 Sun 16:08]
********** DONE + --recover-all-dangling-branches : rien !
CLOSED: [2023-04-30 Sun 16:08]
********* DONE Données filtrées ? apparement non
CLOSED: [2023-04-30 Sun 16:41]
183122 read(s) filtered by: MappingQualityReadFilter
3674 read(s) filtered by: NotDuplicateReadFilter
********** DONE --disable-read-filter MappingQualityReadFilter: idem
CLOSED: [2023-04-30 Sun 16:34]
On a bien - 0 read(s) filtered by: MappingQualityAvailableReadFilter
********** DONE --disable-read-filter NotDuplicateReadFilter: idem
CLOSED: [2023-04-30 Sun 16:40]
********* DONE Essayer freebayes : idem
CLOSED: [2023-04-30 Sun 16:22]
freebayes -f genomeRef.fna -r NC_000015.10 cento_chr15.bam > freebayes-test-chr15.vcf
********* DONE Avec toutes les options : idem
--linked-de-bruijn-graph --recover-all-dangling-branches --min-pruning 0 --bam-output debug.bam
CLOSED: [2023-04-30 Sun 16:50]
********* DONE Vérifier qu'on regarde le même bam : oui
CLOSED: [2023-04-30 Sun 16:50]
********* DONE Désactiver dbSNP : idem
CLOSED: [2023-04-30 Sun 16:52]
********* DONE Changer kmer size : idem
CLOSED: [2023-04-30 Sun 16:56]
par exemple[[https://gatk.broadinstitute.org/hc/en-us/community/posts/360075653152-REAL-Variant-not-called-by-HaplotypeCaller][forum gatk]] --kmer-size 18 --kmer-size 22
********* DONE --adaptive-pruning true
CLOSED: [2023-05-01 Mon 19:57]
******** DONE Mapping quality : est à 0 !!!!
CLOSED: [2023-05-01 Mon 19:58]
******* KILL Comparer VCF avec vcfeval :haplotypecaller:
CLOSED: [2023-06-12 Mon 23:24]
On prépare les données en julia
#+begin_src ~/recherche/bisonex/simuscop
julia --project=. toVCF.jl
#+end_src
Puis on export sur le mésocentre
#+begin_src
scp variants_for_vcfeval.tsv.gz* meso:cento_variants/
#+end_src
#+begin_src
z bis
cd simuscop-200x
rtg vcfeval -b ~/cento_variants/variants_for_vcfeval.tsv.gz -c cento/variantCalling/haplotypecaller/cento.vcf.gz -o compare-haplotypecaller -t /Work/Groups/bisonex/data/giab/GRCh38/genomeRef.sdf
#+end_src
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
82.000 540 540 60 45 0.9000 0.9231 0.9114
None 546 546 329 39 0.6240 0.9333 0.7479
******* KILL Comparer avec hap.py :haplotypecaller:
CLOSED: [2023-06-12 Mon 23:24]
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/checkInserted.nf -profile standard,helios --outdir=compare-simuscop-200x --query=out/simuscop-cento-200x/cento/callVariant/haplotypecaller/cento.vcf.gz --truth=cento_variants/variants_for_vcfeval.tsv.gz --id=simuscop-200x-check
******* DONE Méthode naïve 549/585
CLOSED: [2023-05-04 Thu 21:57]
Haplotypecaller: Nb reference SNV 692 vs found 585
Variant calling, filter technical: reference SNV 692 vs found 521
****** KILL Avant annotation
CLOSED: [2023-06-12 Mon 23:25] SCHEDULED: <2023-04-28 Fri>
#+begin_src
cd cento/variantCalling
bgzip filter-technical.vcf
tabix -p vcf filter-technical.vcf.gz -f
#+end_src
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
12.000 519 519 55 66 0.9042 0.8872 0.8956
None 519 519 55 66 0.9042 0.8872 0.8956
******* DONE Méthode naïve 521/585
CLOSED: [2023-05-04 Thu 21:57]
Haplotypecaller: Nb reference SNV 692 vs found 585
Variant calling, filter technical: reference SNV 692 vs found 521
******* KILL Comparer avec hap.py
CLOSED: [2023-06-12 Mon 23:24]
****** KILL Après filtre annotation
CLOSED: [2023-06-12 Mon 23:25]
******* DONE Méthode naïve : 493/585
CLOSED: [2023-05-04 Thu 22:09]
******* KILL Comparer avec hap.py
CLOSED: [2023-06-12 Mon 23:25]
******* KILL VCf eval
CLOSED: [2023-06-12 Mon 23:25]
cd cento/annotation/
bgzip postvep-filter.vcf
tabix postvep-filter.vcf.gz
cd ../..
rtg vcfeval -b ~/cento_variants/variants_for_vcfeval.tsv.gz -c cento/annotation/postvep-filter.vcf.gz -o compare-vepfilter -t /Work/Groups/bisonex/data/giab/GRCh38/genomeRef.sdf
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
12.000 491 491 50 94 0.9076 0.8393 0.8721
None 491 491 50 94 0.9076 0.8393 0.8721
**** KILL NEAT : trop lent :neat:
CLOSED: [2023-04-29 Sat 22:06]
***** KILL Génération fastq sur exno 5 GATAD2B
CLOSED: [2023-04-29 Sat 22:06]
Trop lent : pour 1 exon : 1500 secondes !
#+begin_src sh
samtools faidx genomeRef.fna NC_000001.11 | save -f genomeRef_chr1.fna
python gen_reads.py -r ../test-simuscop/genomeRef_chr1.fna -o lol -tr ../test-simuscop/gatad2b-exon6.bed -R 147 --pe 150 10
#+end_src
**** KILL ReSeq : exome avec exons comme fasta mais ne gère pas des exons trop petits :reseq:
CLOSED: [2023-04-30 Sun 19:44] SCHEDULED: <2023-04-29 Sat>
#+begin_quote
Can I simulate exome sequencing? Yes. You need to use a reference that only contains the exons as individual scaffolds. Using --refBiasFile you can specify the coverage of individual exons. To simulate intron contamination you can add the whole reference to the reference containing the exons and strongly reduce the coverage for these scaffolds using --refBiasFile.
#+end_quote
Par contre, rapide
***** DONE Fasta pour exons seuls
CLOSED: [2023-04-30 Sun 19:25]
Depuis le GFF
#+begin_src sh :dir ~/code/bisonex/test-reseq :results silent
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz
#+end_src
#+begin_src sh :dir ~/code/bisonex/test-reseq :results silent
gunzip -c GCF_000001405.39_GRCh38.p13_genomic.gff.gz | grep -w "exon" > exons.gff
#+end_src
On génère les exons
#+begin_src sh :dir ~/code/bisonex/test-reseq
bedtools getfasta -fi ../test-simuscop/genomeRef.fna -bed exons.gff -fo exons.fna
#+end_src
A tester avec un profile déjà fait :
https://github.com/schmeing/ReSeq-profiles/tree/master/profiles
On cherche l'exons qui nous intéresse
NC_000001.11 g.153817496 A>T
N'y est pas ??
****** DONE On test sur les 2 premiers : exec
CLOSED: [2023-04-30 Sun 18:39]
#+begin_src
head exons.fa -n 2 > 2exons.fna
#+end_src
#+begin_src sh
../ReSeq/bin/reseq illuminaPE -j 32 -R exons.fa -s Ec-Hi2000-TruSeq.reseq --ipfIterations 0 -1 reseq-sim_1.fq reseq_sim_2.fq
#+end_src
#+begin_quote
error: All reference sequences are too short for simulating. They should have at least 1991 bases
#+end_quote
#+begin_src sh
grep '^>NC_000001.10'
| Threshold | True-pos-baseline | True-pos-call | False-pos | False-neg | Precision | Sensitivity | F-measure |
|-----------+-------------------+---------------+-----------+-----------+-----------+-------------+-----------|
| 3.000 | 42789 | 42416 | 2598 | 8080 | 0.9423 | 0.8412 | 0.8889 |
| None | 42798 | 42425 | 2616 | 8071 | 0.9419 | 0.8413 | 0.8888 |
Indel avec le plus petit seuil : zcat NA12878.non_snp_roc.tsv.gz
Attention à inverser precision et recall !
zcat NA12878.non_snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'
0.71390.7136
SNP avec le plus petit seuil : zcat NA12878.non_snp_roc.tsv.gz
Attention à inverser precision et recall !
$ zcat NA12878.snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'
0.85470.9727
compareNA12878-giab/vcfeval/NA12878.summary.txt
| Threshold | True-pos-baseline | True-pos-call | False-pos | False-neg | Precision | Sensitivity | F-measure |
| 1.000 | 44812 | 44812 | 2878 | 6057 | 0.9397 | 0.8809 | 0.9093 |
| None | 44813 | 44813 | 2882 | 6056 | 0.9396 | 0.8809 | 0.9093 |
SNP:
$ zcat NA12878.snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'
0.89370.9621
indel
$ zcat NA12878.non_snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'
0.75980.7445
compareNA12878-giab/happy/NA12878.summary.csv
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
|-------+--------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------+----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|
| INDEL | ALL | 4871 | 3678 | 1193 | 7036 | 1299 | 2011 | 208 | 217 | 0.755081 | 0.741493 | 0.285816 | 0.748225 | | | 1.6174985978687606 | 2.5240506329113925 |
| INDEL | PASS | 4871 | 3678 | 1193 | 7036 | 1299 | 2011 | 208 | 217 | 0.755081 | 0.741493 | 0.285816 | 0.748225 | | | 1.6174985978687606 | 2.5240506329113925 |
| SNP | ALL | 46032 | 41138 | 4894 | 47694 | 1622 | 4930 | 362 | 31 | 0.893683 | 0.962071 | 0.103367 | 0.926617 | 2.529551552318896 | 2.4124463519313304 | 1.6206857273037931 | 1.6888675840288743 |
| SNP | PASS | 46032 | 41138 | 4894 | 47694 | 1622 | 4930 | 362 | 31 | 0
.893683 | 0.962071 | 0.103367 | 0.926617 | 2.529551552318896 | 2.4124463519313304 | 1.6206857273037931 | 1.688867584028874 |
***** KILL Résultats sans trimming
CLOSED: [2023-06-25 Sun 15:53] SCHEDULED: <2023-06-26 Mon>
***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"
CLOSED: [2023-06-30 Fri 22:08] SCHEDULED: <2023-06-25 Sun>
#+begin_src
nextflow run workflows/compareVCF.nf -profile standard,helios --outdir=out/HG001-SRX11061486_SRR14724513-GRCh38 --query=out/HG001-SRX11061486_SRR14724513-GRCh38/callVariant/haplotypecaller/HG001-SRX11061486_SRR14724513-GRCh38.vcf.gz --compare=vcfeval,happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed --id=HG001
#+end_src
Meilleurs résultats !
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.89071 | 0.88551 | 0.378198 | 0.888102 | | | 1.86096256684492 | 2.247272727272727 |
| INDEL | PASS | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.89071 | 0.88551 | 0.378198 | 0.888102 | | | 1.86096256684492 | 2.247272727272727 |
| SNP | ALL | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.007110300820419 | 2.78468624064479 | 1.5918102430965306 | 1.8161449399656946 |
| SNP | PASS | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.007110300820419 | 2.78468624064479 | 1.5918102430965306 | 1.8161449399656946 |
***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi" gatk-4.4
CLOSED: [2023-08-03 Thu 23:55] SCHEDULED: <2023-06-25 Sun>
#+begin_src
ID="HG001-SRX11061486_SRR14724513-GRCh38"; nextflow run workflows/compareVCF.nf -profile standard,helios --outdir=out/${ID} --query=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --compare=vcfeval,hay -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed --id=HG001 --genome=GRCh38 -bg
#+end_src
***** KILL Utiliser d'autres données brutes ?
CLOSED: [2023-06-25 Sun 15:58]
https://zenodo.org/record/3597727
Capture en hg37 également. Serait intéressant mais pas le temps..
***** KILL Comparer avec UCSCS liftover
CLOSED: [2023-06-26 Mon 19:02] SCHEDULED: <2023-06-25 Sun>
Picard liftoverinterval est basé sur UCSCS
Mais on n'aurait pas la différence pour NA12878 qu'on voit...
**** DONE HG002 :hg002:hg38:
CLOSED: [2023-07-30 Sun 14:25] SCHEDULED: <2023-07-25 Tue>
#+begin_src
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/giabFastq.nf -profile standard,helios
NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios -resume --input="/Work/Groups/bisonex/data/giab/GRCh38/HG002_{1,2}.fq.gz --test.id=HG002
Only the capture file differs. Results are better using the capture file given by Agilent, stored in data/
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareHG002 --test.id=HG002 --test.query=out/HG002_1/variantCalling/haplotypecaller/HG002_1.vcf.gz --test.compare=vcfeval,happy --test.capture=data/AgilentSureSelectv05_hg38.bed
#
#+end_src
***** DONE Mauvais résultats
CLOSED: [2023-04-14 Fri 09:42]
avec vcfeval
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
0.000 24585 24390 10060 39415 0.7080 0.3841 0.4980
None 24585 24390 10060 39415 0.7080 0.3841 0.4980
La sortie du variantCalling est celle d'happy ???
On relance...
***** DONE Vérifier vcf en hg38
CLOSED: [2023-04-12 Wed 10:33] SCHEDULED: <2023-04-12 Wed>
***** KILL Capture en hg19 ?
CLOSED: [2023-04-13 Thu 09:46] SCHEDULED: <2023-04-12 Wed>
***** KILL Vraiment fichier de capture ou zone d'intérêt ?
CLOSED: [2023-04-13 Thu 09:45] SCHEDULED: <2023-04-12 Wed>
"target region" +/- 50bp
[[https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/README.txt][README]]
list file describing the variant calling regions (target regions extended with 50 bp on each end)
***** DONE .bed fourni par AGilent: sensbilité très mauvaise
CLOSED: [2023-04-13 Thu 09:46] SCHEDULED: <2023-04-13 Thu>
Agilent SureSelect Human All Exon V5 kit
Disponible en hg38
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
0.000 19653 19501 6410 21657 0.7526 0.4757 0.5830
None 19653 19501 6410 21657 0.7526 0.4757 0.5830
***** DONE Trier par nom avec samtools sort : bons résultats
CLOSED: [2023-04-14 Fri 09:25] SCHEDULED: <2023-04-13 Thu>
Avec capture fourni par GIAB
vcf eval
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
5.000 57443 57032 984 6557 0.9830 0.8975 0.9383
None 57457 57046 1009 6543 0.9826 0.8978 0.9383
Happy
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
|-------+--------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------+----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|
| INDEL | ALL | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 |
| INDEL | PASS | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 |
| SNP | ALL | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 |
| SNP | PASS | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 |
***** DONE Capture agilent légment meilleur que celui fourni par GIAB (padding ?)
CLOSED: [2023-04-14 Fri 09:48]
GIAB:
vcf eval
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
5.000 57443 57032 984 6557 0.9830 0.8975 0.9383
None 57457 57046 1009 6543 0.9826 0.8978 0.9383
Happy
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
|-------+--------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------+----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|
| INDEL | ALL | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 |
| INDEL | PASS | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 |
| SNP | ALL | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 |
| SNP | PASS | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 |
Agilent
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
6.000 37241 36965 449 4069 0.9880 0.9015 0.9428
None 37248 36972 461 4062 0.9877 0.9017 0.9427
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL | 2909 | 2477 | 432 | 3229 | 207 | 519 | 52 | 50 | 0.851495 | 0.923616 | 0.160731 | 0.886091 | | | 1.4964850615114236 | 1.8339222614840989 |
| INDEL | PASS | 2909 | 2477 | 432 | 3229 | 207 | 519 | 52 | 50 | 0.851495 | 0.923616 | 0.160731 | 0.886091 | | | 1.4964850615114236 | 1.8339222614840989 |
| SNP | ALL | 38406 | 34793 | 3613 | 36935 | 275 | 1868 | 37 | 15 | 0.905926 | 0.992158 | 0.050575 | 0.947083 | 2.6247759222568168 | 2.5752854654538417 | 1.588953331534934 | 1.6192536889897844 |
| SNP | PASS | 38406 | 34793 | 3613 | 36935 | 275 | 1868 | 37 | 15 | 0.905926 | 0.992158 | 0.050575 | 0.947083 | 2.6247759222568168 | 2.5752854654538417 | 1.588953331534934 | 1.6192536889897844 |
***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"
CLOSED: [2023-07-30 Sun 14:24] SCHEDULED: <2023-07-23 Sun>
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL | 626 | 536 | 90 | 900 | 23 | 334 | 6 | 14 | 0.85623 | 0.959364 | 0.371111 | 0.904868 | | | 1.5696202531645569 | 2.406844106463878 |
| INDEL | PASS | 626 | 536 | 90 | 900 | 23 | 334 | 6 | 14 | 0.85623 | 0.959364 | 0.371111 | 0.904868 | | | 1.5696202531645569 | 2.406844106463878 |
| SNP | ALL | 23136 | 22346 | 790 |
0.972274 | 0.380298 | 0.917767 | | | 1.6111111111111112 | 2.3984375 |
| SNP | ALL | 23041 | 22225 | 816 | 26302 | 114 | 3972 | 87 | 5 | 0.964585 | 0.994895 | 0.151015 | 0.979505 | 2.91407709288504 | 2.7368645271229766 | 1.6883829538820783 | 1.8632748665431964 |
| SNP | PASS | 23041 | 22225 | 816 | 26302 | 114 | 3972 | 87 | 5 | 0.964585 | 0.994895 | 0.151015 | 0.979505 | 2.91407709288504 | 2.7368645271229766 | 1.6883829538820783 | 1.8632748665431964 |
***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi" gatk4.4
CLOSED: [2023-08-03 Thu 23:24] SCHEDULED: <2023-08-03 Thu>
#+begin_src sh
ID="HG004-SRX11061489_SRR14724510-GRCh38" ; nextflow run workflows/compareVCF.nf -profile standard,helios --outdir=out/${ID} --query=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --compare=vcfeval,happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed --id=HG003 --genome=GRCh38
#+end_src
**** DONE Refaire la figure pour HG001,2,3,4
CLOSED: [2023-08-05 Sat 09:10] SCHEDULED: <2023-08-04 Fri>
**** DONE Regarder impact changement de version gatk 4.3 -> 4.4: aucun
CLOSED: [2023-08-05 Sat 09:07] SCHEDULED: <2023-08-05 Sat>
**** STRT HG001 :hg001:T2T:
Avec liftover : 10x moins de variants...
Type,Filter,TRUTH.TOTAL,TRUTH.TP,TRUTH.FN,QUERY.TOTAL,QUERY.FP,QUERY.UNK,FP.gt,FP.al,METRIC.Recall,METRIC.Precision,METRIC.Frac_NA,METRIC.F1_Score,TRUTH.TOTAL.TiTv_ratio,QUERY.TOTAL.TiTv_ratio,TRUTH.TOTAL.het_hom_ratio,QUERY.TOTAL.het_hom_ratio
INDEL,ALL,413,246,167,751,289,215,2,93,0.595642,0.460821,0.286285,0.519629,,,2.4285714285714284,2.4651162790697674
INDEL,PASS,413,246,167,751,289,215,2,93,0.595642,0.460821,0.286285,0.519629,,,2.4285714285714284,2.4651162790697674
SNP,ALL,11236,10985,251,23597,9771,2841,26,58,0.977661,0.529245,0.120397,0.686734,3.1146100329549617,2.857049501715406,3.640644361833953,2.1146328578975173
SNP,PASS,11236,10985,251,23597,9771,2841,26,58,0.977661,0.529245,0.120397,0.686734,3.1146100329549617,2.857049501715406,3.640644361833953,2.1146328578975173
***** TODO Comprendre mauvais résultat
****** DONE 2x moins de variants, beaucoup trop de FP : erreur de FILTER
CLOSED: [2023-07-08 Sat 11:17] SCHEDULED: <2023-07-07 Fri>
******* DONE [#A] Certains FP sont des vrais FP: erreur de flag et non d'happy
CLOSED: [2023-07-08 Sat 10:43] SCHEDULED: <2023-07-07 Fri>
******** Ex: chr1:408793
G C 600.64 . BS=408793;Regions=CONF,TS_contained GT:BD:BK:BI:BVT:BLT:QQ ./.:.:.:.:NOCALL:nocall:. 0/1:FP:.:tv:SNP:het:600.64
CLOSED: [2023-07-07 Fri 20:03]
********* DONE Vérifier que l'on est bien dans la zone "high confidence" définie dans le bed
oui:
chr1 408514 414397 . 500 +
********* DONE Vérifier que le variant est bien dans le truth et query
CLOSED: [2023-07-07 Fri 20:14]
truth
chr1 408793 . G C 50 MismatchedRefAllele AttemptedAlleles=C*->G;AttemptedLocus=chr1:408793-408793;SwappedAlleles;callable=CS_HiSeqPE300xGATK_callable,CS_10XLRGATK_callable,CS_CCS15kb_20kbGATK4_callable,CS_CGnormal_callable,CS_HiSeqPE300xfreebayes_callable;callsetnames=HiSeqPE300xGATK,CCS15kb_20kbGATK4,CGnormal,HiSeqPE300xfreebayes,CCS15kb_20kbDV,10XLRGATK;callsets=6;datasetnames=HiSeqPE300x,CCS15kb_20kb,CGnormal,10XChromiumLR;datasets=4;datasetsmissingcall=IonExome,SolidSE75bp;filt=CS_CCS15kb_20kbDV_filt,CS_CCS15kb_20kbGATK4_filt;platformnames=Illumina,PacBio,CG,10X;platforms=4 GT:AD:ADALL:DP:GQ 1/0:153,159:141,132:689:99
query
chr1 408793 . G C 600.64
. AC=1;AF=0.500;AN=2;BaseQRankSum=-1.390;DP=64;ExcessHet=0.0000;FS=0.961;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.53;ReadPosRankSum=-3.146;SOR=0.906 GT:AD:DP:GQ:PL 0/1:33,30:63:99:608,0,798
********* DONE Tester happy sur ce variant: non retrouvé
CLOSED: [2023-07-08 Sat 10:42]
Il faut au moins 2 variant + les index (sinon "no chromosome in common")
Donc on augmente la taille de la région
#+begin_src sh :dir ~/code/bisonex/out
bcftools view HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz -o lifted_test.vcf.gz chr1:408793-408900
bcftools view HG001-SRX11061486_SRR14724513-T2T.vcf.gz -o run_test.vcf.gz chr1:408793-408900
bcftools index lifted_test.vcf.gz
bcftools index run_test.vcf.gz
#+end_src
#+begin_src sh
hap.py lifted_test.vcf.gz run_test.vcf.gz --reference ../data/chm13v2.0.fa -o test
#+end_src
On trouve bien les 2 variants. L'indel est retrouvé mais pas le SNP
chr1 408793 . G C 600.64 . BS=408793 GT:BD:BK:BI:BVT:BLT:QQ ./.:.:.:.:NOCALL:nocall:. 0/1:FP:.:tv:SNP:het:600.64
chr1 408874 . CGAA C 1476.6 . BS=408874 GT:BD:BK:BI:BVT:BLT:QQ 0/1:TP:gm:d1_5:INDEL:het:1476.6 0/1:TP:gm:d1_5:INDEL:het:1476.6
********* DONE Changer flag : mismatch -> PASS: OUI
CLOSED: [2023-07-08 Sat 10:42]
********* DONE Changer haplotype 1/0 -> 0/1 truth: idem
CLOSED: [2023-07-08 Sat 10:35]
********* DONE Tester avec vcfeval : idemnt
CLOSED: [2023-07-08 Sat 10:43]
******* DONE Comparer hg38 et T2T: 2x moinsr de variants, trop de FP et F
N
CLOSED: [2023-07-07 Fri 18:38]
T2T
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL | 413 | 246 | 167 | 751 | 289 | 215 | 2 | 93 | 0.595642 | 0.460821 | 0.286285 | 0.519629 | NaN | NaN | 2.428571 | 2.465116 |
| INDEL | PASS | 413 | 246 | 167 | 751 | 289 | 215 | 2 | 93 | 0.595642 | 0.460821 | 0.286285 | 0.519629 | NaN | NaN | 2.428571 | 2.465116 |
| SNP | ALL | 11236 | 10985 | 251 | 23597 | 9771 | 2841 | 26 | 58 | 0.977661 | 0.529245 | 0.120397 | 0.686734 | 3.11461 | 2.85705 | 3.640644 | 2.114633 |
| SNP | PASS | 11236 | 10985 | 251 | 23597 | 9771 | 2841 | 26 | 58 | 0.977661 | 0.529245 | 0.120397 | 0.686734 | 3.11461 | 2.85705 | 3.640644 | 2.114633 |
Hg38
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.890710 | 0.885510 | 0.378198 | 0.888102 | NaN | NaN | 1.860963 | 2.247273 |
| INDEL | PASS | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.890710 | 0.885510 | 0.378198 | 0.888102 | NaN | NaN | 1.860963 | 2.247273 |
| SNP | ALL | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976
744 | 0.974435 | 0.162184 | 0.975588 | 3.00711 | 2.784686 | 1.591810 | 1.816145 |
| SNP | PASS | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.00711 | 2.7
muscop
simuReads config_wes.txt
#+end_src
#+RESULTS:
Alignement
#+begin_src sh :dir ~/code/bisonex/test-simuscop
bwa mem -R '@RG\tID:sample\tSM:sample\tPL:ILLUMINA\tPM:Miseq\tCN:lol\tLB:definition_to_add' bwa/genomeRef test-gatad2b/single_1.fq test-gatad2b/single_2.fq | samtools sort -o single.bam
#+end_src
#+RESULTS:
******* DONE Profile github HiSeq2000
CLOSED: [2023-04-29 Sat 19:56]
#+begin_src sh :dir ~/code/bisonex/test-simuscop :result file
wget https://raw.githubuserco
84686 | 1.591810 | 1.816145 |
******** Résumé
T2T
| Type | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision |
| INDEL | 413 | 246 | 167 | 751 | 289 | 215 | 2 | 93 | 0.595642 | 0.460821 |
| SNP | 11236 | 10985 | 251 | 23597 | 9771 | 2841 | 26 | 58 | 0.977661 | 0.529245 |
Hg38
| Type | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision |
| INDEL | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.890710 | 0.885510 |
| SNP | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 |
****** DONE Interesection des bed: similaire
CLOSED: [2023-07-04 Tue 23:11]
HG38
#+begin_src sh
bedtools intersect -a capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed -b /Work/Groups/bisonex/data/giab/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed | wc -l
#+end_src
204280
T2T
#+begin_src sh
bedtools intersect -a /Work/Groups/bisonex/data/giab/T2T/Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed -b /Work/Groups/bisonex/data/giab/T2T/HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed | wc -l
#+end_src
204021
****** DONE Vérifier la ligne de commande
CLOSED: [2023-07-04
On démarre la simulation
#+begin_src sh :dir ~/code/bisonex/test-si
Tue 23:38]
#+begin_src sh
hap.py \
HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz \
HG001-SRX11061486_SRR14724513-T2T.vcf.gz \
\
--reference chm13v2.0.fa \
--threads 6 \
\
-T Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed \
--false-positives HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed \
\
-o HG001
#+end_src
****** DONE Corriger FILTER : mieux mais toujours trop de négatifs. 3/4 SNP retrouvés
CLOSED: [2023-07-08 Sat 15:19] SCHEDULED: <2023-07-08 Sat>
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP
https://github.com/lh3/CHM-eval/releases
** TODO Insilico :cento:
*** TODO tous les variants centogène
**** DONE Extraire liste des SNVs
CLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>
***** DONE Corriger manquant à la main
CLOSED: [2023-04-22 Sat 17:31]
La sortie est sauvegardé dans git-annex : variants_success.csv
***** DONE Automatique
CLOSED: [2023-04-22 Sat 17:31]
**** DONE Convert SNVs : transcript -> génomique
CLOSED: [2023-06-03 Sat 17:16]
***** DONE Variant_recoder
CLOSED: [2023-04-26 Wed 21:21] SCHEDULED: <2023-04-22 Sat>
****** KILL Haskell: 160 manquant : recoded-success.csv
CLOSED: [2023-04-25 Tue 18:32]
La liste des variants a été générée en Haskel l et nettoyée à la main.
On générer une liste de variant pour variant_rec oder et on soumet tout d'un coup.
[[file:~/recherche/bisonex/parsevariants/app/Main.hs][parsevariant]]
#+begin_src haskell
recodeVariant = do
prepareVariantRecod er "variant_success.csv" "renamed.csv"
runVariantRecoder "renamed.csv" "recoded.json"
#+end_src
#+RESULTS:
: <interactive>:4:3-19: error:
: Variable not in scope: runVariantRecoder :: String -> String -> t
: gh
Problème : 160 n'ont pas pu être lu sur 820, probablement à cause du numéro mineur de transcrit
La sortie est sauvegardé dans git-annex : variants-recoded-raw.json.
****** KILL Julia
CLOSED: [2023-04-25 Tue 18:32]
On regénère la liste de variant et on passe à Julia pour préparer l'appel en parallèle à variant recoder
[[file:~/recherche/bisonex/parsevariants/variantRecoder.jl][variantRecoder.jl]]
#+begin_src julia
setupVariantRecoder(unique(init), n)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 10
#+end_src
On récupère les résultats
#+begin_src julia
(fails, success) = mergeVariantRecoder(n)
CSV.write(fSuccess, success)
CSV.write(fFailures, fails)
#+end_src
Certains variants ne sont pas trouvé, donc on prépare un nouveau job en enlevant les versionrs mineures des transcrits
#+begin_src julia
# Cleanup json and txt
if isfile(fSuccess) && isfile(fFailures)
foreach(rm, variantRecoderInput())
foreach(rm, variantRecoderOutput())
end
redoFails(fFailures)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 3
#+end_src
Il manque encore 70 transcrits
***** DONE Julia avec mobidetails: recode-failures-mobidetails.csv
CLOSED: [2023-04-25 Tue 18:58]
Nouvelle stratégie : on essaie une fois variant recoder.
Pour tous les échecs, on utilise mobidetails (~170).
Si l'ID n'est pas trouvé, on incrémente le numéro de version 2 fois
***** DONE Reste une dizaine à corriger à la main
CLOSED: [2023-04-26 Wed 21:21]
- [X] certains transcrits ont juste été supprimé
- [X] Erreur de parsing, manque souvent un -
#+begin_src julia
lastTryMobidetails("recoded-failures-mobidetails.csv")
#+end_src
***** DONE Fusionner données
CLOSED: [2023-04-26 Wed 22:35]
#+begin_src julia
function mergeAllGenomic()
dNew = mergeAll("recoded-success.csv",
"recoded-failures-mobidetails.csv",
"recoded-failures-mobidetails-redo.csv")
dInit = @chain DataFrame(CSV.File("variant_success.csv")) begin
@transform :transcript = :transcript .* ":" .* :coding .* :codingPos .* :codingChange
@select :file :transcript :classification :zygosity
@rename :classificationCento = :classification
end
dTmp = outerjoin(dInit, dNew, on = :transcript)
CSV.write("variant_genomic.csv", dTmp)
end
fSuccess = "recoded-success.csv"
fFailures = "recoded-failures.csv"
# variantRecoder(fSuccess, fFailures)
# mobidetailsOnFailures(fFailures)
# lastTryMobidetails("recoded-failures-mobidetails.csv")
mergeAllGenomic()
#+end_src
***** DONE Formatter donner pour simuscop
CLOSED: [2023-04-28 Fri 11:55] SCHEDULED: <2023-04-26 Wed>
**** KILL Extraire liste des CNVs
CLOSED: [2023-08-12 Sat 15:54]
SCHEDULED: <2023-04-17 Mon>
**** KILL Simuscop :simuscop:
CLOSED: [2023-08-12 Sat 15:54]
***** DONE Entrainer le modèle sur 63003856/
CLOSED: [2023-04-29 Sat 19:56]
Relancer le modèle pour être sûr
***** DONE Générer fastq avec simuscop (del et ins seulement) 20x
CLOSED: [2023-04-28 Fri 23:35] SCHEDULED: <2023-04-22 Sat>
****** DONE Génerer un profile avec bed de centogène
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
NA12878 mais à refaire avec un vrai séquencage
Voir [[*Centogène][Bed Centogène]] pour choix
****** DONE Générer les données en 20x
CLOSED: [2023-04-28 Fri 11:54] SCHEDULED: <2023-04-22 Sat>
capture de cento
****** DONE Regénérer en supprimant les doublons
CLOSED: [2023-04-28 Fri 17:28]
***** DONE Quelle couverture ?
CLOSED: [2023-04-29 Sat 18:26]
ex sur chr11:16,014,966 où on a 11 reads dans la simulation contre 200 !
****** 200 est la plus proche
#+attr_html: :width 500px
[[./simuscop-200-chr1-1.png]]
#+attr_html: :width 500px
[[./simuscop-200-chr1-2.png]]
****** DONE 20x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 50x
CLOSED: [2023-04-29 Sat 15:38]
****** DONE 100x
CLOSED: [2023-04-29 Sat 15:39]
****** DONE 200x
CLOSED: [2023-04-29 Sat 15:39]
***** DONE Reads mal centrés sur des petits exons seuls
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
Capture ok : [[https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A153817168%2D153817824&hgsid=296556270_F4fkENLPXHXidi2oALXls2jxNH9l][UCSC]] (track noire)
Mais mauvaise répartitiopn
#+attr_html: :width 800px
[[./simuscop-error.png]]
À tester
- Problème de profile ?
- mauvais patient ?
- mauvaise génération ? -> comparer avec ceux donnés sur github
- nom des chromosomes ?
****** DONE [#A] Tester sur exon 6 GATAD2B pour NC_000001.11:g.153817496A>T
CLOSED: [2023-04-29 Sat 19:56] SCHEDULED: <2023-04-29 Sat>
******* DONE Configuration + Profile 63003856.profile: idem, mal centré
CLOSED: [2023-04-29 Sat 19:18]
Téléchargement des données
#+begin_src sh :dir ~/code/bisonex/test-simuscop
scp meso:/Work/Projects/bisonex/data/genome/GRCh38.p14/genomeRef.fna .
scp meso:Work/Projects/bisonex/data/simuscop/*.profile .
scp -r meso:/Work/Projects/bisonex/data/genome/GRCh38.p13/bwa .
#+end_src
On récupère l'exon (NB: org-mode ne lance pas le code...)
#+begin_src julia
using CSV,DataFramesMeta
d = CSV.read("VCGS_Exome_Covered_Targets_hg38_40.1MB_renamed.bed", header=false, delim="\t", DataFrame)
@subset d :Column1 .== "NC_000001.11" :Column2 .<= 153817496 :Column3 .>= 153817496
#+end_src
NC_000001.11 153817371 153817542
Génération du bed
#+begin_src sh :dir ~/code/bisonex/test-simuscop
echo -e "NC_000001.11\t153817371\t153817542" > gatad2b-exon6.bed
#+end_src
#+RESULTS:
Génération d'un variant
#+begin_src sh :dir ~/code/bisonex/test-simuscop
echo -e "s\tsingle\tNC_000001.11\t153817496\tA\tT\thet"> variant.txt
#+end_src
#+RESULTS:
Génération du fichier de config
#+begin_src sh :dir ~/code/bisonex/test-simuscop
cat > config_wes.txt << EOL
ref = genomeRef.fna
profile = ./63003856.profile
variation = ./variant.txt
target = ./gatad2b-exon6.bed
layout = PE
threads = 1
name = single
output = test-gatad2b
coverage = 20
EOL
#+end_src
#+RESULTS:
.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 413 246 167 751 289 215 2 98 0.595642 0.460821 0.286285 0.519629 NaN NaN 2.428571 2.465116
INDEL PASS 413 246 167 751 289 215 2 98 0.595642 0.460821 0.286285 0.519629 NaN NaN 2.428571 2.465116
SNP ALL 15883 15479 404 23597 5277 2841 46 44 0.974564 0.745760 0.120397 0.844947 3.017198 2.85705 5.560099 2.114633
SNP PASS 15883 15479 404 23597 5277 2841 46 44 0.974564 0.745760 0.120397 0.844947 3.017198 2.85705 5.560099 2.114633
******* DONE Vérifier qu'il ne reste plus de filtre autre que PASS
CLOSED: [2023-07-08 Sat 15:19]
#+begin_src
$ zgrep -c 'PASS' HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz
3730505
$ zgrep -c '^chr' HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz
3730506
#+end_src
****** TODO 1/4 SNP manquant ?
******* DONE Regarder avec Julia si ce sont vraiment des FP: 61/5277 qui ne le sont pas
CLOSED: [2023-07-09 Sun 12:09]
******* DONE Examiner les FP
CLOSED: [2023-07-30 Sun 22:05]
******* DONE Tester un FP
CLOSED: [2023-07-30 Sun 22:05]
2 │ chr1 608765 A G ./.:.:.:.:NOCALL:nocall:. 1/1:FP:.:ti:SNP:homalt:188
liftDown UCSC: rien en GIAB : vrai FP
3 │ chr1 762943 A G ./.:.:.:.:NOCALL:nocall:. 1/1:FP:.:ti:SNP:homalt:287
4 │ chr1 762945 A T ./.:.:.:.:NOCALL:nocall:. 1/1:FP:.:tv:SNP:homalt:287
Remaniements complexes ? Pas dans le gène en HG38
******* DONE La plupart des FP (4705/5566) sont homozygotes: erreur de référence ?
CLOSED: [2023-07-12 Wed 21:10] SCHEDULED: <2023-07-09 Sun>
Sur les 2 premiers variants, ils montrent en fait la différence entre T2T et GRCh38
Erreur à l'alignement ?
******** KILL relancer l'alignement
CLOSED: [2023-07-09 Sun 17:36]
******** DONE vérifier reads identiques hg38 et T2T: oui
CLOSED: [2023-07-09 Sun 16:36]
T2T CHR1608765
38 chr1:1180168-1180168 (
SRR14724513.24448214
SRR14724513.24448214
******* DONE Vérifier quelques variants sur IGV
CLOSED: [2023-07-09 Sun 17:36]
******* KILL Répartition des FP : cluster ?
CLOSED: [2023-07-09 Sun 17:36]
****** DONE Examiner les FP restant après correction selon séquence de référence
CLOSED: [2023-08-12 Sat 15:57]
****** HOLD Examiner les variants supprimé
****** TODO Enlever les FP qui correspondent à un changement dans le génome
******* Condition:
- pas de variation à la position en GRCh38
- variantion homozygote
- la varation en T2T correspond au changement de pair de base GRC38 -> T2T
pour les SNP:
alt_T2T[i] = DNA_GRC38[j]
avec i la position en T2T et j la position en GRCh38
Note: définir un ID n'est pas correct car les variants peuvent être modifié par happy !
******* Idée
- Pour chaque FP, c'est un "faux" FP si
- REF en hg38 == ALT en T2T
- et REF en hg38 != REF en T2T
- et variant homozygote
Comment obtenir les séquences de réferences ?
1. liftover
2. blat sur la séquence autour du variant
3. identifier quelques reads contenant le variant et regarder leur aligneement en hg38
Après discussion avec Alexis: solution 3
******* Algorithme
1. Extraire les coordonnées en T2T des faux positifs *homozygote*
2. Pour chaque faux positif
1. lister 10 reads contenant le variant
2. pour chacun de ces reads, récupérer la séquence en T2T et GRCh38 via le nom du read dans le bam
3. si la séquence en T2T modifiée par le variant est "identique" à celle en GRCh38, alors on ignore ce faux positif
Note: on ignore les reads qui ont changé de chromosome entre les version
******* DONE Résultat préliminaire
CLOSED: [2023-07-23 Sun 14:30]
cf [[file:~/roam/research/bisonex/code/giab/giab-corrected.csv][script julia]]
3498 faux positifs en moins, soit 0.89 sensibilité
julia> tp=15479
julia> fp=5277
julia> tp/(tp+fp)
0.7457602620928888
julia> tp/(tp+(fp-3498))
0.8969173716537258
On est toujours en dessous des 97%
******* HOLD Corriger proprement VCF ou résultats Happy
******* TODO Adapter pour gérer plusieurs variants par read
****** DONE Méthodologie du pangenome
CLOSED: [2023-10-03 Tue 21:28]
Voir biblio[cite:@liao2023] mais ont aligné sur GRCH38
******* DONE Mail alexis
CLOSED: [2023-10-03 Tue 21:28]
****** DONE Méthodologie T2T
CLOSED: [2023-10-16 Mon 19:42]
Mail alexis
SCHEDULED: <2023-10-04 Wed>
***** TODO Rendre simplement le nombre de vrais positifs
SCHEDULED: <2023-12-26 Tue>
***** KILL Mail Yannis
CLOSED: [2023-07-08 Sat 10:44]
***** DONE Mail GIAB pour version T2T
CLOSED: [2023-07-07 Fri 18:37]
**** KILL HG002 :hg002:T2T:
CLOSED: [2023-11-26 Sun 12:30]
**** KILL HG003 :hg003:T2T:
CLOSED: [2023-11-26 Sun 12:30]
**** KILL HG004 :hg004:T2T:
CLOSED: [2023-11-26 Sun 12:30]
**** DONE Plot : ashkenazim trio :hg38:
CLOSED: [2023-07-30 Sun 16:49] SCHEDULED: <2023-07-30 Sun 15:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 16:06]--[2023-07-30 Sun 16:35] => 0:29
CLOCK: [2023-07-30 Sun 15:39]--[2023-07-30 Sun 15:40] => 0:01
:END:
/Entered on/ [2023-04-16 Sun 17:29]
Refaire résultats
**** DONE Mail Paul sur les résultat ashkenazim +/- centogene
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Relancer comparaison GIAB avec GATK 4.4.0
CLOSED: [2023-08-12 Sat 15:55]
/Entered on/ [2023-08-03 Thu 12:42]
**** TODO Re-télécharger proprement dans pipeline dédiés
[[*Résumé][Résumé]]
Cf [[*Validation : Quelles données de référence ?][Validation : Quelles données de référence ?]]
https://medium.com/dnanexus/benchmarking-state-of-the-art-secondary-variant-calling-pipelines-5472ca6bace7
Source:
https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=study&acc=SRP047086
https://zenodo.org/records/3597727
Selon https://github.com/genome-in-a-bottle/giab_data_indexes
***** TODO HG001 :hg001:
SCHEDULED: <2023-11-29 Wed>
****** TODO Avec données en hg38
SCHEDULED: <2023-11-29 Wed>
[[*Résumé][Résumé]]
Ok pour hiseq4000 et sureselect mais utiliser le dernier commit pour symlink
****** TODO Avec données en hg19
SCHEDULED: <2023-12-20 Wed>
Utiliser crossmap ! https://crossmap.readthedocs.io/en/latest/ (inspiré de [[https://github.com/bcbio/bcbio_validation_workflows/blob/master/giab-exome/input/get_data.sh][bcbio]]
pour vérifier
***** TODO HG002 :hg002:
SCHEDULED: <2023-12-21 Thu>
***** TODO HG003 :hg003:
SCHEDULED: <2023-12-21 Thu>
***** TODO HG004 :hg001:
SCHEDULED: <2023-12-21 Thu>
**** TODO Refaire les analyses happy+ rtgeval
SCHEDULED: <2023-12-09 Sat>
On veut les résultats de https://medium.com/dnanexus/benchmarking-state-of-the-art-secondary-variant-calling-pipelines-5472ca6bace7
hap.py avec conda ?
*** TODO Platinum genome :platinum:
https://emea.illumina.com/platinumgenomes.html
**** TODO Tester sur la zone couverte par l'exome centogène
SCHEDULED: <2023-12-26 Tue>
*** DONE Séquencer NA12878 :cento:hg001:
CLOSED: [2023-10-07 Sat 17:59]
Discussion avec Paul : sous-traitant ne nous donnera pas les données, il faut commander l'ADN
**** DONE ADN commandé
CLOSED: [2023-06-30 Fri 22:29]
**** DONE Sauvegarder les données brutes
CLOSED: [2023-07-30 Sun 14:22] SCHEDULED: <2023-07-19 Wed>
K, scality, S
**** KILL Récupérer le fichier de capture
CLOSED: [2023-07-30 Sun 14:25] SCHEDULED: <2023-07-23 Sun>
Candidats donnés dans publication https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354858/
#+begin_quote
In short, the Nextera Rapid Capture Exome Kit (Illumina, San Diego, CA), the SureSelect Human All Exon kit (Agilent, Santa Clara, CA) or the Twist Human Core Exome was used for enrichment, and a Nextseq500, HiSeq4000, or Novoseq 6000 (Illumina) instrument was used for the actual sequencing, with the average coverage targeted to at least 100× or at least 98% of the target DNA covered 20×.
#+end_quote
Par défaut, on utilisera https://www.twistbioscience.com/products/ngs/alliance-panels#tab-3
ANnonce récente pour nouveau panel Twist : https://www.centogene.com/news-events/news/newsdetails/twist-bioscience-and-centogene-launch-three-panels-to-advance-rare-disease-and-hereditary-cancer-research-and-support-diagnostics
Masi pas de fichier BED
***** DONE Mail centogène
CLOSED: [2023-07-30 Sun 14:22] DEADLINE: <2023-07-23 Sun>
**** DONE Tester Nextera Rapid Capture Exome v1.2 (hg19) :giab:
CLOSED: [2023-08-06 Sun 19:05] SCHEDULED: <2023-08-03 Thu 19:00>
https://support.illumina.com/downloads/nextera-rapid-capture-exome-v1-2-product-files.html
***** DONE Liftover capture
CLOSED: [2023-08-06 Sun 18:30] SCHEDULED: <2023-08-06 Sun>
#+begin_src sh
nextflow run -profile standard,helios workflows/lift-nextera-capture.nf -lib lib
#+end_src
Vérification rapide : ok
***** DONE Run
CLOSED: [2023-08-06 Sun 19:05] SCHEDULED: <2023-08-06 Sun>
#+begin_src sh
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_NA12878-63118093_S260-GRCh38/callVariant/haplotypecaller/2300346867_NA12878-63118093_S260-GRCh38.vcf.gz --outdir=out/2300346867_NA12878-63118093_S260-GRCh38/happy-nextera-lifted/ --compare=happy -lib lib --capture=capture/nexterarapidcapture_exome_targetedregions_v1.2-nochrM_lifted.bed --id=HG001 --genome=GRCh38
#+end_src
**** DONE Tester Agilent SureSelect All Exon V8 (hg38) :giab:
CLOSED: [2023-07-31 Mon 23:09] SCHEDULED: <2023-07-31 Mon>
https://earray.chem.agilent.com/suredesign/index.htm
"Find design"
"Agilent catalog"
Fichiers:
- Regions.bed: Targeted exon intervals, curated and targeted by Agilent Technologies
- MergedProbes.bed: Merged probes for targeted enrichment of exons described in Regions.bed
- Covered.bed: Merged probes and sequences with 95% homology or above
- Padded.bed: Merged probes and sequences with 95% homology or above extended 50 bp at each side
- AllTracks.bed: Targeted regions and covered tracks
#+begin_src sh
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy/ --compare=happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v8_hg38_Regions.bed --id=HG001 --genome=GRCh38
#+end_src
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL | 423 | 395 | 28 | 915 | 108 | 405 | 4 | 13 | 0.933806 | 0.788235 | 0.442623 | 0.854868 | | | 1.7012987012987013 | 2.7916666666666665 |
| INDEL | PASS | 423 | 395 | 28 | 915 | 108 | 405 | 4 | 13 | 0.933806 | 0.788235 | 0.442623 | 0.854868 | | | 1.7012987012987013 | 2.7916666666666665 |
| SNP | ALL | 20984 | 20600 | 384 | 26080 | 780 | 4703 | 62 | 10 | 0.9817 | 0.963512 | 0.18033 | 0.972521 | 3.0499710592321048 | 2.7596541786743516 | 1.58256372367935 | 1.8978207694018234 |
| SNP | PASS | 20984 | 20600 | 384 | 26080 | 780 | 4703 | 62 | 10 | 0.9817 | 0.963512 | 0.18033 | 0.972521 | 3.0499710592321048 | 2.7596541786743516 | 1.58256372367935 | 1.8978207694018234 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-01 Tue 23:16] SCHEDULED: <202 3-08-02 Wed>
https://www.twistbioscience.com/resources/data-files/ngs-human-core-exome-panel-bed-file
#+begin_src
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed --id=HG001 --genome=GRCh38 -bg
#+end_src
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL | 328 | 313 | 15 | 722 | 95 | 309 | 4 | 13 | 0.954268 | 0.769976 | 0.427978 | 0.852273 | | | 1.8584070796460177 | 2.8967391304347827 |
| INDEL | PASS | 328 | 313 | 15 | 722 | 95 | 309 | 4 | 13 | 0.954268 | 0.769976 | 0.427978 | 0.852273 | | | 1.8584070796460177 | 2.8967391304347827 |
| SNP | ALL | 19198 | 18962 | 236 | 23381 | 684 | 3738 | 48 | 10 | 0.987707 | 0.965178 | 0.159873 | 0.976313 | 3.1034188034188035 | 2.859264147830391 | 1.5669565217391304 | 1.8578767123287672 |
| SNP | PASS | 19198 | 18962 | 236 | 23381 | 684 | 3738 | 48 | 10 | 0.987707 | 0.965178 | 0.159873 | 0.976313 | 3.1034188034188035 | 2.859264147830391 | 1.5669565217391304 | 1.8578767123287672 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
#+begin_src sh
ID="2300346867_NA12878-63118093_S260-GRCh38"; nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --outdir=out/${ID}/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed --id=HG001 --genome=GRCh38 -bg
#+end_src
**** DONE Tester Agilen SureSelect All Exon V8 (hg38) GATK-4.4:giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
**** DONE Vérifier l'impact gatk 4.3 - 4.4 : aucun
CLOSED: [2023-08-05 Sat 09:25]
**** DONE Figure comparant les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Mail Paul sur les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** KILL Tester si le panel Twist Alliance VCGS Exome suffit
CLOSED: [2023-07-31 Mon 22:31] SCHEDULED: <2023-07-30 Sun>
**** DONE Mail cento pour demande le type de capture
CLOSED: [2023-10-07 Sat 17:59]
/Entered on/ [2023-08-07 Mon 20:40]
Twist exome
*** PROJ Comparer happy et happy-vcfeval :giab:
** TODO Données syndip (CHM-eval) ! :syndip:
https://github.com/lh3/CHM-eval
*** KILL Données officielles : non car génome !!
CLOSED: [2023-11-19 Sun 23:43]
**** KILL Run ERR1341793
CLOSED: [2023-11-19 Sun 23:43] SCHEDULED: <2023-11-18 Sat>
(raw reads ERR1341793_1.fastq.gz and ERR1341793_2.fastq.gz downloaded from https://www.ebi.ac.uk/ena/browser/view/ERR1341793)
**** KILL Run ERR1341796
CLOSED: [2023-11-19 Sun 23:43] SCHEDULED: <2023-11-18 Sat>
*** TODO Données exome Broad institute (nextflow)
SCHEDULED: <2023-12-26 Tue>
https://console.cloud.google.com/storage/browser/broad-public-datasets/CHM1_CHM13_WES;tab=objects?pli=1&prefix=&forceOnObjectsSortingFiltering=false
*** TODO Télécharger VCF
SCHEDULED: <2023-12-01 Fri>
26289 | 103 | 3845 | 77 | 4 | 0.965854 | 0.995411 | 0.146259 | 0.98041 | 2.9282199219412863 | 2.7752583237657866 | 1.6348301800775018 | 1.8423330808354075 |
| SNP | PASS | 23136 | 22346 | 790 | 26289 | 103 | 3845 | 77 | 4 | 0.965854 | 0.995411 | 0.146259 | 0.98041 | 2.9282199219412863 | 2.7752583237657866 | 1.6348301800775018 | 1.8423330808354075 |
***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi" gatk-4.4
CLOSED: [2023-08-03 Thu 23:24] SCHEDULED: <2023-08-03 Thu>
#+begin_src sh
ID="HG002-SRX11061487_SRR14724512-GRCh38" ; nextflow run workflows/compareVCF.nf -profile standard,helios --outdir=out/${ID} --query=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --compare=vcfeval,happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed --id=HG002 --genome=GRCh38
#+end_src
**** DONE HG003 :hg003:hg38:
CLOSED: [2023-07-30 Sun 14:26]
***** Notes
#+begin_src sh
NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios --input /Work/Groups/bisonex/data/giab/GRCh38/HG003_{1,2}.fq.gz -bg
#+end_src
#+begin_src sh
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareHG003 --test.id=HG003 --test.query=out/HG003_1/variantCalling/haplotypecaller/HG003_1.vcf.gz --test.compare=vcfeval,happy --test.capture=data/AgilentSureSelectv05_hg38.bed
#+end_src
vcfeval
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
5.000 36745 36473 486 3988 0.9869 0.9021 0.9426
None 36748 36476 495 3985 0.9866 0.9022 0.9425
$ zcat NA12878.snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'
happy
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 2731 2290 441 3092 208 577 62 53 0.838521 0.917296 0.186611 0.876141 NaN NaN 1.505145 1.888993
INDEL PASS 2731 2290 441 3092 208 577 62 53 0.838521 0.917296 0.186611 0.876141 NaN NaN 1.505145 1.888993
SNP ALL 37997 34481 3516 36861 306 2074 33 13 0.907466 0.991204 0.056265 0.947488 2.611269 2.565915 1.555780 1.621727
SNP PASS 37997 34481 3516 36861 306 2074 33 13 0.907466 0.991204 0.056265 0.947488 2.611269 2.5659
***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"
CLOSED: [2023-07-30 Sun 14:25] SCHEDULED: <2023-07-23 Sun>
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL | 644 | 538 | 106 | 914 | 32 | 337 | 7 | 19 | 0.835404 | 0.944541 | 0.368709 | 0.886626 | | | 1.7444933920704846 | 2.3138686131386863 |
| INDEL | PASS | 644 | 538 | 106 | 914 | 32 | 337 | 7 | 19 | 0.835404 | 0.944541 | 0.368709 | 0.886626 | | | 1.7444933920704846 | 2.3138686131386863 |
| SNP | ALL | 23126 | 22271 | 855 | 26405 | 135 | 4002 | 90 | 20 | 0.963029 | 0.993974 | 0.151562 | 0.978257 | 2.949462182004439 | 2.7766657134686876 | 1.6080333972695475 | 1.8465106245280984 |
| SNP | PASS | 23126 | 22271 | 855 | 26405 | 135 | 4002 | 90 | 20 | 0.963029 | 0.993974 | 0.151562 | 0.978257 | 2.949462182004439 | 2.7766657134686876 | 1.6080333972695475 | 1.8465106245280984 |
***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi" gatk-4.4
CLOSED: [2023-08-03 Thu 23:24] SCHEDULED: <2023-08-03 Thu>
#+begin_src
ID="HG003-SRX11061488_SRR14724511-GRCh38" ; nextflow run workflows/compareVCF.nf -profile standard,helios --outdir=out/${ID} --query=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --compare=vcfeval,happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed --id=HG003 --genome=GRCh38
#+end_src
**** DONE HG004 :hg38:hg004:
CLOSED: [2023-11-26 Sun 12:30]
***** Notes
#+begin_src sh
NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios --input /Work/Groups/bisonex/data/giab/GRCh38/HG004_{1,2}.fq.gz -bg
#+end_src
vcfeval
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
6.000 36938 36678 421 4040 0.9887 0.9014 0.9430
None 36942 36682 432 4036 0.9884 0.9015 0.9429
happy
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 2787 2388 399 3183 195 580 53 38 0.856835 0.925086 0.182218 0.889654 NaN NaN 1.507834 1.848649
INDEL PASS 2787 2388 399 3183 195 580 53 38 0.856835 0.925086 0.182218 0.889654 NaN NaN 1.507834 1.848649
SNP ALL 38185 34560 3625 36921 254 2107 46 7 0.905067 0.992704 0.057068 0.946862 2.589175 2.553546 1.632595 1.653534
SNP PASS 38185 34560 3625 36921 254 2107 46 7 0.905067 0.992704 0.057068 0.946862 2.589175 2.553546 1.632595 1.653534
***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"
CLOSED: [2023-07-30 Sun 14:39] SCHEDULED: <2023-07-23 Sun>
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL | 588 | 511 | 77 | 873 | 15 | 332 | 7 | 8 | 0.869048 | 0.972274 | 0.380298 | 0.917767 | | | 1.6111111111111112 | 2.3984375 |
| INDEL | PASS | 588 | 511 | 77 | 873 | 15 | 332 | 7 | 8 | 0.869048 |
| --create-output-bam-index true |
| --create-output-bam-md5 false | --create-output-bam-md5 false |
| --create-output-variant-index true | --create-output-variant-index true |
| --create-output-variant-md5 false | --create-output-variant-md5 false |
| --max-variants-per-shard 0 | --max-variants-per-shard 0 |
| --lenient false | --lenient false |
| --add-output-sam-program-record true | --add-output-sam-program-record true |
| --add-output-vcf-command-line true | --add-output-vcf-command-line true |
| --cloud-prefetch-buffer 40 | --cloud-prefetch-buffer 40 |
| --cloud-index-prefetch-buffer -1 | --cloud-index-prefetch-buffer -1 |
| --disable-bam-index-caching false | --disable-bam-index-caching false |
| --sites-only-vcf-output false | --sites-only-vcf-output false |
| --help false | --help false |
| --version false | --version false |
| --showHidden false
r}/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz script/files/vcf/NA12878_NIST7035.vcf -f ${dir}/HG001_GRCh38_1_22_v4.2.1_benchmark.bed -o test
#+end_src
****** KILL beaucoup trop de faux négatifs
CLOSED: [2023-02-17 Fri 19:37]
******* DONE Test 1 : vep annot : beaucoup tro
p de faux négatif
CLOSED: [2023-02-06 lun. 13:40]
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 276768 274 276494 1500 257 968 26 15 0.000990 0.516917 0.645333 0.001976 NaN NaN 1
.483361 6.129187
INDEL PASS 276768 274 276494 1500 257 968 26 15 0.000990 0.516917 0.645333 0.001976 NaN NaN 1.483361 6.129187
SNP ALL 1937706 1193 1936513 3338 106
2037 11 2 0.000616 0.918524 0.610246 0.001231 2.0785 1.861183 1.539064 2.703663
SNP PASS 1937706 1193 1936513 3338 106 2037 11 2 0.000616 0.918524 0.610246 0.001231 2.0785 1.861183 1.539064 2.703663
******* KILL Test 3 : indexer vcf de reference
CLOSED: [2023-02-06 lun. 17:19]
Même résultat avec vcfeval, qui a besoin de la version indexée
******* DONE Test 3 sans filtre vep : idem
CLOSED: [2023-02-06 lun. 17:19]
Benchmarking Summary:
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
INDEL ALL 276768 10535 266233 52169 10969 30616 3552 2122 0.038064 0.491069 0.586862 0.070652 NaN NaN 1.483361 0.509510
INDEL PASS 276768 10535 266233 52169 10969 30616 3552 2122 0.038064 0.491069 0.586862 0.070652 NaN NaN 1.483361 0.509510
SNP ALL 1937706 105753 1831953 357652 74634 177259 35111 797 0.054576 0.586270 0.495619 0.099857 2.0785 1.42954 1.539064 0.324923
SNP PASS 1937706 105753 1831953 357652 74634 177259 35111 797 0.054576 0.586270 0.495619 0.099857 2.0785 1.42954 1.539064 0.324923
******* DONE Test 4 avec vcfeval sur vep_annot : idem
CLOSED: [2023-02-06 lun. 17:18]
#+begin_src
#!/bin/bash
#SBATCH -c 4
#SBATCH -p smp
#SBATCH --time=01:00:00
#SBATCH --mem=32G
module load nix/2.11.0
export HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna dir=/Work/Groups/bisonex/data/NA12878/GRCh38
rtg vcfeval -b /Work/Groups/bisonex/data/NA12878/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -c files/vcf/NA12878_NIST7035_vep_annot.vcf.gz -o test-rtg -t /Work/Groups/bisonex/data/genome/GRCh38.p13/genomeRef.sdf
#+end_src
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
1.000 2984 2682 1840 3890296 0.5931 0.0008 0.0015
None 2984 2682 1841 3890296 0.5930 0.0008 0.0015
Exemple du log
2023-02-06 13:50:14 Reference NC_000001.11 baseline contains 307854 variants.
2023-02-06 13:50:14 Reference NC_000001.11 calls contains 426 variants.
2023-02-06 13:50:15 Reference NC_000002.12 baseline contains 325877 variants.
2023-02-06 13:50:15 Reference NC_000002.12 calls contains 320 variants.
******* DONE Regarder quelques variants à la main
CLOSED: [2023-02-07 Tue 22:01]
Ex:
Il manque NC_000001.11 783006 . A G 50 PASS
Il y a A -> G et C -> A sur cette position
***** DONE Restreindre genome de référence
CLOSED: [2023-03-04 Sat 11:15]
****** Discussion Alexis
le pipeline prend en compte 5', 3', variant canoniques d'épissage + prédit spip
Le plus simple pour le moment est de restreindre seulement aux exons
GENCODE (version europénne) vs RefSeq: [[https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S8-S2][article 2015]] en faveur de GENCODE mais Alexis conseille Refseq
****** DONE -f, -R ou -T ?
CLOSED: [2023-02-25 Sat 19:47]
Selon la doc : -f avec le bed fourni et -T pour filtrer sor les exons
******* rtg tools
Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
----------------------------------------------------------------------------------------------------
3.000 1015 910 206 32531 0.8154 0.0303 0.0583
None 1015 910 206 32531 0.8154 0.0303 0.0583
***** KILL Exons seuls
CLOSED: [2023-04-02 Sun 17:11]
****** DONE BestRefSeq
CLOSED: [2023-02-19 Sun 12:05]
Dans refseq,[[https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/][2 types de modèles pour le gène]]
- basé sur refseq (NM_, NP_), curée
- basé sur gnomon (XM_ , XP_), prédite
Les modèles basés sur refseq ont la préférénce (cf lien)
On se restreint donc à bestrefseq
#+begin_src sh
wget https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz
gunzip https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz
#+end_src
On se restrein aux exons codant (NM_)
#+begin_src
awk '/BestRefSeq\texon/ && /transcript_id=NM/ {print $1"\t"$4"\t"$5;}' GRCh38_latest_genomic.gff > exons.csv
#+end_src
Puis intersection
******* DONE Tests après correction bug dans noms de chromosome : precision ~ ok, recall très mauvais -> trop de FN ?
CLOSED: [2023-02-19 Sun 12:05]
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision
INDEL ALL 7230 321 6909 1500 290 888 27 18 0.044398 0.526144
INDEL PASS 7230 321 6909 1500 290 888 27 18 0.044398 0.526144
SNP ALL 59052 1653 57399 3338 101 1583 12 2 0.027992 0.942450
SNP PASS 59052 1653 57399 3338 101 1583 12 2 0.027992 0.942450
METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
0.592000 0.081887 NaN NaN 1.54733 6.129187
0.592000 0.081887 NaN NaN 1.54733 6.129187
0.474236 0.054370 2.433271 1.861183 1.57523 2.703663
0.474236 0.054370 2.433271 1.861183 1.57523 2.703663
******* DONE Vérifier exons: on a l'union des exons de tous les transcripts...
CLOSED: [2023-02-19 Sun 12:05]
Il faudrait un .bed d'illumina
On teste Twist for Illumina Exome 2.0 Plus BED File (hg19) sur https://support.illumina.com/downloads/nextera-flex-for-enrichment-BED-files.html
Conversion en hg38 avec ucsc
Renommage des chromosomes
#+begin_src
sed 's:^:s/chr:;s:chrMT:chrM:;s:\s:\\t/:;s:$:\\t/:' ../../genome/GRCh38.p13/chromosome_mapping.txt > pattern.sed
sed -i.bak -f pattern.sed illumina_exons.bed
bedtools intersect -a HG001_GRCh38_1_22_v4.2.1_benchmark.bed -b illumina_exons.bed > HG001_GRCh38_1_22_v4.2.1_benchmark_illumina_exons.bed
#+end_src
Intersection
****** KILL Bed illumina
CLOSED: [2023-02-24 Fri 23:44]
******* KILL Sans filtre vep: Inversion truth et query... on recommence
CLOSED: [2023-02-19 Sun 13:15]
******* KILL Sans filtre vep: mieux mais pas exceptionnel
CLOSED: [2023-02-24 Fri 23:44]
cd work/00/2c72e62400956c96fb101ac7af405e/
$ cat .command.out
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision
INDEL ALL
922 490 432 942 439 0 32 56 0.531453 0.533970
INDEL PASS 922 490 432 942 439 0 32 56 0.531453 0.533970
SNP ALL 24618 18689 5929 21257 2571 0 239 17 0.759160 0.879052
SNP PASS 24618 18689 5929 21257 2571 0 239 17 0.759160 0.879052
METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
0.0 0.532709 NaN NaN 1.628743 2.799180
0.0 0.532709 NaN NaN 1.628743 2.799180
0.0 0.814719 2.899604 2.881526 1.598479 1.564378
0.0 0.814719 2.899604 2.881526 1.598479 1.564378
******* KILL Comprendre pour les FN explosent avec vep annot
CLOSED: [2023-02-24 Fri 23:44]
NC_000001.11 924024 . C G
non couverte dans bam -> 1er exons de SAMD11 mais non couverte
Il est dans NM_001385641.1 mais pas dans NM_152486.4
****** KILL Obtenir les zones couvertes depuis le bam directement
CLOSED: [2023-02-24 Fri 23:44]
#+begin_src sh
samtools sort NA12878_chr1.bam -o NA12878_chr1_sorted.bam
bedtools genomecov -ibam NA12878_chr1_sorted.bam -bg > chr1.bedgraph
head chr1.bedgraph
#+end_src
#+RESULTS:
: NC_000001.11 10001 10021 1
: NC_000001.11 10021 10059 2
: NC_000001.11 10059 10063 1
: NC_000001.11 10063 10087 2
: NC_000001.11 10087 10110 1
: NC_000001.11 10110 10113 3
: NC_000001.11 10113 10121 2
On prend les régions avec 20 reads
awk '$4 > 20 {print $1"\t"$2"\t"$3}' chr1.bedgraph > tomerge.bed
On fusionne les régions
bedtools merge -i tomerge.bed > exons_from_bam.bed
Problème : on manque parfois le bord des exons...
****** KILL Vérifier un bam de référence de NA12878
CLOSED: [2023-02-24 Fri 23:44]
Notamment pour la définitions des exons, on a des reads qui ne semblent pas alignés sur les bons exons selon IGV
On donne directemet à IGV le bam d'illuma WES ( https://github.com/genome-in-a-bottle/giab_data_indexes )
IGV n'aime pas le ftp apparement...
On récupére 2 échantillons pour ce patient sur HiSeq Exome
#+begin_src sh :dir /ssh:meso:/Work/Groups/bisonex/data/giab/GRCh38
wget https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/NA12878/alignment.index.NA12878_HiSeq_Exome_Garvan_GRCh37_09252015 -O todl.txt
awk '{print $1}' todl.txt | wget -i -
#+end_src
On récupére le premier échantillons en prenant just le chromosome 1
#+begin_src
samtools merge NA12878-NIST7035-HiSeq_Exome_Garan_GRCh37.bam project
.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.bam project.NIST_NIST7035_H7AP8ADXX_TA
AGGCGA_2_NA12878.bwa.markDuplicates.bam
samtools index NA12878-NIST7035-HiSeq_Exome_Garan_GRCh37.bam
#+end_src
******* Étude
NC_000001.11:924024 :
- bed d’illumina : pas correct
- bed refseq : meux
- bam : exon non ciblé, probablement parce que Mane select n’a pas été utilisé mais refseq (https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:28706)
NC_000001.11:924310: idem
NC_000001.11:924321: idem
NC_000001.11:924533: idem
NC_000001.11:966227: le bed ne couvre pas le bon exon !
https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A965863%2D966591&hgsid=295298291_vhDbIv5YIckCKLpGB7UUaZi2cAkr
NC_000001.11:966272
****** KILL Filtrer variants introniques de référence avec vep
CLOSED: [2023-02-24 Fri 23:44]
******* KILL variant calling seulf + seulement -f: nombreux FP
CLOSED: [2023-02-24 Fri 23:44]
/Work/Users/apraga/bisonex/work/68/f1cf72a5a4078fdf743fb3844b369a
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision
INDEL ALL 519 284 235 52169 37789 14094 12 64 0.547206 0.007511
INDEL PASS 519 284 235 52169 37789 14094 12 64 0.547206 0.007511
SNP ALL 22131 17434 4697 357652 305313 34904 189 32 0.787764 0.054020
SNP PASS 22131 17434 4697 357652 305313 34904 189 32 0.787764 0.054020
METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
0.270160 0.014820 NaN NaN 1.775956 0.509510
0.270160 0.014820 NaN NaN 1.775956 0.509510
0.097592 0.101108 2.971834 1.429533 1.579776 0.324923
0.097592 0.101108 2.971834 1.429533 1.579776 0.324923
****** DONE Bed donnés par GIAB (en hg19) : résultats corrects :resultats:
CLOSED: [2023-03-09 Thu 22:42] SCHEDULED: <2023-03-02 Thu>
Téléchargé à la main et converti via UCSCS. À automatiser, voir : *hg38
Sans oublier de renommer les chromosomes !
| Type | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision |
|-------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------|
| INDEL | 4871 | 3461 | 1410 | 7048 | 1554 | 1987 | 193 | 346 | 0.710532 | 0.692946 |
| SNP | 46032 | 39369 | 6663 | 44600 | 1186 | 4041 | 304 | 30 | 0.855253 | 0.970759 |
Type Ssensibilité VPP
INDEL 0.710532 0.692946
SNP 0.855253 0.970759
| METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
|----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|
| 0.281924 | 0.701629 | | | 1.6174985978687606 | 3.0674091441969518 |
| 0.090605 | 0.909353 | 2.529551552318896 | 2.4019675131548843 | 1.6206857273037931 | 1.6274012964054214 |
****** DONE Re-tester avec exons Refseq et option -T: résultats un peu moins bons
CLOSED: [2023-03-09 Thu 22:42] SCHEDULED: <2023-03-08 Wed>
On utilise directement les coordonées données par refseq
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision
INDEL ALL 7226 3417 3809 6978 1599 1918 228 353 0.472876 0.683992
SNP ALL 59052 37825 21227 43480 1913 3740 675 35 0.640537 0.951862
METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
0.274864 0.559171 NaN NaN 1.547733 2.756151
0.086017 0.765767 2.433271 2.350281 1.575230 1.492346
****** DONE Vérifier que la zone de capture a vraiment besoin d'un liftover...
CLOSED: [2023-04-02 Sun 14:13]
D'après la documentation, oui
https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-captur
| --showHidden false |
| --QUIET false | --QUIET false |
| --use-jdk-deflater false | --use-jdk-deflater false |
| --use-jdk-inflater false | --use-jdk-inflater false |
| --gcs-max-retries 20 | --gcs-max-retries 20 |
| --gcs-project-for-requester-pays | --gcs-project-for-requester-pays |
| --disable-tool-default-read-filters false PN:GATK ApplyBQSR | --disable-tool-default-read-filters false PN:GATK ApplyBQSR |
****** KILL Vérifier sha256sum
CLOSED: [2023-01-24 Tue 23:00]
alignment: différent
****** KILL Comparer bam
CLOSED: [2023-01-25 Wed 21:58]
/Work/Users/apraga/bisonex/script/files〉picard CompareSAMs LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_DUP=true tmp_63003856_S135/63003856_S135.bam /Work/Groups/bisonex/ref/tmp_63003856_S135/63003856_S135.bam O=compare-bam.tsv
picard CompareSAMs -LENIENT_LOW_MQ_ALIGNMENT true -LENIENT_DUP true tmp_63003856_S135/63003856_S135.bam /Work/Groups/bisonex/ref/tmp_63003856_S135/63003856_S135.bam -O compare-bam.tsv
VN Program Record attribute differs.
File 1: 1.13
File 2: 1.10
SAM files differ.
[Tue Jan 24 23:12:50 CET 2023] picard.sam.CompareSAMs done. Elapsed time: 7.32 minutes.
***** DONE Relancer avec la même version de samtools
CLOSED: [2023-01-25 Wed 21:58]
Pas d'impact
***** KILL Comparer tsv de sortie
CLOSED: [2023-05-23 Tue 08:45]
***** KILL Regarder où sont les variants différents
CLOSED: [2023-05-23 Tue 08:45]
** TODO GIAB Validation :giab:
https://github.com/ga4gh/benchmarking-tools
Prérequis :
- [[*hap.py][hap.py]]
- [[*NA12878][NA12878]]
*** TODO GIAB : exome :giab:
**** Notes
https://github.com/genome-in-a-bottle/giab_FAQ
**** Résultats résumés :resultats:
***** DONE HG001 :
CLOSED: [2023-04-06 Thu 21:41] SCHEDULED: <2023-04-02 Sun>
| Données | Algorithm | Type | Recall | Precision |
|---------+-----------+---------+--------+-----------|
| Bisonex | Happy | SNP | 0.8552 | 0.9708 |
| Bisonex | vcfeval | SNP | 0.8547 | 0.9727 |
| Bisonex | Happy | INDEL | 0.7105 | 0.6929 |
| Bisonex | vcfeval | Non-SNP | 0.7139 | 0.7136 |
|---------+-----------+---------+--------+-----------|
| GIAB | happy | INDEL | 0.7551 | 0.7415 |
| GIAB | vcfeval | INDEL | 0.7598 | 0.7445 |
| GIAB | happy | SNP | 0.8937 | 0.9621 |
| giab | vcfeval | SNP | 0.8937 | 0.9621 |
***** DONE HG002, HG003, HG004
CLOSED: [2023-04-14 Fri 11:36] SCHEDULED: <2023-04-14 Fri>
Capture Agilent
| Patient | Algorithm | Type | Recall | Precision |
| HG002 | happy | INDEL | 0.851495 | 0.923616 |
| HG002 | happy | SNP | 0.905926 | 0.992158 |
| HG002 | vcfeval | indel | 0.8523 | 0.9212 |
| HG002 | vcfeval | snp | 0.9054 | 0.9934 |
| HG003 | vcfeval | indel | 0.8363 | 0.9115 |
| HG003 | vcfeval | snp | 0.9069 | 0.9928 |
| HG003 | happy | INDEL | 0.838521 | 0.917296 |
| HG003 | happy | SNP | 0.907466 | 0.991204 |
| HG004 | happy | INDEL | 0.856835 | 0.925086 |
| HG004 | happy | SNP | 0.905067 | 0.992704 |
| HG004 | vcfeval | indel | 0.8568 | 0.9240 |
| HG004 | vcfeval | snp | 0.9048 | 0.9938 |
**** DONE télécharger données avec Nextflow :hg38:
CLOSED: [2023-11-26 Sun 12:30]
***** DONE Renommer les chromosomes
CLOSED: [2023-02-17 Fri 19:30]
****** DONE Genome de reference NCBI
CLOSED: [2023-02-25 Sat 19:46]
****** DONE Bed avec les exons
CLOSED: [2023-03-29 Wed 23:04]
****** DONE hg19
CLOSED: [2023-02-26 Sun 22:37]
****** DONE hg38
CLOSED: [2023-03-29 Wed 23:04]
- [X] Télécharger hg19 : ok
- [X] convertir bed en interval list
picard BedToIntervalList -I exons_illumina.bed -O exons_illumina.list -SD ../../genome/GRCh19/genomeRef.dict
- [X] puis en hg38
picard LiftOverIntervalList -I exons_illumina.list -O exons_illumina_hg38.list --CHAIN hg19ToHg38.over.chain -SD ../../genome/GRCh38.p13/genomeRef.dict
- [X] puis en bed
***** KILL VCF de référence
CLOSED: [2023-04-16 Sun 16:32]
****** DONE NA12878 (HG001)
CLOSED: [2023-11-26 Sun 12:29]
******* DONE Fastq HiSeq
CLOSED: [2023-02-25 Sat 19:46]
On prend le Hiseq, qui est probablement ce qu'utilise Centogène :
https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/
On utilisé les données "trimmés" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1069-7), i.e qui ont enlevé les fragments plus petits que la taille d'un read.
Informations:
- https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/Garvan_NA12878_HG001_HiSeq_Exome.README
- Sequencer: HiSeq2500
- kit: Nextera Rapid Capture Exome and Expanded Exome
Il y a 2 samples (NIST7035 et NIST7086), chacun sur 2 lanes -> à concaténer
NB : liste techno illumina https://www.illumina.com/systems/sequencing-platforms.html
Hiseq postérieur nextseq 550
******* KILL Fastq hiseq sans trimming
CLOSED: [2023-11-26 Sun 12:29]
******* DONE Capture : Exons (bed)
CLOSED: [2023-02-25 Sat 19:46]
https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/nexterarapidcapture_expandedexome_targetedregions.bed.gz
******* DONE Bed, vcf
CLOSED: [2023-02-24 Fri 23:45]
****** DONE Ashkenazy trio HG002, HG003, HGQ004
CLOSED: [2023-04-06 Thu 21:43] SCHEDULED: <2023-04-01 Sat>
****** KILL Chinese trio HG005, 6, 7
CLOSED: [2023-04-16 Sun 16:32]
***** KILL Fastq :fastq:
CLOSED: [2023-04-16 Sun 16:32]
****** DONE NA12878 (HG001)
CLOSED: [2023-02-25 Sat 19:46]
******* DONE Fastq HiSeq
CLOSED: [2023-02-25 Sat 19:46]
On prend le Hiseq, qui est probablement ce qu'utilise Centogène :
https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/
On utilisé les données "trimmés" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1069-7), i.e qui ont enlevé les fragments plus petits que la taille d'un read.
Informations:
- https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/Garvan_NA12878_HG001_HiSeq_Exome.README
- Sequencer: HiSeq2500
- kit: Nextera Rapid Capture Exome and Expanded Exome
Il y a 2 samples (NIST7035 et NIST7086), chacun sur 2 lanes -> à concaténer
NB : liste techno illumina https://www.illumina.com/systems/sequencing-platforms.html
Hiseq postérieur nextseq 550
******* DONE Capture : Exons (bed)
CLOSED: [2023-02-25 Sat 19:46]
https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/nexterarapidcapture_expandedexome_targetedregions.bed.gz
****** DONE Ashkenazy trio HG002, HG003, HG004
CLOSED: [2023-04-15 Sat 23:24] SCHEDULED: <2023-04-05 Wed>
******* DONE Capture
CLOSED: [2023-04-15 Sat 23:24]
https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/wex_Agilent_SureSelect_v05_b37.baits.slop50.merged.list
******* DONE Capture Agilent
CLOSED: [2023-04-15 Sat 23:24]
******* DONE Bam à partir des fastq
CLOSED: [2023-04-15 Sat 23:24]
Bam + index + checksum
https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/Ashkena
/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna
dir=/Work/Groups/bisonex/data/NA12878/GRCh38
hap.py ${di
zimTrio/alignment.index.AJtrio_OsloUniversityHospital_IlluminaExome_bwamem_GRCh37_11252015
****** KILL Chinese trio
CLOSED: [2023-04-16 Sun 16:32]
Whole exome pour HG005 seulement
******* KILL HG005
CLOSED: [2023-04-16 Sun 16:32]
https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/ChineseTrio/alignment.index.Chinesetrio_HG005_OsloUniversityHospital_IlluminaExome_bwamem_GRCh37_11252015
**** DONE Télécharger FASTQ directement avec aws (via SRA)
CLOSED: [2023-06-30 Fri 22:30] SCHEDULED: <2023-06-27 Tue>
***** Remarques
Numéro d'accession : https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08365-3/tables/1
Fastq disponible via SRA. Avec AWS, on peut accéder au fastq directement.
(Sinon il faut convertir SRA -> Fastq avec le toolkit : compliqué à configurer)
Exemple: https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR2962669&display=data-access
Avantage:
- pas de conversion BAM -> fASTQ
- détail des capture
- capture en hg38 sur site du constructeur !!
- capture semblable pour ashkenazi
Inconvénient :
- NA12878 : discordance pour le nombre de paires de bases : NA12878 = 49G (donc 24G de fastq)
- capture non disponible en ligne (site agilent)
- format SRA (le lien pour les fastq n'est pas gratuit): utiliser HTTP ou leur toolkit (télécharge au format SRA puis convertit en fastq). Exemple: pour avoir 2 fastq
fastq-dump --split-files --gzip SRR2962669
Important:
- ne pas compresser la sortie avec fasta-dump directement (lent++)
- Fasterq-dump est plus rapide
***** Liste des runs :
Voir [[*En cherchant dans SRA directement][En cherchant dans SRA directement]]
https://www.ncbi.nlm.nih.gov/sra
***** DONE HiSeq 4000 + agilent sureselect :sra:
CLOSED: [2023-06-28 Wed 22:06] SCHEDULED: <2023-06-28 Wed>
- [ ] HG001 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061486 SRR14724513
- [ ] HG002 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061487 SRR14724512
- [ ] HG003 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061488 SRR14724511
- [ ] HG004 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061489 SRR14724510
Other
- HG005 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061491 SRR14724508
- HG006 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061492 SRR14724507
- HG007 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061493 SRR14724506
******* DONE Capture agilent sureselect
CLOSED: [2023-06-30 Fri 22:30] SCHEDULED: <2023-06-28 Wed>
**** KILL Lift T2T :T2T:
CLOSED: [2023-11-26 Sun 12:30]
#+begin_quote
We performed liftover using the GATK release 4.1.9 LiftoverVcf (Picard Version 2.23.3) tool with the default parameters. This successfully lifts over variants that map exactly from GRCh38 to T2T-CHM13v2.0 but does not recover variants with swapped reference and alternative alleles. To recover variants with swapped reference/alternative alleles, we ran LiftoverVCF again, with the RECOVER_SWAPPED_REF_ALT flag. Notably, this feature does not recover multiallelic variants, so to recover these variants, we first separated them into multiple biallelic variants, performed liftover using the RECOVER_SWAPPED_REF_ALT tag, and converted them back to their multiallelic representations.
#+end_quote
***** KILL Liftovervcf avec valeur par défaut
CLOSED: [2023-07-02 Sun 23:09] SCHEDULED: <2023-06-30 Fri>
HG002 : il manque la moitié des valeurs
hg001
[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ less HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.lifted.vcf.gz
[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ zgrep -c '^chr' HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.lifted.vcf.gz
2168972
[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ zgrep -c '^chr' HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.unlifted.vcf.gz
1862374
[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ zgrep -c '^chr' HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
4031346
***** DONE liftover bed
CLOSED: [2023-07-02 Sun 23:09] SCHEDULED: <2023-06-30 Fri>
792 of 217488 intervals failed (0.364158%) to liftover, encompassing 219109 of 35718732 bases (0.613429%).
wc -l capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed
217488 capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed
wc -l work/e4/9981dc539a2373c2beeaa0affc3497/Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38.interval_list
On a donc perdu 1000 zones
***** DONE Liftovervcf avec variant échangé référence/alternative ?
CLOSED: [2023-07-02 Sun 23:09]
**** DONE NA12878 :na12878:hg38:
CLOSED: [2023-06-30 Fri 22:30]
***** DONE Discussion alexis : Mail
CLOSED: [2023-03-29 Wed 22:40]
Avec le patient NA12878 et comparaison avec hap.py du VCF de Genome In A Bottle ("gold" standard), on avait pour rappel
- sensibilité (=recall) 71% pour indel, 85% SNP
- précision (= VPP) 69 et 97% respectivement
| Type | TRUTH | TP | FN | QUERY | FP | UNK | FP.gt | FP.al | Recall | Precision |
| INDEL | 4871 | 3461 | 1410 | 7048 | 1554 | 1987 | 193 | 346 | 0.710532 | 0.692946 |
| SNP | 46032 | 39369 | 6663 | 44600 | 1186 | 4041 | 304 | 30 | 0.855253 | 0.970759 |
Les statistiques sur les génomes sont bien meilleurs (cf precisionFDA challenge).
Pour les exome, un article [1] a fait a des meilleures stats sur ce patient avec BWA et GATK mais ils ont moins de variant (on a presque un facteur 2 !).
Je soupçonne qu'on ne travaille pas sur les mêmes zones de capture (pas réussi à récupérer leur .bed)
| Exome | Type | TP | FP | FN | Sensitivity | Precision | F-Score | FDR |
| 1 | SNV | 23689 | 1397 | 613 | 0.975 | 0.944 | 0.959 | 0.057 |
| 2 | SNV | 23946 | 865 | 356 | 0.985 | 0.965 | 0.975 | 0.036 |
| 1 | indel | 1254 | 72 | 75 | 0.944 | 0.946 | 0.945 | 0.054 |
| 2 | indel | 1309 | 10 | 20 | 0.985 | 0.992 | 0.989 | 0.008 |
Pour essayer d'améliorer les statistiques :
- La version du génome GRC38 vs GRCh38.p13 ne change quasiment rien
- Désactiver dbSNP ne change strictement rien pour le variant calling
J'ai exploré les faux négatifs :
- la grande majorité n'est juste pas vue (ce n'est pas un problème d'haploïde/génotype)
- la répartition par chromosome est relativement homogène, sauf sur le 6 ()
- la majorité est en 5' et 3'UTR (selon Best refseq)
Conclusion: je pense m'arrêter là pour la validation du variant calling par manque de temps. Il faudrait creuser pour savoir pourquoi certains variants ne sont pas vus par GATK mais ce n'est pas la majorité. En tout cas, je peux justifier d'une première analyse pour la thèse.
Ça te va ?
[1]
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2928-9
Résultats ici https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-019-2928-9/MediaObjects/12859_2019_2928_MOESM8_ESM.pdf
***** DONE Comparaison
CLOSED: [2023-03-04 Sat 11:14]
HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna ./result/bin/hap.py /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1
_benchmark_renamed.vcf.gz script/files/vcf/NA12878_NIST7035_vep_annot.vcf -f /Work/Groups/bison
ex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.bed -o test
na1878.slurm
#+begin_src slurm
#!/bin/bash
#SBATCH -c 4
#SBATCH -p smp
#SBATCH --time=01:00:00
#SBATCH --mem=32G
module load nix/2.11.0
export HGREF=
|
| --create-output-variant-md5 false | --create-output-variant-md5 false |
| --max-variants-per-shard 0 | --max-variants-per-shard 0 |
| --lenient false | --lenient false |
| --add-output-sam-program-record true | --add-output-sam-program-record true |
| --add-output-vcf-command-line true | --add-output-vcf-command-line true |
| --cloud-prefetch-buffer 40 | --cloud-prefetch-buffer 40 |
| --cloud-index-prefetch-buffer -1 | --cloud-index-prefetch-buffer -1 |
| --disable-bam-index-caching false | --disable-bam-index-caching false |
| --sites-only-vcf-output false | --sites-only-vcf-output false |
| --help false | --help false |
| --version false | --version false |
| --showHidden false | --showHidden false |
| --QUIET false | --QUIET false |
| --use-jdk-deflater false | --use-jdk-deflater false |
| --use-jdk-inflater false | --use-jdk-inflater false |
| --gcs-max-retries 20 | --gcs-max-retries 20 |
| --gcs-project-for-requester-pays | --gcs-project-for-requester-pays |
| --disable-tool-default-read-filters false | --disable-tool-default-read-filters false |
| --minimum-mapping-quality 20 | --minimum-mapping-quality 20 |
| --disable-tool-default-annotations false | --disable-tool-default-annotations false |
| --enable-all-annotations false | --enable-all-annotations false |
| --allow-old-rms-mapping-quality-annotation-data false | --allow-old-rms-mapping-quality-annotation-data false" |
| ",Version="4.2.4.1" | Version="4.2.4.1", |
Prod helios
/Work/Users/apraga/bisonex/script/files/tmp_63003856_S135〉less 63003856_S135_DP_over_30.vcf
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller
,Date="January 10, 2023 at 12:26:57 AM CET">
******* DONE VCF : même différence
CLOSED: [2023-01-20 Fri 22:48]
/Work/Projects/bisonex/ref-63003856_S135〉ls *.vcf* | insert nblines {|e| (^zgrep -v '^#' $e.name | wc -l)} | select name nblines 01/14/2023 08:04:02 PM
╭───┬───────────────────────────────────────────────────────────────────────────┬─────────╮
│ # │ name │ nblines │
├───┼───────────────────────────────────────────────────────────────────────────┼─────────┤
│ 0 │ 63003856_S135_DP_over_30.vcf.gz │ 84708 │
│ 1 │ 63003856_S135_DP_over_30.vcf.gz.tbi │ 1 │
│ 2 │ 63003856_S135_DP_over_30_not_SNP.recode.vcf │ 11362 │
│ 3 │ 63003856_S135_DP_over_30_not_SNP_consensual_sequence.vcf │ 8864 │
│ 4 │ 63003856_S135_DP_over_30_not_SNP_consensual_sequence_not_technical.vcf.gz │ 6478 │
╰───┴───────────────────────────────────────────────────────────────────────────┴─────────╯
/Work/Users/apraga/bisonex/script/files/tmp_63003856_S135〉ls *.vcf* | insert nblines {|e| (^zgrep -v '^#' $e.name | wc -l)} | select name nblines 01/14/2023 08:05:23 PM
╭───┬───────────────────────────────────────────────────────────────────────────┬─────────╮
│ # │ name │ nblines │
├───┼───────────────────────────────────────────────────────────────────────────┼─────────┤
│ 0 │ 63003856_S135_DP_over_30.vcf │ 84724 │
│ 1 │ 63003856_S135_DP_over_30_not_SNP.recode.vcf │ 11377 │
│ 2 │ 63003856_S135_DP_over_30_not_SNP_consensual_sequence.vcf │ 8884 │
│ 3 │ 63003856_S135_DP_over_30_not_SNP_consensual_sequence_not_technical.vcf.gz │ 6759 │
╰───┴───────────────────────────────────────────────────────────────────────────┴─────────╯
***** KILL Relancer avec 4 coeurs
CLOSED: [2023-05-23 Tue 08:45]
-c 4
****** DONE Alignement ok !!
CLOSED: [2023-01-20 Fri 23:24]
$ samtools view -c files/tmp_63003856_S135/63003856_S135.bam
128077207
****** KILL Vérifier les flags de chaque étape
CLOSED: [2023-05-23 Tue 08:44]
post_cleanSam = _cleaned.bam
post_markDuplicate = _marked_dup.ba
/DP<=30' 63003856_S135.vcf.gz | bcftools filter -e 'FORMAT/AD[0:1]<=10' -o two-filters.vcf
$ grep '^NC' two-filters.vcf | wc -l
82054
***** DONE Tester bwa en séquentiel
CLOSED: [2023-01-07 Sat 00:05]
**** DONE (save) Version d'Alexis 24 threads, sans télécharger les bases de données, gatk 4.2.4.1
CLOSED: [2023-01-07 Sat 00:06]
***** Bwa mem 24 threads: comme la version test...
$ cd /Work/Users/apraga/bisonex/script/files/tmp_63003856_S135
$ samtools view -c 63003856_S135.bam
128077211
$ samtools view -c /Work/Groups/bisonex/ref_63003856_S135/63003856_S135.bam
128077207
En ne conservant que les mapped reads, minime différence
$ samtools view -c -F 260 /Work/Groups/bisonex/ref_63003856_S135/63003856_S135.bam
127941051
$ samtools view -c -F 260 files/tmp_63003856_S135/63003856_S135.bam
127941054
**** DONE Version prod à la maison
CLOSED: [2023-01-15 Sun 23:22]
preprocessing + variant calling sans alignement
***** DONE GATK nix
CLOSED: [2023-01-15 Sun 23:22]
❯ samtools view -c 63003856_S135_marked_dup.bam
128077211
On a le même nombre
***** DONE GATK compilé: idem
CLOSED: [2023-01-15 Sun 23:22]
script/files-src/tmp_63003856_S135 on prod [$!?]
❯ samtools view -c 63003856_S135_marked_dup.bam
128077211
Idem...
**** KILL GATK : tests de non régression ??
CLOSED: [2023-05-23 Tue 08:44]
**** DONE Compiler gatk: idem
CLOSED: [2023-01-19 Thu 22:03]
***** DONE Compilation
CLOSED: [2023-01-14 Sat 22:45]
Requirements :
- java8 avec jDK
- git lfs
#+begin_src sh
git clone https://github.com/broadinstitute/gatk
git checkout tags/4.2.4.0 -b 4.2.4.0
nix-shell -p jdk8 git-lfs
# We need the datasets for testing (otherwise it fails)
git lfs install
git lfs pull --include src/main/resources/large
./gradlew bundle
#+end_src
***** DONE Vérifier tests
CLOSED: [2023-01-19 Thu 22:03]
#+begin_src
./gradlew test
#+end_src
267064 tests completed, 444 failed, 1966 skipped
> There were failing tests. See the report at: file:///Home/Users/apraga/gatk/build/reports/tests/test/index.html
BUILD FAILED in 37m 1s
6 actionable tasks: 1 executed, 5 up-to-date
Ceux qui ont planté sont liés à spark + erreurs d'authentification kerberos
***** KILL Lancer calcul : maison
CLOSED: [2023-01-19 Thu 22:03]
JAVA_HOME=/nix/store/r1r5jr7gv6hcchpiggjmfqjkzbi8y5ja-openjdk-8u322-ga/lib/openjdk PATH=$PATH:$JAVA_HOME/bin ./gatk --version
**** KILL Comparer tsv à la sortie (Alexis)
CLOSED: [2023-05-23 Tue 08:44]
- diff
- Nombre de lignes
**** KILL Version de prod + nix sur Helios
CLOSED: [2023-05-23 Tue 08:45]
***** DONE 24 coeurs : idem
CLOSED: [2023-01-20 Fri 22:49]
****** DONE Preprocessing : idem
CLOSED: [2023-01-20 Fri 22:49]
******* DONE Alignement
CLOSED: [2023-01-19 Thu 22:28]
******** DONE Nombre lignes : idem
CLOSED: [2023-01-19 Thu 22:48]
/Work/Users/apraga/bisonex/script/files/tmp_63003856_S135〉samtools view -c 63003856_S135.bam 01/19/2023 10:16:19 PM
128077211
/Work/Projects/bisonex/ref-63003856_S135〉samtools view -c 63003856_S135.bam 01/19/2023 10:11:39 PM
128077207
******** DONE Bwa version ok, arguments ok
CLOSED: [2023-01-20 Fri 22:49]
/Work/Users/apraga/bisonex/script/files/tmp_63003856_S135〉samtools view -H 63003856_S135.bam | grep PN 01/19/2023 10:46:55 PM
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem -R @RG\tID:63003856_S135\tSM:63003856_S135\tPL:ILLUMINA\tPM:Miseq\tCN:CHU_Minjoz\tLB:definition_to_add -v 2 -t 24 /Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna files/fastq/63003856_S135_R1_001.fastq.gz files/fastq/63003856_S135_R2_001.fastq.gz
@PG ID:samtools PN:samtools PP:bwa VN:1.13 CL:samtools sort -@ 24 -O BAM -o files/tmp_63003856_S135/63003856_S135.bam
@PG ID:samtools.1 PN:samtools PP:samtools VN:1.13 CL:samtools view -H 63003856_S135.bam
/Work/Projects/bisonex/ref-63003856_S135〉samtools view -H 63003856_S135.bam | grep PN 01/19/2023 10:49:25 PM
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:/bin/bwa mem -R @RG\tID:63003856_S135\tSM:63003856_S135\tPL:ILLUMINA\tPM:Miseq\tCN:CHU_Minjoz\tLB:definition_to_add -t 4 /mnt/j/bases_de_donnees/genome/GRCh38_latest_genomic.fna /mnt/j/working_directory_pipeline_analyse_exome/fastq/2200467051_63003856/63003856_S135_R1_001.fastq.gz /mnt/j/working_directory_pipeline_analyse_exome/fastq/2200467051_63003856/63003856_S135_R2_001.fastq.gz
@PG ID:samtools PN:samtools PP:bwa VN:1.10 CL:/mnt/h/tools/samtools sort -@ 4 -O BAM -o /mnt/j/working_directory_pipeline_analyse_exome/tmp_63003856_S135/63003856_S135.bam
@PG ID:samtools.1 PN:samtools PP:samtools VN:1.13 CL:samtools view -H 63003856_S135.bam
******* KILL ApplyBQSR
CLOSED: [2023-01-20 Fri 22:48]
/Work/Users/apraga/bisonex/script/files/bam〉samtools view -c 63003856_S135_recalibrated_hg38.bam 01/19/2023 10:21:00 PM
128077211
??
****** DONE Variant calling
CLOSED: [2023-01-20 Fri 22:48]
******* DONE Re vérifier flags
CLOSED: [2023-01-19 Thu 22:44]
/Work/Projects/bisonex/ref-63003856_S135〉less 63003856_S135_DP_over_30.vcf.gz
##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller
| Ref | Prod helios |
|-------------------------------------------------------------------------------------------------+-----------------------------------------------------------------------------------------|
| --dbsnp /mnt/j/bases_de_donnees/dbSNP/GCF_000001405.39.gz | --dbsnp /Work/Groups/bisonex/data-alexis-reference/dbSNP/GCF_000001405.39.gz |
| --max-mnp-distance 2 | --max-mnp-distance 2 |
| --output /mnt/j/working_directory_pipeline_analyse_exome/vcf/63003856_S135.vcf | --output files/vcf/63003856_S135.vcf |
| --input /mnt/j/working_directory_pipeline_analyse_exome/bam/63003856_S135_recalibrated_hg38.bam | --input files/bam/63003856_S135_recalibrated_hg38.bam |
| --reference /mnt/j/bases_de_donnees/genome/GRCh38_latest_genomic.fna | --reference /Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna |
| --verbosity WARNING | --verbosity WARNING |
| --use-posteriors-to-calculate-qual false | --use-posteriors-to-calculate-qual false |
| --dont-use-dragstr-priors false | --dont-use-dragstr-priors false |
| --use-new-qual-calculator true | --use-new-qual-calculator true |
| --annotate-with-num-discovered-alleles false | --annotate-with-num-discovered-alleles false |
| --heterozygosity 0.001 | --heterozygosity 0.001 |
| --indel-heterozygosity 1.25E-4 | --indel-heterozygosity 1.25E-4 |
| --heterozygosity-stdev 0.01
ty |
| ------ | | | | | |
| NC_000020.11 | 33412656 | rs35938843 | C | G,T | |
| NC_000020.11 | 33412656 | 220958 | C | T | Conflicting_interpretations_of_pathogenicity |
| ------ | | | | | |
| NC_000020.11 | 45891622 | rs181943893 | G | A,C,T | |
| NC_000020.11 | 45891622 | 459632 | G | C | Conflicting_interpretations_of_pathogenicity |
| NC_000020.11 | 45891622 | 797035 | G | T | Likely_benign |
| NC_000020.11 | 45891622 | 1572689 | GCTA | G | Likely_benign |
| ------ | | | | | |
| NC_000020.11 | 54171651 | rs35873579 | G | A,T | |
| NC_000020.11 | 54171651 | 285894 | G | A | Conflicting_interpretations_of_pathogenicity |
| NC_000020.11 | 54171651 | 1373583 | G | C | Uncertain_significance |
| NC_000020.11 | 54171651 | 895614 | G | T | Benign/Likely_benign |
| ------ | | |
| 8 | 97 | 0.893816 | 0.996963 | 0.020633 | 0.942576 |
**** KILL Version avec rtg-tools
CLOSED: [2023-07-30 Sun 14:38]
**** HOLD Faire fonctionner Tests
***** HOLD Essai 2 : depuis nix develop:
#+begin_src
nix develop .#hap-py
genericBuild
#+end_src
Lancé initialement à la main, mais on peut maintenant utiliser run_tests
#+begin_src
HCDIR=bin/ ../src/sh/run_tests.sha
#+end_src
- [X] test boost
- [X] multimerge
- [X] hapenum
- [X] fp accuracy
- [X] faulty variant
- leftshift fails
- [X] other vcf
- [X] chr prefix
- [X] gvcf
- [X] decomp
- [X] contig lengt
- [X] integration test
- [ ] scmp fails sur le type
- [X] giab
- [X] performance
- [ ] quantify fails sur le type
- [ ] stratified échec sur les résultats !
- [X] pg counting
- [ ] sompy: ne trouve pas Strelka dans somatic
phases="buildPhase checkPhase installPhase fixupPhase" genericBuild
#+end_src
**** KILL Reproduire les performances precisionchallenge : attention à HG002 et HG001!
CLOSED: [2023-04-01 Sa
t 19:43]
https://www.nist.gov/programs-projects/genome-bottle
***** KILL 0GOOR
CLOSED: [2023-04-01 Sat 19:40]
Le problème venait 1. de l'ADN et 2. du renommage des chromosomes qui était faux
****** DONE HG002
CLOSED: [2023-02-17 Fri 19:31]
Type Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score
INDEL ALL 525466 491355 34111 1156702 57724 605307 9384 25027 0.935084 0.895313 0.523304 0.914766
INDEL PASS 525466 491355 34111 1156702 57724 605307 9384 25027 0.935084 0.895313 0.523304 0.914766
SNP ALL 3365115 3358399 6716 5666020 21995 2284364 4194 1125 0.998004 0.993496 0.403169 0.995745
SNP PASS 3365115 3358399 6716 5666020 21995 2284364 4194 1125 0.998004 0.993496 0.403169 0.995745
TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratio
NaN NaN 1.528276 2.752637
NaN NaN 1.528276 2.752637
2.100129 1.473519 1.581196 1.795603
2.100129 1.473519 1.581196 1.795603
***** KILL Avec python2
CLOSED: [2023-02-17 Fri 19:25]
****** KILL avec nix
CLOSED: [2023-02-17 Fri 19:25]
conda create -n python2 python=2.7 anaconda
****** KILL avec conda
CLOSED: [2023-02-17 Fri 19:25]
******* Gentoo: regex_error sur test...
Ok avec bash !
#+begin_src
anaconda3/bin/conda create --name py2 python=2.7
conda activate py2
conda install -c bioconda hap.py
#+end_src
******** Faire tou
|
| NM_000249:c.589-10T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37012001 | substitution | T>A | Intron 7 | 148 | NM_000249 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0No | 10 | 37012002 | Acc | 0.009529819 | No | Acc | 37012010 | -9 | 0 | 0 | No | 37012010 | 0.028437574 | No | 0.000009275960 | No | |
| NM_000249:c.791-7T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37017499 | substitution | T>A | Intron 9 | 2961 | NM_000249 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0No | 10 | 37017500 | Acc | 0.015564917 | No | Acc | 37017505 | -6 | 0 | 0 | No | 37017505 | 0.023995855 | No | 0.000022606476 | No | |
Test sur mobidetails : 98% pour spip (! différent du fichier excel...)
Second variant: ok en VCf également
***** DONE Lifter les variants T2T : ok ! mais multiples trnascrits en génomique ...
CLOSED: [2023-08-09 Wed 23:23] SCHEDULED
: <2023-08-09 Wed>
##fileformat=VCFv4.0
##assembly=GRCh38/hg38
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
#CHROM POS ID REF ALT QUAL FILTER INFO
chr11 108264994 lol T G . . .
chr17 32146124 lol T A . . .
chr3 31588185 lol T G . . .
chr3 37013346 lol T A . . .
chr3 37018844 lol T A . . .
❯ ./result/bin/spip -I test-spip-T2T.vcf -O test-spip-T2T.out -g hs1 --refseq dataRefSeqhs1.RData --transcriptome transcriptome_hs1.RData
#+RESULTS:
| CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | varID | Interpretation | InterConfident | SPiPscore | strand | gNomen | varType | ntChange | ExonInfo | exonSize | transcript | gene | NearestSS | DistSS | RegType | SPiCEproba | SPiCEinter_2thr | deltaMES | BP | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut | probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT | probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut |
| chr11 | 108264994 | lol | T | G | . | . | . | NM_000051:g.108264994:T>G | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.986 | + | 108264994 | substitution | T>G | Intron 14 | 1140 | NM_000051 | ATM | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 108264994 | Acc | 0.02483600258856 | No | Acc | 108265003 | -10 | 0 | 0.00000000000000 | No | 108265003 | 0.006489079 | No | 0.000004368542 | No |
| chr11 | 108264994 | lol | T | G | . | . | . | NM_001351834:g.108264994:T>G | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.986 | + | 108264994 | substitution | T>G | Intron 15 | 1140 | NM_001351834 | ATM | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 108264994 | Acc | 0.02483600258856 | No | Acc | 108265003 | -10 | 0 | 0.00000000000000 | No | 108265003 | 0.006489079 | No | 0.000004368542 | No |
| chr17 | 32146124 | lol | T | A | . | . | . | NM_000267:g.32146124:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 1.000 | + | 32146124 | substitution | T>A | Intron 8 | 17755 | NM_000267 | NF1 | acceptor | -12 | IntronCons | 1 | high | 0 | 0 | No | 10 | 32146125 | Acc | 0.00908289924996 | No | Acc | 32146135 | -11 | 0 | 0.00000000000000 | No | 32146135 | 0.005160854 | No | 0.000003718518 | No |
| chr17 | 32146124 | lol | T | A | . | . | . | NM_001128147:g.32146124:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 1.000 | + | 32146124 | substitution | T>A | Intron 8 | 17755 | NM_001128147 | NF1 | acceptor | -12 | IntronCons | 1 | high | 0 | 0 | No | 10 | 32146125 | Acc | 0.00908289924996 | No | Acc | 32146135 | -11 | 0 | 0.00000000000000 | No | 32146135 | 0.005160854 | No | 0.000003718518 | No |
| chr17 | 32146124 | lol | T | A | . | . | . | NM_001042492:g.32146124:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 1.000 | + | 32146124 | substitution | T>A | Intron 8 | 17755 | NM_001042492 | NF1 | acceptor | -12 | IntronCons | 1 | high | 0 | 0 | No | 10 | 32146125 | Acc | 0.00908289924996 | No | Acc | 32146135 | -11 | 0 | 0.00000000000000 | No | 32146135 | 0.005160854 | No | 0.000003718518 | No |
| chr3 | 31588185 | lol | T | G | . | . | . | NM_178862:g.31588185:T>G | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 31588185 | substitution | T>G | Intron 3 | 16710 | NM_178862 | STT3B | donor | 5663 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 31588184 | Don | 0.00000002308527 | No | Don | 31582522 | 5662 | 31588181 | 0.00000000129731 | No | 31582522 | 0.071835522 | Yes | 0.071835521718 | Yes |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_000249:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_000249 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001167617:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001167617 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001167618:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001167618 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001167619:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001167619 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001258271:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001258271 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001258273:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001258273 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001258274:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 8 | 148 | NM_001258274 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354615:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354615 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354616:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354616 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354617:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354617 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354618:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354618 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354619:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 8 | 148 | NM_001354619 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354620:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354620 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354621:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354621 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354622:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354622 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354623:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354623 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354624:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354624 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354625:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354625 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354626:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354626 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354627:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354627 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354628:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354628 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354629:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354629 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354630:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354630 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_000249:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_000249 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001167617:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001167617 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001167618:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001167618 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001167619:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001167619 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001258271:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001258271 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001258273:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001258273 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001258274:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 10 | 2961 | NM_001258274 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354615:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001354615 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354616:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001354616 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354617:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354617 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354618:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354618 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354619:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 10 | 2961 | NM_001354619 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354620:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354620 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354621:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 8 | 8209 | NM_001354621 | MLH1 | acceptor | -2810 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37021653 | -2809 | 37018850 | 0.02399585516738 | No | 37021653 | 0.241893494 | Yes | 0.241893494461 | Yes |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354622:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 9 | 5764 | NM_001354622 | MLH1 | acceptor | -2810 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37021653 | -2809 | 37018850 | 0.02399585516738 | No | 37021653 | 0.241893494 | Yes | 0.241893494461 | Yes |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354623:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 8 | 5764 | NM_001354623 | MLH1 | acceptor | -2810 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37021653 | -2809 | 37018850 | 0.02399585516738 | No | 37021653 | 0.241893494 | Yes | 0.241893494461 | Yes |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354624:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 9 | 11091 | NM_001354624 | MLH1 | donor | 2955 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Don | 37015889 | 2956 | 37018850 | 0.02399585516738 | No | 37026980 | 0.028353019 | No | 0.028353019047 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354625:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 8 | 11091 | NM_001354625 | MLH1 | donor | 2955 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Don | 37015889 | 2956 | 37018850 | 0.02399585516738 | No | 37026980 | 0.028353019 | No | 0.028353019047 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354626:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 9 | 11091 | NM_001354626 | MLH1 | donor | 2955 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Don | 37015889 | 2956 | 37018850 | 0.02399585516738 | No | 37026980 | 0.028353019 | No | 0.028353019047 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354627:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 9 | 11091 | NM_001354627 | MLH1 | donor | 2955 | DeepIntron | 0 | Outside SPiCE Interpretation |
0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Don | 37015889 | 2956 | 37018850 | 0.02399585516738 | No | 37026980 | 0.028353019 | No | 0.028353019047 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354628:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354628 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354629:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001354629 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354630:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354630 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
**** DONE 1 variant avec score = 38% (mobidetails)
CLOSED: [2023-08-10 Thu 23:16]
chr10:g.89010760A>G
Avec
#+begin_src sh
varID
NM_000043.4:c.513A>G
#+end_src
On a bien 35.81%
| varID | Interpretation | InterConfident | SPiPscore | strand | gNomen | varType | ntChange | ExonInfo | exonSize | transcript | gene | NearestSS | DistSS | RegType | SPiCEproba | SPiCEinter_2thr | deltaMES | BP | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut | probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT | probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut |
| NM_000043.4:c.513A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89010760 | substitution | A>G | Exon 6 | 63 | NM_000043 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 00 | No | -1.67753 | 89010759 | Acc | 0.0000003317384 | No | Acc | 89010752 | 7 | 89010759 | 0.0000002205815 | No | 89010752 | 0.02545572 | No | 0.02545572 | No | |
Avec les coordonnées génomiques en hg38, on ne retrouve pas le transcrit (non visible sur UCSCS...) parmi les nombreux transcrit.
Mais en T2T oui !
##fileformat=VCFv4.0
##assembly=CHM18v2.0/hs1
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
#CHROM POS ID REF ALT QUAL FILTER INFO
chr10 89894645 lol A G . . .
❯ ./result/bin/spip -I test-spip-T2T.vcf -O test-spip-T2T.out -g hs1 --refseq dataRefSeqhs1.RData --transcriptome transcriptome_hs1.RData
| CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | varID | Interpretation | InterConfident | SPiPscore | strand | gNomen | varType | ntChange | ExonInfo | exonSize | transcript | gene | NearestSS | DistSSRegType | SPiCEproba | SPiCEinter_2thr | deltaMES | BP | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut | probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT | probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut | |
| chr10 | 89894645 | lol | A | G | . | . | . | NM_000043:g.89894645:A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89894645 | substitution | A>G | Exon 6 | 63 | NM_000043 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 0 | 0 | No | -1.67753 | 89894644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| chr10 | 89894645 | lol | A | G | . | . | . | NM_001320619:g.89894645:A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89894645 | substitution | A>G | Exon 6 | 63 | NM_001320619 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 0 | 0 | No | -1.67753 | 89894644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| chr10 | 89894645 | lol | A | G | . | . | . | NM_152871:g.89894645:A>G | NTR | 00 % [00 % - 00
.92 %] | 0.000 | + | 89894645 | substitution | A>G | Intron 5 | 1398 | NM_152871 | FAS | donor | 160 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10.00000 | 89894644 | Don | 0.0001360257829 | No | Don | 89894485 | 159 | 0 | 0.0000000000000 | No | 89894485 | 0.07177992 | Yes | 0.07177992 | Yes |
| chr10 | 89894645 | lol | A | G | . | . | . | NM_152872:g.89894645:A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89894645 | substitution | A>G | Exon 6 | 63 | NM_152872 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 0 | 0 | No | -1.67753 | 89894644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| chr10 | 89894645 | lol | A | G | . | . | . | NR_028033:g.89894645:A>G | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 89894645 | substitution | A>G | Intron 4 | 1398 | NR_028033 | FAS | donor | 160 | De
delta_scores
y_ref = np.mean([ann.models[m].predict(x_ref) for m in range(5)], axis=0)
File "/Home/Users/apraga/.local/lib/python3.9/site-packages/spliceai/utils.p
y", line 159, in <listcomp>
y_ref = np.mean([ann.models[m].predict(x_ref) for m in range(5)], axis=0)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler
return fn(*args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/training.py", line 2382, in predict
tmp_batch_outputs = self.predict_function(iterator)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/training.py", line 2169, in predict_function
return step_function(self, iterator)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/training.py", line 2155, in step_function
outputs = model.distribute_strategy.run(run_step, args=(data,))
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/training.py", line 2143, in run_step
outputs = model.predict_step(data)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/training.py", line 2111, in predict_step
return self(x, training=False)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler
return fn(*args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/training.py", line 558, in __call__
return super().__call__(*args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler
return fn(*args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/base_layer.py", line 1145, in __call__
outputs = call_fn(inputs, *args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler
return fn(*args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/functional.py", line 512, in call
return self._run_internal_graph(inputs, training=training, mask=mask)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/functional.py", line 669, in _run_internal_graph
outputs = node.layer(*args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/utils/traceback_utils.py", line 65, in error_handler
return fn(*args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/engine/base_layer.py", line 1145, in __call__
outputs = call_fn(inputs, *args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/utils/traceback_utils.py", line 96, in error_handler
return fn(*args, **kwargs)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/layers/convolutional/base_conv.py", line 290, in call
outputs = self.convolution_op(inputs, self.kernel)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/layers/convolutional/base_conv.py", line 262, in convolution_op
return tf.nn.convolution(
Node: 'model_1/conv1d_3/Conv1D'
DNN library is not found.
[[{{node model_1/conv1d_3/Conv1D}}]] [Op:__inference_predict_function_22195]
#+end_quote
***** DONE GPU: chr20 ok
CLOSED: [2023-09-26 Tue 11:50]
LD_PRELOAD=/lib64/libcuda.so spliceai -I NA12878-sanger-20-2-T2T.vep.vcf.gz -O output-20-2-gpu.vcf -R /Work/Groups/bisonex/data/fasta/chm13v2.0/chm13v2.0.fa -A ~/t2t.txt
temps d'exécution : 5min
***** DONE GPU: toutes les données :GPU:spliceai:
CLOSED: [2023-09-28 Thu 01:34]
****** DONE Run : 70GB, 3h30
CLOSED: [2023-09-27 Wed 10:37] SCHEDULED: <2023-09-26 Tue>
32G insufissant ! Il faut 70GB :
Job ID: 17340
Cluster: mesoubfc
User/Group: apraga/mesousers
State: COMPLETED (exit code 0)
Cores: 1
CPU Utilized: 03:11:53
CPU Efficiency: 93.55% of 03:25:07 core-walltime
Job Wall-clock time: 03:25:07
Memory Utilized: 67.75 GB
Memory Efficiency: 52.93% of 128.00 GB
#+begin_src slurm
#!/bin/bash -l
# Fichier submission.SBATCH
#SBATCH --job-name="spliceai-gpu"
#SBATCH --output=%x.%J.out ## %x=nom_du_job, %J=id du job
#SBATCH --error=%x.%J.out
# walltime (hh:mm::ss) max is 8 days
#SBATCH -t 24:00:00
#SBATCH --partition=gpu
#SBATCH --gres=gpu:1
## To request more memory, use --mem option.
## Please don't use more than 128g.
#SBATCH --mem=64G
## votre dresse mail pour les notifs
#SBATCH --mail-user=apraga@chu-besancon.fr
#SBATCH --mail-type=END,FAIL
nvidia-smi
module purge
module load nix/2.11.0
LD_PRELOAD=/lib64/libcuda.so spliceai -I NA12878-sanger-all-T2T.vep.vcf.gz -O output-all-gpu.vcf -R /Work/Groups/bisonex/data/fasta/chm13v2.0/chm13v2.0.fa -A ~/t2t.txt
#+end_src
****** DONE Annoter la sortie de VEP avec ce VCF
CLOSED: [2023-09-28 Thu 01:32]
Problème: SpliceAI est dans un INFO différent et donc pas avec les transcrits. filter_vep ne semble pas gérer ce cas.
On doit donc fusionner : le plus simple est de le convertir en fichier d'annotation et d'utiliser vep (comme pour Spip )
Générer un fichier d'annotation
#+begin_src
bcftools annotate -x INFO/CSQ output-all-gpu.vcf -o spliceai.vcf.gz
bcftools index spliceai.vcf.gz
#+end_src
Annoter avec vep
#+begin_src sh
ln -s /Work/Projects/bisonex/data/fasta/chm13v2.0/chm13v2.0.fa .
ln -s /Work/Projects/bisonex/data/fasta/chm13v2.0/chm13v2.0.fa.fai .
ln -s /Work/Projects/bisonex/data/vep/chm13v2.0/106 .
ln -s /Work/Projects/bisonex/data/clinvar/chm13v2.0/clinvar.vcf.gz .
ln -s /Work/Projects/bisonex/data/clinvar/chm13v2.0/clinvar.vcf.gz.tbi .
#+end_src
Essai 1: on coupe le fichier en 2 pour utiliser le plugin spliceai
filter -i 'POS<15000' spliceai.vcf.gz -o spliceai1.vcf.gz
bcftools filter -i 'POS>=15000' spliceai.vcf.gz -o spliceai2.vcf.gz
vep -i output-all-gpu.vcf -o output-all-gpu-annotated.vcf.gz --appris --biotype --canonical --ccds --compress_output bgzip --domains --exclude_predicted --flag_pick --hgvs --hgvsg --gene_phenotype --numbers --mane --protein --offline --uniprot --symbol --tsl --use_given_ref --variant_class --vcf --plugin NMD --custom clinvar.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN --plugin SpliceAI,snv=spliceai1.vcf.gz,indel=spliceai2.vcf.gz --fasta chm13v2.0.fa --assembly T2T-CHM13v2.0 --species homo_sapiens_gca009914755v4/ --cache --cache_version 106 --dir_cache 106
test
filter_vep -i output-all-gpu-annotated.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA) or (SpliceAI_pred_DS_AG and SpliceAI_pred_DS_AG >= 0.2) or (SpliceAI_pred_DS_AL and SpliceAI_pred_DS_AL >= 0.2) or (SpliceAI_pred_DS_DG and SpliceAI_pred_DS_DG >= 0.2) or (SpliceAI_pred_DS_DL and SpliceAI_pred_DS_DL >= 0.2) " --only_matched -o output-all-gpu-filtered.vcf.gz
Méthode un peu sale car on a des "." dans l'annotation spliceai
****** KILL Save
CLOSED:
1 Thu 10:38] SCHEDULED: <2023-08-29 Tue>
**** DONE Grantham
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-30 Wed>
**** DONE Corriger spliceAI
CLOSED: [2023-08-31 Thu 13:51] SCHEDULED: <2023-08-31 Thu>
Pas d'annotation
- chromosome ? essai 1 au lieu de chr1 : idem. Et fonctionne pour CADD
- index ?
- retélécharger
- indexer nous-meme
**** DONE Supprimer score spip en double
CLOSED: [2023-08-31 Thu 14:17] SCHEDULED: <2023-08-31 Thu>
**** DONE Vérifier variant 63126867
CLOSED: [2023-08-31 Thu 10:52] SCHEDULED: <2023-08-31 Thu>
**** DONE Ajouter tronquant ou non
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-31 Thu>
**** DONE Ajouter récessif
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-31 Thu>
**** KILL Corriger allelic depth
CLOSED: [2023-08-31 Thu 11:18] SCHEDULED: <2023-08-31 Thu>
Problème lié à libre office
**** DONE Regénérer annotation pour na12878, inserted et patient PEX1
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-31 Thu>
**** TODO ACMG incidental
**** DONE Sortie VCF (pour avoir la fraction allélique AF)
CLOSED: [2023-08-28 Mon 17:22]
**** DONE VCF -> tsv avec bcftools
CLOSED: [2023-08-29 Tue 11:03] SCHEDULED: <2023-08-28 Mon>
**** DONE Un seul transcrit après VEP avec filter_vep :filter:
CLOSED: [2023-08-29 Tue 11:03] SCHEDULED: <2023-08-28 Mon>
Avec mise à jour VEP 110, pick_flag semble fonctionner.
***** DONE Test chr20: Pas de variant "perdus"
CLOSED: [2023-08-28 Mon 17:31] SCHEDULED: <2023-08-28 Mon>
contrairement au résultat communiqué à alexis par mail
#+begin_src sh :dir out/annotate
bcftools +counts vep/NA12878-sanger-chr20-GRCh38/NA12878-sanger-chr20-GRCh38.vep.vcf.gz
#+end_src
Number of samples: 1
Number of SNPs: 123
Number of INDELs: 32
Number of MNPs: 53
Number of others: 0
Number of sites: 208
#+begin_src sh
filter_vep -i vep/NA12878-sanger-chr20-GRCh38/NA12878-sanger-chr20-GRCh38.vep.vcf.gz --filter 'PICK' | bcftools +counts
#+end_src
Number of samples: 1
Number of SNPs: 123
Number of INDELs: 32
Number of MNPs: 53
Number of others: 0
Number of sites: 208
2nd vérification
#+begin_src sh :dir out/annotate
f
ilter_vep -i vep/NA12878-sanger-chr20-GRCh38/NA12878-sanger-chr20-GRCh38.vep.vcf.gz --filter 'PICK' --soft_filter | grep fail
#+end_src
***** DONE Test NA12878 + variants sanger : variants perdus avec --pick ?
CLOSED: [2023-08-29 Tue 10:36] SCHEDULED: <2023-08-28 Mon>
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/out/annotate
~/.nix-profile/bin/bcftools +counts vep/NA12878-sanger-all-GRCh38/NA12878-sanger-all-GRCh38.vep.vcf.gz
#+end_src
#+RESULTS:
| Number | of | samples: | 1 |
| Number | of | SNPs: | 6293 |
| Number | of | INDELs: | 1515 |
| Number | of | MNPs: | 1588 |
| Number | of | others: | 0 |
| Number | of | sites: | 9322 |
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/out/annotate
~/.nix-profile/bin/filter_vep -i vep/NA12878-sanger-all-GRCh38/NA12878-sanger-all-GRCh38.vep.vcf.gz --filter 'PICK' | bcftools +counts
#+end_src
| Number | of | samples: | 1 |
| Number | of | SNPs: | 6293 |
| Number | of | INDELs: | 1515 |
| Number | of | MNPs: | 1588 |
| Number | of | others: | 0 |
| Number | of | sites: | 9322 |
***** DONE Test NA12878 + variants sanger: vérifier sortie avec julia : ok
CLOSED: [2023-08-29 Tue 10:21] SCHEDULED: <2023-08-28 Mon>
143 variants/146 comme avant
***** DONE Relancer en T2T pour vérifier compatibilité :T2T:
CLOSED: [2023-08-29 Tue 11:03] SCHEDULED: <2023-08-29 Tue>
**** DONE Repasser les tests sanger sur NA12878
CLOSED: [2023-09-01 Fri 10:32] SCHEDULED: <2023-08-31 Thu>
2 variants manquants après filter vep
**** DONE Choisir le meilleur transcript nous-meme
CLOSED: [2023-09-01 Fri 10:32] SCHEDULED: <2023-09-01 Fri>
**** DONE Vérifier T2T passe
CLOSED: [2023-08-31 Thu 22:10] SCHEDULED: <2023-08-31 Thu>
**** DONE Revoir choix du transcrit + filtre avec paul
CLOSED: [2023-09-08 Fri 22:46] SCHEDULED: <2023-09-06 Wed>
**** DONE Filtrer les variants selon les filtres d'Alexis et garder tous les résultat
CLOSED: [2023-09-10 Sun 15:39] SCHEDULED: <2023-09-09 Sat>
**** DONE Ajout colonne MANE SELECT et garder les autres
CLOSED: [2023-09-10 Sun 15:39] SCHEDULED: <2023-09-09 Sat>
**** DONE v1.0
CLOSED: [2023-09-11 Mon 19:11] SCHEDULED: <2023-09-09 Sat>
***** DONE Branche prod
CLOSED: [2023-09-10 Sun 15:44] SCHEDULED: <2023-09-09 Sat>
Merge depuis debug
***** DONE Mail alexis
CLOSED: [2023-09-01 Fri 10:32] SCHEDULED: <2023-08-31 Thu>
***** DONE Relancer test sanger
CLOSED: [2023-09-11 Mon 19:11] SCHEDULED: <2023-09-10 Sun>
***** DONE Mail Paul pour validation
CLOSED: [2023-09-11 Mon 19:11] SCHEDULED: <2023-09-10 Sun>
**** DONE Utiliser spliceAI >= 0.2 pour filtre au lieu de spip
CLOSED: [2023-09-11 Mon 21:48] SCHEDULED: <2023-09-11 Mon>
**** DONE Repasser tests sanger avec spliceAI
CLOSED: [2023-09-14 Thu 22:45] SCHEDULED: <2023-09-11 Mon>
**** DONE Corriger colonne récessive
CLOSED: [2023-09-14 Thu 22:57] SCHEDULED: <2023-09-14 Thu>
soit 1/1, soit 1/2
soit 0/1 avec 2 variants par gene
*** KILL Comparer les annotations sur 63003856
CLOSED: [2023-08-28 Mon 17:28]
**** Relancer le nouveau pipeline
*** KILL Ancienne version
CLOSED: [2023-08-28 Mon 17:24]
**** KILL HGVS
CLOSED: [2023-08-28 Mon 17:24]
**** KILL Filtrer après VEP
CLOSED: [2023-08-28 Mon 17:24]
**** KILL OMIM
CLOSED: [2023-08-28 Mon 17:24]
**** KILL clinvar
CLOSED: [2023-08-28 Mon 17:24]
**** KILL ACMG incidental
CLOSED: [2023-08-28 Mon 17:24]
**** KILL Grantham
CLOSED: [2023-08-28 Mon 17:24]
**** KILL LRG
CLOSED: [2023-04-18 mar. 17:22] SCHEDULED: <2023-04-18 Tue>
Vu avec alexis, n’est plus à jour
**** KILL Gnomad
CLOSED: [2023-08-28 Mon 17:24]
*** DONE Réordonner les colonnes :annotation:
CLOSED: [2023-08-31 Thu 10:38] SCHEDULED: <2023-08-28 Mon>
Pas d'OMIM, pas de CADD, pas de spliceAI
*** DONE Ajouter gnomAD v3 :gnomadv3:
CLOSED: [2023-10-01 Sun 15:34] SCHEDULED: <2023-09-29 Fri>
/Entered on/ [2023-09-29 Fri 22:38]
Après discussion avec Mathieu sur le problème de certaines régions corrigées dans la v3 !
VEP utilise la v2 pour les exomes et v3 pour génomes
Il manquera pour les patients 1-107
On ne l'a pas dans la sortie de VEP jusque là
**** DONE Test sur 1 patient
CLOSED: [2023-09-30 Sat 23:54] SCHEDULED: <2023-09-29 Fri>
**** DONE Reprendre run batch
CLOSED: [2023-10-01 Sun 15:34]
** DONE Porter exactement la version d'Alexis sur Helios
CLOSED: [2023-01-14 Sat 17:56]
Branche "prod"
** KILL Tester version d'alexis avec Nix
CLOSED: [2023-06-14 Wed 22:37]
*** DONE Ajouter clinvar
CLOSED: [2022-11-13 Sun 19:37]
*** DONE Alignement
CLOSED: [2022-11-13 Sun 12:52]
*** DONE Haplotype caller
CLOSED: [2022-11-13 Sun 13:00]
*** KILL Filter
CLOSED: [2023-06-14 Wed 22:37]
- [X] depth
- [ ] comon snp not path
Problème avec liste des ID
**** KILL variant annotation
CLOSED: [2023-06-14 Wed 22:37]
Besoin de vep
*** KILL Variant calling
CLOSED: [2023-06-14 Wed 22:37]
** KILL Tester sarek
CLOSED: [2023-08-12 Sat 15:53]
#+begin_src sh
module load apptainer/1.1.8
nextflow run nf-core/sarek -profile test,singularity --outdir test-sarek
#+end_src
Les dépendences ne se téléchargent pas correctement, on les extrait à la main
#+begin_src sh
rg -IN galaxyproject modules | sed 's/ //g;s/:$//' | sort | uniq > deps.txt
#+end_src
Nettoyage à la main
Puis
#+begin_src sh
cat deps.txt | xargs -L1 singularity pull
#+end_src
** DONE Support pour samplesheet
CLOSED: [2023-08-03 Thu 14:24] SCHEDULED: <2023-08-03 Thu 13:00>
/Entered on/ [2023-08-03 Thu 13:12]
** DONE Petit jeu de données : chr22 sur HG001
CLOSED: [2023-08-05 Sat 14:21] SCHEDULED: <2023-08-05 Sat>
** DONE Corriger OMIM annotation: manquant pour NMNAT1
CLOSED: [2023-09-16 Sat 22:47] SCHEDULED: <2023-09-16 Sat>
/Entered on/ [2023-09-16 Sat 19:32]
** PROJ Regarder la profondeur des variants rendus
/Entered on/ [2023-10-05 Thu 21:44]
* Documentation
:PROPERTIES:
:CATEGORY: doc
:END:
** DONE Procédure d'installation nix + dependences pour VM CHU
CLOSED: [2023-04-22 Sat 15:27] SCHEDULED: <2023-04-13 Thu>
* Bibliographie
** DONE Finir[cite:@alser2021]
CLOSED: [2023-09-26 Tue 11:26] SCHEDULED: <2023-09-22 Fri>
* Manuscript
:PROPERTIES:
:CATEGORY: manuscript
:END:
** DONE Flowchart pipeline (avec T2T)
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** Aligneur
*** DONE Figure: nombre de publication par aligneur
CLOSED: [2023-09-19 Tue 16:54] SCHEDULED: <2023-09-19 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
*** DONE Biblio performance aligneur <(biblio aligneur)> <(aligneur)>
CLOSED: [2023-10-13 Fri 17:40] SCHEDULED: <2023-10-01 Sun>
*** DONE Figure: nombre d'articles citant les principaux aligneur par année
CLOSED: [2023-10-11 Wed 23:54] SCHEDULED: <2023-10-03 Tue>
Il faudrait utiliser pubmed en local, sinon c'est 10 000 requete par aligner !
*** DONE Figure: nombre d'articles citant les principaux aligneur
CLOSED: [2023-10-12 Thu 23:58] SCHEDULED: <2023-10-12 Thu>
Il faudrait utiliser pubmed en local, sinon c'est 10 000 requete par aligner !
On se base sur
** DONE Appel de variant
CLOSED: [2023-12-14 Thu 23:25]
*** DONE Biblio <(biblio appel variant)> <(appel variant)>
CLOSED: [2023-11-25 Sat 23:29] SCHEDULED: <2023-11-25 Sat 11:00>
*** DONE Finir biblio avec comparatifs [0/3]
CLOSED: [2023-12-14 Thu 23:24] SCHEDULED: <2023-11-26 Sun 13:00>
*** KILL Figure: nombre de publication par appel de variant
CLOSED: [2023-11-25 Sat 19:00] SCHEDULED: <2023-11-07 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
Impossible d'utiliser pubmed car certains sont sur arxiv
** TODO Genome
SCHEDULED: <2023-12-14 Thu>
** TODO Figure: nombre d'exomes par années
SCHEDULED: <2023-12-23 Sat>
/Entered on/ [2023-09-19 Tue 08:43]
* Tests :tests:
** KILL Non régression : version prod
CLOSED: [2023-05-23 Tue 08:46]
*** DONE ID common snp
CLOSED: [2022-11-19 Sat 21:36]
#+begin_src
$ wc -l ID_of_common_snp.txt
23194290 ID_of_common_snp.txt
$ wc -l /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
23194290 /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
#+end_src
*** DONE ID common snp not clinvar patho
CLOSED: [2022-12-11 Sun 20:11]
**** DONE Vérification du problème
CLOSED: [2022-12-11 Sun 16:30]
Sur le J:
21155134 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref
Version de "non-régression"
21155076 database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt
Nouvelle version
23193391 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt
Si on enlève les doublons
$ sort database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | uniq > old.txt
$ wc -l old.txt
21107097 old.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt | uniq > new.txt
$ wc -l new.txt
21174578 new.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref | uniq > ref.txt
$ wc -l ref.txt
21107155 ref.txt
Si on regarde la différence
comm -23 ref.txt old.txt
rs1052692
rs1057518973
rs1057518973
rs11074121
rs112848754
rs12573787
rs145033890
rs147889095
rs1553904159
rs1560294695
rs1560296615
rs1560310926
rs1560325547
rs1560342418
rs1560356225
rs1578287542
...
On cherche le premier
bcftools query -i 'ID="rs1052692"' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 1619351 C A,T
Il est bien patho...
$ bcftools query -i 'POS=1619351' database/clinvar/clinvar.vcf.gz -f '%CHROM %POS %REF %ALT %INFO/CLNSIG\n'
19 1619351 C T Conflicting_interpretations_of_pathogenicity
On vérifie pour tous les autres
$ comm -23 ref.txt old.txt > tocheck.txt
On génère les régions à vérifier (chromosome number:position)
$ bcftools query -i 'ID=@tocheck.txt' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM\t%POS\n' > tocheck.pos
On génère le mapping inverse (chromosome number -> NC)
$ awk ' { t = $1; $1 = $2; $2 = t; print; } ' database/RefSeq/refseq_to_number_only_consensual.txt > mapping.txt
On remap clinvar
$ bcftools annotate --rename-chrs mapping.txt database/clinvar/clinvar.vcf.gz -o clinvar_remapped.vcf.gz
$ tabix clinvar_remapped.vcf.gz
Enfin, on cherche dans clinvar la classification
$ bcftools query -R tocheck.pos clinvar_remapped.vcf.gz -f '%CHROM %POS %INFO/CLNSIG\n'
$ bcftools query -R tocheck.pos database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %ID \n' | grep '^NC'
#+RESULTS:
**** DONE Comprendre pourquoi la nouvelle version donne un résultat différent
CLOSED: [2022-12-11 Sun 20:11]
***** DONE Même version dbsnp et clinvar ?
CLOSED: [2022-12-10 Sat 23:02]
Clinvar différent !
$ bcftools stats clinvar.gz
clinvar (Alexis)
SN 0 number of samples: 0
SN 0 number of records: 1492828
SN 0 number of no-ALTs: 965
SN 0 number of SNPs: 1338007
SN 0 number of MNPs: 5562
SN 0 number of indels: 144580
SN 0 number of others: 3714
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0
clinvar (new)
SN 0 number of samples: 0
SN 0 number of records: 1493470
SN 0 number of no-ALTs: 965
SN 0 number of SNPs: 1338561
SN 0 number of MNPs: 5565
SN 0 number of indels: 144663
SN 0 number of others: 3716
SN 0 number of multiallelic sites: 0
SN 0 number of multiallelic SNP sites: 0
***** DONE Mettre à jour clinvar et dbnSNP pour travailler sur les mêm bases
CLOSED: [2022-12-11 Sun 12:10]
Problème persiste
***** DONE Supprimer la conversion en int du chromosome
CLOSED: [2022-12-10 Sat 19:29]
***** KILL Même NC ?
CLOSED: [2022-12-10 Sat 19:29]
$ zgrep "contig=<ID=NC_\(.*\)" clinvar/GRCh38/clinvar.vcf.gz > contig.clinvar
$ diff contig.txt contig.clinvar
< ##contig=<ID=NC_012920.1>
***** DONE Tester sur chromosome 19: ok
CLOSED: [2022-12-11 Sun 13:53]
On prépare les données
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -o dbSNP_common_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar.vcf.gz -o clinvar_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data-alexis/dbSNP/dbSNP_common.vcf.gz -o dbSNP_common_19_old.vcf.gz
bcftools filter -i 'CHROM="19"' /Work/Groups/bisonex/data-alexis/clinvar/clinvar.vcf.gz -o clinvar_19_old.vcf.gz
#+end_src
On récupère les 2 versions du script
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
git checkout regression ../../script/pythonScript/clinvar_sbSNP.py
cp ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP_old.py
git checkout HEAD ../../script/pythonScript/clinvar_sbSNP.py
#+end_src
#+RESULTS:
On compare
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
#+end_src
#+RESULTS:
| 535155 | old.txt |
| 535194 | new.txt |
| 1070349 | total |
Si on prend le premier manquant dans new, il est conflicting patho donc il ne devrait pas y être...
$ bcftools query -i 'ID="rs10418277"' dbSNP
_common_19.vcf.gz -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'ID="rs10418277"' dbSNP_common_19_old.vcf.gz -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'POS=54939682' clinvar_19.vcf.gz -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ bcftools query -i 'POS=54939682' clinvar_19_old.vcf.gz -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ grep rs10418277 *.txt
new.txt:rs10418277
tmp.txt:rs10418277
Le problème venait de la POS qui n'était plus convertie en int (suppression de la ligne par erreur ??)
On vérifie
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
diff old.txt new.txt
#+end_src
#+RESULTS:
| 535155 | old.txt |
| 535155 | new.txt |
| 1070310 | total |
***** DONE Tester sur chromosome 19 et 20: ok
CLOSED: [2022-12-11 Sun 15:56]
On prépare les données
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools filter -i 'CHROM="NC_000019.10" | CHROM="NC_000020.11"' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -o dbSNP_common_19_20.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10" | CHROM="NC_000020.11"' /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar.vcf.gz -o clin
[2023-09-27 Wed 21:40]
# ****** DONE Filtre vep avec spliceAI: 37365 -> 6130. SpliceAI n'apporte rien
# CLOSED: [2023-09-27 Wed 19:37] SCHEDULED: <2023-09-27 Wed>
# :PROPERTIES:
# :ID: c9b2009a-503b-4561-94c6-29ae21a3188d
# :END:
# #+begin_src sh
# filter_vep -i output-all-gpu.vcf --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA) or (SpliceAI_pred_DS_AG and SpliceAI_pred_DS_AG >= 0.2) or (SpliceAI_pred_DS_AL and SpliceAI_pred_DS_AL >= 0.2) or (SpliceAI_pred_DS_DG and SpliceAI_pred_DS_DG >= 0.2) or (SpliceAI_pred_DS_DL and SpliceAI_pred_DS_DL >= 0.2) " --only_matched -o output-all-gpu-filtered.vcf
# #+end_src
# filter_vep -i output-all-gpu.vcf --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched | grep -c -v '^#'
# 6130
# $ grep -c -v '^#' output-all-gpu-filtered.vcf
# 6130
# ****** DONE Re-vérifier filtre avec spip: 7730 -> probable problème avec spip
# CLOSED: [2023-09-27 Wed 20:54] SCHEDULED: <2023-09-27 Wed>
# filter_vep -i NA12878-sanger-all-T2T.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA) or (SPIP_spipScore and SPIP_spipScore >= 20)" --only_matched | grep -c -v '^#'
# perl: warning: Setting locale failed.
# perl: warning: Please check that your locale settings:
# LANGUAGE = (unset),
# LC_ALL = (unset),
# LANG = "en_US.utf8"
# are supported and installed on your system.
# perl: warning: Falling back to the standard locale ("C").
# 7730
****** DONE vérifier si tests sanger passent: ok
CLOSED: [2023-09-28 Thu 01:32] SCHEDULED: <2023-09-27 Wed>
ok !
Haplotypecaller : /Work/Users/apraga/bisonex/out//call_variant/haplotypecaller/NA12878-sanger-all-T2T/NA12878-sanger-all-T2T.haplotypecaller.vcf.gz/Work/Users/apraga/bisonex/out//call_variant/haplotypecaller/NA12878-sanger-all-T2T/NA12878-sanger-all-T2T.haplotypecaller.vcf.gz
144 found over 146
2×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼──────────────────────────────────────
1 │ chr12:g.13594572C>T 60.0 1
2 │ chr17:g.10204026T>A 60.0 1
/Work/Users/apraga/bisonex/tests/spliceai/output-all-gpu-filtered.vcf.gz
144 found over 146
spliceai : another 0 missed variants
0×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┴──────────────────────────
***** KILL Avec pip: echec
CLOSED: [2023-09-28 Thu 01:34]
2023-09-24 08:28:46.361434: W tensorflow/core/common_runtime/gpu/gpu_device.cc:1956] Cannot dlopen some GPU libraries. Please make sure the missing libraries mentioned above are installed properly if you would like to use GPU.
***** DONE Tester conda: echec
CLOSED: [2023-09-23 Sat 21:43] SCHEDULED: <2023-09-23 Sat>
Ananconda: N'arrive pas à installer
#+begin_quote
- feature:/linux-64::__glibc==2.28=0
- python=3.11 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']
- spliceai -> tensorflow[version='>=1.13.0'] -> __cuda
- spliceai -> tensorflow[version='>=1.13.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.28
#+end_quote
Il faut utiliser mamba
***** DONE Mail Paul
CLOSED: [2023-09-28 Thu 09:30] SCHEDULED: <2023-09-28 Thu>
Au total:
- pas de filtre sur l'épissage pour "rattraper" variants intronique : 6130 variants mais on en perd 4 (donner un exemple)
- avec spip: pas de variant perdu (hormis les 2 lié au bam) mais 7 332 variants au total et exécution lente (1H) mais possible sur serveur
- avec spliceai sur GPU (annotation "à la volée"): pas de variant perdu mais 6609 variants au total. 3h30 de calcul sur le mésocentre, impossible à faire chez nous car GPU
Rejoint ce que disait Yannis....
J'ai l'impression que c'est lié à un grand nombre de missense [1]
Note: j'ai plus confiance dans l'annottaion spliceAI pour T2T car moins compliqué à porter
[1] en prenant le transcrit avec la "pire" conséquences, on a 80% de missense (total = 6609)
11 3_prime_utr_variant
9 3_prime_utr_variant&nmd_transcript_variant
6 5_prime_utr_variant
48 coding_sequence_variant
5 coding_sequence_variant&nmd_transcript_variant
121 frameshift_variant
9 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
9 frameshift_variant&splice_region_variant
78 inframe_deletion
3 inframe_deletion&nmd_transcript_variant
2 inframe_deletion&splice_region_variant
84 inframe_insertion
2 inframe_insertion&nmd_transcript_variant
1 inframe_insertion&splice_region_variant
156 intron_variant
8 intron_variant&nmd_transcript_variant
24 intron_variant&non_coding_transcript_variant
5305 missense_variant
205 missense_variant&nmd_transcript_variant
3 missense_variant&splice_donor_5th_base_variant
110 missense_variant&splice_region_variant
9 missense_variant&splice_region_variant&nmd_transcript_variant
11 non_coding_transcript_exon_variant
12 splice_acceptor_variant
1 splice_acceptor_variant&nmd_transcript_variant
2 splice_acceptor_variant&non_coding_transcript_variant
9 splice_donor_5th_base_variant&intron_variant
1 splice_donor_5th_base_variant&intron_variant&nmd_transcript_variant
16 splice_donor_region_variant&intron_variant
4 splice_donor_region_variant&intron_variant&non_coding_transcript_variant
19 splice_donor_variant
1 splice_donor_variant&nmd_transcript_variant
3 splice_donor_variant&non_coding_transcript_variant
1 splice_donor_variant&splice_donor_5th_base_variant&3_prime_utr_variant&intron_variant&nmd_transcript_variant
3 splice_donor_variant&splice_donor_5th_base_variant&coding_sequence_variant&intron_variant
1 splice_donor_variant&splice_donor_5th_base_variant&intron_variant
39 splice_polypyrimidine_tract_variant&intron_variant
5 splice_polypyrimidine_tract_variant&intron_variant&nmd_transcript_variant
10 splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant
1 splice_region_variant&3_prime_utr_variant
1 splice_region_variant&5_prime_utr_variant
9 splice_region_variant&intron_variant
1 splice_region_variant&intron_variant&nmd_transcript_variant
2 splice_region_variant&intron_variant&non_coding_transcript_variant
5 splice_region_variant&non_coding_transcript_exon_variant
1 splice_region_variant&non_coding_transcript_variant
43 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant
2 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&nmd_transcript_variant
6 splice_region_variant&splice_polypyrimidin
e_tract_variant&intron_variant&non_coding_transcript_variant
15 splice_region_variant&synonymous_variant
14 start_lost
44 stop_gained
4 stop_gained&frameshift_variant
2 stop_gained&frameshift_variant&splice_region_variant
3 stop_gained&nmd_transcript_variant
3 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&nmd_transcript_variant
2 stop_lost
1 stop_lost&nmd_transcript_variant
6 stop_retained_variant
2 stop_retained_variant&nmd_transcript_variant
89 synonymous_variant
2 synonymous_variant&nmd_transcript_variant
1 transcript_ablation
1 upstream_gene_variant
En prenant tous les transcrits, 66% missense (total = 22085)
39 3_prime_UTR_variant
120 3_prime_UTR_variant&NMD_transcript_variant
22 5_prime_UTR_variant
2 5_prime_UTR_variant&NMD_transcript_variant
94 coding_sequence_variant
13 coding_sequence_variant&NMD_transcript_variant
527 downstream_gene_variant
257 frameshift_variant
21 frameshift_variant&NMD_transcript_variant
2 frameshift_variant&splice_donor_region_variant
20 frameshift_variant&splice_region_variant
1 frameshift_variant&splice_region_variant&NMD_transcript_variant
1 incomplete_terminal_codon_variant&coding_sequence_variant
211 inframe_deletion
18 inframe_deletion&NMD_transcript_variant
6 inframe_deletion&splice_region_variant
242 inframe_insertion
22 inframe_insertion&NMD_transcript_variant
4 inframe_insertion&splice_region_variant
983 intron_variant
244 intron_variant&NMD_transcript_variant
358 intron_variant&non_coding_transcript_variant
14690 missense_variant
1416 missense_variant&NMD_transcript_variant
6 missense_variant&splice_donor_5th_base_variant
374 missense_variant&splice_region_variant
34 missense_variant&splice_region_variant&NMD_transcript_variant
383 non_coding_transcript_exon_variant
53 splice_acceptor_variant
11 splice_acceptor_variant&NMD_transcript_variant
11 splice_acceptor_variant&non_coding_transcript_variant
20 splice_donor_5th_base_variant&intron_variant
4 splice_donor_5th_base_variant&intron_variant&NMD_transcript_variant
9 splice_donor_5th_base_variant&intron_variant&non_coding_transcript_variant
59 splice_donor_region_variant&intron_variant
11 splice_donor_region_variant&intron_variant&NMD_transcript_variant
24 splice_donor_region_variant&intron_variant&non_coding_transcript_variant
79 splice_donor_variant
6 splice_donor_variant&NMD_transcript_variant
17 splice_donor_variant&non_coding_transcript_variant
1 splice_donor_variant&splice_donor_5th_base_variant&3_prime_UTR_variant&intron_variant&NMD_transcript_variant
21 splice_donor_variant&splice_donor_5th_base_variant&coding_sequence_variant&intron_variant
3 splice_donor_variant&splice_donor_5th_base_variant&intron_variant
1 splice_donor_variant&splice_donor_5th_base_variant&non_coding_transcript_exon_variant&intron_variant
176 splice_polypyrimidine_tract_variant&intron_variant
27 splice_polypyrimidine_tract_variant&intron_variant&NMD_transcript_variant
48 splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant
1 splice_region_variant&3_prime_UTR_variant
24 splice_region_variant&3_prime_UTR_variant&NMD_transcript_variant
9 splice_region_variant&5_prime_UTR_variant
61 splice_region_variant&intron_variant
23 splice_region_variant&intron_variant&NMD_transcript_variant
37 splice_region_variant&intron_variant&non_coding_transcript_variant
26 splice_region_variant&non_coding_transcript_exon_variant
5 splice_region_variant&non_coding_transcript_variant
145 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant
27 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&NMD_transcript_variant
41 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant
37 splice_region_variant&synonymous_variant
3 splice_region_variant&synonymous_variant&NMD_transcript_variant
30 start_lost
5 start_lost&NMD_transcript_variant
135 stop_gained
13 stop_gained&frameshift_variant
3 stop_gained&frameshift_variant&NMD_transcript_variant
2 stop_gained&frameshift_variant&splice_region_variant
14 stop_gained&NMD_transcript_variant
5 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&NMD_transcript_variant
4 stop_lost
1 stop_lost&NMD_transcript_variant
9 stop_retained_variant
6 stop_retained_variant&NMD_transcript_variant
311 synonymous_variant
24 synonymous_variant&NMD_transcript_variant
1 transcript_ablation
390 upstream_gene_variant
**** KILL Ajout LOEUF et pli
CLOSED: [2023-10-07 Sat 17:57]
plugin VEP
**** DONE NMD
CLOSED: [2023-10-07 Sat 17:57]
plugin VEP
**** KILL Ajout LOEUF
CLOSED: [2023-04-19 mer. 16:32]
plugin VEP
**** DONE Spip
CLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>
BED ne semble pas bien marcher (il faut définir une zone)
VCF : trop d’information
Attention, plusieurs transcripts mais résultats identiques. On supprimer les doublons
***** DONE interpretation + score + intervalle de confiance séparé
CLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>
Tests :
dans tests/
vep -i 63004925-small.vcf -o postvep.vcf --vcf --fasta genomeRef.fna --dir 109 --merged --pick --offline --custom ../script/spip_annotation.vcf.gz,SPIP,vcf,exact,0,spipInterp,spipScore,spipConfidence
***** DONE Score
CLOSED: [2023-04-22 Sat 15:30]
**** DONE CADD: remplacer par plugin VEP
CLOSED: [2023-05-07 Sun 14:45] SCHEDULED: <2023-05-07 Sun>
***** Test
#+begin_src
vep -i test.vcf -o lol.vcf --offline --dir /Work/Projects/bisonex/data/vep/GRCh38/ --merged --vcf --fasta /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna --plugin CADD,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.snv.tsv.gz,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.indel.tsv.gz --dir_plugins ../VEP_plugins/ -v
#+end_src
Test
#+begin_src sh
vep --id "1 230710048 230710048 A/G 1" --offline --dir /Work/Projects/bisonex/data/vep/GRCh38/ --merged --vcf --fasta /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna --plugin CADD,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.snv.tsv.gz,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.indel.tsv.gz --hgvsg --plugin pLI --plugin LOEUF -o lol
#+end_src
CSQ=G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000366667|protein_coding|2/5||||843|776|259|M/T|aTg/aCg|||-1||HGNC|HGNC:333||Ensembl||A|A||1:g.230710048A>G|0.347|-0.277922|
Correspond bien à https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=I7ZsIbrj14P6lD43-9115494
***** DONE Utiliser whole genome
CLOSED: [2023-04-29 Sat 15:46]
***** KILL Renommer les chromosome avant ...
CLOSED: [2023-05-01 Mon 09:14] SCHEDULED: <2023-04-30 Sun>
Trop long !
- Téléchargement de CADD: 4h20
- renommer les chromosome pour SNV : 6h20
- tabix sur les SNV : job tué au bout de 21h....
***** DONE annoter séparément et fusionner les tableaux
CLOSED: [2023-05-07 Sun 14:45] SCHEDULED: <2023-05-01 Mon>
NB: on pourrait filtrer CADD avec tabix pour se restreindre à nos variants
**** DONE clinvar
CLOSED: [2023-04-22 Sat 15:31]
**** KILL Vérifier résultats HGVS avec mutalyzer
CLOSED: [2023-05-01 Mon 09:26]
**** HOLD Parallélisation
***** HOLD par chromosome avec workflow VEP
https://github.com/Ensembl/ensembl-vep/blob/release/109/nextflow/workflows/run_vep.nf
***** HOLD Avec option --fork
**** DONE Utiliser la version de nf-core de VEP
CLOSED: [2023-05-13 Sat 18:27] SCHEDULED: <2023-05-07 Sun>
**** DONE OMIM
CLOSED: [2023-08-31 Thu 10:38] SCHEDULED: <2023-08-29 Tue>
**** DONE plI et LOEUF depuis gnomad
CLOSED: [2023-08-3
epIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10.00000 | 89894644 | Don | 0.0001360257829 | No | Don | 89894485 | 159 | 0 | 0.0000000000000 | No | 89894485 | 0.07177992 | Yes | 0.07177992 | Yes |
|chr10129957338-T-C chr10 | 89894645 | lol | A | G | . | . | . | NR_028034:g.89894645:A>G | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 89894645 | substitution | A>G | Intron 3 | 1398 | NR_028034 | FAS | donor | 160 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10.00000 | 89894644 | Don | 0.0001360257829 | No | Don | 89894485 | 159 | 0 | 0.0000000000000 | No | 89894485 | 0.07177992 | Yes | 0.07177992 | Yes |
| chr10 | 89894645 | lol | A | G | . | . | . | NR_028035:g.89894645:A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89894645 | substitution | A>G | Exon 4 | 63 | NR_028035 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 0 | 0 | No | -1.67753 | 89894644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| chr10 | 89894645 | lol | A | G | . | . | . | NR_028036:g.89894645:A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89894645 | substitution | A>G | Exon 5 | 63 | NR_028036 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 0 | 0 | No | -1.67753 | 89894644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| chr10 | 89894645 | lol | A | G | . | . | . | NR_135313:g.89894645:A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89894645 | substitution | A>G | Exon 5 | 63 | NR_135313 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 0 | 0 | No | -1.67753 | 89894644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| chr10 | 89894645 | lol | A | G | . | . | . | NM_001410956:g.89894645:A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89894645 | substitution | A>G | Exon 6 | 63 | NM_001410956 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 0 | 0 | No | -1.67753 | 89894644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| chr10 | 89894645 | lol | A | G | . | . | . | NR_135314:g.89894645:A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89894645 | substitution | A>G | Exon 6 | 63 | NR_135314 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 0 | 0 | No | -1.67753 | 89894644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| chr10 | 89894645 | lol | A | G | . | . | . | NR_135315:g.89894645:A>G | Alter ESR | 35.81 % [28.11 % - 44.1 %] | 0.288 | + | 89894645 | substitution | A>G | Exon 4 | 63 | NR_135315 | FAS | acceptor | 8 | ExonESR | 0 | Outside SPiCE Interpretation | 0 | 0 | No | -1.67753 | 89894
runtime/gpu/gpu_device.cc:1635] Created device /job:localhost/replica:0/task:0/device:GPU:0 with 38188 MB memory: -> device: 0, name: NVIDIA A100-PCIE-40GB, pci bus id: 0000:21:00.0, compute capability: 8.0
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
WARNING:tensorflow:No training configuration found in the save file, so the model was *not* compiled. Compile it manually.
2023-09-24 09:37:54.143021: I tensorflow/compiler/xla/stream_executor/cuda/cuda_blas.cc:637] TensorFloat-32 will be used for the matrix multiplication. This will only be logged once.
2023-09-24 09:37:54.217160: E tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:429] Could not create cudnn handle: CUDNN_STATUS_NOT_INITIALIZED
2023-09-24 09:37:54.217220: E tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:438] Possibly insufficient driver version: 510.108.3
2023-09-24 09:37:54.217245: W tensorflow/core/framework/op_kernel.cc:1830] OP_REQUIRES failed at conv_ops.cc:1068 : UNIMPLEMENTED: DNN library is not found.
2023-09-24 09:37:54.217262: I tensorflow/core/common_runtime/executor.cc:1197] [/job:localhost/replica:0/task:0/device:GPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): UNIMPLEMENTED: DNN library is not found.
[[{{node model_1/conv1d_3/Conv1D}}]]
Traceback (most recent call last):
File "/Home/Users/apraga/.local/bin/spliceai", line 8, in <module>
sys.exit(main())
File "/Home/Users/apraga/.local/lib/python3.9/site-packages/spliceai/__main__.py", line 72, in main
scores = get_delta_scores(record, ann, args.D, args.M)
File "/Home/Users/apraga/.local/lib/python3.9/site-packages/spliceai/utils.py", line 159, in get_delta_scores
y_ref = np.mean([ann.models[m].predict(x_ref) for m in range(5)], axis=0)
File "/Home/Users/apraga/.local/lib/python3.9/site-packages/spliceai/utils.py", line 159, in <listcomp>
y_ref = np.mean([ann.models[m].predict(x_ref) for m in range(5)], axis=0)
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/keras/utils/traceback_utils.py", line 70, in error_handler
raise e.with_traceback(filtered_tb) from None
File "/Softs/helios/gpu/anaconda3/2023.03-1/envs/tensorflow-gpu-2.12.0+py3.9/lib/python3.9/site-packages/tensorflow/python/eager/execute.py", line 52, in quick_execute
tensors = pywrap_tfe.TFE_Py_Execute(ctx._handle, device_name, op_name,
tensorflow.python.framework.errors_impl.UnimplementedError: Graph execution error:
Detected at node 'model_1/conv1d_3/Conv1D' defined at (most recent call last):
File "/Home/Users/apraga/.local/bin/spliceai", line 8, in <module>
sys.exit(main())
File "/Home/Users/apraga/.local/lib/python3.9/site-packages/spliceai/__main__.py", line 72, in main
scores = get_delta_scores(record, ann, args.D, args.M)
File "/Home/Users/apraga/.local/lib/python3.9/site-packages/spliceai/utils.py", line 159, in get_
j63gbsa5irq3/bin/nextflow -c /nix/store/q46gdjil6bbap0bcghpqimh1camzmlpx-nextflow.config"
#+end_src
Avec user.name= on a une exécution correcte :
#+begin_src sh
#!/bin/bash -l
# Fichier submission.SBATCH
#SBATCH --job-name="bisonex"
#SBATCH --output=%x.%J.out ## %x=job name, %J=job id
#SBATCH --error=%x.%J.out
# walltime (hh:mm::ss) max is 8 days
#SBATCH -t 24:00:00
#SBATCH --partition=smp
#SBATCH -c 1 ## request 16 cores (MAX is 32)
#SBATCH --mem=12G ## (MAX is 96G)
#SBATCH --mail-user=apraga@chu-besancon.fr
#SBATCH --mail-type=END,FAIL # notify when job end/fail
module load nix/2.11.0
# Otherwise job fails as it cannot write to $HOME/.nextflow
export NXF_HOME=/Work/Users/apraga/.nextflow
# user.name must be forced (again... our fix does not seem to work in nix)
nextflow -Duser.name=apraga run main.nf -profile standard,helios --input=samples.csv --genome=GRCh38
#+end_src
**** DONE Mettre à jour documentation
CLOSED: [2023-10-13 Fri 11:44] SCHEDULED: <2023-10-13 Fri>
** DONE Mettre à jour spip pour corriger bug 62982239 : variant trop long (?)
CLOSED: [2023-09-22 Fri 22:22] SCHEDULED: <2023-09-21 Thu>
/Entered on/ [2023-09-21 Thu 23:11]
Rapporté par https://github.com/raphaelleman/SPiP/issues/9
*** DONE Relance run
CLOSED: [2023-09-22 Fri 22:22] SCHEDULED: <2023-09-21 Thu>
*** DONE Mise à jour spip
CLOSED: [2023-09-21 Thu 23:41] SCHEDULED: <2023-09-21 Thu>
** DONE nixpkgs unstable -> 23.05
CLOSED: [2023-09-22 Fri 22:22] SCHEDULED: <2023-09-21 Thu>
*** DONE repasser tests sanger
CLOSED: [2023-09-22 Fri 22:22] SCHEDULED: <2023-09-21 Thu>
** TODO Preprocessing avec nextflow
*** TODO Map to reference
**** TODO Sample ID dans header
/Work/Users/apraga/bisonex/out/63003856_S135/preprocessing/baserecalibrator
*** DONE Mark duplicate
CLOSED: [2022-10-09 Sun 22:30]
*** DONE Recalib
rate base quality score
CLOSED: [2022-10-09 Sun 22:30]
** DONE Variant calling avec Nextflow
CLOSED: [2022-11-19 Sat 21:34]
*** DONE Haplotype caller
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter variants
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter common snp not clinvar path
CLOSED: [2022-11-07 Mon 23:00]
Voir [[*common dbSNP not clinvar patho][common dbSNP not clinvar patho]]
*** DONE Filter variant only in consensual sequence
CLOSED: [2022-11-08 Tue 22:23]
*** DONE Filter technical variants
CLOSED: [2022-11-19 Sat 21:34]
*** DONE Utilise AVX pour accélerer l'exécution
CLOSED: [2023-04-29 Sat 15:46]
Sans cela, on a l'avertissement
#+begin_quote
17:28:00.720 INFO PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported
17:28:00.721 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/nix/store/cy9ckxqwrkifx7wf02hm4ww1p6lnbxg9-gatk-4.2.4.1/bin/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
17:28:00.733 WARN NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/Work/Users/apraga/bisonex/out/NA12878_NIST7035/preprocessing/applybqsr/libgkl_utils821485189051585397.so: libgomp.so.1: cannot open shared object file: No such file or directory)
17:28:00.733 WARN IntelPairHmm - Intel GKL Utils not loaded
17:28:00.733 WARN PairHMM - ***WARNING: Machine does not have the AVX instruction set support needed for the accelerated AVX PairHmm. Falling back to the MUCH slower LOGLESS_CACHING implementation!
17:28:00.763 INFO ProgressMeter - Starting traversal
#+end_quote
libgomp.so est fourni par gcc donc il faut charger le module
module load gcc@11.3.0/gcc-12.1.0
** KILL Utiliser subworkflow
CLOSED: [2023-04-02 Sun 18:08]
Notre version permet d'être plus souple
*** KILL Alignement
CLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>
*** KILL Vep
CLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>
vcf_annotate_ensemblvep
** TODO Annotation avec nextflow :annotation:
*** KILL VEP : --gene-phenotype ?
CLOSED: [2023-04-18 mar. 18:32]
Vu avec alexis : bases de données non à jour
https://www.ensembl.org/info/genome/variation/phenotype/sources_phenotype_documentation.html
*** DONE plugin VEP
CLOSED: [2023-04-18 mar. 18:32]
Cloner dépôt git avec plugin
Puis utiliser --dir_plugins
*** HOLD Utiliser code d’Alexis
*** TODO Nouvelle version avec VEP
Example avec --custom
https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html
**** DONE Ajout spliceAI
CLOSED: [2023-05-18 Thu 11:02] SCHEDULED: <2023-04-30 Sun>
plugin VEP
***** DONE Télécharger les données
CLOSED: [2023-05-11 Thu 19:01]
Difficile d'automatiser, le lien est temporaire...
***** DONE PLugin
CLOSED: [2023-05-11 Thu 20:16]
***** DONE Séparer score en plusieurs colonnes
CLOSED: [2023-05-11 Thu 20:16]
Test avec ce fichier pour avoir une ligne avec annotation et une ligne sans
#CHROM POS ID REF ALT
1 9091 . A C
1 69091 . A C
et
#+begin_src sh
rm -f postvep.tsv* && vep -i testspliceai.vcf.gz -o postvep.tsv --tab --dir 109 --merged --pick --use_given_ref --offline --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz
#+end_src
#+begin_src
$ bgzip postvep.tsv
$ python spliceai.py
$ cat postvep2.tsv
,variation,Location,Allele,Gene,Feature,Feature_type,Consequence,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,IMPACT,DISTANCE,STRAND,FLAGS,REFSEQ_MATCH,SOURCE,REFSEQ_OFFSET,SpliceAI_AG,SpliceAI_AL,SpliceAI_DG,SpliceAI_DL
0,1_9091_A/C,1:9091,C,ENSG00000290825,ENST00000456328,Transcript,upstream_gene_variant,-,-,-,-,-,-,MODIFIER,2778,1,-,-,Ensembl,-,,,,
1,1_69091_A/C,1:69091,C,ENSG00000186092,ENST00000641515,Transcript,missense_variant,124,64,22,M/L,Atg/Ctg,-,MODERATE,-,1,-,-,Ensembl,-,0.
-A ~/t2t.txt
#+end_src
Échec: librarie DNN not found...
#+begin_quote
To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-09-24 09:37:45.892545: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2023-09-24 09:37:47.759421: I tensorflow/core/common_
01,0.00,0.00,0.01
#+end_src
Test
cp work/bf/437ae511958509e43072f032f4d495/small.tab.gz tests/vep-spip.tab.gz
cp work/d5/3b1244b5ae83d54409ee0d456e8c55/small_cadd.tab.gz tests/vep-cadd-splice.tab.gz
**** DONE Package Nix spliceAI
CLOSED: [2023-10-07 Sat 18:00]
On utilise le tensorflow fourni avec nix (branche spliceai)
Il faut LD_PRELOAD=/lib64/libcuda.so pour l'exécution
***** DONE Version CPU non optimisé
CLOSED: [2023-09-23 Sat 21:34]
****** DONE Vérifier annotation hg19 et 38
CLOSED: [2023-09-23 Sat 18:49]
****** DONE Annotation maison T2T
CLOSED: [2023-09-23 Sat 21:33] SCHEDULED: <2023-09-23 Sat>
***** DONE Version CPU optismisée
CLOSED: [2023-09-23 Sat 21:34]
Activer flag dans le package nix
***** DONE Version CPU: Test chr20
CLOSED: [2023-09-23 Sat 22:25] SCHEDULED: <2023-09-23 Sat>
10min ?
***** DONE Version CPU: NA12878 sanger complet: kill car trop long
CLOSED: [2023-09-24 Sun 08:22] SCHEDULED: <2023-09-23 Sat>
10min ?
***** DONE GPU avec la version sur mésocentre: mail envoyé
CLOSED: [2023-09-26 Tue 11:49]
#+begin_src sh
module unload nix/2.11.0
module load anaconda3@2021.05/gcc-12.1.0
module load deep/tensorflow-gpu
pip install spliceai
#+end_src
Puis on teste sur la queue gpu
#+begin_src sh
srun -p gpu -t 4:00:00 --gres=gpu:1 --pty bash
cd /Work/Users/apraga/bisonex/tests/spliceai/
module load deep/tensorflow-gpu
module unload nix/2.11.0
time spliceai -I NA12878-sanger-chr20-T2T.vep.vcf.gz -O output-20-2.vcf -R /Work/Groups/bisonex/data/fasta/chm13v2.0/chm13v2.0.fa
64
4 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
**** DONE Vérifier multiples transcripts en hg38 avec coordonées génomiquues: ok
CLOSED: [2023-08-10 Thu 23:00]
Beaucoup plus de transcrits en T2T
Ex: 1 transcrit refseq curated
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A108257446%2D108257496&hgsid=1672963428_J5aWAqack2FpJ7mvhFTNVw7bKzxo
vs 2 transcrits en T2T
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_3671779_hs1&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A108264969%2D108265019&hgsid=1672963612_Eso9frdQ7z6RkKkcKsIf2Waq3pec
C'est bien ce qu'on retrouve avec spip
*** DONE [#A] Filtre vep avec spip
CLOSED: [2023-08-13 Sun 00:39] SCHEDULED: <2023-08-12 Sat 19:00>
*** DONE Annotation CADD + spliceAI GRCh38 avec nouvelle version :annotation:
CLOSED: [2023-08-28 Mon 17:21] SCHEDULED: <2023-08-20 Sun>
*** DONE OMIM: possible seulement sur nom du gènes:annotation:
CLOSED: [2023-08-13 Sun 11:57] SCHEDULED: <2023-08-13 Sun 16:00>
Base de données non disponible et compliqué de faire la mise à jour nous.
Si on essaie de prendre les gènes de GRCH38, ils ne sont pas forcément en T2T
Ex: DDX11L17 n'existe pas dans T2T à ces coordonées
zgrep DDX11L17 GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz
Note: c'est un pseudogene
https://www.genecards.org/cgi-bin/carddisp.pl?gene=DDX11L17
Si on prend les gènes de T2T, il y en a des nouveaux.
Ex: le premier est LOC101928626.
À cette position, rien en GRCh38
Si on essaye avec ENSEMBL: non car n'ont pas le même identifiant
Ex: ACHE
Idéalement, il faudrait l'identifiant NCBI (disponible dans OMIM) mais n'est pas en sortie de VEP
Et cela demande la version "merged" donc impossible en T2T
Est-ce faisable de faire une chr10129957338-T-Ccorrespondance sur le nom du gène ?
Tous les gènes de T2T:
#+begin_src sh :dir ~/Downloads
zgrep -o "ID=gene[^;]*;" GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz | sed 's/ID=gene-//;s/;//' | sort | uniq > t2t-genes.txt
wc -l t2t-genes.txt
#+end_src
#+RESULTS:
: 57660 t2t-genes.txt
#+begin_src sh :dir ~/Downloads
zgrep -o "ID=gene[^;]*;" GCF_000001405.40_GRCh38.p14_genomic.gff.gz | sed 's/ID=gene-//;s/;//' | sort | uniq > hg38-genes.txt
wc -l hg38-genes.txt
#+end_src
#+RESULTS:
: 67127 hg38-genes.txt
Gènes communs aux 2
#+begin_src sh :dir ~/Downloads
comm -12 t2t-genes.txt hg38-genes.txt | wc -l
#+end_src
#+RESULTS:
: 54506
Gènes uniquements dans t2t
#+begin_src sh :dir ~/Downloads
comm -23 t2t-genes.txt hg38-genes.txt | wc -l
#+end_src
#+RESULTS:
: 3154
Gènes uniquements dans GRCh38
#+begin_src sh :dir ~/Downloads
comm -13 t2t-genes.txt hg38-genes.txt | wc -l
#+end_src
#+RESULTS:
: 12621
*** HOLD OMIM sur nom du gène :annotation:
*** DONE Mobidetails API
CLOSED: [2023-09-10 Sun 16:44]
Trop long ... 1h à 1h30 d'exécution
Disponible dans module
*** DONE Filtre vep avec spip for T2T et spliceAI pour GRCh38
CLOSED: [2023-09-16 Sat 22:47]
*** DONE Repasser tests en GRCh38 avec nouveau filtre (spip ou splice ai) :sanger:
CLOSED: [2023-09-17 Sun 09:07] SCHEDULED: <2023-09-16 Sat>
*** HOLD Franklin API
https://www.postman.com/genoox-ps/workspace/franklin-api-documentation-s-public-workspace/documentation/6621518-4335389d-12e3-445f-8182-339df95b2a09
*** KILL Regarder si clinique disponible avec vep :annotation:
CLOSED: [2023-09-10 Sun 16:44]
*** TODO Filtrer suffisament après annotation
**** DONE Tester filtre sans splice: 6130 mais il en manque 4
CLOSED: [2023-10-18 Wed 22:50] SCHEDULED: <2023-09-27 Wed>
Mail Paul: Exome donc hors splice, peu intéressant
***** DONE Enlever complètement condition splice: 6130 variants restants...
CLOSED: [2023-09-27 Wed 19:37] SCHEDULED: <2023-09-26 Tue>
Cf [[id:c9b2009a-503b-4561-94c6-29ae21a3188d][Filtre vep avec spliceAI: 37365 -> 6130]]
Dans tests/splicai
#+begin_src sh
filter_vep -i output-all-gpu.vcf --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched -o test.vcf
grep -c -v '^#' test.vcf
6130
#+end_src
***** DONE Remplacer par impact fonctionnel: peu d'impact : majorité = MODERATE
CLOSED: [2023-09-27 Wed 19:45] SCHEDULED: <2023-09-26 Tue>
filter_vep -i output-all-gpu-filtered.vcf --format vcf --filter "IMPACT is HIGH" --only_matched | grep -c -v '^#'
258
filter_vep -i output-all-gpu-filtered.vcf --format vcf --filter "IMPACT is LOW" --only_matched | grep -c -v '^#'
11
filter_vep -i output-all-gpu-filtered.vcf --format vcf --filter "IMPACT is MODERATE" --only_matched | grep -c -v '^#'
5824
***** DONE Regarder les conséquences pour tes les transcripts
CLOSED: [2023-09-27 Wed 21:04]
/Work/Users/apraga/bisonex/out/annotate/vep/NA12878-sanger-all-T2T
filter_vep -i NA12878-sanger-all-T2T.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched -o filtered.vcf
bcftools +split-vep filtered.vcf -f '%Consequence\n' -d | sort | uniq -c
94 coding_sequence_variant
13 coding_sequence_variant&NMD_transcript_variant
257 frameshift_variant
21 frameshift_variant&NMD_transcript_variant
2 frameshift_variant&splice_donor_region_variant
20 frameshift_variant&splice_region_variant
1 frameshift_variant&splice_region_variant&NMD_transcript_variant
1 incomplete_terminal_codon_variant&coding_sequence_variant
211 inframe_deletion
18 inframe_deletion&NMD_transcript_variant
6 inframe_deletion&splice_region_variant
242 inframe_insertion
22 inframe_insertion&NMD_transcript_variant
4 inframe_insertion&splice_region_variant
14689 missense_variant
1416 missense_variant&NMD_transcript_variant
6 missense_variant&splice_donor_5th_base_variant
374 missense_variant&splice_region_variant
34 missense_variant&splice_region_variant&NMD_transcript_variant
53 splice_acceptor_variant
11 splice_acceptor_variant&NMD_transcript_variant
79 splice_donor_variant
6 splice_donor_variant&NMD_transcript_variant
30 start_lost
5 start_lost&NMD_transcript_variant
135 stop_gained
13 stop_gained&frameshift_variant
3 stop_gained&frameshift_variant&NMD_transcript_variant
2 stop_gained&frameshift_variant&splice_region_variant
14 stop_gained&NMD_transcript_variant
5 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&NMD_transcript_variant
4 stop_lost
1 stop_lost&NMD_transcript_variant
9 stop_retained_variant
6 stop_retained_variant&NMD_transcript_variant
1 transcript_ablation
Idem tests/spliceai
bcftools +split-vep output-all-gpu-filtered.vcf -f '%Consequence\n' -d | sort | uniq -c
94 coding_sequence_variant
13 coding_sequence_variant&NMD_transcript_variant
257 frameshift_variant
21 frameshift_variant&NMD_transcript_variant
2 frameshift_variant&splice_donor_region_variant
20 frameshift_variant&splice_region_variant
1 frameshift_variant&splice_region_variant&NMD_transcript_variant
1 incomplete_terminal_codon_variant&coding_sequence_variant
211 inframe_deletion
18 inframe_deletion&NMD_transcript_variant
6 inframe_deletion&splice_region_variant
242 inframe_insertion
22 inframe_insertion&NMD_transcript_variant
4 inframe_insertion&splice_region_variant
14689 missense_variant
1416 missense_variant&NMD_transcript_variant
6 missense_variant&splice_donor_5th_base_variant
374 missense_variant&splice_region_variant
34 missense_variant&splice_region_variant&NMD_transcript_variant
53 splice_acceptor_variant
11 splice_acceptor_variant&NMD_transcript_variant
79 splice_donor_variant
6 splice_donor_variant&NMD_transcript_variant
30 start_lost
5 start_lost&NMD_transcript_variant
135 stop_gained
13 stop_gained&frameshift_variant
3 stop_gained&frameshift_variant&NMD_transcript_variant
2 stop_gained&frameshift_variant&splice_region_variant
14 stop_gained&NMD_transcript_variant
5 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&NMD_transcript_variant
4 stop_lost
1 stop_lost&NMD_transcript_variant
9 stop_retained_variant
6 stop_retained_variant&NMD_transcript_variant
1 transcript_ablation
***** DONE Regarder les conséquences pour -s worst
CLOSED: [2023-09-27 Wed 21:04]
/Work/Users/apraga/bisonex/out/annotate/vep/NA12878-sanger-all-T2T
Après filtre_vep sans splice
]$ bcftools +split-vep filtered.vcf -f '%Consequence\n' -d -s worst | sort | uniq -c
48 coding_sequence_variant
6 coding_sequence_variant&nmd_transcript_variant
121 frameshift_variant
9 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
9 frameshift_variant&splice_region_variant
79 inframe_deletion
3 inframe_deletion&nmd_transcript_variant
2 inframe_deletion&splice_region_variant
85 inframe_insertion
2 inframe_insertion&nmd_transcript_variant
1 inframe_insertion&splice_region_variant
5309 missense_variant
207 missense_variant&nmd_transcript_variant
3 missense_variant&splice_donor_5th_base_variant
110 missense_variant&splice_region_variant
9 missense_variant&splice_region_variant&nmd_transcript_variant
19 splice_acceptor_variant
1 splice_acceptor_variant&nmd_transcript_variant
21 splice_donor_variant
1 splice_donor_variant&nmd_transcript_variant
14 start_lost
44 stop_gained
4 stop_gained&frameshift_variant
2 stop_gained&frameshift_variant&splice_region_variant
3 stop_gained&nmd_transcript_variant
3 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&nmd_transcript_variant
2 stop_lost
1 stop_lost&nmd_transcript_variant
6 stop_retained_variant
2 stop_retained_variant&nmd_transcript_variant
1 transcript_ablation
Dans tests/spliceai
$ bcftools +split-vep output-all-gpu-filtered.vcf -f '%Consequence\n' -s worst -d | sort | uniq -c
48 coding_sequence_variant
6 coding_sequence_variant&nmd_transcript_variant
121 frameshift_variant
9 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
9 frameshift_variant&splice_region_variant
79 inframe_deletion
3 inframe_deletion&nmd_transcript_variant
2 inframe_deletion&splice_region_variant
85 inframe_insertion
2 inframe_insertion&nmd_transcript_variant
1 inframe_insertion&splice_region_variant
5309 missense_variant
207 missense_variant&nmd_transcript_variant
3 missense_variant&splice_donor_5th_base_variant
110 missense_variant&splice_region_variant
9 missense_variant&splice_region_variant&nmd_transcript_variant
19 splice_acceptor_variant
1 splice_acceptor_variant&nmd_transcript_variant
21 splice_donor_variant
1 splice_donor_variant&nmd_transcript_variant
14 start_lost
44 stop_gained
4 stop_gained&frameshift_variant
2 stop_gained&frameshift_variant&splice_region_variant
3 stop_gained&nmd_transcript_variant
3 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&nmd_transcript_variant
2 stop_lost
1 stop_lost&nmd_transcript_variant
6 stop_retained_variant
2 stop_retained_variant&nmd_transcript_variant
1 transcript_ablation
***** KILL Vérifier si tests sanger passent: non
CLOSED: [2023-09-28 Thu 01:33] SCHEDULED: <2023-09-27 Wed>
│ String Float64 Int64
─────┼───────────────────────────────────────
1 │ chr10:g.130884530 60.0 67
2 │ chr10:g.240362 60.0 79
3 │ chr14:g.52665581 60.0 51
4 │ chr19:g.41325390 60.0 180
***** DONE Comparer aux filtres en GRCh38: ce sont bien les filtres hors splice...
CLOSED: [2023-10-17 Tue 21:12]
T2T:
filter_vep -i 2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched | bcftools +counts
Number of samples: 1
Number of SNPs: 5362
Number of INDELs: 325
Number of MNPs: 323
Number of others: 0
Number of sites: 5991
GRCh38
filter_vep -i 2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched | bcftools +counts
Number of samples: 1
Number of SNPs: 1182
Number of INDELs: 143
Number of MNPs: 535
Number of others: 0
Number of sites: 1840
***** DONE Proportions de conséquence : T2T vs GRCh38 avec multiqc: idem
CLOSED: [2023-10-17 Tue 21:00]
À l'oeil
***** Réexaminer les conséquences
****** DONE Impact fonctionnel: plus de LOW et de MODIFIER++
CLOSED: [2023-10-17 Tue 21:22]
T2T
bcftools +split-vep 2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.filtervep.vcf -f '%IMPACT\n' -d | sort | uniq -c
596 HIGH
2828 LOW
16314 MODERATE
11261 MODIFIER
GRCh38
bcftools +split-vep 2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.filtervep.vcf -f '%IMPACT\n' -d | sort | uniq -c
414 HIGH
466 LOW
10054 MODERATE
550 MODIFIER
****** DONE Pire conséquence: trop de missense
CLOSED: [2023-10-17 Tue 21:23]
GRCh38
$ bcftools +split-vep 2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.filtervep.vcf -f '%Consequence\n' -d -s worst | sort | uniq -c
2 3_prime_utr_variant&nmd_transcript_variant
1 5_prime_utr_variant
2 coding_sequence_variant
47 frameshift_variant
6 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
1 frameshift_variant&splice_region_variant
1 frameshift_variant&start_lost&start_retained_variant
37 inframe_deletion
9 inframe_deletion&nmd_transcript_variant
27 inframe_insertion
5 inframe_insertion&nmd_transcript_variant
21 intron_variant
1593 missense_variant
37 missense_variant&nmd_transcript_variant
17 missense_variant&splice_region_variant
1 missense_variant&splice_region_variant&nmd_transcript_variant
1 protein_altering_variant
1 splice_acceptor_variant
1 splice_acceptor_variant&frameshift_variant
2 splice_acceptor_variant&nmd_transcript_variant
3 splice_donor_5th_base_variant&intron_variant
1 splice_donor_5th_base_variant&intron_variant&non_coding_transcript_variant
2 splice_donor_region_variant&intron_variant
1 splice_donor_region_variant&intron_variant&nmd_transcript_variant
1 splice_donor_region_variant&intron_variant&non_coding_transcript_variant
10 splice_donor_variant
1 splice_donor_variant&non_coding_transcript_variant
11 splice_polypyrimidine_tract_variant&intron_variant
1 splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant
1 splice_region_variant&intron_variant
9 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant
3 splice_region_variant&synonymous_variant
1 splice_region_variant&synonymous_variant&nmd_transcript_variant
4 start_lost
19 stop_gained
2 stop_gained&frameshift_variant
2 stop_gained&nmd_transcript_variant
1 stop_gained&splice_region_variant
1 stop_gained&splice_region_variant&nmd_transcript_variant
3 stop_lost
2 stop_lost&nmd_transcript_variant
1 stop_retained_variant
18 synonymous_variant
1 synonymous_variant&nmd_transcript_variant
1 transcript_ablation
T2T
[apraga@mesointeractive filter]$ bcftools +split-vep 2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.filtervep.vcf -f '%Consequence\n' -d -s worst | sort | uniq -c
15 3_prime_utr_variant
11 3_prime_utr_variant&nmd_transcript_variant
51 5_prime_utr_variant
3 5_prime_utr_variant&nmd_transcript_variant
48 coding_sequence_variant
5 coding_sequence_variant&nmd_transcript_variant
3 downstream_gene_variant
121 frameshift_variant
9 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
9 frameshift_variant&splice_region_variant
78 inframe_deletion
2 inframe_deletion&nmd_transcript_variant
2 inframe_deletion&splice_region_variant
84 inframe_insertion
2 inframe_insertion&nmd_transcript_variant
1 inframe_insertion&splice_region_variant
16 intergenic_variant
368 intron_variant
21 intron_variant&nmd_transcript_variant
71 intron_variant&non_coding_transcript_variant
5187 missense_variant
207 missense_variant&nmd_transcript_variant
3 missense_variant&splice_donor_5th_base_variant
105 missense_variant&splice_region_variant
9 missense_variant&splice_region_variant&nmd_transcript_variant
33 non_coding_transcript_exon_variant
12 splice_acceptor_variant
1 splice_acceptor_variant&5_prime_utr_variant&intron_variant&nmd_transcript_variant
1 splice_acceptor_variant&nmd_transcript_variant
3 splice_acceptor_variant&non_coding_transcript_variant
1 splice_acceptor_variant&splice_polypyrimidine_tract_variant&intron_variant&nmd_transcript_variant
16 splice_donor_5th_base_variant&intron_variant
2 splice_donor_5th_base_variant&intron_variant&non_coding_transcript_variant
33 splice_donor_region_variant&intron_variant
4 splice_donor_region_variant&intron_variant&nmd_transcript_variant
7 splice_donor_region_variant&intron_variant&non_coding_transcript_variant
19 splice_donor_variant
1 splice_donor_variant&nmd_transcript_variant
2 splice_donor_variant&non_coding_transcript_variant
3 splice_donor_variant&splice_donor_5th_base_variant&coding_sequence_variant&intron_variant
64 splice_polypyrimidine_tract_variant&intron_variant
6 splice_polypyrimidine_tract_variant&intron_variant&nmd_transcript_variant
8 splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant
2 splice_region_variant&3_prime_utr_variant
2 splice_region_variant&5_prime_utr_variant
4 splice_region_variant&intron_variant
6 splice_region_variant&non_coding_transcript_exon_variant
54 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant
4 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&nmd_transcript_variant
5 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant
27 splice_region_variant&synonymous_variant
13 start_lost
31 stop_gained
4 stop_gained&frameshift_variant
2 stop_gained&frameshift_variant&splice_region_variant
3 stop_gained&nmd_transcript_variant
2 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&nmd_transcript_variant
2 stop_lost
1 stop_lost&nmd_transcript_variant
6 stop_retained_variant
2 stop_retained_variant&nmd_transcript_variant
349 synonymous_variant
17 synonymous_variant&nmd_transcript_variant
1 transcript_ablation
2 upstream_gene_variant
**** DONE Regarder annotation VEP des variants sur NA12878 non trataié :na12878:
CLOSED: [2023-10-18 Wed 22:50] SCHEDULED: <2023-10-16 Mon>
/Entered on/ [2023-10-16 Mon 19:39]
**** DONE Regarder si les variants sont dans des zones modifiées de T2T
CLOSED: [2023-10-19 Thu 17:19] SCHEDULED: <2023-10-18 Wed>
/Entered on/ [2023-10-18 Wed 22:49]
Liftover des variants de GRCh38 -> T2T
Cf ~/roam/research/bisonex/code/t2t/comparePositions.jl
#+begin_quote
Successfully converted 1896 records: View Conversions
Conversion failed on 17 records.
#+end_quote
On utilise t2tOnly()
Proportion par chromosome
julia> @by d :Column1 $nrow
24×2 DataFrame
Row │ Column1 nrow
│ String7 Int64
─────┼────────────────
1 │ chr1 678
2 │ chr2 369
3 │ chr3 287
4 │ chr4 224
5 │ chr5 258
6 │ chr6 430
7 │ chr7 321
8 │ chr8 218
9 │ chr9 251
10 │ chr10 275
11 │ chr11 489
12 │ chr12 350
13 │ chr13 74
14 │ chr14 185
15 │ chr15 171
16 │ chr16 283
17 │ chr17 364
18 │ chr18 82
19 │ chr19 550
20 │ chr20 142
21 │ chr21 93
22 │ chr22 171
23 │ chrX 98
24 │ chrY 1
**** DONE Regarder si les variants sont sur des nouveaux gènes
CLOSED: [2023-10-19 Thu 20:18] SCHEDULED: <2023-10-19 Thu>
Cf ~/roam/reasearch/bisonex/code/t2t/compareGene.jl
Test de la fonction pour extraire les gènes:
Important: les chiffres ne sont pas données sur le nom du gène seul mais sur le nom + la position. On ne supprime donc pas les noms en double"
- T2T
- refseq + liftoff, 20 008, The official webpage says 20 006 for v4 https://ccb.jhu.edu/T2T.shtml.
- Gencode38 19490
- GRCh38
- refseq we have 23 314, so 4 less than the official website : https://www.ncbi.nlm.nih.gov/datasets/gene/GCF_000001405.40/?gene_type=protein-coding
On choisit refseq:: Il y a 170 gènes (unique sur le nom du gène !) dans T2T non présents dans GRCh38-p14
À noter qu'il y a plus de gènes dans Refseq en GRC38-p14 qu'en T2T (20 080 > 19 748 )
Avec compareGene.j, on retrouve 0.73%
**** DONE Annotation avec vep + GTF (dernière versio): n'aide pas
CLOSED: [2023-10-20 Fri 00:16] SCHEDULED: <2023-10-19 Thu>
https://www.science.org/doi/10.1126/science.abj6987#core-R61
/Entered on/ [2023-10-19 Thu 10:41]
#+begin_src sh :dir "meso://Work/Users/apraga/bisonex/test/t2t"
wget https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_RefSeq_Liftoff_v5.1.gff3.gz
zgrep -v "#" chm13v2.0_RefSeq_Liftoff_v5.1.gff3.gz | sort -k1,1 -k4,4n -k5,5n -t$'\t' | bgzip -c > chm13v2.0_RefSeq_prepared.gff3.gz
tabix -p gff chm13v2.0_RefSeq_prepared.gff3.gz
#+end_src
# ./vep -i input.vcf --gff data.gff.gz --fasta genome.fa.gz
Dans ce dossier, on annote
#+begin_src sh
vep -i ../../out/annotate/vep/2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.vep.vcf.gz --gff chm13v2.0_RefSeq_prepared.gff3.gz --fasta /Work/Groups/bisonex/data/fasta/chm13v2.0/chm13v2.0.fa --vcf -o na12878_annotated.vcf
#+end_src
Et on filtre
#+begin_src sh
filter_vep -i na12878_annotated.vcf --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched > na12878_annotated_filtered.vcf
#+end_src
Idem
grep -c -v '#' na12878_annotated_filtered.vcf
6368
**** DONE Figure propre pour position des variants
CLOSED: [2023-10-19 Thu 15:41] SCHEDULED: <2023-10-19 Thu>
**** DONE Nombre de variants dans les zones exclusives à T2T
CLOSED: [2023-10-19 Thu 16:39] SCHEDULED: <2023-10-19 Thu>
Zones unique à T2T données par : https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1735553302_OcJ6esPoUFcSykF6hKiRmIGU24KD&db=hub_3267197_GCA_009914755.4&c=CP068269.2&g=hub_3267197_hgUnique
Note: le .fai donné ( https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz.gzi ) cause un problème aec bcftools :
Chromosome "" defined twice in chm13v2.0.fa.gz.gzi
On utilise donc l'index regénér sur le mésocentre
#+begin_src sh :dir "/home/alex/roam/research/bisonex/code/t2t"
wget https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/chain/v1_nflo/grch38-chm13v2.paf
scp meso:/Work/Projects/bisonex/data/fasta/chm13v2.0/chm13v2.0.fa.fai .
cut -f 1,3,4 grch38-chm13v2.paf | bedtools sort -i - -g chm13v2.0.fa.fai | bedtools merge | bedtools complement -g chm13v2.0.fa.fai -i - | bedtools merge | save T2T-CHM13v2.0_unique_regions_hg38.bed -f
#+end_src
#+RESULTS:
On génère le BED des variants supplémentaires en T2T avec
Puis
#+begin_src sh :dir "/home/alex/roam/research/bisonex/code/t2t"
bedtools intersect -a na12878-t2t-only.bed -b T2T-CHM13v2.0_unique_regions_hg38.bed > na12878-t2t-only-unique.bed
wc -l na12878-t2t-only.bed
wc -l na12878-t2t-only-unique.bed
#+end_src
#+RESULTS:
| 6364 | na12878-t2t-only.bed |
| 47 | na12878-t2t-only-unique.bed |
Donc 0.73% sont dans des zones unique
**** KILL Comparer l'annotation sur 1 variant filtré en GRCh388 et non filtré en T2T
CLOSED: [2023-10-19 Thu 22:54] SCHEDULED: <2023-10-19 Thu>
**** KILL Snpeff
SCHEDULED: <2023-10-19 Thu>
CLOSED: [2023-10-19 Thu 10:42]
Base de données non disponible
**** DONE Garder les transcrits canonique: reste nombreux
CLOSED: [2023-10-20 Fri 23:46] SCHEDULED: <2023-10-19 Thu>
/Entered on/ [2023-10-19 Thu 11:23]
***** Test GRCH38
Dans /Work/Users/apraga/bisonex/test/t2t
On vérifie qu'afficher CANONICAL ne montre que les transcrits canoniques
#+begin_src sh
bcftools +split-vep /Work/Users/apraga/bisonex/out/annotate/vep/2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.vep.vcf.gz -f '%CHROM:%POS %CANONICAL\n' -d | wc -l
20366
bcftools +split-vep /Work/Users/apraga/bisonex/out/annotate/vep/2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.vep.vcf.gz -f '%CHROM:%POS\n' -d | wc -l
90865
#+end_src
On peut aussi filtrer les transcrits canoniques seuls
#+begin_src sh
bcftools +split-vep /Work/Users/apraga/bisonex/out/annotate/vep/2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.vep.vcf.gz -f '%CHROM:%POS %Consequence\n' -i 'CANONICAL="YES"' -d | wc -l
20366
#+end_src
****** Après VEP: canonique et missense ou pire: 1528 transcrits
#+begin_src sh
bcftools +split-vep /Work/Users/apraga/bisonex/out/annotate/vep/2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.vep.vcf.gz -f '%CHROM:%POS %Consequence\n' -i 'CANONICAL="YES"' -d -s worst:missense+ | wc -l
1528
****** Après filtre vep: canonique et missense ou pire: 1255 transcrits
#+begin_src sh
bcftools +split-vep /Work/Users/apraga/bisonex/out/annotate/filter/2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.filtervep.vcf -f '%CHROM:%POS %Consequence\n' -i 'CANONICAL="YES"' -d | wc -l
3519
bcftools +split-vep /Work/Users/apraga/bisonex/out/annotate/filter/2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.filtervep.vcf -f '%CHROM:%POS %Consequence\n' -i 'CANONICAL="YES"' -d -s worst:missense+| wc -l
1255
#+end_src
****** Notre filtre vep + canonique: 2216 variants
#+begin_src
filter_vep -i /Work/Users/apraga/bisonex/out/annotate/vep/2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --filter "CANONICAL is YES" --only_matched | wc -l
2216
#+end_src
***** Test T2T
50 000 vs 30 000
#+begin_src sh
bcftools +split-vep /Work/Users/apraga/bisonex/out/annotate/vep/2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.vep.vcf.gz -f '%CHROM:%POS %Consequence\n' -i 'CANONICAL="YES"' -d | wc -l
50142
#+end_src
****** Apres VEP: canonique et missense ou pire: 4615 transcrits
#+begin_src sh
bcftools +split-vep /Work/Users/apraga/bisonex/out/annotate/vep/2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.vep.vcf.gz -f '%CHROM:%POS %Consequence\n' -i 'CANONICAL="YES"' -d -s worst:missense+ | wc -l
#+end_src
****** Après filtre vep: canonique et missense ou pire : 3734 transcrits (et 3734 variants)
#+begin_src sh
bcftools +split-vep /Work/Users/apraga/bisonex/out/annotate/filter/2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.filtervep.vcf -f '%CHROM:%POS %Consequence\n' -i 'CANONICAL="YES"' -d -s worst:missense+ | wc -l
#+end_src
****** Notre filtre vep + canonique: 5539 variants
#+begin_src sh
filter_vep -i /Work/Users/apraga/bisonex/out/annotate/vep/2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --filter "CANONICAL is YES" --only_matched | wc -l
5539
#+end_src
**** KILL Vérifier fréquence gnomad: non disponible dans cache
CLOSED: [2023-10-20 Fri 23:24] SCHEDULED: <2023-10-20 Fri>
Pas de sortie gnomad ? On teste dans /Work/Users/apraga/bisonex/test/t2t/gnomad
On copie les smlink
#+begin_src sh
cp -P /Work/Users/apraga/bisonex/work/98/967730e87f1bd228dbd68725a1ef7d/* .
cp /Work/Users/apraga/bisonex/work/98/967730e87f1bd228dbd68725a1ef7d/.command.sh .
rm *.spip.*
rm *.vep.*
#+end_src
** DONE [#B] Indicateurs qualité :qualité:
CLOSED: [2023-09-10 Sun 16:46]
*** Idée
Raredisease:
- FastQC : nombreuses statistiques. Non disponible Nix
- Mosdepth : calcule la profondeur (2x plus rapide que samtools depth). Nix
- MultiQC : fusionne juste les résultats des analyses. Non disponible nix
- Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics
- Qualimap : alternative fastqc ? Non disponible nix
- Sentieon's WgsMetricsAlgo : propriétaire
- TIDDIT's cov : TIDIT = remaninement chromosomique
Sarek:
- alignment statistics : samtools stats, mosdepth
- QC : MultiQC
MultiQC : non disponible Nix
*** DONE FastqQC
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
*** DONE Mosdepth
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
Pour exomple, il faut le fichier de capture
subworkflows/local/bam_markduplicates/
*** DONE Samtools stats
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
*** DONE [#B] Compte-redu exécution avec MultiQC
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
*** DONE Résultats sur NA12878 : 98% à 20x
CLOSED: [2023-08-19 Sat 20:45] SCHEDULED: <2023-08-17 Thu>
**** DONE Comprendre 91% à 20x seulement: SNVs inséré
CLOSED: [2023-08-18 Fri 22:25]
***** DONE Tester autre kit : Twist exome comprehensive
CLOSED: [2023-08-18 Fri 22:24]
Moins bon
***** DONE Tester génome sans alt
CLOSED: [2023-08-18 Fri 22:25]
Idem
***** DONE Tester NA12878 sans SNVs inséré: cause !!
CLOSED: [2023-08-18 Fri 22:25]
***** DONE Tester hg19 sur NA12878 non inséré
CLOSED: [2023-08-18 Fri 22:25]
**** DONE Comprendre pourquoi SNVs diminuent le score: reads manquants
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-18 Fri>
Voir [[id:5c1c36f3-f68e-4e6d-a7b6-61dca89abc37][Bug: perte de nombreux reads avec NA12878]]
*** DONE Relancer résultats avec NA1287 et NA12878 + sanger
CLOSED: [2023-08-29 Tue 10:30] SCHEDULED: <2023-08-29 Tue>
*** DONE Comparer avec hg19
CLOSED: [2023-08-28 Mon 17:22] SCHEDULED: <2023-08-20 Sun>
*** DONE Comparer avec autres kit de capture
CLOSED: [2023-08-28 Mon 17:22] SCHEDULED: <2023-08-20 Sun>
*** DONE Comparer avec no-alt
CLOSED: [2023-08-28 Mon 17:22] SCHEDULED: <2023-08-20 Sun>
** HOLD vérifier si normalisation
** KILL [#B] Vérification nomenclature hgvs :hgvs:
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-15 Tue>
*** KILL mutalyzer
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
*** KILL API variantvalidator
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
** DONE Exécution
CLOSED: [2022-09-13 Tue 21:37]
*** KILL test Bionix
*** KILL Implémenter execution avec Nix ?
Voir https://academic.oup.com/gigascience/article/9/11/giaa121/5987272?login=false
pour un exemple.
Probablement plus simple d’utiliser Nix pour gestion de l’environnement et snakemake pour l’exécution
Pas d’accès internet depuis le cluster
*** DONE nextflow
CLOSED: [2022-09-13 Tue 21:37]
**** TODO Bug scheduler SGE
Le job se fait tuer car l'utilisateur n'est pas passé correctement à nextflow
***** DONE Forcer l'utilisateur à l'exécution
CLOSED: [2023-04-01 Sat 17:57]
NXF_OPTS=-D"user.name=alex"
***** DONE Vérifier si le problème persiste avec 22.10.6
CLOSED: [2023-04-01 Sat 18:38] SCHEDULED: <2023-04-01 Sat>
oui
***** KILL Packager l'utilisateur dans le programme ?
Mauvaise idée..
*** DONE Diminuer mémoire pour haplotypecaller
CLOSED: [2023-09-20 Wed 21:44] SCHEDULED: <2023-09-19 Tue>
/Entered on/ [2023-09-19 Tue 15:30]
Medium = 32Go pour 6 coeurs => 4 jobs (donc tout le noeud) prend plus que les 96GB...
On essaie 16Gb
Puis commit
*** DONE Report multiqc avec 10 runs
CLOSED: [2023-09-19 Tue 15:31] SCHEDULED: <2023-09-19 Tue>
/Entered on/ [2023-09-19 Tue 15:31]
Cf mail 2023-09-19
*** DONE Bug: variant sur 7788314 pour patient 62982193 filtré : DP < 30
CLOSED: [2023-10-02 Mon 21:58] SCHEDULED: <2023-09-25 Mon>
/Entered on/ [2023-09-22 Fri 22:59]
35 selon IGV mais 27 en pratique dans le VCF.
VCF cento: 26 reads également...
VOUS, non confirmé sanger
Mail envoyé Alexis
Vu avec Paul : on laisse DP >= 30 si c'est la seule occurence
*** DONE Bug mésohelios: les jobs se font killer :bug:
CLOSED: [2023-10-13 Fri 11:44]
/Entered on/ [2023-10-11 Wed 12:06]
**** DONE Comprendre pourquoi
CLOSED: [2023-10-11 Wed 16:06] SCHEDULED: <2023-10-11 Wed>
Utilisateurs déconnectés à 4h du matin tous les jours
**** DONE Démarrer nextflow avec sbatch
CLOSED: [2023-10-13 Fri 11:07] SCHEDULED: <2023-10-11 Wed>
On retrouve le même bug avec squeue qui n'arrive pas à retrouver l'utilisateur en utilisant nextflow+nix
Même en forcant USER et export NXF_OPTS='-D"user.name=apraga"'
Test avec la version packagée sur mésocentre (il faut mettre à la main le dossier...): ok
#+begin_src sh
module load nextflow@23.04.3/gcc-12.1.0
# Force it
nextflow="/Softs/spack/opt/spack/linux-rocky8-x86_64/gcc-12.1.0/nextflow-23.04.3-qputqf2dmtvabpv76miz
-9 | IntronCons | 1 | high | 0 | 0No | 10 | 32370947 | Acc | 0.004449623 | No | Acc | 32370955 | -9 | 0 | 0 | No | 32370955 | 0.005060308 | No | 0.000005609419 | No |
var_19_20.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10" | C
HROM="NC_000020.11"' /Work/Groups/bisonex/data-alexis/dbSNP/dbSNP_common.vcf.gz -o dbSNP_common_19_20_old.vcf.gz
bcftools filter -i 'CHROM="19" | CHROM="20"' /Work/Groups/bisonex/data-alexis/clinvar/clinvar.vcf.gz -o clinvar_19_20_old.vcf.gz
#+end_src
#+RESULTS:
On récupère les 2 versions du script
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
git checkout regression ../../script/pythonScript/clinvar_sbSNP.py
cp ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP_old.py
git checkout HEAD ../../script/pythonScript/clinvar_sbSNP.py
#+end_src
#+RESULTS:
On compare
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP.py --clinvar clinvar_19_20.vcf.gz --dbSNP dbSNP_common_19_20.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_20_old.vcf.gz --dbSNP dbSNP_common_19_20_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
#+end_src
***** DONE Regarder la répartition des différences
CLOSED: [2022-12-11 Sun 16:29]
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt | uniq > notpatho.new
sort /Work/Groups/bisonex/data-alexis/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | uniq > notpatho.old
comm -23 notpatho.new notpatho.old > nopatho.diff
#+end_src
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools query -i 'ID=@nopatho.diff' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -f '%CHROM\n' | sort | uniq -c
#+end_src
On a principalement des coordonnées non consensuelles (non "NC_", voir notes)
#+RESULTS:
: 2 NC_000002.12
: 18 NC_000003.12
: 2 NC_000004.12
: 2 NC_000005.10
: 14 NC_000006.12
: 6 NC_000007.14
: 2 NC_000009.12
: 1 NC_000010.11
: 6 NC_000014.9
: 1 NC_000015.10
: 3 NC_000016.10
: 3 NC_000017.11
: 1 NC_000019.10
: 1 NC_000020.11
: 1 NC_000021.9
: 2 NC_000022.11
: 16018 NT_113793.3
: 17010 NT_113796.3
: 14 NT_113891.3
: 1 NT_167244.2
: 13 NT_167245.2
: 2 NT_167246.2
: 13 NT_167247.2
: 7 NT_167248.2
: 14 NT_167249.2
: 14857 NT_187361.1
: 92 NT_187367.1
: 1 NT_187369.1
: 13 NT_187381.1
: 54 NT_187383.1
: 6 NT_187499.1
: 46 NT_187502.1
: 13754 NT_187513.1
: 611 NT_187517.1
: 1 NT_187520.1
: 1 NT_187524.1
: 249 NT_187526.1
: 18 NT_187532.1
: 1 NT_187546.1
: 886 NT_187562.1
: 1 NT_187564.1
: 346 NT_187576.1
: 13 NT_187600.1
: 5 NT_187601.1
: 494 NT_187606.1
: 1 NT_187607.1
: 12 NT_187613.1
: 307 NT_187614.1
: 1 NT_187625.1
: 445 NT_187633.1
: 43 NT_187648.1
: 18 NT_187649.1
: 1 NT_187652.1
: 512 NT_187661.1
: 18 NT_187678.1
: 49 NT_187681.1
: 1 NT_187682.1
: 18 NT_187688.1
: 12 NT_187689.1
: 18 NT_187690.1
: 18 NT_187691.1
: 404 NT_187693.1
: 2 NW_003315952.3
: 1 NW_003315970.2
: 203 NW_003571054.1
: 322 NW_003571055.2
: 16 NW_003571056.2
: 16 NW_003571057.2
: 16 NW_003571058.2
: 16 NW_003571059.2
: 16 NW_003571060.1
: 213 NW_003571061.2
: 2 NW_009646201.1
: 322 NW_009646205.1
: 321 NW_009646206.1
: 371 NW_012132914.1
: 1 NW_012132915.1
: 13 NW_012132918.1
: 2 NW_013171801.1
: 1 NW_013171807.1
: 49 NW_015148966.1
: 14 NW_015495298.1
: 2 NW_015495299.1
: 1 NW_016107298.1
: 4 NW_017363813.1
: 2 NW_017852933.1
: 1 NW_018654722.1
: 38 NW_021160001.1
: 1 NW_021160003.1
: 1 NW_021160007.1
: 7 NW_021160017.1
***** DONE Regarder la différence avec la version sans les sites non consensuels: ok !
CLOSED: [2022-12-11 Sun 20:11]
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt | uniq > notpatho.new
sort /Work/Groups/bisonex/data-alexis/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | uniq > notpatho.old
comm -13 notpatho.new notpatho.old > notpatho.diff
wc -l
#+end_src
#+RESULTS:
: 528 notpatho.diff
Il manque 528 variants
rs1057520103
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools query -i 'ID=@notpatho.diff' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -f '%CHROM\n' | sort | uniq -c
#+end_src
#+RESULTS:
: 528 NC_012920.1
Donc la nouvelle version fonctionne mieux !
ON vérifie bien qu'ils sont dans l'ancienne version et la nouvelle:
$ grep -w -f notpatho.diff /Work/Groups/bisonex/data-alexis/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | wc -l
528
$ grep -w -f notpatho.diff /Work/Groups/bisonex/data/d
bSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt
#+end_src
**** DONE Supprimer les sites non consensuels
CLOSED: [2022-12-11 Sun 19:51]
**** DONE Rajouter les mitochondries (vu avec Paul)
CLOSED: [2022-12-13 Tue 17:26]
Ok avec notre version générée. Sur le J: 21155134
$ wc -l dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt
21155065 dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt
$ wc -l ../data-alexis/dbSNP/ID_of_common_snp_not_clinvar_patho.txt
21155065 ../data-alexis/dbSNP/ID_of_common_snp_not_clinvar_patho.txt
La différence vient probablement d'une vieille version de clinvar
**** KILL Comprendre la différence nouvelle version et prod
CLOSED: [2023-05-23 Tue 08:46]
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
#sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt | uniq > notpatho.new
#sort /Work/Groups/bisonex/data-alexis/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | uniq > notpatho.old
comm -13 notpatho.new notpatho.old > missing-from-old
comm -23 notpatho.new notpatho.old > missing-from-new
wc -l missing-from-old
wc -l missing-from-new
#+end_src
#+RESULTS:
| 75 | missing-from-old |
| 6 | missing-from-new |
Il manque 75 variants et on a 6 en trop
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools query -i 'ID=@missing-from-old' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -f '%CHROM\n' | sort | uniq -c
#+end_src
#+RESULTS:
| 16 | NC_000001.11 |
| 2 | NC_000002.12 |
| 18 | NC_000003.12 |
| 7 | NC_000004.12 |
| 1 | NC_000005.10 |
| 5 | NC_000006.12 |
| 3 | NC_000007.14 |
| 2 | NC_000009.12 |
| 1 | NC_000010.11 |
| 5 | NC_000011.10 |
| 3 | NC_000015.10 |
| 1 | NC_000016.10 |
| 4 | NC_000017.11 |
| 2 | NC_000019.10 |
| 1 | NC_000020.11 |
| 3 | NC_000022.11 |
| 1 | NC_000023.11 |
| 2 | NT_113891.3 |
| 2 | NT_167245.2 |
| 2 | NT_167247.2 |
| 1 | NT_167248.2 |
| 2 | NT_167249.2 |
| 18 | NT_187532.1 |
| 1 | NT_187562.1 |
| 1 | NT_187633.1 |
| 18 | NT_187649.1 |
| 18 | NT_187678.1 |
| 18 | NT_187688.1 |
| 12 | NT_187689.1 |
| 18 | NT_187690.1 |
| 18 | NT_187691.1 |
| 1 | NW_013171807.1 |
Donc la nouvelle version fonctionne mieux !
ON vérifie bien qu'ils sont dans l'ancienne version et la nouvelle:
$ grep -w -f notpatho.diff /Work/Groups/bisonex/data-alexis/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | wc -l
528
$ grep -w -f notpatho.diff /Work/Groups/bisonex/data/d
bSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt
#+end_src
*** DONE Comparer les versions
CLOSED: [2023-01-26 jeu. 17:42]
**** DONE bases de données
CLOSED: [2023-01-26 jeu. 17:42]
***** DONE Genome de référénce:
CLOSED: [2023-01-06 Fri 00:00]
Version calculée
$ find . -type f -name "genomeRef.*" -exec sh -c 'echo {}; sha256sum {}' \;
e0761a7ba5d10de9e7e97fa331667963925531c0199575bcceafbb13c3147e3f ./genomeRef.fna
d121084c35037763ea58c59726545eaa1c11025a7bf2d75634677c72ddb72fd1 ./genomeRef.dict
0a6e215314659929dbcdffc1881714e311e3d149bdc33978a6f5e28206fcc675 ./genomeRef.fna.fai
45a4aa0d8dc1095d090b13e4df180763b2e24d133ec81f026beaead6d41ebafc ./bwa/genomeRef.ann
ac6e465f230da6d9f8339ebdf4cb05bcfc47d03f3a3889cae7256983c7809210 ./bwa/genomeRef.bwt
058ffaf8cd38e7bc33c31e86e54e99869a8a4fbabb6737d7420d6b89e8b5988e ./bwa/genomeRef.sa
f665b64275eb76111463966bcb8e91e550c63c9b58263d43e19bae8552be2815 ./bwa/genomeRef.amb
d0d3731d1203cb4a0d0dd1279c37c85480b85a91da2d1dc543ac391ff927c272 ./bwa/genomeRef.pac
Version de référence
$ find . -type f -exec sh -c 'echo {}; sha256sum {}' \;
e0761a7ba5d10de9e7e97fa331667963925531c0199575bcceafbb13c3147e3f ./GRCh38_latest_genomic.fna
dd87d628a8179fc1e37a33b99101eece8282bec88dc17b1998a07ff0b912d4a3 ./GRCh38_latest_genomic.fna.index
0a6e215314659929dbcdffc1881714e311e3d149bdc33978a6f5e28206fcc675 ./GRCh38_latest_genomic.fna.fai
974cc313146aedd9ec2ae3f86b382b1317180e078621c1d53e8a803d4ec0d3a9 ./GRCh38_latest_genomic.dict
ac6e465f230da6d9f8339ebdf4cb05bcfc47d03f3a3889cae7256983c7809210 ./GRCh38_latest_genomic.fna.bwt
45a4aa0d8dc1095d090b13e4df180763b2e24d133ec81f026beaead6d41ebafc ./GRCh38_latest_genomic.fna.ann
f665b64275eb76111463966bcb8e91e550c63c9b58263d43e19bae8552be2815 ./GRCh38_latest_genomic.fna.amb
058ffaf8cd38e7bc33c31e86e54e99869a8a4fbabb6737d7420d6b89e8b5988e ./GRCh38_latest_genomic.fna.sa
d0d3731d1203cb4a0d0dd1279c37c85480b85a91da2d1dc543ac391ff927c272 ./GRCh38_latest_genomic.fna.pac
Dict ok si on renome le ficdhier d'origine
#+begin_src sh :dir /ssh:meso:/Work/Groups/bisonex/
sed 's/UR:.*/UR:genomeRef.fna/' data-alexis-reference/genome/GRCh38_latest_genomic.dict > lol.dict
diff lol.dict data/genome/GRCh38.p13/genomeRef.dict
#+end_src
#+RESULTS:
***** DONE dbSNP et dbSNP common: ok
CLOSED: [2023-01-03 Tue 23:17]
sha256sum GCF_000001405.39.gz
452e1112b6339a9b19821c2a226a8a3ba946e92a47e03e6ae464ef8820ee130d GCF_000001405.39.gz
sha256sum data-alexis-reference/dbSNP/GCF_000001405.39.gz
452e1112b6339a9b19821c2a226a8a3ba946e92a47e03e6ae464ef8820ee130d data-alexis-reference/dbSNP/GCF_000001405.39.gz"
sha256sum dbSNP_common.vcf.gz
70dfd9be859c39916598d23b5744cc1fbda04add5840cd90a6d0cd005bd3075b dbSNP_common.vcf.gz
sha256sum data-alexis-reference/dbSNP/dbSNP_common.vcf.gz
70dfd9be859c39916598d23b5744cc1fbda04add5840cd90a6d0cd005bd3075b data-alexis-reference/dbSNP/dbSNP_common.vcf.gz
***** DONE Clinvar : version différente
CLOSED: [2023-01-06 Fri 22:51]
$ zgrep -v '^#' data-alexis-reference/clinvar/clinvar.vcf.gz | wc -l
1474547
$ zgrep -v '^#' data/clinvar/GRCh38/clinvar.vcf.gz | wc -l
1571404
***** DONE Revérifer checksum de GRCh38 et dbSNP
CLOSED: [2023-01-26 jeu. 17:42]
****** DONE GRCh38
CLOSED: [2023-01-26 jeu. 17:42]
/Work/Projects/bisonex/data-alexis-reference/genome>sha256sum GRCh38_latest_genomic.fna
e0761a7ba5d10de9e7e97fa331667963925531c0199575bcceafbb13c3147e3f GRCh38_latest_genomic.fna
PS J:\bases_de_donnees\genome> cat .\checksum.txt
e0761a7ba5d10de9e7e97fa331667963925531c0199575bcceafbb13c3147e3f GRCh38_latest_genomic.fna
****** DONE dbSNP
CLOSED: [2023-01-26 jeu. 17:42]
/Work/Projects/bisonex/data-alexis-reference/dbSNP>sha256sum GCF_000001405.39.gz 01/26/2023 04:40:48 PM
452e1112b6339a9b19821c2a226a8a3ba946e92a47e03e6ae464ef8820ee130d GCF_000001405.39.gz
PS J:\bases_de_donnees\dbSNP> cat .\checksums.txt
452e1112b6339a9b19821c2a226a8a3ba946e92a47e03e6ae464ef8820ee130d GCF_000001405.39.gz
**** DONE Outils
CLOSED: [2023-01-26 jeu. 17:42]
| | Prod | Test |
| VCFtools | 0.1.17 | 0.1.16 |
| bcftools | 1.14 | 1.16 |
| samtools | 1.14 | 1.13 |
| gatk | 4.2.4.1 | 4.3.0.0 |
| bwa | ? | 0.7.17-r1188 |
On a des versions plus vieilles sauf (le plus important) Gatk
*** KILL 63003856_S135
CLOSED: [2023-05-23 Tue 08:45]
**** KILL Notes : bonne reproductibilité sur le cluster mais diff avec la version "de prod"
CLOSED: [2023-01-09 Mon 23:03]
tester sequential puis version spécifique bwa mem
Note: clinvar est plus ancien dans la version d'Alexis, cela explique les 8884 de la version pseudo-prod (via ID not clinvar patho)
Attention : le nombre de lignes = celles sans commentaires (et pas just NC... car il devrait y avoir les mitochondries !)
$ find . -name filter-depth.vcf -exec sh -c 'echo {}; grep -c -v '^#' {}' \;
Attention, on a un vcf.gz pour la version de test !!! ne pas utiliser le vcf
| | prod | prod | prod | prod | prod | test | test | test |
|---------------------+------------+-----------+------------+------------+------------+------------+------------+------------|
| PC | Karine | helios | helios | helios | Helios | Helios | Helios | Helios |
| cores | 4 | 4 | 4 | 24 | 1 | 24 | 24 | 1 |
| gatk | 4.2.4.1 | 4.2.4.1 | 4.2.4.1 | 4.2.4.1 | 4.2.4.1 | 4.2.4.1 | 4.3.0 | 4.2.3.1 |
| samtools | 1.10 | 1.10 | 1.13 | 1.13 | 1.13 | 1.13 | | |
| clinvar | 2022-09-03 | | 2022-09-03 | 2022-09-03 | 2022-09-03 | 2022-12-03 | 2022-12-03 | 2022-12-03 |
|---------------------+------------+-----------+------------+------------+------------+------------+------------+------------|
| bwa mem | 128077207 | 128077207 | 128077207 | 128077211 | 128077210 | 128077211 | 128077211 | 128077210 |
| cleanSam | 128077207 | | | | 128077210 | 128077211 | 128077211 | 128077210 |
| applybqsr | | | | 128077211 | | | | |
| haplotypecaller | 1528059 | 1528066 | 1528066 | 1528093 | 1528089 | 1528093 | 1528093 | 1528093 |
| DP_over_30 | 84708 | 84716 | 84716 | 84724 | 84725 | 84724 | 84724 | 84725 |
| not_SNP | 11362 | 11366 | 11366 | 11377 | 11384 | NA | NA | NA |
| consensual_sequence | 8864 | 8868 | 8868 | 8884 | 8886 | 8898 | 8898 | 8900 |
| tsv | 1087 | | 1121 | | | | | |
***** Convention
post_cleanSam = _cleaned.bam
post_markDuplicate = _marked_dup.bam
post_BaseRecalibrator = _recal.table
post_ApplyBQSR = _recalibrated_hg38.bam
post_haplotypecaller = .vcf
post_depth_filter = _DP_over_30.vcf
post_exclude_SNP = _DP_over_30_not_SNP
post_consensual = _DP_over_30_not_SNP_consensual_sequence.vcf
post_technical = _DP_over_30_not_SNP_consensual_sequence_not_technical.vcf.gz
On a vérifié que grep -c et grep | wc -l donnent le même résultat
#
**** KILL Gatk 4.3.0
CLOSED: [2023-01-04 Wed 19:16]
***** KILL Alignement
CLOSED: [2023-01-04 Wed 19:16]
****** DONE Brut
CLOSED: [2022-12-26 Mon 22:03]
Bam alexis
$ samtools view -c /Work/Groups/bisonex/ref_63003856_S135/63003856_S135.bam
128077207
Notre
9f/26cf3d] Cached process > preprocess:BWA_MEM (63003856_S135)
$ samtools view -c work/9f/26cf3deb07b425a3e851be2a7bd782/63003856_S135.bam
On vérifie la sortie
$ samtools view -c out/63003856_S135/preprocessing/mapped/63003856_S135.bam
128077211
Petite différence (< 1e-8) mais selon Alexis, bwa mem est non reproductible. d'autant qu'on utilise une version parallélisée
128077211
****** On vérifie les arguments: ok
#+begin_src
bwa mem \
-R '@RG\tID:sample\tSM:sample\tPL:ILLUMINA\
rner les tests.
Il faut remplace bin/test_haplotypes par test_haplotypes dans src/sh/run_tests.sh
#+begin_src sh
HGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta HCDIR=~/anaconda3/envs/py2/bin bash src/sh/run_tests.sh
#+end_src
Echec:
test_haplotypes: /opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/lib/tools/Fasta.cpp:81: MMappedFastaFile::MMappedFastaFile(const string&): Assertion `fd != -1' failed.
unknown location(0): fatal error in "testVariantPrimitiveSplitter": signal: SIGABRT (application abort requested)
/opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/test/test_align.cpp(298): last checkpoint
******** Chr21
HGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta hap.py example/happy/PG_NA12878_chr21.vcf.gz example/happy/NA12878_chr21.vcf.gz -f example/happy/PG_Conf_chr21.bed.gz -o test
******* Helios
échec
** TODO T2T :T2T:
Toutes les ressourcs sont décrites ici
https://github.com/marbl/CHM13
Détails sur le pipeline
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_hgLiftOver
*** Liftover pipelines
:PROPERTIES:
:ID: d2280207-3f65-4a31-a291-41fa9a9658c2
:END:
Contient les chain files
*** DONE Alignement
CLOSED: [2023-06-26 Mon 19:42]
NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios --input="/Work/Groups/bisonex/data/giab/*_R{1,2}_001.fastq.gz" --id=NA12878-T2T -bg
SCHEDULED: <2023-06-14 Wed>
*** DONE Haplotypecaller
CLOSED: [2023-06-26 Mon 19:42] SCHEDULED: <2023-06-15 Thu>
*** DONE Faire fonctionner le filtre technical variant
CLOSED: [2023-08-03 Thu 14:24] SCHEDULED: <2023-08-03 Wed 10:30>
*** DONE Annotation vep seule
CLOSED: [2023-08-05 Sat 08:59] SCHEDULED: <2023-08-05 Sat>
T2T n'a pas
- de version merged
- polyphen
- gnomAD
On désactive l'annotation spip pour le moment
*** DONE Générer la base de donnée spip :spip:
CLOSED: [2023-08-09 Wed 21:41] SCHEDULED: <2023-08-03 Thu 11:30>
**** KILL Vérifier la génération du transcriptome en hg38: checksum différent
CLOSED: [2023-08-09 Wed 21:41]
- [X] Nettoyer et vérifier sur hg38 avec ediff les RData : différent
- [X] Sinon, ne pas nettoyer et générer: idem
**** DONE Récupérer ncbi RefSeq curated
CLOSED: [2023-08-07 Mon 22:59] SCHEDULED: <2023-08-06 Sun>
.txt sur UCSC mais pas en T2T: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
Format: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1173061381_UepaHnvaOKFZKMOV4o7DtcNUHGVa&hgta_doSchemaDb=chlSab2&hgta_doSchemaTable=ncbiRefSeqCurated
Ancient format vs nouveau
| 1 | bin | 1 | chrom |
| 2 | name | 2 | chromStart |
| 3 | chrom | 3 | chromEnd |
| 4 | strand | 4 | name |
| 5 | txStart | 5 | score |
| 6 | txEnd | 6 | strand |
| 7 | cdsStart | 7 | thickStart |
| 8 | cdsEnd | 8 | thickEnd |
| 9 | exonCount | 9 | reserved |
| 10 | exonStarts | 10 | blockCount |
| 11 | exonEnds | 11 | blockSizes |
| 12 | score | 12 | chromStarts |
| 13 | name2 | 13 | name2 |
| 14 | cdsStartStat | 14 | cdsStartStat |
| 15 | cdsEndStat | 15 | cdsEndStat |
| 16 | exonFrames | 16 | exonFrames |
| | | 17 | type |
| | | 18 | geneName |
| | | 19 | geneName2 |
| | | 20 | geneType |
En T2T, seulement au format bigBed : https://hgdownload.soe.ucsc.edu/gbdb/hs1/ncbiRefSeq/
Il y a un exécutable pour convertir en bed : http://hgdownload.soe.ucsc.edu/admin/exe/
Sous gentoo, il faut instaler mit-krb5 (pour libkrb5)
#+begin_src
./bigBedToBed ncbiRefSeqCurated.bb ncbiRefSeqCurated.bed
#+end_src
Exemple:
chr1 7505 13582 NR_182076.1 0 - 13582 13582 0 2 5477,138, 0,5939, LOC127239154 none none -1,-1, NR_182076.1 LOC127239154
Dans R:
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
1 585 NR_046018 chr1 + 11873 14409 14409 14409 3 11873,12612,13220,
V11 V12 V13 V14 V15 V16 V17 V18
1 12227,12721,14409, 0 DDX11L1 none none -1,-1,-1, 354,109,1189, 0,739,1347,
Ne pas oublier les headers car ils sont dans un ordre différent:
Colonnes en GRGh38 =
3, 5, 6, 2, 12, 4, 7, 8, 12, 9, 17, 18, 13
Correspondance en T2T
1, 7, 8, 4, 5, 6, 14, 15, 5, ?, ?, ?, 13
En fait, il suffit d'avoir
- le gène
- le début du transcrit
- la fin du transcrit
- le brin
pour générer
***** KILL Tester correspondance partielle ?
CLOSED: [2023-08-07 Mon 22:58]
pas de CDS et pas de colonne 17 et 18
seules les colonnes (dans la nouvelle dataframe) 10,11,12 causent problèmes (9,17,18 dans les ancienne)
NB: on peut retrouver le nombre d'exons colonnes 9 à partir de la lons
***** DONE Correspondance totale
CLOSED: [2023-08-07 Mon 22:59]
> dataRefSeq[1,]
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12
1 chr1 11873 14409 NR_046018 0 + 14409 14409 0 3 354,109,1189, 0,739,1347,
V13
1 DDX11L1
> source("pkgs/getRefSeqDatabaseT2T.r")
Use the URL: http://hgdownload.cse.ucsc.edu/goldenPath/
read files...
> dataRefSeq[1,]
V1 V2 V3 V4 V5 V6 V7 V8 V5.1 V10 V11 V12
1 chr1 7505 13582 NR_182076 0 - 13582 13582 0 2 5477,138, 0,5939,
V13
1 LOC127239154
*** DONE Inclure génération refseq + transcriptom T2T dans dérivation nix :spip:
CLOSED: [2023-08-12 Sat 18:08] SCHEDULED: <2023-08-12 Sat 15:00>
**** DONE [#A] Tester nouvelle dérivation
CLOSED: [2023-08-12 Sat 18:08] SCHEDULED: <2023-08-12 Sat 15:00>
***** DONE En hg38
CLOSED: [2023-08-12 Sat 17:59]
test-spip-hg38.txt
varID
NM_000051:c.2251-10T>G
NM_000267:c.889-12T>A
NM_000059:c.8488-9T>G
NM_000249:c.589-10T>A
NM_000249:c.791-7T>A
#+begin_src
❯ ../result/bin/spip -I test-spip-hg38.txt -O test-spip-hg38.out -g hg38
#+end_src
#+RESULTS:
| varID | Interpretation | InterConfident | SPiPscore | strand | gNomen | varType | ntChange | ExonInfo | exonSize | transcript | gene | NearestSS | DistSS | RegType | SPiCEproba | SPiCEinter_2thr | deltaMES | BP | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut | probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT | probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut | | | | | | | | |
| NM_000051:c.2251-10T>G | Alter | by | SPiCE | 98.41 | % | [91.47 | % | - | 99.96 | %] | 0.986 | + | 108257471 | substitution | T>G | Intron | 14 | 1140 | NM_000051 | ATM | acceptor | -10 | IntronCons | 1 | high | 0 | 0No | 10 | 108257471 | Acc | 0.024836003 | No | Acc | 108257480 | -10 | 0 | 0 | No | 108257480 | 0.006489079 | No | 0.000004368542 | No |
| NM_000267:c.889-12T>A | Alter | by | SPiCE | 98.41 | % | [91.47 | % | - | 99.96 | %] | 1.000 | + | 31200410 | substitution | T>A | Intron | 8 | 17756 | NM_000267 | NF1 | acceptor | -12 | IntronCons | 1 | high | 0 | 0No | 10 | 31200411 | Acc | 0.009082899 | No | Acc | 31200421 | -11 | 0 | 0 | No | 31200421 | 0.005160854 | No | 0.000003718518 | No |
| NM_000059:c.8488-9T>G | Alter | by | SPiCE | 98.41 | % | [91.47 | % | - | 99.96 | %] | 0.994 | + | 32370947 | substitution | T>G | Intron | 19 | 398 | NM_000059 | BRCA2 | acceptor | -9 | IntronCons | 1 | high | 0 | 0No | 10 | 32370947 | Acc | 0.004449623 | No | Acc | 32370955 | -9 | 0 | 0 | No | 32370955 | 0.005060308 | No | 0.000005609419 | No |
| NM_000249:c.589-10T>A | Alter | by | SPiCE | 98.41 | % | [91.47 | % | - | 99.96 | %] | 0.978 | + | 37012001 | substitution | T>A | Intron | 7 | 148 | NM_000249 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0No | 10 | 37012002 | Acc | 0.009529819 | No | Acc | 37012010 | -9 | 0 | 0 | No | 37012010 | 0.028437574 | No | 0.000009275960 | No |
| NM_000249:c.791-7T>A | Alter | by | SPiCE | 98.41 | % | [91.47 | % | - | 99.96 | %] | 0.988 | + | 37017499 | substitution | T>A | Intron | 9 | 2961 | NM_000249 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0No | 10 | 37017500 | Acc | 0.015564917 | No | Acc | 37017505 | -6 | 0 | 0 | No | 37017505 | 0.023995855 | No | 0.000022606476 | No |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
***** DONE En T2T
CLOSED: [2023-08-12 Sat 18:08]
****** DONE Sur 1 variant avec score 35.01%: ok
CLOSED: [2023-08-12 Sat 18:05]
##fileformat=VCFv4.0
##assembly=CHM18v2.0/hs1
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
#CHROM POS ID REF ALT QUAL FILTER INFO
chr10 89894645 lol A G . . .
#+begin_src
../result/bin/spip -I test-spip-T2T.vcf -O test-spip-T2T.out -g hs1
#+end_src
#+RESULTS:
| CHROM POS ID REF ALT QUAL FILTER INFO varID Interpretation InterConfident SPiPscore strand gNomen varType ntChange ExonInfo exonSize transcript gene NearestSS DistSS RegType SPiCEproba SPiCEinter_2thr deltaMES BP mutInPBarea deltaESRscore posCryptMut sstypeCryptMut probaCryptMut classProbaCryptMut nearestSStoCrypt nearestPosSStoCrypt nearestDistSStoCrypt posCryptWT probaCryptWT classProbaCryptWT posSSPhysio probaSSPhysio classProbaSSPhysio probaSSPhysioMut classProbaSSPhysioMut |
| chr10 89894645 lol A G . . . NM_000043:g.89894645:A>G Alter ESR 35.81 % [28.11 % - 44.1 %] 0.288 + 89894645 substitution A>G Exon 6 63 NM_000043 FAS acceptor 8 ExonESR 0 Outside SPiCE Interpretation 0 0 No -1.67753 89894644 Acc 0.0000003317384 No Acc 89894637 7 89894644 0.0000002205815 No 89894637 0.02545572 No 0.02545572 No |
| chr10 89894645 lol A G . . . NM_001320619:g.89894645:A>G Alter ESR 35.81 % [28.11 % - 44.1 %] 0.288 + 89894645 substitution A>G Exon 6 63 NM_001320619 FAS acceptor 8 ExonESR 0 Outside SPiCE Interpretation 0 0 No -1.67753 89894644 Acc 0.0000003317384 No Acc 89894637 7 89894644 0.0000002205815 No 89894637 0.02545572 No 0.02545572 No |
| chr10 89894645 lol A G . . . NM_152871:g.89894645:A>G NTR 00 % [00 % - 00.92 %] 0.000 + 89894645 substitution A>G Intron 5 1398 NM_152871 FAS donor 160 DeepIntron 0 Outside SPiCE Interpretation 0 0 No 10.00000 89894644 Don 0.0001360257829 No Don 89894485 159 0 0.0000000000000 No 89894485 0.07177992 Yes 0.07177992 Yes |
| chr10 89894645 lol A G . . . NM_152872:g.89894645:A>G Alter ESR 35.81 % [28.11 % - 44.1 %] 0.288 + 89894645 substitution A>G Exon 6 63 NM_152872 FAS acceptor 8 ExonESR 0 Outside SPiCE Interpretation 0 0 No -1.67753 89894644 Acc 0.0000003317384 No Acc 89894637 7 89894644 0.0000002205815 No 89894637 0.02545572 No 0.02545572 No |
| chr10 89894645 lol A G . . . NR_028033:g.89894645:A>G NTR 00 % [00 % - 00.92 %] 0.000 + 89894645 substitution A>G Intron 4 1398 NR_028033 FAS donor 160 DeepIntron 0 Outside SPiCE Interpretation 0 0 No 10.00000 89894644 Don 0.0001360257829 No Don 89894485 159 0 0.0000000000000 No 89894485 0.07177992 Yes 0.07177992 Yes |
| chr10 89894645 lol A G . . . NR_028034:g.89894645:A>G NTR 00 % [00 % - 00.92 %] 0.000 + 89894645 substitution A>G Intron 3 1398 NR_028034 FAS donor 160 DeepIntron 0 Outside SPiCE Interpretation 0 0 No 10.00000 89894644 Don 0.0001360257829 No Don 89894485 159 0 0.0000000000000 No 89894485 0.07177992 Yes 0.07177992 Yes |
| chr10 89894645 lol A G . . . NR_028035:g.89894645:A>G Alter ESR 35.81 % [28.11 % - 44.1 %] 0.288 + 89894645 substitution A>G Exon 4 63 NR_028035 FAS acceptor 8 ExonESR 0 Outside SPiCE Interpretation 0 0 No -1.67753 89894644 Acc 0.0000003317384 No Acc 89894637 7 89894644 0.0000002205815 No 89894637 0.02545572 No 0.02545572 No |
| chr10 89894645 lol A G . . . NR_028036:g.89894645:A>G Alter ESR 35.81 % [28.11 % - 44.1 %] 0.288 + 89894645 substitution A>G Exon 5 63 NR_028036 FAS acceptor 8 ExonESR 0 Outside SPiCE Interpretation 0 0 No -1.67753 89894644 Acc 0.0000003317384 No Acc 89894637 7 89894644 0.0000002205815 No 89894637 0.02545572 No 0.02545572 No |
| chr10 89894645 lol A G . . . NR_135313:g.89894645:A>G Alter ESR 35.81 % [28.11 % - 44.1 %] 0.288 + 89894645 substitution A>G Exon 5 63 NR_135313 FAS acceptor 8 ExonESR 0 Outside SPiCE Interpretation 0 0 No -1.67753 89894644 Acc 0.0000003317384 No Acc 89894637 7 89894644 0.0000002205815 No 89894637 0.02545572 No 0.02545572 No |
| chr10 89894645 lol A G . . . NM_001410956:g.89894645:A>G Alter ESR 35.81 % [28.11 % - 44.1 %] 0.288 + 89894645 substitution A>G Exon 6 63 NM_001410956 FAS acceptor 8 ExonESR 0 Outside SPiCE Interpretation 0 0 No -1.67753 89894644 Acc 0.0000003317384 No Acc 89894637 7 89894644 0.0000002205815 No 89894637 0.02545572 No 0.02545572 No |
| chr10 89894645 lol A G . . . NR_135314:g.89894645:A>G Alter ESR 35.81 % [28.11 % - 44.1 %] 0.288 + 89894645 substitution A>G Exon 6 63 NR_135314 FAS acceptor 8 ExonESR 0 Outside SPiCE Interpretation 0 0 No -1.67753 89894644 Acc 0.0000003317384 No Acc 89894637 7 89894644 0.0000002205815 No 89894637 0.02545572 No 0.02545572 No |
| chr10 89894645 lol A G . . . NR_135315:g.89894645:A>G Alter ESR 35.81 % [28.11 % - 44.1 %] 0.288 + 89894645 substitution A>G Exon 4 63 NR_135315 FAS acceptor 8 ExonESR 0 Outside SPiCE Interpretation 0 0 No -1.67753 89894644 Acc 0.0000003317384 No Acc 89894637 7 89894644 0.0000002205815 No 89894637 0.02545572 No 0.02545572 No |
| |
****** DONE 5 variants patho
CLOSED: [2023-08-12 Sat 18:08]
##fileformat=VCFv4.0
##assembly=CHM13v2.0/hs1
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
#CHROM POS ID REF ALT QUAL FILTER INFO
chr11 108264994 lol T G . . .
chr17 32146124 lol T A . . .
chr3 31588185 lol T G . . .
chr3 37013346 lol T A . . .
chr3 37018844 lol T A . . .
#+begin_src
../result/bin/spip -I test-spip-T2T.vcf -O test-spip-T2T.out -g hs1
#+end_src
#+RESULTS:
| CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | varID | Interpretation | InterConfident | SPiPscore | strand | gNomen | varType | ntChange | ExonInfo | exonSize | transcript | gene | NearestSS | DistSS | RegType | SPiCEproba | SPiCEinter_2thr | deltaMES | BP | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut | probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT | probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut |
| chr11 | 108264994 | lol | T | G | . | . | . | NM_000051:g.108264994:T>G | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.986 | + | 108264994 | substitution | T>G | Intron 14 | 1140 | NM_000051 | ATM | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 108264994 | Acc | 0.02483600258856 | No | Acc | 108265003 | -10 | 0 | 0.00000000000000 | No | 108265003 | 0.006489079 | No | 0.000004368542 | No |
| chr11 | 108264994 | lol | T | G | . | . | . | NM_001351834:g.108264994:T>G | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.986 | + | 108264994 | substitution | T>G | Intron 15 | 1140 | NM_001351834 | ATM | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 108264994 | Acc | 0.02483600258856 | No | Acc | 108265003 | -10 | 0 | 0.00000000000000 | No | 108265003 | 0.006489079 | No | 0.000004368542 | No |
| chr17 | 32146124 | lol | T | A | . | . | . | NM_000267:g.32146124:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 1.000 | + | 32146124 | substitution | T>A | Intron 8 | 17755 | NM_000267 | NF1 | acceptor | -12 | IntronCons | 1 | high | 0 | 0 | No | 10 | 32146125 | Acc | 0.00908289924996 | No | Acc | 32146135 | -11 | 0 | 0.00000000000000 | No | 32146135 | 0.005160854 | No | 0.000003718518 | No |
| chr17 | 32146124 | lol | T | A | . | . | . | NM_001128147:g.32146124:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 1.000 | + | 32146124 | substitution | T>A | Intron 8 | 17755 | NM_001128147 | NF1 | acceptor | -12 | IntronCons | 1 | high | 0 | 0 | No | 10 | 32146125 | Acc | 0.00908289924996 | No | Acc | 32146135 | -11 | 0 | 0.00000000000000 | No | 32146135 | 0.005160854 | No | 0.000003718518 | No |
| chr17 | 32146124 | lol | T | A | . | . | . | NM_001042492:g.32146124:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 1.000 | + | 32146124 | substitution | T>A | Intron 8 | 17755 | NM_001042492 | NF1 | acceptor | -12 | IntronCons | 1 | high | 0 | 0 | No | 10 | 32146125 | Acc | 0.00908289924996 | No | Acc | 32146135 | -11 | 0 | 0.00000000000000 | No | 32146135 | 0.005160854 | No | 0.000003718518 | No |
| chr3 | 31588185 | lol | T | G | . | . | . | NM_178862:g.31588185:T>G | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 31588185 | substitution | T>G | Intron 3 | 16710 | NM_178862 | STT3B | donor | 5663 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 31588184 | Don | 0.00000002308527 | No | Don | 31582522 | 5662 | 31588181 | 0.00000000129731 | No | 31582522 | 0.071835522 | Yes | 0.071835521718 | Yes |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_000249:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_000249 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001167617:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001167617 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001167618:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001167618 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001167619:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001167619 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001258271:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001258271 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001258273:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001258273 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001258274:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 8 | 148 | NM_001258274 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354615:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354615 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354616:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354616 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354617:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354617 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354618:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354618 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354619:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 8 | 148 | NM_001354619 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354620:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354620 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354621:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354621 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354622:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354622 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354623:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354623 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354624:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354624 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354625:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354625 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354626:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354626 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354627:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354627 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354628:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354628 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354629:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 6 | 148 | NM_001354629 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37013346 | lol | T | A | . | . | . | NM_001354630:g.37013346:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.978 | + | 37013346 | substitution | T>A | Intron 7 | 148 | NM_001354630 | MLH1 | acceptor | -10 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37013347 | Acc | 0.00952981867149 | No | Acc | 37013355 | -9 | 0 | 0.00000000000000 | No | 37013355 | 0.028437574 | No | 0.000009275960 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_000249:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_000249 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001167617:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001167617 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001167618:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001167618 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001167619:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001167619 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001258271:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001258271 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001258273:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001258273 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001258274:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 10 | 2961 | NM_001258274 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354615:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001354615 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354616:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001354616 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354617:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354617 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354618:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354618 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354619:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 10 | 2961 | NM_001354619 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354620:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354620 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354621:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 8 | 8209 | NM_001354621 | MLH1 | acceptor | -2810 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37021653 | -2809 | 37018850 | 0.02399585516738 | No | 37021653 | 0.241893494 | Yes | 0.241893494461 | Yes |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354622:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 9 | 5764 | NM_001354622 | MLH1 | acceptor | -2810 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37021653 | -2809 | 37018850 | 0.02399585516738 | No | 37021653 | 0.241893494 | Yes | 0.241893494461 | Yes |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354623:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 8 | 5764 | NM_001354623 | MLH1 | acceptor | -2810 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37021653 | -2809 | 37018850 | 0.02399585516738 | No | 37021653 | 0.241893494 | Yes | 0.241893494461 | Yes |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354624:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 9 | 11091 | NM_001354624 | MLH1 | donor | 2955 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Don | 37015889 | 2956 | 37018850 | 0.02399585516738 | No | 37026980 | 0.028353019 | No | 0.028353019047 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354625:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 8 | 11091 | NM_001354625 | MLH1 | donor | 2955 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Don | 37015889 | 2956 | 37018850 | 0.02399585516738 | No | 37026980 | 0.028353019 | No | 0.028353019047 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354626:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 9 | 11091 | NM_001354626 | MLH1 | donor | 2955 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Don | 37015889 | 2956 | 37018850 | 0.02399585516738 | No | 37026980 | 0.028353019 | No | 0.028353019047 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354627:g.37018844:T>A | NTR | 00 % [00 % - 00.92 %] | 0.000 | + | 37018844 | substitution | T>A | Intron 9 | 11091 | NM_001354627 | MLH1 | donor | 2955 | DeepIntron | 0 | Outside SPiCE Interpretation | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Don | 37015889 | 2956 | 37018850 | 0.02399585516738 | No | 37026980 | 0.028353019 | No | 0.028353019047 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354628:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354628 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354629:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 8 | 2961 | NM_001354629 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
| chr3 | 37018844 | lol | T | A | . | . | . | NM_001354630:g.37018844:T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.988 | + | 37018844 | substitution | T>A | Intron 9 | 2961 | NM_001354630 | MLH1 | acceptor | -7 | IntronCons | 1 | high | 0 | 0 | No | 10 | 37018845 | Acc | 0.01556491731833 | No | Acc | 37018850 | -6 | 0 | 0.00000000000000 | No | 37018850 | 0.023995855 | No | 0.000022606476 | No |
*** DONE Vérifier annotation SPIP sur variants confirmé
CLOSED: [2023-08-10 Thu 23:16] SCHEDULED: <2023-08-09 Wed>
**** DONE 5 variants patho tirés de l'article princips
CLOSED: [2023-08-10 Thu 23:00]
On trié par SQUIRLS décroissant
#+begin_src sh
varID
NM_000051:c.2251-10T>G
NM_000267:c.889-12T>A
NM_000059:c.8488-9T>G
NM_000249:c.589-10T>A
NM_000249:c.791-7T>A
#+end_src
***** DONE En hg38
CLOSED: [2023-08-09 Wed 22:01]
#+begin_src
spip --input test-spip.txt --output test-spip.out --GenomeAssenbly hg38 --threads 1 --maxLines 1000
#+end_src
#+RESULTS:
| varID | Interpretation | InterConfident | SPiPscore | strand | gNomen | varType | ntChange | ExonInfo | exonSize | transcript | gene | NearestSS | DistSS | RegType | SPiCEproba | SPiCEinter_2thr | deltaMES | BP | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut | probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT | probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut |
| NM_000051:c.2251-10T>G | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.986 | + | 108257471 | substitution | T>G | Intron 14 | 1140 | NM_000051 | ATM | acceptor | -10 | IntronCons | 1 | high | 0 | 0No | 10 | 108257471 | Acc | 0.024836003 | No | Acc | 108257480 | -10 | 0 | 0 | No | 108257480 | 0.006489079 | No | 0.000004368542 | No | |
| NM_000267:c.889-12T>A | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 1.000 | + | 31200410 | substitution | T>A | Intron 8 | 17756 | NM_000267 | NF1 | acceptor | -12 | IntronCons | 1 | high | 0 | 0No | 10 | 31200411 | Acc | 0.009082899 | No | Acc | 31200421 | -11 | 0 | 0 | No | 31200421 | 0.005160854 | No | 0.000003718518 | No | |
| NM_000059:c.8488-9T>G | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] | 0.994 | + | 32370947 | substitution | T>G | Intron 19 | 398 | NM_000059 | BRCA2 | acceptor |
| | |
| NC_000020.11 | 62172726 | rs36106901 | G | A | |
| NC_000020.11 | 62172726 | 981031 | G | A | Conflicting_interpretations_of_pathogenicity |
| ------ | | | | | |
| NC_000020.11 | 63349782 | rs1044396 | G | A,C | |
| NC_000020.11 | 63349782 | 93427 | G | A | Benign |
| NC_000020.11 | 63349782 | 857384 | G | C | Conflicting_interpretations_of_pathogenicity |
| ------ | | | | | |
| NC_000020.11 | 63414925 | rs1801545 | G | A,C,T | |
| NC_000020.11 | 63414925 | 194284 | G | A | Conflicting_interpretations_of_pathogenicity |
| NC_000020.11 | 63414925 | 129337 | G | C | Benign |
| NC_000020.11 | 63414925 | 851545 | GG | CA | Uncertain_significance |
| ------ | | | | | |
On a donc plusieurs problèmes :
1. isec devrait fonctionner au moins sur
| NC_000020.11 | 25390747 | rs373200654 | G | C | |
| NC_000020.11 | 25390747 | 338000 | G | C | Conflicting_interpretations_of_pathogenicity |
On teste juste sur cette ligne
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools filter -i 'POS=25390747' clinvar_chr20.vcf.gz -o clinvar_test.vcf.gz
bcftools filter -i 'POS=25390747' dbSNP_common_chr20.vcf.gz -o dbSNP_test.vcf.gz
#+end_src
On retrouve bien la ligne dans l'intersection...
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools filter -i 'POS=25390747' clinvar_chr20.vcf.gz -o clinvar_test.vcf.gz
bcftools index dbSNP_test.vcf.gz dbSNP_test.vcf.gz
bcftools index dbSNP_test.vcf.gz clinvar_test.vcf.gz
bcftools isec dbSNP_test.vcf.gz clinvar_test.vcf.gz -p test
#+end_src
#+RESULTS:
2. isec ne semble pas fonctionner sur en cas d'ALT multiples
| NC_000020.11 | 32800145 | rs2424926 | C | G,T | |
| NC_000020.11 | 32800145 | 338173 | C | G | Benign |
| NC_000020.11 | 32800145 | 338174 | C | T | Conflicting_interpretations_of_pathogenicity |
| | | | | | |
3. s'il y a plusieurs variantions à une position, il faut bien vérifier que tous ne sont pas patho.
La version d'Alexis le fait bien
| NC_000020.11 | 3234173 | rs3827075 | T | A,C,G | |
| NC_000020.11 | 3234173 | 262001 | T | G | Conflicting_interpretations_of_pathogenicity |
| NC_000020.11 | 3234173 | 1072511 | T | TGGCGAAGC | Pathogenic |
| NC_000020.11 | 3234173 | 208613 | TGGCGAAGC | G | Pathogenic |
| NC_000020.11 | 3234173 | 1312 | TGGCGAAGC | T | Pathogenic |
****** DONE Voir si isec gère les multiallélique (chr20) : non, impossible de faire marcher
CLOSED: [2022-11-27 Sun 00:37]
******* DONE chr20 en prenant un patho clinvar aussi dans dbSNP
CLOSED: [2022-11-27 Sun 00:37]
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools filter dbSNP_common_chr20.vcf.gz -i 'POS=10652589' -o test_dbsnp.vcf.gz
bcftools filter clinvar_chr20.vcf.gz -i 'POS=10652589' -o test_clinvar.vcf.gz
bcftools index test_dbsnp.vcf.gz
bcftools index test_clinvar.vcf.gz
#+end_src
#+RESULTS:
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools isec test_dbsnp.vcf.gz test_clinvar.vcf.gz -p tmp
grep '^[^#]' tmp/0002.vcf
grep '^[^#]' tmp/0003.vcf
#+end_src
#+RESULTS:
Même en biallélique, ne fonctionne pas.
Testé en modifiant test_dbsnp !
Fonctionne avec un variant par ligne
****** DONE isec en coupant les sites multialléliques: non
CLOSED: [2022-11-27 Sun 00:37]
******* DONE Exemple simple ok
CLOSED: [2022-11-27 Sun 00:34]
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools filter -i 'POS=10652589' dbSNP_common_chr20.vcf.gz -o dbsnp_mwi.vcf.gz
bcftools filter -i 'POS=10652589' clinvar_chr20.vcf.gz -o clinvar_mwi.vcf.gz
bcftools index -f dbsnp_mwi.vcf.gz
bcftools index -f clinvar_mwi.vcf.gz
bcftools isec dbsnp_mwi.vcf.gz clinvar_mwi.vcf.gz -n=2
#+end_src
#+RESULTS:
Même en biallélique, ne fonctionne pas.
Chr 20
Avec les fichiers du teste précédent
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools norm -m -any dbsnp_mwi.vcf.gz -o dbsnp_mwi_norm.vcf.gz
bcftools index dbsnp_mwi_norm.vcf.gz
bcftools isec dbsnp_mwi_norm.vcf.gz clinvar_mwi.vcf.gz -n=2
#+end_src
#+RESULTS:
| NC_000020.11 | 10652589 | G | A | 11 |
| NC_000020.11 | 10652589 | G | C | 11 |
******* DONE Sur dbSNP chr20 non
CLOSED: [2023-10-07 Sat 17:57]
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools norm -m -any dbSNP_common_chr20 -o dbSNP_common_chr20_norm.vcf.gz
#+end_src
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools isec -i 'INFO/CLNSIG="Pathogenic"' dbSNP_common_chr20_norm.vcf.gz clinvar_chr20.vcf.gz -p tmp
#+end_src
#+RESULTS:
***** DONE Essai bedtools intersect
#+begin_src sh
bedtools intersect -a dbSNP_common.vcf.gz -b clinvar.vcf.gz
#+end_src
$ wc -l intersect.vcf
220206 intersect.vcf
** TODO Dépendences avec Nix
*** DONE GATK
CLOSED: [2022-10-21 Fri 21:59]
*** WAIT BioDBHTS
Contribuer pull request
*** DONE BioExtAlign
CLOSED: [2022-10-22 Sat 00:38]
*** DONE BioBigFile
CLOSED: [2023-11-30 Thu 21:57]
Revoir si on peut utliser kent dernière version
Contribuer pull request
*** HOLD rtg-tools
Convertir clinvar NC
*** DONE simuscop
CLOSED: [2022-12-30 Fri 22:31]
*** DONE Spip
CLOSED: [2022-12-04 Sun 12:49]
Pas de pull request
*** DONE R + packages
CLOSED: [2022-11-19 Sat 21:05]
*** TODO hap.py
https://github.com/Illumina/hap.py
**** DONE Version sans rtgtools avec python 3
CLOSED: [2023-02-02 Thu 22:15]
Procédure pour tester
#+begin_src
nix develop .#hap-py
$ genericBuild
#+end_src
1. Supprimer l’appel à make_dependencies dans cmakelist.txt : on peut tout installer avec nix
2. Patch Roc.cpp pour avoir numeric_limits ( error: 'numeric_limits' is not a member of 'std')
3. ajout de flags de link (essai, error)
set(ZLIB_LIBRARIES -lz -lbz2 -lcurl -lcrypto -llzma)
4. Changer les appels à print en print() dans le code python et suppression de quelques import
[nix-shell:~/source]$ sed -i.orig 's/print \"\(.*\)"/print(\1)/' src/python/*.py
**** DONE Sérialiser json pour écrire données de sorties
CLOSED: [2023-02-17 Fri 19:25]
**** DONE Tester sur example
CLOSED: [2023-02-04 Sat 00:25]
#+begin_src sh
$ cd hap.py
$ ../result/bin/hap.py example/happy/PG_NA12878_chr21.vcf.gz example/happy/NA12878_chr21.vcf.gz -f example/happy/PG_Conf_chr21.bed.gz -o test -r example/chr21.fa
#+end_src
#+RESULTS:
| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score |
| INDEL | ALL | 8937 | 7839 | 1098 | 11812 | 343 | 3520 | 45 | 283 | 0.877140 | 0.958635 | 0.298002 | 0.916079 |
| INDEL | PASS | 8937 | 7550 | 1387 | 9971 | 283 | 1964 | 30 | 242 | 0.844803 | 0.964656 | 0.196971 | 0.900760 |
| SNP | ALL | 52494 | 52125 | 369 | 90092 | 582 | 37348 | 107 | 354 | 0.992971 | 0.988966 | 0.414554 | 0.990964 |
| SNP | PASS | 52494 | 46920 | 5574 | 48078 | 143 | 992
bam
: bam/2200074722_62948298/62948298_S131.bqrt.bam
: bam/2200074990_62948306/62948306_S218.bqrt.bam
: bam/2200214581_62967331/62967331_S267.bqrt.bam
: bam/2200225399_62972187/62972187_S85.bqrt.bam
: bam/2200293962_62979117/62979117_S63.bqrt.bam
: bam/2200423985_62999352/62999352_S1.bqrt.bam
: bam/2200495073_63010427/63010427_S20.bqrt.bam
: bam/2200511274_63012586/63012586_S114.bqrt.bam
: bam/2200669188_63036688/63036688_S150.bqrt.bam
* Nouveau workflow :workflow:
** TODO Bases de données
*** KILL Nix pour télécharger les données brutes
**** Conclusion
Non viable sur cluster car en dehors de /nix/store
On peut utiliser des symlink mais trop compliqué
**** KILL Axel au lieu de curl pour gérer les timeout?
CLOSED: [2022-08-19 Fri 15:18]
*** DONE Tester patch de @pennae pour gros fichiers
SCHEDULED: <2022-08-19 Fri>
*** KILL Télécharger les données avec nextflow: hg38
CLOSED: [2023-06-12 Mon 23:29]
**** DONE Genome de référence
**** DONE dbSNP
**** DONE VEP 20G
CLOSED: [2023-06-12 Mon 23:29]
Ajout vérification checksum -> à vérifier
**** DONE VEP version 1.10
CLOSED: [2023-08-06 Sun 09:45] SCHEDULED: <2023-08-06 Sun>
**** DONE transcriptome (spip)
CLOSED: [2023-06-12 Mon 23:29]
Rajouter checksum manuel
**** KILL Refseq
**** KILL OMIM
CLOSED: [2023-06-12 Mon 23:29]
codé, à vérifier
**** KILL ACMG incidental
CLOSED: [2023-06-12 Mon 23:29]
*** DONE Données :T2T:
CLOSED: [2023-09-10 Sun 16:45]
:PROPERTIES:
:ID: 5d915178-ca96-44ef-87f1-6702af114f2b
:END:
**** DONE fasta
CLOSED: [2023-06-12 Mon 23:30]
***** DONE compatibilité hg38
CLOSED: [2023-06-12 Mon 23:30]
**** DONE fasta index
CLOSED: [2023-06-13 Tue 00:07]
***** DONE compatibilité hg38
CLOSED: [2023-06-13 Tue 00:07]
**** DONE fasta dictionnaire
CLOSED: [2023-06-13 Tue 00:07]
**** DONE dbSNP
CLOSED: [2023-06-12 Mon 23:30]
***** DONE compatibilité hg38
CLOSED: [2023-06-12 Mon 23:30]
**** DONE commonSNP
CLOSED: [2023-06-14 Wed 22:32]
***** DONE compatibilité hg38
CLOSED: [2023-06-14 Wed 22:32]
cd /Work/Groups/bisonex/data/dbsnp/GRCh38.p14
❯ ga@mesointeractive GRCh38.p14]$ zgrep -c '^NC' dbSNP_common.vcf.gz
21340485
[apraga@mesointeractive GRCh38.p14]$ pwd
[apraga@mesointeractive GRCh38.p14]$ zgrep -c '^NC'
dbSNP_common.vcf.gz ID_of_common_snp_not_clinvar_patho.txt
dbSNP_common.vcf.gz.tbi ID_of_common_snp.txt
[apraga@mesointeractive dbsnp]$ cd chm13v2.0/
[apraga@mesointeractive chm13v2.0]$ ls
chm13v2.0_dbSNPv155.vcf.gz dbSNP_common.vcf.gz.tbi versions.yml
chm13v2.0_dbSNPv155.vcf.gz.tbi ID_of_common_snp_not_clinvar_patho.txt
dbSNP_common.vcf.gz ID_of_common_snp.txt
[apraga@mesointeractive chm13v2.0]$ zgrep -c '^chr' dbSNP_common.vcf.gz
19433713
[apraga@mesointeractive chm13v2.0] $
❯ man tmux
**** DONE commonSNP non patho
CLOSED: [2023-06-14 Wed 22:35]
***** DONE compatibilité hg38
CLOSED: [2023-06-14 Wed 22:35]
**** DONE cache vep
CLOSED: [2023-06-30 Sun 14:20] SCHEDULED: <2023-07-25 Tue>
*** HOLD Processing bases de données
**** DONE dbSNP common
**** DONE Seulement les ID dans dbSNP common !
CLOSED: [2022-11-19 Sat 21:42]
172G au lieu de 253M...
**** HOLD common dbSNP not clinvar patho
***** DONE Conclusion partielle
CLOSED: [2022-12-12 Mon 22:25]
- vcfeval : prometteur mais n'arrive pas à traiter toutes les régions
- isec : trop de problèmes avec
- classif clinvar directement dans dbSNP: le plus simple
Et ça permet de rattraper quelques erreurs dans le script d'Alexis
***** KILL Utiliser directement le numéro dbSNP dans clinvar ? Non
CLOSED: [2022-11-20 Sun 19:51]
Ex: chr20
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f 'rs%INFO/RS \n' -i 'INFO/RS != "." & INFO/CLNSIG="Pathogenic"' clinvar_chr20.vcf.gz | sort > ID_clinvar_patho.txt
bcftools query -f '%ID\n' dbSNP_common_chr20.vcf.gz | sort > ID_of_common_snp.txt
comm -23 ID_of_common_snp.txt ID_clinvar_patho.txt > ID_of_common_snp_not_clinvar_patho.txt
wc -l ID_of_common_snp_not_clinvar_patho.txt
# sort ID
#+end_src
#+RESULTS:
: 518846 ID_of_common_snp_not_clinvar_patho.txt
Version d'alexis
#+begin_src sh :dir ~/code/bisonex/test_isec
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20_notremapped.vcf.gz
python ../script/pythonScript/clinvar_sbSNP.py \
--clinvar $clinvar \
--chrm_name_table ../database/RefSeq/refseq_to_number_only_consensual.txt \
--dbSNP $snp --output prod.txt
wc -l prod.txt
zgrep '^NC' dbSNP_common_chr20.vcf.gz | wc -l
#+end_src
#+RESULTS:
| 518832 | prod.txt |
| 518846 | |
***** KILL classification clinvar codée dbSNP ?
CLOSED: [2022-12-04 Sun 14:38]
Sur le chromosome 20
*Attention* CLNSIG a plusieurs champs (séparé par une virgule)
On y accède avec INFO/CLNSIG[*]
Ensuite, chaque item peut avoir plusieurs haploïdie (séparé par un |). IL faut donc utiliser une regexp
NB: *ne pas mettre la condition* dans une variable !!
Pour avoir les clinvar patho, on veut 5 mais pas 255 (= autre) pour la classification !`
Il faut également les likely patho et conflicting
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f '%INFO/CLNSIG\n' dbSNP_common_chr20.vcf.gz -i \
'INFO/CLNSIG[*]~"^5|" | INFO/CLNSIG[*]=="5" | INFO/CLNSIG[*]~"|5" | INFO/CLNSIG[*]~"^4|" | INFO/CLNSIG[*]=="4" | INFO/CLNSIG[*]~"|4" | INFO/CLNSIG[*]~"^12|" | INFO/CLNSIG[*]=="12" | INFO/CLNSIG[*]~"|12"' | sort
#+end_src
#+RESULTS:
| . | . | 12 | | | | | | | | |
| . | 12 | 0 | 2 | | | | | | | |
| 2 | 3 | 2 | 2 | 2 |
)
#+end_src
On groupe les résultat par identifiant (résultats = liste de records qui doit être convertie en table)
et on trie ceux qui n'ont qu'un fastq ou un bam
#+begin_src
let single = ( $bam | append $fastq | group-by id | transpose id files | get files | where {|x| ($x | length) == 1})
#+end_src
On convertit en table et on récupère seulement les bam
#+begin_src
$single | reduce {|it, acc| $acc | append $it} | where dir == bam | get id | each {|e| ^ls $"bam/*_($e)/*.bam"}
#+end_src
#+RESULTS:
: bam/2100656174_62913201/62913201_S52.bqrt.bam
: bam/2100733271_62925220/62925220_S33.bqrt.bam
: bam/2100738763_62926502/62926502_S108.bqrt.bam
: bam/2100746726_62926498/62926498_S105.bqrt.bam
:
bam/2100787936_62931955/62931955_S4.bqrt.bam
: bam/2200066374_62948290/62948290_S130.bqrt.
5 | . | | | | |
| . | 2 | 3 | 2 | 2 | 4 | | | | | |
| . | . | 3 | 12 | 3 | | | | | | |
| . | 5 | 2 | . | | | | | | | |
| . | . | . | 5 | 2 | 2 | | | | | |
| . | 9 | 9 | 9 | 5 | 5 | 2 | 3 | 2 | 3 | 2 |
Si on les exclut :
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f '%ID\n' dbSNP_common_chr20.vcf.gz -e \
'INFO/CLNSIG[*]~"^5|" | INFO/CLNSIG[*]=="5" | INFO/CLNSIG[*]~"|5" | INFO/CLNSIG[*]~"4" | INFO/CLNSIG[*]~"12"' | sort | uniq > common-notpatho.txt
#+end_src
#+RESULTS:
#+begin_src sh :dir ~/code/bisonex/test_isec
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20_notremapped.vcf.gz
python ../script/pythonScript/clinvar_sbSNP.py \
--clinvar $clinvar \
--chrm_name_table ../database/RefSeq/refseq_to_number_only_consensual.txt \
--dbSNP $snp --output tmp.txt
sort tmp.txt | uniq > common-notpatho-alexis.txt
wc -l common-notpatho-alexis.txt
#+end_src
#+RESULTS:
: 518832 common-notpatho-alexis.txt
On en a 6 de plus que la version d'Alexis mais quelques différences
Ceux d'Alexis qui manquent:
#+begin_src sh :dir ~/code/bisonex/test_isec
comm -23 common-notpatho-alexis.txt common-notpatho.txt > alexis-only.txt
cat alexis-only.txt
#+end_src
#+RESULTS:
| rs1064039 |
| rs3833341 |
| rs73598374 |
On les teste dans clinvar et dbSNP
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'ID=@alexis-only.txt' dbSNP_common_chr20.vcf.gz
bcftools query -f '%POS\n' -i 'ID=@alexis-only.txt' dbSNP_common_chr20.vcf.gz > alexis-only-pos.txt
while read -r line; do
bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'POS='$line clinvar_chr20.vcf.gz
done < alexis-only-pos.txt
# bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'POS=23637790' clinvar_chr20.vcf.gz
#+end_src
#+RESULTS:
| 764018 | A | ACAGGTCAAT,ACAGGT | .,5 | 2,. | |
| 23637790 | C | G,T | .,.,12 | | |
| 44651586 | C | A,G,T | .,.,.,5 | 2 | 2 |
| 764018 | A | ACAGGTCAAT | Benign | | |
| 23637790 | C | T | Benign | | |
| 44651586 | C | T | Benign | | |
On a donc une discordance entre clinvar et dbSNP.
On dirait qu'ils ont mal fait l'intersection avec clinvar.
Par exemple https://www.ncbi.nlm.nih.gov/snp/rs3833341#clinical_significance
Tu as l'impression qu'il y a un 1 clinvar bénin et 1 patho.
En cherchant par NM, tu vois qu'il est bénin sur clinvar car il y a d'autres soumissions ! https://www.ncbi.nlm.nih.gov/clinvar/variation/262235/
Confirmation sur nos bases de données :
$ bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'POS=764018' dbSNP_common_chr20.vcf.gz
764018 A ACAGGTCAAT,ACAGGT .,5|2,.
$ bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'POS=764018' clinvar_chr20.vcf.gz
764018 A ACAGGTCAAT Benign
***** KILL Corriger script alexi
CLOSED: [2022-12-04 Sun 13:03]
Gère clinvar patho, probablement patho ou conflicting !
***** HOLD Rtg tools
****** Test
1. Générer SDf file
#+begin_src sh
rtg format genomeRef.fna -o genomeRef.sdf
#+end_src
2. Pour les bases de donnés, il faut l'option --sample ALT sinon on a
#+begin_src
$ rtg vcfeval -b dbSNP_common.vcf.gz -c clinvar.vcf.gz -o test -t genomeRef.sdf/^C
VCF header does not contain a FORMAT field named GQ
Error: Record did not contain enough samples: NC_000001.11 10001 rs1570391677 A,C . PASS RS=1570391677;dbSNPBuildID=154;SSR=0;PSEUDOGENEINFO=DDX11L1:100287102;VC=SNV;R5;GNO;FREQ=KOREAN:0.9891,0.0109,.|SGDP_PRJ:0,1,.|dbGaP_PopFreq:1,.,0;COMMON
#+end_src
Essai intersection clinvar (patho ou non) dbSNP
- faux négatif = dbSNP common qui ne sont pas dans clinvar
- faux positif = clinvar qui ne sont pas dbSNP common
- vrai positif = clinvar qui sont dans dbSNP common
- vrai positif baseline = dbSNP common qui sont dans clinvar
On calcule le nombre de lignes
#+begin_src ssh
zgrep '^[^#]' /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar.vcf.gz | wc -l
for i in *.vcf.gz; do echo $i; zgrep '^[^#]' $i | wc -l; done
#+end_src
| clinvar | 1493470 |
| fn.vcf.gz | 22330220 |
| fp.vcf.gz | 1222529 |
| tp-baseline.vcf.gz | 131040 |
| tp.vcf.gz | 136638 |
À noter qu'on ne retrouve pas tout clinvar...
1222529 + 131040 = 1353569 < 1493470
certains régions ne sont pas traitées :
#+begin_quote
Evaluation too complex (50002 unresolved paths, 34891 iterations) at reference region NC_000001.11:790930-790970. Variants in this region will not be included in results
#+end_quote
#+begin_src sh
grep 'not be included' vcfeval.log | wc -l
56192
#+end_src
Le total est quand même inférieur
On veut les clinvar non patho dans dbSNP soit les faux négatif (dbSNP common not contenu dans clinvar patho)
#+begin_src sh
bcftools filter -i 'INFO/CLNSIG="Pathogenic"' /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar.vcf.gz -o /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar-patho.vcf.gz
tabix /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar-patho.vcf.gz
#+end_src
On lance le script (dbSNP common et clinvar = 9h)
#+begin_src sh
#!/bin/bash
#SBATCH --nodes=1
#SBATCH -p smp
#SBATCH --time=12:00:00
#SBATCH --mem=12G
dir=/Work/Groups/bisonex/data
dbSNP=$dir/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz
clinvar=$dir/clinvar/GRCh38/clinvar-patho.vcf.gz
genome=$dir/genome/GRCh38.p13/genomeRef.sdf
srun rtg vcfeval -b $dbSNP -c $clinvar -o common-not-patho -t $genome --sample ALT
#+end_src
****** HOLD Voir pour régions complexes non traitées
***** DONE bcftools isec : non
CLOSED: [2022-11-27 Sun 00:38]
#+begin_src sh
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -p common
#+end_src
On vérifie bien que les 2 fichiers commons on le même nombre de lignes
#+begin_src sh
$ grep -e '^NC' 0002.vcf | wc -l
74302
alex@gentoo ~/code/bisonex/data/common $ grep -e '^NC' 0003.vcf | wc -l
74302
#+end_src
****** DONE Impact option -n
CLOSED: [2022-10-23 Sun 13:56]
Mais en spécifiant -n =2:
#+begin_src sh
$ bedtools intersect -a dbSNP_common.vcf.gz -b clinvar.vcf.gz
74978
#+end_src
Si on ne regarde que les variants, on retrouve bien 74302
#+begin_src sh
rg "^NC" none_sorted.vcf | wc -l
#+end_src
NB : test fait avec
#+begin_src
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c none -n =2 -w 1 | sort > none.vcf
sort common/0003.vcf > common/0003_sorted.vcf
comm -13 common/0003_sorted.vcf none_sorted.vcf
#+end_src
****** DONE Géstion des duplicates: -c none
CLOSED: [2022-10-23 Sun 13:56]
Si on ne garde que ceux avec REF et ALT identiques
#+begin_src sh
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c none -n =2 -w 1 | wc -l
74978
#+end_src
Si on garde tout
#+begin_src sh
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c all -n =2 -w 1 | wc -l
137777
#+end_src
Pour regarder la différence :
#+begin_src sh
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c none -n =2 -w 1 | sort > none_sorted.vcf
bcftools isec dbSNP_common.vcf.gz clinvar.vcf.gz -c all -n =2 -w 1 | sort > all_sorted.vcf
comm -13 none_sorted.vcf all_sorted.vcf | head
#+end_src
Sur un exemple,on a bien des variants différents
****** DONE Suppression des clinvar patho
CLOSED: [2022-10-23 Sun 18:55]
Semble faire le travail vu que dbSNP_commo a 23194960 lignes (donc ~80 000 de moins)
#+begin_src sh
$ bcftools isec -e 'INFO/CLNSIG="Pathogenic" & INFO/CLNSIG="Pathogenic/Likely_pathogenic"' -c none -n~10 dbSNP_common.vcf.gz clinvar.vcf.gz | wc -l
Note: -w option not given, printing list of sites...
23119984
#+end_src
Par contre, l'o'ption -w ou -p fait des ficher "data"...
Après un nouvel essai, plus de problème
#+begin_src
$ bcftools isec -e 'INFO/CLNSIG="Pathogenic" & INFO/CLNSIG="Pathogenic/Likely_pathogenic"' -c none -n=1 dbSNP_common.vcf.gz clinvar.vcf.gz -w 1 -o lol.vcf.gz
$ zcat lol.vcf.gz | wc -l
23120660
#+end_src
À noter le choix de l'option -n qui change entre "=1" et "~10"...
En effet "=1" = au moins 1 fichier et "~10" fait exactement dans le premier et non dans le second
#+begin_src
$ bcftools isec -e 'INFO/CLNSIG="Pathogenic" & INFO/CLNSIG="Pathogenic/Likely_pathogenic"' -c none -n~10 dbSNP_common.vcf.gz clinvar.vcf.gz -w 1 -o lol.vcf.gz
$ zcat lol.vcf.gz | wc -l
23120660
#+end_src
****** DONE Valider avec Alexis : bcftool isec
CLOSED: [2022-11-07 Mon 21:42 ]
****** DONE Pourquoi nombre de lignes différentes avec la version d'Alexis -> isec ne gère pas plusieurs ALT
CLOSED: [2022-11-26 Sat 23:36]
Grosse différence !
#+begin_src
$ wc -l ID_of_common_snp_not_clinvar_patho.txt
23119915 ID_of_common_snp_not_clinvar_patho.txt
$ wc -l /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt
85820 /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt
#+end_src
À noter que tout dbSNP = 23194960
******* Clinvar classe 4 ? Moins mais toujours trop
#+begin_src
$ zgrep '^NC' tmp.vcf.gz | wc -l
21081654
#+end_src
******* Comparer les ID et regarder ceux en plus
#+begin_src sh
bcftools isec -e 'INFO/CLNSIG="Pathogenic"' -c none -n~10 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar.vcf.gz -w 1 -o tmp.vcf.gz
zgrep -o -e 'rs[[:digit:]]\' tmp.vcf.gz | sort | id_sorted.txt
sort ../database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt > reference_sorted.txt
comm -23 id_sorted.txt reference_sorted.txt > unique1.txt
#+end_src
Par exemple
#+begin_src sh
zgrep rs1000000561 ../database/dbSNP/dbSNP_common.vcf.gz
#+end_src
NC_000002.12 136732859 rs1000000561 ACG A,ACGCG . PASS RS=1000000561;dbSNPBuildID=151;SSR=0;VC=INDEL;GNO;FREQ=ALSPAC:0.2506,0.7494,.|TOMMO:0.9971,0.002865,.|TWINSUK:0.2473,0.7527,.|dbGaP_PopFreq:0.993,0.006943,8.902e-05;COMMON
Attention, clinvar est en numéro de chromosomoe et dbSNP en NC...
Normalement, géré lors du calcul d'intersection !
Ce SNP n'est pas dans clinvar (vérifié dans UCSC)
******* Tester sur chromosome 20
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools view --regions NC_000020.11 ../database/dbSNP/dbSNP_common.vcf.gz -o dbSNP_common_chr20.vcf.gz
bcftools view --regions 20 ../database/clinvar/clinvar.vcf.gz -o clinvar_chr20.vcf.gz
tabix dbSNP_common_chr20.vcf.gz
tabix clinvar_chr20.vcf.gz
#+end_src
#+RESULTS:
Attention à bien renommer clinvar !
#+begin_src sh :dir ~/code/bisonex/test_isec
mv clinvar_chr20.vcf.gz clinvar_chr20_notremapped.vcf.gz
bcftools annotate --rename-chrs chromosome_mapping.txt clinvar_chr20_notremapped.vcf.gz -o clinvar_chr20.vcf.gz
#+end_src
#+RESULTS:
*ATTENTION*: sans indexer les vcf, les fichiers seront *VIDES*
*ATTENTION*: par défaut les filtres s'appliquent sur les 2. Cela est un problème si on joue sur l'inclusion et non l'exclusion
Attention: vérifier la conventdion de nommage des chromosomes
******** Test pathogene: ne prend pas en compte les multi-allèles ????
On teste l'intersection dbsnp et clinvar patho ainsi que le complémentaire
#+begin_src sh :dir ~/code/bisonex/test_isec
clinvar=clinvar_chr20_patho.vcf.gz
snp=dbSNP_common_chr20.vcf.gz
bcftools index $clinvar
bcftools index $snp
bcftools filter -i 'INFO/CLNSIG="Pathogenic"' clinvar_chr20.vcf.gz -o $clinvar
bcftools isec $snp $clinvar -p tmp
for i in tmp/*.vcf ; do echo $i; grep '^[^#]' $i | wc -l; done
#+end_src
#+RESULTS:
| tmp/0000.vcf |
| 518846 |
| tmp/0001.vcf |
| 0 |
| tmp/0002.vcf |
| 0 |
| tmp/0003.vcf |
| 0 |
Aucun clinvar patho... Clairement faux !
Autre méthode : on inclut tous les SNP et clinvar patho et on regarde ceux uniq
#+title: Bisonex
#+category: bisonex
* Idées
** Validation analytique
mail Yannis : données patients +/- simulées
*** Utiliser données GCAT et uploader le notre ?
https://www.nature.com/articles/ncomms7275
*** [#A] Variant calling : Genome in a bottle : NA12878 + autres
Résumé : https://www.nist.gov/programs-projects/genome-bottle
Manuscript : https://www.nature.com/articles/s41587-019-0054-x.epdf?author_access_token=E_1bL0MtBBwZr91xEsy6B9RgN0jAjWel9jnR3ZoTv0OLNnFBR7rUIZNDXq0DIKdg3w6KhBF8Rz2RWQFFc0St45kC6CZs3cDYc87HNHovbWSOubJHDa9CeJV-pN0BW_mQ0n7cM13KF2JRr_wAAn524w%3D%3D
Article comparant les variant calling : https://www.biorxiv.org/content/10.1101/2020.12.11.422022v1.full.pdf
**** Tester le séquencage aussi
Depuis un fastq correspondant à Illumina https://github.com/genome-in-a-bottle/giab_data_indexes
puis on compare le VCF avec les "high confidence"
On séquence directement NA12878 -> inutile pour le pipeline seul
**** Tester seul la partie bioinformatique
Tout résumé ici : https://www.nist.gov/programs-projects/genome-bottle
- methode https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/analysis/Illumina_PlatinumGenomes_NA12877_NA12878_09162015/IlluminaPlatinumGenomes-user-guide.pdf
- vcf
https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/latest/GRCh38/
NB: à quoi correspond https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/analysis/Illumina_PlatinumGenomes_NA12877_NA12878_09162015/hg38/2.0.1/NA12878/ ??
Article comparant les variant calling : https://www.biorxiv.org/content/10.1101/2020.12.11.422022v1.full.pdf
Article pour vcfeval : https://www.nature.com/articles/s41587-019-0054-x
La version 4 ajoute 273 gènes "clinically relevant" https://www.biorxiv.org/content/10.1101/2021.06.07.444885v3.full.pdf
Ajout des zones "difficiles"
https://www.biorxiv.org/content/10.1101/2020.07.24.212712v5.full.pdf
*** [#B] Pipeline : générer patient avec tous les variants retrouvés à Cento
Comparaison de génération ADN (2019)
https://academic.oup.com/bfg/article/19/1/49/5680294
**** SimuSCop (exome)
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03665-5
https://github.com/qasimyu/simuscop
1. Crééer un modèle depuis bam + vcf : Setoprofile
2. Génerer données NGS
** Annotation :
*** Comparaison vep / snpeff et annovar
* Changement nouvelle version
- Dernière version du génome (la version "prête à l'emploi" est seulement GRCh38 sans les version patchées)
* Notes
** Nextflow
*** afficher les résultats d'un process/workflow
#+begin_src
lol.out.view()
#+end_src
Attention, ne fonctionne pas si plusieurs sortie:
#+begin_src
lol.out[0].view()
#+end_src
ou si /a/ est le nom de la sortie
#+begin_src
lol.out.a.view()
#+end_src
** Quelle version du génome ?
- T2T: notation chromose = chR1,2 : ok genome, clinvar, dbSNP
- GRCh38: notation chromose = NC_... : ok genome, clinvar, dbSNP
** Performances
Ordinateur de Carine (WSL2) : 4h dont 1h15 alignement (parallélisé) et 1h15 haplotypecaller (séquentiel)
** Chromosomes NC, NT, NW
Correspondance :
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&chromInfoPage=
Signification
https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloadAlt
- alt = séquences alternatives (utilisables)
- fix = patch (correction ou amélioration)
- random = séquence connue sur un chromosome mais non encore utilisée
** Pipelines prêt-à-l’emploi nextflow
Problème : nécessite singularity ou docker (ou conda)
Potentiellement utilisable avec nix...
** Validation : Quelles données de référence ?
Discussion avec Alexis
*** KILL Platinum genomes = génome seul
CLOSED: [2023-11-26 Sun 23:29]
]] Que du génome « sequenced to 50x depth on a HiSeq 2000 system”
*** [[https://github.com/genome-in-a-bottle/giab_data_indexes][Genome in a bottle]]
**** Illumina
- NA12878 :
- Illumina HiSeq Exome : fastq + capture en hg37
- Illumina TruSeq Exome : bam, pas de capture
- VCF en hg37 https://zenodo.org/record/3597727 mais avec capture. Raw data ne semblent pas être accessibles...
- HiSeq2000
- NextSeq 500
- HiSeq 2500
- HG002,3,4
- Illumina Whole Exome : bam. le kit de capture est "Agilent SureSelect Human All Exon V5 kit" selon [[https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/README.txt][README]]. On il faut les régions [[https://kb.10xgenomics.com/hc/en-us/articles/115004150923-Where-can-I-find-the-Agilent-Target-BED-files-][selon ce site]]
Un autre fichier est disponible (capture ???)
https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/wex_Agilent_SureSelect_v05_b37.baits.slop50.merged.list
"target region" +/- 50bp
testé sur chr311780-312086 : ok
**** KILL Autres technologies : non adaptées au pipeline (vu avec Alexis)
CLOSED: [2023-11-26 Sun 23:29]
*** KILL 1000 genomes: trop compliqué pour capture
CLOSED: [2023-11-26 Sun 23:52]
- [[https://www.internationalgenome.org/data-portal/sample/NA12878][NA12878]]
- Quelle capture ? Réponse ici https://www.internationalgenome.org/category/targets/
- ceux marqués "exons targetted" ont ce [[http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/][BED]] pour 1000 gènes
- ceux marqués exomes ont tout le CCDS (en hg19...)
- [[http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/exome_pull_down_targets/][BED pour phase 3]]
- [[http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/exome_pull_down_targets_phases1_and_2/][BED pour phase 1 ou 2]]
- Librairie selon les centres : https://www.internationalgenome.org/category/exome/
#+begin_quote
- Baylor College of Medicine : NimbleGen SeqCap_EZ_Exome_v2 for its Solid based exome sequencing. For its more recent Illumina based exome sequencing it used a custom array HSGC VCRome.
- The Broad Institute has used Agilent SureSelect_All_Exon_V2 (https://earray.chem.agilent.com/earray/ using ELID: S0293689).
- The BGI used NimbleGen SeqCap EZ exome V1 for the phase 1 samples and NimbleGen SeqCap_EZ_Exome_v2 for phase 2 and 3 (the v1 files were obtained from BGI directly; they are discontinued from Nimblegen).
- The Washington University Genome Center used Agilent SureSelect_All_Exon_V2 (https://earray.chem.agilent.com/earray/ using ELID: S0293689) for phase 1 and phase 2, and NimbleGen SeqCap_EZ_Exome v3 for phase 3
#+end_quote
- Un BED a été créé avec l' [[ http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/exome_pull_down_targets_phases1_and_2/README.20120518.exome.consensus][intersection des capture et CCDS]] Mais en GRCh37...
- intersection des capture + CCDS [[id:b77e64fa-06a8-4ffa-8b5b-ab3fda684b61][Données brutes exome 1000 Genomes (fastq + capture)]]
*** TODO NA12878
**** DONE En cherchant dans SRA directement
CLOSED: [2023-11-29 Wed 23:37] SCHEDULED: <2023-11-28 Tue>
https://www.ncbi.nlm.nih.gov/sra avec NA12878 et en filtrant par exome
- NovaSeq 6000 TruSeq capture SRX11061536
- NovaSeq 6000 IDT capture SRX11061526
- NovaSeq 6000 Agilent SureSelect v7 capture SRX11061516
- HiSeq 4000 TruSeq capture SRX11061506
- HiSeq 4000 IDT capture SRX11061496
- HiSeq 4000 Agilent SureSelect v7 capture SRX11061486
Note: SRX = expérience, SRR = run
Note trueseq non disponible ?
hg19 : https://www.biostars.org/p/144554/
IDT: lequel
https://www.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-hybridization-capture/pre-designed-hyb-cap-panels/exome-hyb-panel-v2
**** DONE Run avec [cite:@hwang2015]
CLOSED: [2023-11-29 Wed 23:37] SCHEDULED: <2023-11-28 Tue>
HiSeq2000 SRR515199 SureSelect v4 WES 298.45×
HiSeq2000 SRR098401 SureSelect v2 WES 116.84×
HiSeq2000 SRR1611178 SeqCap EZ Human Exome Lib v3.0 WES 79.93×
HiSeq2000 SRR1611179 SeqCap EZ Human Exome Lib v3.0 WES 79.84×
HiSeq2000 SRR292250 SeqCap EZ Exome SeqCap v2 WES 116.06×
HiSeq2500 SRR1611183 SeqCap EZ Human Exome Lib v3.0 WES 129.94×
HiSeq2500 SRR1611184 SeqCap EZ Human Exome Lib v3.0 WES 11
1.90×
Kit acessible ?
**** TODO Run selon [cite:@Kumaran_2019]
NA12878 SRR098401
NA24385 SRR2962669
NA24631 SRR2962693
**** Résumé
Kit disponible en hg38
| HiSeq 4000 | Agilent SureSelect v7 | SRX11061486 | https://github.com/kevinblighe/agilent |
| NovaSeq 6000 | Agilent SureSelect v7 | SRX11061516 | idem |
Kit disponible en hg19
| HiSeq2000 | SeqCap EZ Human Exome Lib v3.0 | SRR1611178 |http://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
| HiSeq2000 | SeqCap EZ Human Exome Lib v3.0 | SRR1611179 |idem
| HiSeq2500 | SeqCap EZ Human Exome Lib v3.0 | SRR1611183 |idem
| HiSeq2500 | SeqCap EZ Human Exome Lib v3.0 | SRR1611184 |idem
https://emea.support.illumina.com/downloads/truseq-exome-product-files.html
*** Autres
**** Selon [cite:@Kumaran_2019]
NA24385 SRR2962669
NA24631 SRR2962693
*** Liste de capture
Agilent sureselect v7 hg19 et 38 https://github.com/kevinblighe/agilent
**** UCSCS
- [[http://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/][hg19]]
- [[http://hgdownload.soe.ucsc.edu/gbdb/hg38/exomeProbesets/][hg38]]
**** github aztrazeneca
https://github.com/AstraZeneca-NGS/reference_data
- IDT xGen Exome Research Panel v1.0
- Agilent SureSelect Human All Exon V6
- Agilent SureSelect Clinical Research Exome
- Nimblegen SeqCap EZ MedExome
- Nmblegen SeqCap EZ Exome v3
**** Trueseq
https://emea.support.illumina.com/downloads/truseq-exome-product-files.html
*** Exemple de validation avec bcbio:
Télécharge données + bed + liftover avec crossmap
https://github.com/bcbio/bcbio_validation_workflows/blob/master/giab-exome/input/get_data.sh
*** TODO Comment télécharger
**** DONE Tester ligne de commande
CLOSED: [2023-11-29 Wed 23:37] SCHEDULED: <2023-11-28 Tue>
***** KILL Tester aws
CLOSED: [2023-11-28 Tue 23:47] SCHEDULED: <2023-11-28 Tue>
Semble télécharger le .sra vu la taille (manque l'extension)
#+begin_src
aws s3 cp s3://sra-pub-run-odp/sra/SRR1611178/SRR1611178 --no-sign-request .
#+end_src
***** KILL Tester sra faster dump
CLOSED: [2023-11-29 Wed 22:20] SCHEDULED: <2023-11-28 Tue>
Selon la doc https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump, il faut faire un "pré" - téléchargement
#+begin_src sh
prefetch SRR1611178
fastqer-dump SRR1611178
#+end_src
Note fasterq-dump créé un répertoire temporaire de la taille de prefetch et le supprime. Les fastq ne sont pas compressés
***** DONE Passer par ENA qui donne un lien vers FTP directement
CLOSED: [2023-11-29 Wed 23:37]
**** KILL Nextflow
CLOSED: [2023-12-04 Mon 23:46]
***** KILL fromSRA
CLOSED: [2023-11-29 Wed 23:15]
Ne renvoie pas le FTP pour SRR1611178/SRR1611178 même avec clé API
**** TODO DataToolkit.jl
SCHEDULED: <2023-11-28 Tue>
- plusieurs datasets par patient appelé NA12878 par exemple mais avec attributs différents (séquencer, kit, pair1, pair2)
- FTP depuis ENA (FTP)
- "meta"-dataset for the 2 fastq. Ex:
#+begin_src toml
[[data1]]
uuid = "4ac8e6a5-9430-4745-8027-551fa620c2a8"
description = "1"
[[data1.storage]]
driver = "filesystem"
checksum = "crc32c:96646914"
path = "1.txt"
[[data1.loader]]
driver = "io->file"
path = "lol.txt"
[[sequence]]
uuid = "adbaa0af-71fc-43f1-aa5d-408e9c2dc5be"
[[sequence.storage]]
driver = "raw"
value = { forward = "📇DATASET<<data1::DataToolkitBase.FilePath>>"}
[[sequence.loader]]
driver = "passthrough"
#+end_src
*** Zone de capture GIAB fourni le .bed pour l'exome . INfo : https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-exome-kit/downloads.html
*** Valider la méthode
- 1000 genomes + SureSelect human all exon v2 target capture kit : non disponible sur le site d'agilent (V6 ou plus)
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2928-9
- GIAB + liftover du fichire de capture en hg38
Ce qui est aussi fait par
https://bcbio-nextgen.readthedocs.io/en/stable/contents/germline_variants.html
Mais avec UCSC liftover
** Centogène
https://www.twistbioscience.com/node/23906
Bed non fourni pour exactement cette capture
On prend https://www.twistbioscience.com/resources/data-files/twist-alliance-vcgs-exome-401mb-bed-files
qui content la majeure partie
* Réunion
** <2023-08-10 Thu> Alexis
Ok pour bloquer le développment d'ici mardi prochain
Dév:
- pipeline jusque VEP en T2T + GRCh38
- ok pour valider spip T2T sur quelques variant => à intégrer au pipeline
- annotation :
- ok pour mobidetails hg38
- +OMIM T2T+ non
- +franklin hg38+ non pour le moment
- métriques (fastq a minima) + rapport multiqc
- optionnel
- reformater la sortie
- on abandonne
- XAMScissors ave indel
- parallélisation haplotype caller
- spliceai à la vollée
- pangolin
Test
- GIAB:
- hg38: ok pour refaire les tests NA12878 avec données cento, sinon ok pour "c'est difficile" sur les 3 fichiers de capture
- T2T: ok pour faire des tests rapides mais probablement pas assez de temps !
- patient de synthèse : variant cento confirém par sanger seuls
Résultats
- ok pour scale up bwa mem et haplotyecaller
Manuscrit
- validation de méthode : laisser tomber la version actuelle et faire comme strasbourg (cf ngs diag) dans la présentatino
- a envoyé le powerponit avec les références des différsences articles
- ok pour robo4 si résultat
- architecture cible = VM : 78 coeurs 54Go RAUM et 1To espace disque
Passage en production : ok pour présentation rapide du code
* Nixpkgs :nix:
** DONE GATK
CLOSED: [2023-05-06 Sat 08:51]
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185819][Binaire]]
CLOSED: [2022-09-10 Sat 23:53] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** KILL Corriger code pour utiliser source
CLOSED: [2022-09-11 Sun 22:05]
*** DONE Corriger PATH pour include java et python
CLOSED: [2022-10-11 Tue 11:46]
https://github.com/NixOS/nixpkgs/pull/191548
Review <2022-10-10 Mon> , corrigé dans la journée
*** DONE Update 4.3.0.0
CLOSED: [2023-04-13 Thu 09:01]
** HOLD Nextflow
*** KILL version script seule
CLOSED: [2023-04-01 Sat 18:29]
Fix pour SGE et nextflow
https://github.com/NixOS/nixpkgs/issues/192396
*** KILL Version avec gradle
CLOSED: [2022-10-09 Sun 22:51]
*** HOLD [[https://github.com/NixOS/nixpkgs/issues/192396][Bug report Version 22.10.6]]
**** Notes
Erreur :
ERROR: Cannot download nextflow required file -- make sure you can connect to the internet
Alternatively you can try to download this file:
https://www.nextflow.io/releases/v22.10.6/nextflow-22.10.6-all.jar
and save it as:
.//nix/store/md2b1ah4d7ivj82k8xxap30dmdci00pa-nextflow-22.10.6/bin/.nextflow-wrapped
Dans la mise à jour, il y a la création d'un environnement virtuel qui casse l'exécution de nextflow (besoin de télécharger)
Fix = désactiver
**** KILL Patch NXF_OFFLINE=true
CLOSED: [2023-07-02 Sun 11:02] SCHEDULED: <2023-06-11 Sun>
** TODO [[https://github.com/NixOS/nixpkgs/pull/249329][Multiqc]]
SCHEDULED: <2023-12-17 Sun>
HG002,sanger-chr20,data/HG002-sanger-inserted-chr20_1.fq.gz,data/HG002-sanger-inserted-chr20_2.fq.gz
** KILL Mutalyzer
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
Packaging faisable mais nombreux paquet python
** TODO Variant validator -> hgvs
C'est juste une interface autour d'hgvs mais il faut
- postgresql
- un accès ou télécharger des bases de données
Dépendences
s: wcwidth, pyee, pure-eval, ptyprocess, pickleshare, parsley, parse, fake-useragent, executing, backcall, appdirs, zipp, websockets, w3lib, urllib3, traitlets, tqdm, tabulate, sqlparse, soupsieve, six, pygments, psycopg2, prompt-toolkit, pexpect, parso, lxml, idna, humanfriendly, decorator, cython, cssselect, configparser, charset-normalizer, certifi, attrs, requests, pysam, pyquery, matplotlib-inline, jedi, importlib-metadata, coloredlogs, beautifulsoup4, asttokens, yoyo-migrations, stack-data, pyppeteer, bs4, bioutils, requests-html, ipython, biocommons.seqrepo, hgvs
** TODO SPIP :spip:
*** DONE PR upstream
CLOSED: [2023-08-12 Sat
dir id | uniq )
let bam = (ls bam/*/*.bam | get name | parse "{dir}/{full_id}/{id}_{S}.bqrt.bam" | select dir id
id}_{R}_001.fastq.gz" | select
18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** DONE Mail R. Lemann :T2T:
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** KILL Mise à jour T2T :T2T:
*** WAIT Corriger PR
SCHEDULED: <2024-01-02 Tue>
** TODO VEP :vep:
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185691][BioPerl]]
SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** DONE BioDBBBigFile
CLOSED: [2023-11-30 Thu 21:52]
:PROPERTIES:
:ORDERED: t
:END:
/Entered on/ [2022-08-10 Wed 14:28]
On utilise la dernière version de kent, donc plus de problème.
PRête à être mergé. Rebase faite<2023-07-02 Sun>
**** DONE Version de kent déjà packagée : forcer version 335
CLOSED: [2023-07-02 Sun 11:20]
***** KILL [[https://github.com/NixOS/nixpkgs/pull/206991][Restore building kent 404]]
CLOSED: [2023-05-06 Sat 17:40]
Review faite <2023-03-26 Sun> , atteinte merge]
Relancé <2023-05-06 Sat>
Kent 446 n'a pas ce problème donc PR inutile
***** DONE [[https://github.com/NixOS/nixpkgs/pull/223411][Ajouter les header to package]] (inc folder)
CLOSED: [2023-05-08 Mon 10:18] SCHEDULED: <2023-05-07 Sun>
Review à faire
https://github.com/NixOS/nixpkgs/pull/223411
Corrigé et plus besoin de la PR précédente
***** KILL [[https://github.com/NixOS/nixpkgs/pull/186462][BioDBBBigFile]] avec ces 2 changements
CLOSED: [2023-07-02 Sun 11:20]
**** KILL Version de kent déjà packagée : 404
CLOSED: [2023-03-27 Mon 16:43]
Compile mais les tests de passent pas
**** DONE Modifier selon PR https://github.com/NixOS/nixpkgs/pull/186462
CLOSED: [2023-07-30 Sun 22:01] SCHEDULED: <2023-07-30 Sun 20:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 19:13]--[2023-07-30 Sun 20:50] => 1:37
:END:
Modification nécessaire pour kent :
- plus de patch
- suppression d'une boucle dans postPatch
On supprime aussi NIX_BUILD_TOP
**** DONE Corriger PR biobigfile
CLOSED: [2023-11-30 Thu 21:52] SCHEDULED: <2023-12-05 Tue>
/Entered on/ [2023-10-15 Sun 17:21]
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186459][BioDBHTS]]
CLOSED: [2023-05-06 Sat 08:49] SCHEDULED: <2023-04-15 Sat>
/Entered on/ [2022-08-10 Wed 14:28]
Correction pour review faites <2022-10-10 Mon>
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186464][BioExtAlign]]
CLOSED: [2022-10-22 Sat 12:43] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-10 Wed 14:28]
Review <2022-10-10 Mon>, correction dans la journée.
Correction 2e passe, attente
Impossible de faire marcher les tests Car il ne trouve pas le module Bio::Tools::Align, qui est dans un dossier ailleurs dans le dépôt. Même en compilant tout le dépôt, cela ne fonctionne pas... On skip les tests.
*** TODO VEP
SCHEDULED: <2023-12-21 Thu>
** WAIT [[https://github.com/NixOS/nixpkgs/pull/230394][rtg-tools]] :vcfeval:
Soumis
** WAIT Package Spip https://github.com/NixOS/nixpkgs/pull/247476
** TODO Happy :happy:
*** TODO PR python 3 upstream
SCHEDULED: <2023-12-27 Wed>
*** TODO nixpkgs en l'état
SCHEDULED: <2023-12-27 Wed>
** PROJ SpliceAI
** TODO Bamsurgeon
/Entered on/ [2023-05-13 Sat 19:11]
*** TODO Velvet
** TODO PR Picard avec option pour gérer la mémoire
Similaire à
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/picard.sh
** DONE Gatk 4.5.0
CLOSED: [2023-12-17 Sun 22:02] SCHEDULED: <2023-12-15 Fri>
/Entered on/ [2023-12-15 Fri 18:58]
* Julia :julia:
** KILL XAM.jl: PR pour modification record :julia:
CLOSED: [2023-05-29 Mon 15:40] SCHEDULED: <2023-05-28 Sun>
/Entered on/ [2023-05-27 Sat 22:39]
** TODO XAMscissors.jl :xamscissors:
Modification de la séquence dans BAM.
*Pas de mise à jour de CIGAR*
On convertit en fastq et on lance le pipeline pour "corriger"
#+begin_src sh
cd /home/alex/code/bisonex/out/63003856/preprocessing/mapped
samtools view 63003856_S135.bam NC_000022.11 -o 63003856_S135_chr22.bam
cd /home/alex/recherche/bisonex/code/BamScissors.jl
cp ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135_chr22.bam .
samtools index 63003856_chr22.bam
#+end_src
Le script va modifier le bam, le trier et générer le fastq. !!!
Attention: ne pas oublier l'option -n !!!
#+begin_src sh
time julia --project=.. insertVariant.jl
scp 63003856_S135_chr22_{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
*** WAIT Implémenter les SNV avec VAF :snv:
Stratégie :
1. calculer la profondeur sur les positions
2. créer un dictionnaire { nom du reads : position dataframe }
3. itérer sur tous les reads et changer ceux marqués
**** DONE VAF = 1
CLOSED: [2023-05-29 Mon 15:34]
**** DONE VAF selon loi normale
CLOSED: [2023-05-29 Mon 15:35]
Tronquée si > 1
**** WAIT Tests unitaires
***** DONE NA12878: 1 gène sur chromosome 22
CLOSED: [2023-05-30 Tue 23:55]
root = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/"
#+begin_src sh
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878.bwa.markDuplicates.bam chr22 -o project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam chr22:19419700-19424000 -o NIST7035_H7AP8ADXX_NA12878_chr22_MRPL40_hg19.bam
#+end_src
***** WAIT Pull request formatspeciment
https://github.com/BioJulia/FormatSpecimens.jl/pull/8
***** DONE Formatspecimens
CLOSED: [2023-05-29 Mon 23:03]
****** DONE 1 read
CLOSED: [2023-05-29 Mon 23:02]
****** DONE VAF sur 1 exon
CLOSED: [2023-05-29 Mon 23:03]
**** DONE [#A] Bug: perte de nombreux reads avec NA12878
CLOSED: [2023-08-19 Sat 20:45] SCHEDULED: <2023-08-18 Fri>
:PROPERTIES:
:ID: 5c1c36f3-f68e-4e6d-a7b6-61dca89abc37
:END:
Ex: chrX:g.124056226 : on passe de 65 reads à 1
Test xamscissors: pas de soucis...
On teste sur cette position +/- 200bp
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
samtools view /home/alex/code/bisonex/out/2300346867_NA12878-63118093_S260-GRCh38/preprocessing/mapped/2300346867_NA12878-63118093_S260-GRCh38.bam chrX:124056026-124056426 -o chrXsmall.bam
#+end_src
#+RESULTS:
***** DONE Vérifier profondeur avec dernière version :
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
****** DONE chr20: profondeur ok
SCHEDULED: <2023-08-19 Sat>
****** DONE toutes les données
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
Ok pour 7 variants (IGV) notament chromosome X
*** TODO Implémenter les indel avec VAF :indel:
*** TODO Soumission paquet
* Données
:PROPERTIES:
:CATEGORY: data
:END:
** DONE Remplacer bam par fastq sur mesocentre
CLOSED: [2023-04-16 Sun 16:33]
Commande
*** DONE Supprimer les fastq non "paired"
CLOSED: [2023-04-16 Sun 16:33]
nushell
Liste des fastq avec "paired-end" manquant
#+begin_src nu
ls **/*.fastq.gz | get name | path basename | split column "_" | get column1 | uniq -u | save single.txt
#+end_src
#+RESULTS:
: 62907927
: 62907970
: 62899606
: 62911287
: 62913201
: 62914084
: 62915905
: 62921595
: 62923065
: 62925220
: 62926503
: 62926502
: 62926500
: 62926499
: 62926498
: 62931719
: 62943423
: 62943400
: 62948290
: 62949205
: 62949206
: 62949118
: 62951284
: 62960792
: 62960785
: 62960787
: 62960617
: 62962561
: 62962692
: 62967473
: 62972194
: 62979102
On vérifie
#+begin_src nu
open single.txt | lines | each {|e| ls $"fastq/*_($in)/*" | get 0 }
open single.txt | lines | each {|e| ls $"fastq/*_($in)/*" | get 0.name } | path basename | split column "_" | get column1 | uniq -c
#+end_src
On met tous dans un dossier (pas de suppression )
#+begin_src
open single.txt | lines | each {|e| ls $"fastq/*_($in)/*" | get 0 } | each {|e| ^mv $e.name bad-fastq/}
#+end_src
On vérifie que les dossiier sont videsj
open single.txt | lines | each {|e| ls $"fastq/*_($in)" | get 0.name } | ^ls -l $in
Puis on supprime
open single.txt | lines | each {|e| ls $"fastq/*_($in)" | get 0.name } | ^rm -r $in
*** DONE Supprimer bam qui ont des fastq
CLOSED: [2023-04-16 Sun 16:33]
On liste les identifiants des fastq et bam dans un tableau avec leur type :
#+begin_src
let fastq = (ls fastq/*/*.fastq.gz | get name | parse "{dir}/{full_id}/{
# -*- mode: org -*-
* DONE Reading task leçon 8
:PROPERTIES:
:ARCHIVE_TIME: 2022-03-26 Sat 13:09
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japonais
:END:
* DONE Reading task leçon 9
:PROPERTIES:
:ARCHIVE_TIME: 2022-03-26 Sat 13:09
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japonais
:END:
* DONE Notes leçon <2022-03-20 Sun>
SCHEDULED: <2022-04-03 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-09 Sat 00:16
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japonais
:END:
* DONE Notes leçon <2022-03-27 Sun>
SCHEDULED: <2022-04-03 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-09 Sat 00:16
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japonais
:END:
* DONE Notes leçon <2022-04-03 Sun>
SCHEDULED: <2022-04-03 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-09 Sat 00:16
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japonais
:END:
* DONE Prendre RV dermotologue
CLOSED: [2022-04-03 Sun 11:47] DEADLINE: <2022-04-02 Sat>
:PROPERTIES:
:CATEGORY: sante
:ARCHIVE_TIME: 2022-04-09 Sat 00:16
:ARCHIVE_CATEGORY: sante
:ARCHIVE_TODO: DONE
:END:
* DONE Convertir tâches Taskarrior en attente -> org mode
DEADLINE: <2022-03-26 Sat 14:00>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-09 Sat 00:16
:ARCHIVE_OLPATH: Emacs
:ARCHIVE_CATEGORY: emacs
:ARCHIVE_TODO: DONE
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:END:
:LOGBOOK:
CLOCK: [2022-03-26 Sat 12:28]--[2022-03-26 Sat 12:58] => 0:30
:END:
[[file:/usr/home/alex/.doom.d/config.el::setq org-directory "~/org/"]]
* DONE Mail avec notmuch
DEADLINE: <2022-03-27 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-09 Sat 00:16
:ARCHIVE_OLPATH: Emacs
:ARCHIVE_CATEGORY: emacs
:ARCHIVE_TODO: DONE
:END:
* DONE Finir importer org-mode tâches finies depus taskwarrior
DEADLINE: <2022-03-26 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-09 Sat 00:16
:ARCHIVE_OLPATH: Emacs
:ARCHIVE_CATEGORY: emacs
:ARCHIVE_TODO: DONE
:END:
:LOGBOOK:
CLOCK: [2022-03-26 Sat 13:27]
:END:
* DONE Billets de train + carte réduction :florian:
DEADLINE: <2022-03-27 Sun>
:PROPERTIES:
:CATEGORY: mariage
:ARCHIVE_TIME: 2022-04-09 Sat 00:16
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: mariage
:ARCHIVE_TODO: DONE
:END:
* DONE novembre 2021
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-09 Sat 00:17
:ARCHIVE_OLPATH: Ledger
:ARCHIVE_CATEGORY: compta
:ARCHIVE_TODO: DONE
:END:
* DONE décembre 2021
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-09 Sat 00:17
:ARCHIVE_OLPATH: Ledger
:ARCHIVE_CATEGORY: compta
:ARCHIVE_TODO: DONE
:END:
Il faut l'avis de l'amende donc on peut s'assoir dessus...
* DONE Notes leçon <2022-03-20 Sun>
SCHEDULED: <2022-04-03 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-17 Sun 11:13
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japonais
:END:
* DONE Notes leçon <2022-03-27 Sun>
SCHEDULED: <2022-04-03 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-17 Sun 11:14
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japonais
:END:
* DONE Notes leçon <2022-04-03 Sun>
SCHEDULED: <2022-04-03 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-17 Sun 11:14
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: japonais
:END:
* DONE Rendre le coran
CLOSED: [2022-04-16 Sat 21:40] DEADLINE: <2022-04-14 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-23 Sat 17:14
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Certificat trail
SCHEDULED: <2022-04-21 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-23 Sat 17:16
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* Genome
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-19 Thu 22:28
:ARCHIVE_OLPATH: Projet
:ARCHIVE_CATEGORY: projets
:END:
** KILL Regarder trafic réseau
SCHEDULED: <2022-04-12 Tue>
1. /Login avec
nomNetbios ""
username "XXXX"
password "YYY"
returnUrl "/"
operation ""
emailOuSms ""
Mais on peut directvement faire
emailOuSms "sms"
2. Générer le cookie puis avoir le token en faisant une requête get
* DONE taskwarrior tui 0.22
CLOSED: [2022-04-10 Sun 17:41] SCHEDULED: <2022-04-10 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-20 Fri 22:17
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: freebsd
:END:
* DONE opengraph v 0.6.3
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-20 Fri 22:17
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: freebsd
:END:
Ok 3.10->3.7
* DONE Kitty 0.25
CLOSED: [2022-04-17 Sun 17:19] SCHEDULED: <2022-04-13 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-20 Fri 22:17
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: freebsd
:END:
* DONE Revoir progression pour anneaux
SCHEDULED: <2022-05-03 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-30 Mon 22:07
:ARCHIVE_OLPATH: Sport
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Préparer <2022-04-17 Sun>
CLOSED: [2022-04-17 Sun 17:18] DEADLINE: <2022-04-17 Sun 12:30>
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-12 Sun 15:20
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:END:
* DONE Notes <2022-04-24 Sun>
SCHEDULED: <2022-04-24 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-12 Sun 15:20
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:END:
*
* DONE Échanger T-shirt Chullanka
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-18 Sat 17:39
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Renvoyé<2022-05-07 Sat>
Rappeler pour voir avec code postal
Vont renvoyer
* KILL Demande interchu Grenoble novembre 2022
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-09 Sat 13:35
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
** DONE Mail PrThevenon
* DONE Changer ampoule
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-09 Sat 13:35
:ARCHIVE_OLPATH: Electricité
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: maison
:END:
Chèque envoyé<2022-07-16 Sat>
* DONE Notes <2022-04-17 Sun>
SCHEDULED: <2022-04-17 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-16 Sat 17:51
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:END:
* DONE Notes <2022-06-12 Sun>
DEADLINE: <2022-06-12 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-16 Sat 17:51
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:END:
** DONE Récupérer compte-rendu IRM mère
** DONE Relecture via Chloé à Bordeaux
LOSED: [2022-05-12 Thu 15:15]
ransmis<2022-05-05 jeu.>
** KILL Relecture par le Dr Pomero
*** KILL Appeler au téléphone
DEADLINE: <2022-06-01 Wed>
* DONE Mémoire
:PROPERTIES:
:CATEGORY: memoire
:ARCHIVE_TIME: 2022-07-21 Thu 14:30
:ARCHIVE_CATEGORY: memoire
:ARCHIVE_TODO: DONE
:END:
** DONE Plan
CLOSED: [2022-05-05 jeu. 17:56] DEADLINE: <2022-05-04 mer. 19:00>
** DONE V1
*** DONE Introduction
*** DONE BPAN
**** Phenotype
**** WDR45
*** DONE Case report
**** DONE Family 1
**** DONE Family 2
**** DONE Discussion
*** DONE Conclusion
*** DONE Correction Juliette BPAN + clinique
ok -> intro
** DONE envoyer intro + context + clinique à Juliette pour relecture
DEADLINE: <2022-05-22 Sun>
** KILL Figure avec tikz des variant sur la séquence d'acide aminé
Missense seulement
* KILL Article
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 14:31
:ARCHIVE_CATEGORY: wdr45
:ARCHIVE_TODO: KILL
:END:
** Réunion du <2022-05-05 jeu.> : on commence le fonctionnel, attendre de leur nouvelles pour publier
** Rajouter Sandrine Passemard dans les co-auteurs
* DONE Fonctionnel
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 14:31
:ARCHIVE_CATEGORY: wdr45
:ARCHIVE_TODO: DONE
:END:
** DONE Mail Patricia Maurin
ajouter âge du patient et IRM mère
** DONE Réunion avec Patricia Maurin
CLOSED: [2022-05-05 jeu. 17:44]
Vont lancer les tests mais ne sera pas prêt pour le mémoire
atients intéressant car phénotype mild
** KILL Mail Binnaz Yalcin
egarder sa biblio avant !
** DONE Démarré analyse
LOSED: [2022-05-05 jeu. 17:57]
** DONE Demander si on peut rajouter des patients
* DONE Reprendre le phénotype des garçons
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 14:40
:ARCHIVE_OLPATH: Recherche/WDR45/Biblio
:ARCHIVE_CATEGORY: wdr45
:ARCHIVE_TODO: DONE
:END:
* KILL ATCD familiaux pour fammile d’Alain Verloes
CLOSED: [2022-05-05 jeu. 17:57]
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 14:49
:ARCHIVE_CATEGORY: wdr45
:ARCHIVE_TODO: KILL
:END:
* DONE taskwarrior tui 0.23.4
SCHEDULED: <2022-05-20 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 15:18
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: freebsd
:END:
* DONE Réclamer pour majoration pour taxe foncière :maison:
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 22:45
:ARCHIVE_CATEGORY: inbox
:ARCHIVE_TODO: DONE
:END:
Mail envoyé<2022-07-16 Sat>
* Base de données
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 22:54
:ARCHIVE_OLPATH: Recherche/Mustard
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_ITAGS: mustard
:END:
** KILL Mysql
*** DONE Biblio
*** DONE Conception papier
*** DONE Prototype
*** DONE import tsv labkey
*** KILL ajout pièces jointes
*** KILL Demande hébergement
*** DONE Point avec Pierre
**On essaye avec excel ?
**Trop ambitieux (long, compliqué et problèmes de droits)
** KILL Site
*** KILL Prototype django/flask
* KILL Vc-darcs
:PROPERTIES:
:CUSTOM_ID: vc-darcs
:ARCHIVE_TIME: 2022-07-23 Sat 00:14
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_OLPATH: Projets personnels
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: KILL
:END:
- ☐ Corriger record
- Ajouter support pour push
* KILL org-nutrition Tracker de calories (lisp)
:PROPERTIES:
:CUSTOM_ID: org-nutrition-tracker-de-calories-lisp
:ARCHIVE_TIME: 2022-07-23 Sat 00:14
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_OLPATH: Projets personnels
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: KILL
:END:
*** Offline ?
:PROPERTIES:
:CUSTOM_ID: offline
:END:
1. Data [[https://fdc.nal.usda.gov/download-datasets.html]] Notamment :
full
[[https://fdc.nal.usda.gov/fdc-datasets/FoodData_Central_csv_2021-04-28.zip]]
CSV [[https://github.com/mrc/el-csv]] SQL
[[https://github.com/skeeto/emacsql]]
*** KILL REST ?
:PROPERTIES:
:CUSTOM_ID: kill-rest
:END:
[[https://tkf.github.io/emacs-request/]]
[[https://fdc.nal.usda.gov/api-guide.html]]
*** KILL Comparer REST et offline en performances
:PROPERTIES:
:CUSTOM_ID: kill-comparer-rest-et-offline-en-performances
:END:
REST: search renvoie vraiment trop de résultats... Plus logique de le
faire avec le CSV mais les données sont éparpillées
*** KILL comprendr les données
:PROPERTIES:
:CUSTOM_ID: comprendr-les-données
:END:
1. Exploration
Doc: [[https://fdc.nal.usda.gov/portal-data/external/dataDictionary]]
food.csv: contient l'identifiant (fdc_{id}) et le nom (description)
ex:
"fdc_{id}","data_{type}","description","food_{categoryid}","publication_{date}"
food_{nutrient}.csv contient l'information intéressante pour l'ID
(fdc_{id})
"id","fdc_{id}","nutrient_{id}","amount","data_{points}","derivation_{id}","min","max","median","footnote","min_{yearacquired}"
Exemple : huile WESSON (fdc_{id} = 1105904) : foods.csv:
"1105904","branded_{food}","WESSON Vegetable Oil 1
GAL","","2020-11-13"
A beaucoup de nutrients : food_{nutrients}.csv:
"1009437","1105904","","","Ingredients","3"
"13706913","1105904","203","0","","71","","","","",""
"13706914","1105904","204","93.33","","71","","","","",""
"13706915","1105904","205","0","","75","","","","",""
"13706916","1105904","208","867","","71","","","","",""
"13706917","1105904","269","0","","71","","","","",""
"13706918","1105904","291","0","","75","","","","",""
"13706919","1105904","301","0","","75","","","","",""
"13706920","1105904","303","0","","75","","","","",""
"13706921","1105904","306","0","","75","","","","",""
"13706922","1105904","307","0","","75","","","","",""
"13706923","1105904","318","0","","75","","","","",""
"13706924","1105904","324","0","","75","","","","",""
"13706925","1105904","401","0","","75","","","","",""
"13706926","1105904","601","0","","75","","","","",""
"13706927","1105904","605","0","","71","","","","",""
"13706928","1105904","606","13.33","","71","","","","",""
"13706929","1105904","645","20","","71","","","","",""
"13706930","1105904","646","53.33","","71","","","","",""
En enlevant ceux qui sont nul (amount = 0)
"1009437","1105904","","","Ingredients","3"
"13706914","1105904","204","93.33","","71","","","","",""
"13706916","1105904","208","867","","71","","","","",""
"13706914","1105904","204","93.33","","71","","","","",""
"13706916","1105904","208","867","","71","","","","",""
En enlevant ceux qui sont redondant, on retrouve 5 (différents des 3
mentionnés ??) food_{nutrients}.csv
"13706914","1105904","204","93.33","","71","","","","",""
"13706916","1105904","208","867","","71","","","","",""
"13706928","1105904","606","13.33","","71","","","","",""
"13706929","1105904","645","20","","71","","","","",""
"13706930","1105904","646","53.33","","71","","","","",""
Les codes ne correspondent pas à nutrient.csv ou
nutrient_{incomingname}. mais d'après le site
[[https://fdc.nal.usda.gov/fdc-app.html#/food-details/1455596/nutrients]]
(au passage, l'ID est encore différent) :
- 204 = lipid
- 208 = énergie
- 606 = fat total saturated
- 645 = fat total monounsaturated
- 646 = fat total polyunsaturated
En fait, le code est donné par nutrient_{nbr} dans nutrients.csv (!)
2. En résumé
Requirements : food.csv, nutrient.csv, food_{nutrients}.csv
1. Chercher l'ID dans food.csv (nom = description, id = fdc_{id})
2. Pour fdc_{id}, obtenir la liste des nutriments (nutrient_{id})
avec leurs valeurs (amonut) dans food_{nutrients}.csv
3. Convertir l'Id nutrient (nutrient_{nbr} = nutrient_{id}) en son
nom (nutrient_{nbr})avec nutrient.csv
* DONE Mémoire
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-23 Sat 11:04
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Génétique/DIU dysmorpho
:ARCHIVE_CATEGORY: dysmorpho
:ARCHIVE_TODO: DONE
:END:
* DONE Mail Dijon pour expliquer que c’est décalé :interchu:
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-23 Sat 11:04
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Envoyer fiche de salaire
:PROPERTIES:
:ARCHIVE_TIME: 2022-08-20 sam. 21:51
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Banque/Compte et CB société générale
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: banque
:END:
Non reproductible
* DONE v25.2
:PROPERTIES:
:ARCHIVE_TIME: 2022-09-07 Wed 23:26
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: FreeBSD/Kitty
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: freebsd
:END:
** DONE Soumettre
** DONE PR upstream pour _Static_assert (cf https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=265393)
SCHEDULED: <2022-08-20 sam.>
Si confirmé, fermé la PR
Sinon, enlevé <assert.h>
** DONE Plus de patch nécessaire ? Réouvert bug sur bugzilla
* DONE Payer amende majorée 75€ , provenance inconnue
:PROPERTIES:
:ARCHIVE_TIME: 2022-09-07 Wed 23:27
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Divers/Amendes
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
- [X] Chèque envoyé parti <2022-08-20 sam.>
- [X] Envoyer un mail
- [X] Virement boursorama pour anticiper
* KILL SGE: sur ancien cluster donc plus d’actualité
:PROPERTIES:
:ARCHIVE_TIME: 2022-09-10 Sat 12:46
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/Pipeline exome/Nouveau workflow/Bases de données/Processing bases de données
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: KILL
:END:
* KILL Problèmes rencontrés à l’install
CLOSED: [2022-09-19 Mon 22:37]
:PROPERTIES:
:ARCHIVE_TIME: 2022-09-19 Mon 22:37
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/Pipeline exome
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: KILL
:END:
- [X] Dossier de log non créé
- [ ] Pourquoi avoir ne pas simplement utiliser list_of_fastq.txt directement ?
- [ ] Supprimé du code
- [ ] Rajouter boucle sur plusieurs fichiers
* DONE Problème de scheduling Slurm sur helios :
CLOSED: [2022-10-09 Sun 22:27]
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-09 Sun 22:28
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/Pipeline exome/Nouveau workflow/Bases de données/Processing bases de données
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: DONE
:END:
- squeue ne fonctionne pas
- nextflow finit par quitter alors que le job tourne
Issue soumis sur github: https://github.com/nextflow-io/nextflow/issues/1644
Seule la version Nix ne fonctionne pas alors que c’est le même executable... !!
* DONE Utiliser nf-core plutôt que nos fonction
CLOSED: [2022-10-09 Sun 22:27]
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-09 Sun 22:28
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/Pipeline exome/Nouveau workflow/Bases de données/Processing bases de données
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: DONE
:END:
* KILL Utiliser 1000 genome pour known_snp ?
CLOSED: [2022-09-19 Mon 22:37]
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-09 Sun 22:30
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/Pipeline exome/Améliorations
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: KILL
:END:
Apparement, déjà dans dbSNP
https://www.internationalgenome.org/category/dbsnp/
* Libraries
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-16 Sun 09:32
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Learning Haskell
:ARCHIVE_CATEGORY: projects
:ARCHIVE_ITAGS: haskell
:END:
- [X] Shelly - [X] Xmonad
= - Récup de l'écran=\\
= - Faire un projet cabal=
* Concepts
:PROPERTIES:
:CUSTOM_ID: concepts
:ARCHIVE_TIME: 2022-10-16 Sun 09:32
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Learning Haskell
:ARCHIVE_CATEGORY: projects
:ARCHIVE_ITAGS: haskell
:END:
- [X] Functional dependencies
= - [X] =[[https://www.youtube.com/watch?v=JleVecHAad4][=An`` ``introduction`` ``to`` ``Haskell's`` ``kinds=]]= =\\
= - [X] =[[https://www.youtube.com/watch?v=Qy_yxVkO8no][=Getting`` ``a`` ``little`` ``fancy`` ``with`` ``Haskell's`` ``kinds=]]
- [ ] Backpack
= - [ ] =[[http://blog.ezyang.com/2016/10/try-backpack-ghc-backpack/][=Part`` ``1=]]\\
= - [ ] =[[https://sebfisch.github.io/haskell-regexp/regexp-play.pdf][=https://sebfisch.github.io/haskell-regexp/regexp-play.pdf=]]\\
= - [ ] =[[http://blog.ezyang.com/2017/01/try-backpack-cabal-packages/][=Part`` ``2=]]
- [X]
[[https://www.quora.com/What-are-some-practical-uses-of-bifunctors-in-Haskell/answer/James-Bowen-13][Bifunctors]]
* Concepts
:PROPERTIES:
:CUSTOM_ID: concepts
:ARCHIVE_TIME: 2022-10-16 Sun 09:32
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Learning Haskell
:ARCHIVE_CATEGORY: projects
:ARCHIVE_ITAGS: haskell
:END:
- [X] Functional dependencies
= - [X] =[[https://www.youtube.com/watch?v=JleVecHAad4][=An`` ``introduction`` ``to`` ``Haskell's`` ``kinds=]]= =\\
= - [X] =[[https://www.youtube.com/watch?v=Qy_yxVkO8no][=Getting`` ``a`` ``little`` ``fancy`` ``with`` ``Haskell's`` ``kinds=]]
- [ ] Backpack
= - [ ] =[[http://blog.ezyang.com/2016/10/try-backpack-ghc-backpack/][=Part`` ``1=]]\\
= - [ ] =[[https://sebfisch.github.io/haskell-regexp/regexp-play.pdf][=https://sebfisch.github.io/haskell-regexp/regexp-play.pdf=]]\\
= - [ ] =[[http://blog.ezyang.com/2017/01/try-backpack-cabal-packages/][=Part`` ``2=]]
- [X]
[[https://www.quora.com/What-are-some-practical-uses-of-bifunctors-in-Haskell/answer/James-Bowen-13][Bifunctors]]
* KILL taskwarrior v0.23.5
CLOSED: [2022-10-20 Thu 23:06] SCHEDULED: <2022-07-31 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-20 Thu 23:06
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: FreeBSD
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: freebsd
:END:
/Entered on/ [2022-07-31 Sun 09:59]
* DONE Nettoyer canapé cuir
CLOSED: [2022-10-22 Sat 23:33] SCHEDULED: <2022-09-06 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-22 Sat 23:33
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
Acheter lait démaquillant
* DONE Corriger erreur de facturation bouyges + renouveler
SCHEDULED: <2022-09-03 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-22 Sat 23:33
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
* DONE Abstract club génétique de l’est
CLOSED: [2022-10-22 Sat 23:33] DEADLINE: <2022-09-15 Thu> SCHEDULED: <2022-09-13 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-22 Sat 23:33
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/NF1/Tâches
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: nf1
:END:
* DONE Avis Paul sur arguments
CLOSED: [2022-09-11 Sun 22:03]
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-22 Sat 23:33
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/NF1/Tâches
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: nf1
:END:
Envoyé <2022-08-09 Tue>
* DONE Accord Domiinque VIAUD
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-22 Sat 23:33
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/NF1/Tâches
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: nf1
:END:
Mail envoyé par Juliette
* DONE Observatoire TED
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-22 Sat 23:33
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/NF1/Tâches
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: nf1
:END:
Non
* Droit au remords
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-25 Tue 16:40
:ARCHIVE_FILE: ~/org-home/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:END:
** DONE Envoi scolarité
CLOSED: [2022-10-25 Tue 16:40]
** DONE Négocier avec Xavier Bertrand pour stage de clinique
SCHEDULED: <2022-07-28 Thu>
Revient de vacances à ce moment environ
* DONE Quillbot
CLOSED: [2023-01-03 Tue 22:54]
:PROPERTIES:
:ARCHIVE_TIME: 2023-01-03 Tue 22:54
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Projets personnels
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
Possible d'utiliser selenium tout le long
Mais si on copy lese cookies et headers depuis le navigateur:
- on peut bypasser cloudflare (vu qu'on a le résultat)
- mais au lieu d'avoir un json, on a du binaire...
* DONE CVEC
CLOSED: [2022-11-20 Sun 21:30]
:PROPERTIES:
:ARCHIVE_TIME: 2023-02-12 Sun 23:16
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Déclaration stage
CLOSED: [2022-11-20 Sun 21:31]
:PROPERTIES:
:ARCHIVE_TIME: 2023-02-12 Sun 23:16
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
Corrigée ce jour
* DONE Inscription fac
CLOSED: [2023-02-12 Sun 23:16] DEADLINE: <2022-12-01 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-02-12 Sun 23:16
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
** DONE Payer
CLOSED: [2022-12-05 Mon 21:23]
** DONE Documents
CLOSED: [2022-12-05 Mon 21:23]
manque fiche attestation
* DONE Compte et CB société générale :banque:
CLOSED: [2023-02-12 Sun 23:16]
:PROPERTIES:
:ARCHIVE_TIME: 2023-02-12 Sun 23:16
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
** KILL Envoyer relevé
** DONE Transfert compte bancaire
CLOSED: [2022-10-22 Sat 23:35] SCHEDULED: <2022-07-21 Thu>
*** DONE Virement pour éviter les défauts de rélèvements
** DONE Demander chequier
CLOSED: [2023-02-12 Sun 23:16] SCHEDULED: <2023-01-02 Mon>
*** DONE Demander au CHU pour le transfert (cela fait 2 mois)
CLOSED: [2022-12-03 Sat 12:34] SCHEDULED: <2022-10-24 Mon>
** DONE Demander DAM transfert compte bancaire
CLOSED: [2023-02-12 Sun 23:16]
Mail envoyé <2022-11-26 Sat>
* DONE Renouveler abonnement
CLOSED: [2022-12-05 Mon 21:22] SCHEDULED: <2022-12-05 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2023-02-12 Sun 23:18
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
"Je veux changer d'abonnement sur la hotline" pour avoir le service commercial
* DONE pkg-config problème avec 0.26.2
CLOSED: [2022-09-22 Thu 10:45]
:PROPERTIES:
:ARCHIVE_TIME: 2023-04-13 Thu 09:01
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: FreeBSD/Kitty
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: freebsd
:END:
* DONE 0.26.4
CLOSED: [2022-10-20 Thu 23:05]
:PROPERTIES:
:ARCHIVE_TIME: 2023-04-13 Thu 09:01
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: FreeBSD/Kitty
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: freebsd
:END:
* DONE Patch pour utiliser openssl base
CLOSED: [2022-10-20 Thu 23:05]
:PROPERTIES:
:ARCHIVE_TIME: 2023-04-13 Thu 09:01
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: FreeBSD/Kitty
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: freebsd
:END:
* KILL Amsteriskm
CLOSED: [2023-05-28 Sun 10:03]
:PROPERTIES:
:ARCHIVE_TIME: 2023-05-28 Sun 10:03
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Projets personnels
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: KILL
:END:
** Objectif
Plus courte distance entre 2 films
** Données
https://datasets.imdbws.com/
Autres : https://www.kaggle.com/datasets/rounakbanik/the-movies-dataset
Acteurs + crédits
** Langage
Chargement des donnése IMDB (title.principals.tsv): 4min en python, du killer le processus en haskell...
Attention, prend toute la RAM
** Outils
Référence :
https://medium.com/web-mining-is688-spring-2021/network-graphs-of-actors-based-on-popular-movies-in-common-69d30e7b5e07
Faire le graphe + visualisation avec pandas + viscc + dash : https://towardsdatascience.com/visualizing-networks-in-python-d70f4cbeb259 (option 3)
** Stratégie
1ere version : noeud = acteur, arête = film en commun
2ere version : noeud = film , arête = acteur en commun
Plutôt la seconde version
* KILL Mettre à jour juliastats
CLOSED: [2023-05-28 Sun 10:04]
:PROPERTIES:
:ARCHIVE_TIME: 2023-05-28 Sun 10:04
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Julia
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: julia
:END:
https://discourse.julialang.org/t/suggestion-for-homepage-of-https-juliastats-org/94948/2
* Stockage
:PROPERTIES:
:ARCHIVE_TIME: 2023-05-28 Sun 10:04
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/Mustard
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_ITAGS: mustard
:END:
** DONE Accès scality au travail
** KILL VPN pour Jehanne
CLOSED: [2023-05-28 Sun 10:04]
* DONE Demander accès
CLOSED: [2022-11-19 Sat 17:36]
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-02 Sun 10:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Gentoo/GURU
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
* FreeBSD :freebsd:
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-07 Fri 18:46
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_CATEGORY: projects
:END:
** KILL ormolu 0.5.0.0
CLOSED: [2022-10-22 Sat 23:36] SCHEDULED: <2022-07-30 Sat>
** Kitty
*** KILL Problème sur fetchdir
CLOSED: [2022-09-22 Thu 10:45]
Commiter au courant, attente de résolution
** KILL [[https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=264158][pkgconf est trop lent sur freebsd]]
CLOSED: [2023-07-07 Fri 18:46]
Problème persiste avec dernière version
* DONE Ordure ménagères
CLOSED: [2023-06-11 Sun 21:40]
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-07 Fri 18:51
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
Envoyé RIB le <2023-06-11 Sun>
* DONE Badge déchetterie
CLOSED: [2023-07-07 Fri 18:48] SCHEDULED: <2023-07-12 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-07 Fri 18:51
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-07-02 Sun 11:03]
* DONE Changer kit chaine
CLOSED: [2023-04-01 Sat 17:24] SCHEDULED: <2023-04-01 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-07 Fri 18:51
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Moto
:ARCHIVE_CATEGORY: moto
:ARCHIVE_TODO: DONE
:END:
RV pris yamah
41000km
* DONE Cadeaux Maxence + Emy
CLOSED: [2023-07-07 Fri 18:40]
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:46
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Famille
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-07-02 Sun 10:53]
Maxence : Éveil musical
* Japonais
:PROPERTIES:
:CATEGORY: japonais
:ARCHIVE_TIME: 2023-07-30 Sun 14:46
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Langues
:ARCHIVE_CATEGORY: japonais
:END:
** Miura [7/7]
*** DONE Leçon 1 [/]
**** DONE Lire
**** DONE Anki
*** KILL Leçon 2 [2/2]
CLOSED: [2023-07-07 Fri 18:48]
**** DONE Lire
**** KILL Anki
CLOSED: [2023-07-07 Fri 18:48]
***** KILL Grammaire
CLOSED: [2023-07-07 Fri 18:48]
*** KILL Leçon 3
CLOSED: [2023-07-07 Fri 18:44]
**** DONE Lire
**** KILL Anki
CLOSED: [2023-07-07 Fri 18:44]
***** KILL Grammaire
CLOSED: [2023-07-07 Fri 18:44]
*** KILL Leçon 4
CLOSED: [2023-07-07 Fri 18:44]
**** DONE Lire
**** KILL Anki
CLOSED: [2023-07-07 Fri 18:44]
***** KILL Grammaire
CLOSED: [2023-07-07 Fri 18:44]
*** KILL Leçon 5
CLOSED: [2023-07-07 Fri 18:44]
**** DONE Lire
**** KILL Anki
CLOSED: [2023-07-07 Fri 18:44]
***** KILL Grammaire
CLOSED: [2023-07-07 Fri 18:44]
*** KILL Leçon 6
CLOSED: [2023-07-07 Fri 18:44]
**** DONE Lire
**** KILL Anki
CLOSED: [2023-07-07 Fri 18:44]
***** KILL Grammaire
CLOSED: [2023-07-07 Fri 18:44]
*** KILL Leçon 7
CLOSED: [2023-07-07 Fri 18:44]
**** KILL Lire
CLOSED: [2023-07-07 Fri 18:44]
**** KILL Anki
CLOSED: [2023-07-07 Fri 18:44]
***** KILL Grammaire
CLOSED: [2023-07-07 Fri 18:44]
*** Lire
** Leçon Aya
:PROPERTIES:
:CATEGORY: aya
:END:
*** KILL Lire dialogue fin leçon 10
CLOSED: [2022-12-03 Sat 12:34] SCHEDULED: <2022-07-30 Sat>
* CentoX
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:47
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Projets personnel
:ARCHIVE_CATEGORY: projects
:END:
** Raw data
*** DONE Ne plus utiliser les .size mais récupérer directement la taille sur le serveur
CLOSED: [2022-07-26 Tue 17:36]
*** DONE Faire fonctionner taches récurrente avec Windows
CLOSED: [2022-11-19 Sat 17:34]
Erreur 0x1 : a priori résolu en démarrant le script dans le bon répertoire...
** Notes
*** Extraction de données
- Trop compliqué de travailles sur la structure du pdf
- Extraire le tableau avec python ?
- Comparaison
- pdftotext : bon résultats sur page 1. Sur les ségrégations, il n’y a pas de retour à la ligne avant l’indication
- pdfminer donne des résultats légèrement supérieurs, beaucoup d’espaces sur les ségrégations
- pypdf2 : trop de retours à la lignes intempestifs dans le texte
La structure du tableau est perdue dans tous les cas
*** Parser
Liste de parser : https://tomassetti.me/parsing-in-python/
* Assistant
:PROPERTIES:
:CATEGORY: assistant
:ARCHIVE_TIME: 2023-07-30 Sun 14:47
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Projets personnel
:ARCHIVE_CATEGORY: assistant
:END:
** DONE Regarder ce qu'Yvain a fait
* DONE Amende
CLOSED: [2023-07-30 Sun 14:47]
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:47
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
** DONE Changement d'adresse carte grise
CLOSED: [2023-06-11 Sun 21:40]
** DONE Envoyer photocopie carte grise pour éviter majoration
CLOSED: [2023-07-02 Sun 10:52] SCHEDULED: <2023-06-18 Sun>
* DONE Contrôle technique
CLOSED: [2023-07-27 Thu 23:32] DEADLINE: <2023-06-01 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:47
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
** DONE Prendre RV
CLOSED: [2023-05-28 Sun 10:03] SCHEDULED: <2023-05-07 Sun>
** DONE Changer amortisseurs
CLOSED: [2023-07-02 Sun 10:52] SCHEDULED: <2023-06-13 Tue>
** DONE Changer phare avant
CLOSED: [2023-07-02 Sun 10:52] SCHEDULED: <2023-06-13 Tue>
** DONE Contrôle pollution
CLOSED: [2023-07-02 Sun 10:52] SCHEDULED: <2023-06-13 Tue>
** DONE Prendre rendez-vous pour contre-visite
CLOSED: [2023-07-21 Fri 17:45] SCHEDULED: <2023-07-02 Sun>
** DONE Contre-visite
CLOSED: [2023-07-27 Thu 23:31] DEADLINE: <2023-07-26 Wed>
* KILL Changer plaquettes +/- disques
CLOSED: [2023-06-11 Sun 18:39] SCHEDULED: <2023-05-09 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:47
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: voiture
:END:
Écrou grippé ? Voir avec fils M. Chouffe à Gennes, chemin du vernois (voiture 607 bleue)
* DONE Changer pneus avant
CLOSED: [2022-09-11 Sun 22:05] SCHEDULED: <2022-09-03 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:47
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
Trop abimé pour prendre le risque, on changera les arrières plus tard
* DONE Héberger arbre généaloqiue
CLOSED: [2023-06-24 Sat 15:42] SCHEDULED: <2023-04-14 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:49
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
- Github : genealogy
- Sourcehut : genealogy
- Proton drive
- Mail <2023-06-24 Sat>
* DONE Enterrement Mme Karl
CLOSED: [2023-05-28 Sun 10:02]
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:49
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
** DONE Commander bouquets
CLOSED: [2023-04-13 Thu 09:11] SCHEDULED: <2023-04-12 Wed>
** DONE Message avec les bouquets
CLOSED: [2023-04-13 Thu 09:11] SCHEDULED: <2023-04-13 Thu>
** DONE Remboursement [5/5]
CLOSED: [2023-05-28 Sun 10:02] SCHEDULED: <2023-04-20 Thu>
*** DONE Aurélien
CLOSED: [2023-04-22 Sat 15:27]
*** DONE Élise
CLOSED: [2023-04-22 Sat 15:27]
*** DONE Yvain
CLOSED: [2023-05-28 Sun 10:02]
*** DONE Papa
CLOSED: [2023-04-22 Sat 15:27]
*** DONE Thierry
CLOSED: [2023-04-13 Thu 09:12]
** DONE Carte personnalisée
CLOSED: [2023-04-26 Wed 21:10] SCHEDULED: <2023-04-17 Mon>
* DONE Don index nzb
CLOSED: [2023-04-22 Sat 15:27] SCHEDULED: <2023-04-19 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:49
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-04-16 Sun 16:53]
* DONE Remboursement TER Grenoble du 9 avril
CLOSED: [2023-05-06 Sat 09:06] SCHEDULED: <2023-05-03 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:49
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-04-26 Wed 21:03]
Demande envoyé <2023-04-26 Wed>
Refusé
* DONE Demander accès déchetteries Saône
CLOSED: [2023-07-30 Sun 14:49]
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:49
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-05-28 Sun 10:02]
* Mustard :mustard:
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 14:51
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche
:ARCHIVE_CATEGORY: recherche
:END:
** Scripts
*** DONE Script pour données labkey
on convertit tous les pdf en png puis OCR avec tesseract pour les transformer en texte
On supprimer les header et footer à la main
Cf ~/code/scripts/python/mustard/courrier.py
*** DONE Renommer les dossiers PED
#+begin_src python :results output
import pandas as pd
import os
import os.path
dir1 = "/alexi/Documents/mustard/"
dir2 = "/alexi/Documents/mustard-new/"
p = pd.read_csv(os.path.join(dir1, "Patients_2022-02-02_11-44-03.tsv"), sep='\t')
# id + p.nom + " " + p.prenom + " " + p.date_de_naissance
for i in p.index:
split = p['patientID'][i].split(".")
# Only store the index case
if split[1] == "1":
dest = p.nom[i].upper() + " " + p.prenom[i] + " " + p.date_de_naissance[i]
print(f"ok {split[0]} {dest}")
src = os.path.join(dir1, split[0])
if os.path.exists(src):
if p.nom[i] != "Non renseigné":
os.rename(src, os.path.join(dir2, dest))
else:
os.rename(src, os.path.join(dir2, split[0]))
#+end_src
*** DONE Générer clinique
#+begin_src python :results output
import pandas as pd
import os
import os.path
dir = "/alexi/Documents/mustard/"
p = pd.read_csv(os.path.join(dir, "Patients_2022-02-02_11-44-03.tsv"), sep='\t')
# id + p.nom + " " + p.prenom + " " + p.date_de_naissance
f = open(os.path.join(dir, "clinique2.csv"), 'w')
for i in p.index:
split = p['patientID'][i].split(".")
# Only store the index case
if split[1] == "1":
folder = p.nom[i].upper() + " " + p.prenom[i] + " " + p.date_de_naissance[i]
if os.path.exists(os.path.join(dir, folder)):
f.write(split[0] + ";" + p.nom[i].upper() + ";" + p.prenom[i] + ";" + p.date_de_naissance[i] + "\n")
#+end_src
*** KILL Stats sur la balance allélique pour Paul
CLOSED: [2023-07-07 Fri 18:47]
**** DONE Besançon seul : total, par variant
CLOSED: [2022-10-28 Fri 10:57]
**** DONE Dijon + Besançon seul : total, par variant et par type de prélèvement
CLOSED: [2022-12-03 Sat 12:35]
Dans "variations à vérifier". 1 seul variant normalement en miseq, parfois plusieurs en exome
AB = "allelic balance"
**** KILL Rajouter une colonne balance allélique
CLOSED: [2023-07-07 Fri 18:47]
***** KILL Ancien panel
CLOSED: [2023-07-07 Fri 18:44]
***** KILL Nouveau panel
CLOSED: [2023-07-07 Fri 18:44]
***** KILL Dijon
CLOSED: [2023-07-07 Fri 18:44]
**** KILL Version executable pour paul
CLOSED: [2023-07-07 Fri 18:44]
Avec colonne dédiée
** Données
*** DONE Import Labkey
*** KILL Clinique, OCR et nettoyage données labkey [1199/1199]
CLOSED: [2023-07-07 Fri 18:44]
DONE = sur scality (mis dans ~/annex/mustard/done)
SRT = traité, non transféré (en attente dans ~/annex/mustard)
**** DONE PED0052
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**** DONE PED1004
**** DONE PED1007
**** DONE PED1009
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CLOSED: [2022-08-01 Mon 09:44]
**** DONE PED1034
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**** DONE PED1035
CLOSED: [2022-08-01 Mon 09:44]
**** DONE PED1036
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CLOSED: [2022-11-08 Tue 22:20]
**** DONE PED1040
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**** DONE PED1075
CLOSED: [2022-11-08 Tue 22:20]
**** DONE PED1077
CLOSED: [2022-11-08 Tue 22:20]
**** KILL PED1078
CLOSED: [2023-07-07 Fri 18:44]
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*** DONE Fusionner exome dijon pour Paul
CLOSED: [2022-08-04 Thu 17:42]
**** DONE Enlever les doublons
CLOSED: [2022-09-13 Tue 21:36]
*** DONE Fusionner panel Dijons
*** DONE Fusion variants à vérifier de dijon
CLOSED: [2022-12-04 Sun 22:32]
*** KILL Dxcare
**** DONE Demande Dijon
**** KILL Demande DPO Besançon
*** KILL donnée pierre
**CLOSED: [2022-05-05 jeu. 17:53]
***** KILL Format de données final
CLOSED: [2023-07-07 Fri 18:44]
Voir avec Paul
** Stockage
*** DONE Accès scality au travail
*** KILL VPN pour Jehanne
CLOSED: [2023-05-28 Sun 10:04]
** Notes
- Sur phénotype mélanocytaire, il peut valoir le coup de faire de la CGH sur biopsie
Inconvénient du panel : on passe à côté
Inconvénient de l’exome : faible profondeur
En général, pas d’ADN suffisant pour les 3 !
- Idée de pipeline : CNV (mais il faut les références)
- 2 approches : exome direct ou CGH + panel
- Exome envoyé à integragen (ou CNR): problème = perte de financement car plus de centre de référence à Dijon
envoi dans le privé compliqué vu le coût...
* KILL DIU dysmorpho
:PROPERTIES:
:CATEGORY: dysmorpho
:ARCHIVE_TIME: 2023-07-30 Sun 15:03
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Génétique
:ARCHIVE_CATEGORY: dysmorpho
:ARCHIVE_TODO: KILL
:END:
** KILL Relire + notes [1/92]
*** KILL Intro dysmorpho - Verloes
CLOSED: [2023-07-07 Fri 18:43]
*** KILL Empreinte génomique
*** KILL Beckwith, Silver Russel
*** KILL Scoliose
*** KILL Syndromes cytogénétique - Salanville
*** KILL Dysostose mandibulo faciale
*** KILL Williams dup 7p11.2
*** KILL Pathologie génétique de la reproduction
*** KILL Malformations oculaires
*** KILL Comprendre les test génétiques
*** KILL Fente
*** KILL Gonosome
*** KILL Smith-Mangenis
*** KILL 22q11
*** KILL Dysmorpho nouveau-né
*** KILL Autopsie foetale
*** KILL Dysmorphologie - généralités (A Verloes)
*** KILL Dysmorphologie du nouveau né (M Vincent)
*** KILL Registre des malformations (N Lelong)
*** KILL Comprendre les tests génétiques - Mutations - NGS (Y Vial)
*** KILL Cytogénétique (C Missirian)
*** KILL NGS et syndromologie (F Tran-Mau-Them)
*** KILL Empreinte génomique (F Brioudé) (seq 15 Beckwith Wiedemann Syndrome et SRussel S)
*** KILL Autopsie foetale (F Guimiot)
*** KILL Tumeur et développement (H Cave)
*** KILL Dysmorphologie foetale (MH Saint Frison)
*** KILL Pathologie génétique de la reproduction (F Vialard)
*** KILL Le dysmorphologiste en prénatal (N Gruchy)
*** KILL Régulation génique et anomalies du développement (F Petit)
*** KILL Echographie fœtale et dysmorphologie (C Rozel)
*** KILL Déficience intellectuelle (A Curie)
*** KILL Autisme et génétique (A Maruani)
*** KILL Tests neuropsy
*** KILL XLID(A Toutain)
*** KILL Anomalies du développement embryonnaire précoce (C Quelin)
*** KILL Anomalies de fermeture du tube neural (C Quelin)
*** KILL FAS (D Germanaud)
*** KILL Médicaments et grossesse (C Vauzelle)
*** KILL Syndromes avec fentes oro-faciales- (J Van-Gils)
*** KILL Syndromes avec craniosténose (C Collet)
*** KILL Dents & syndromes (I Bailleul)
*** KILL Dysostoses Mandibulo faciales (J Amiel)
*** KILL Avances staturales (A Putoux)
*** KILL Retards staturaux syndromiques (A Putoux)
*** KILL Syndromes avec obésité (G Diene)
*** KILL Spliceosomopathies (P Edery)
*** KILL Microcéphalies (S Passemard)
*** KILL Anomalies du cervelet : Joubert, NPH ... (L Burglen)
*** KILL Epilepsie et syndromes (C Mignot)
*** KILL Holoprosencéphalie (S Odent)
*** KILL Hydrocephalie (S Odent)
*** KILL Anomalies de migration (S Passemard)
*** KILL Chondrodysplasies (G Baujat)
*** KILL Anomalies de segmentation et scoliose (J Thévenon)
*** KILL Génétique du développement des membres et principaux syndromes (F Petit)
*** KILL Classification des malformations des membres (F Petit)
*** KILL Prise en charge des anomalies des membres (N Quintero)
*** KILL Syndromes avec anomalies uro-néphrologiques pré- et postnatal (G Morin)
*** KILL Syndromes avec anomalies génitales et DSD (B Leheup)
*** KILL Du coeur au syndrome (D Genevieve)
*** KILL Malformation cardiaque en anténatal (D Genevieve)
*** KILL Base génétique du déterminisme du sexe (C Colson)
*** KILL Surdités syndromiques (S Marlin)
*** KILL Malformations oculaires (N Chassaing)
*** KILL Dermatologie et développement (P Vabres)
*** KILL Dysmorphologie et métabolisme (M Barth)
*** KILL Maladies de surcharge (D Germain)
*** KILL Trisomie 21 (R Touraine)
*** KILL S. Williams - duplication 7q11.2 (M Rossi)
*** KILL Délétion 22q11.2 (L Perrin)
*** KILL Syndromes cytogénétiques (D Sanlaville)
*** KILL Gonosomes (J Leger)
*** KILL Parcours de soin des patients avec anomalies du développement (N Jean-Marçais)
*** KILL Prise en charge médicosociale du handicap (D Juzeau)
*** KILL Fanconi (T Leblanc)
*** KILL Ehlers-Danlos (D Germain)
*** KILL Chromatinopathies: TAD - Kabuki, Rubinstein-Taybi, Wiedemann-Steiner, SBYSS... (D Genevieve)
*** KILL Marfan et syndromes apparentés (G Jondeau)
*** KILL RASopathies (Y Capri)
*** KILL Syndromes de Pitt Hopkins, Angelman, Rett et Rett-like (N Bahi-Buisson)
*** KILL Filaminopathies A (C Goizet)
*** KILL Achondroplasie (G Baujat)
*** KILL OI (G Baujat)
*** KILL Ciliopathies: approche globale (T Attie-Bitach)
*** KILL Smith-Magenis (L Perrin)
*** KILL Cohésinopathies : Cornelia de Lange, Coffin-Siris/NB, CHOPS... (A Goldenberg)
*** KILL Albinisme et syndromes apparentés (B Arveiler)
*** KILL Beckwith Wiedemann Syndrome & Silver Russel Syndrome (F Brioude)
*** KILL Neurofibromatoses - STB (C Goizet)
*** KILL Cowden, Gorlin (P Goizet)
*** KILL Syndrome de Kleefstra (L Perrin)
*** KILL Téloméropathies (T Leblanc)
* DONE DES [4/4]
CLOSED: [2023-07-07 Fri 18:47]
:PROPERTIES:
:ARCHIVE_TIME: 2023-07-30 Sun 15:03
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Génétique
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
** DONE Valider cours sur sides
** KILL Vérifier que toutes les diapos sont sur one drive
CLOSED: [2023-07-07 Fri 18:47]
** DONE Examen sur sides
** KILL Lire les cours
CLOSED: [2023-07-07 Fri 18:47]
*** KILL Presentiel session 1 [9/9]
CLOSED: [2022-11-19 Sat 17:43]
**** DONE Introduction à la dysmorphologie
**** DONE Structuration du génome et mécanismes mutationnels
**** DONE Oncogénétique: introduction
**** KILL Diagnostic prénatal
CLOSED: [2022-11-19 Sat 17:35]
**** DONE Grandes technologies et bioinformatique
**** DONE Aspects réglementaires et éthiques
**** DONE Mucoviscidose
CLOSED: [2022-09-10 Sat 18:34]
**** KILL Bases sur le conseil génétique
CLOSED: [2022-11-19 Sat 17:35]
**** KILL SEPI et TD
CLOSED: [2022-11-19 Sat 17:35]
*** DONE E-learning session 1 [6/6]
**** DONE maladies endocriniennes et métabolisme
**** DONE anomalies de la croissance
**** DONE hématologie
**** DONE maladies du tissu conjonctif
**** DONE Oncogénétique
**** DONE dermatogénétique
*** KILL Presentiel session 2 [0/5]
CLOSED: [2022-11-19 Sat 17:43]
**** KILL Déficience intellectuelle
CLOSED: [2022-11-19 Sat 17:35]
**** KILL Génétique clinique et formelle
CLOSED: [2022-11-19 Sat 17:35]
**** KILL Pathologies fréquentes en génétique clinique
CLOSED: [2022-11-19 Sat 17:35]
**** KILL Génome humain : normal et pathologique
CLOSED: [2022-11-19 Sat 17:35]
**** KILL Maladies métaboliques
CLOSED: [2022-11-19 Sat 17:35]
*** KILL E-learning session 2 [6/6]
CLOSED: [2023-07-07 Fri 18:47]
**** DONE Infertilité
-> cours 1, diapo 31
**** DONE Syndromes microdélétionnels
**** DONE Dysgonosomies
**** DONE Cancer du colon: Maladie de Lynch et CMMRD
**** DONE Déficience intellectuelle
**** KILL Pathologies neuromusculaires
CLOSED: [2023-07-07 Fri 18:47]
* DONE Nettoyer public
CLOSED: [2023-09-30 Sat 17:36] SCHEDULED: <2023-09-30 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-10-01 Sun 21:35
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Backups
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-09-30 Sat 16:21]
* KILL Télécharger les données avec makefile
CLOSED: [2022-10-09 Sun 22:27]
:PROPERTIES:
:ARCHIVE_TIME: 2022-10-09 Sun 22:28
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Recherche/Pipeline exome/Nouveau workflow/Bases de données
:ARCHIVE_CATEGORY: recherche
:ARCHIVE_TODO: KILL
:END:
:END:
* KILL ne compile plus
SCHEDULED: <2022-07-17 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-08-21 Sun 09:15
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: FreeBSD/Kitty
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: freebsd
:ARCHIVE_ITAGS: banque
:ARCHIVE_TODO: DONE
:END:
* DONE Donner cours dysmorpho à Clarisse
SCHEDULED: <2022-08-20 sam.>
:PROPERTIES:
:ARCHIVE_TIME: 2022-08-20 sam. 21:51
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:END:
* DONE Souscription
CLOSED: [2022-04-23 Sat 17:13]
:PROPERTIES:
:ARCHIVE_TIME: 2022-08-20 sam. 21:51
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Banque/Compte et CB société générale
:ARCHIVE_CATEGORY: projects
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: banque
:END:
* DONE Carte bancaire
DEADLINE: <2022-05-21 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2022-08-20 sam. 21:51
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Banque/Compte et CB société générale
:ARCHIVE_CATEGORY: projects
* DONE QROC 3
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-23 Sat 11:04
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Génétique/DIU dysmorpho
:ARCHIVE_CATEGORY: dysmorpho
:ARCHIVE_TODO: DONE
:END:
*DEADLINE: <2022-06-18 Sat>
* DONE QROC S2
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-23 Sat 11:04
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Génétique/DIU dysmorpho
:ARCHIVE_CATEGORY: dysmorpho
:ARCHIVE_TODO: DONE
:END:
*CLOSED: [2022-04-16 Sat 23:42] DEADLINE: <2022-04-16 Sat 23:59>
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:END:
* DONE Liste des videos tricks
DEADLINE: <2022-04-27 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 22:35
:ARCHIVE_OLPATH: Projet
:ARCHIVE_CATEGORY: projets
:ARCHIVE_TODO: DONE
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE_TODO: DONE
:END:
* DONE Passer en heures creuses
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 14:47
:ARCHIVE_OLPATH: Electricité
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: maison
:END:
* KILL Voir avec proprio pour changer disjoncteur
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 14:47
:ARCHIVE_OLPATH: Electricité
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: maison
:END:
* DONE Vérifier l’intérêt de l’article
CLOSED: [2022-05-05 jeu. 17:56]
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-27 Fri 14:08
:ARCHIVE_OLPATH: Recherche/WDR45/Mémoire
:ARCHIVE_CATEGORY: memoire
:ARCHIVE_TODO: DONE
:END:
*** DONE Variant déjà rapporté ?
CLOSED: [2022-05-01 Sun 19:52]
Non, NM différente (non canonique)
Cf mail de Saffari
*** DONE Phénotype : garçon moins atteint que les filles ?
CLOSED: [2022-05-05 jeu. 17:56]
Bien lire les 3 revues
* DONE Lister variants et clinique
CLOSED: [2022-05-05 jeu. 17:56]
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-27 Fri 14:08
:ARCHIVE_OLPATH: Recherche/WDR45/Mémoire
:ARCHIVE_CATEGORY: memoire
:ARCHIVE_TODO: DONE
:END:
*** DONE Déjà fait par saffari2021
CLOSED: [2022-04-18 Mon 21:56]
*** DONE Regarder 2 autres review Cong2021 et Adang2020
CLOSED: [2022-05-05 jeu. 17:56]
Pourquoi plus de variants chez Cong2021 ?
* DONE Récupérer résultat Cyril et mère
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-09 Thu 17:58
:ARCHIVE_OLPATH: Recherche/WDR45/IRM
:ARCHIVE_CATEGORY: wdr45
:ARCHIVE_TODO: DONE
:END:
LOSED: [2022-05-01 Sun 19:52]
* DONE Copie dossier
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-09 Thu 17:58
:ARCHIVE_OLPATH: Recherche/WDR45/IRM
:ARCHIVE_CATEGORY: wdr45
:ARCHIVE_TODO: DONE
:END:
LOSED: [2022-05-01 Sun 19:52]
* DONE Mémoire
:PROPERTIES:
:CATEGORY: memoire
:ARCHIVE_TIME: 2022-07-21 Thu 14:29
:ARCHIVE_CATEGORY: memoire
:ARCHIVE_TODO: DONE
:END:
** DONE Plan
CLOSED: [2022-05-05 jeu. 17:56] DEADLINE: <2022-05-04 mer. 19:00>
** DONE V1
*** DONE Introduction
*** DONE BPAN
**** Phenotype
**** WDR45
*** DONE Case report
**** DONE Family 1
**** DONE Family 2
**** DONE Discussion
*** DONE Conclusion
*** DONE Correction Juliette BPAN + clinique
ok -> intro
** DONE envoyer intro + context + clinique à Juliette pour relecture
DEADLINE: <2022-05-22 Sun>
** KILL Figure avec tikz des variant sur la séquence d'acide aminé
Missense seulement
* DONE cas clinique 3e jeudi
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 14:29
:ARCHIVE_OLPATH: Recherche/WDR45/Présentations
:ARCHIVE_CATEGORY: wdr45
:ARCHIVE_TODO: DONE
:END:
* DONE IRM
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-21 Thu 14:30
:ARCHIVE_CATEGORY: wdr45
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:END:
* KILL Commander nouvelle CB :banque:
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-16 Sat 17:45
:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: KILL
:END:
Demande faite <2022-04-03 Sun>
Reçue mais pas de chiffre en relief
Mail envoyé pour savoir si on peut louer avec mais a priori non (carte de débit !)
Renvoyer un mail car n’ont pas compris la question
* DONE Payer taxe foncière :maison:
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-16 Sat 17:51
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Chèque envoyé<2022-07-16 Sat>
* DONE Payer taxes ordures ménagères :maison:
DEADLINE: <2022-06-06 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2022-07-16 Sat 17:51
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_ITAGS: florian
:END:
* DONE Réparer
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-12 Sun 11:19
:ARCHIVE_OLPATH: Moto
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: moto
:END:
** DONE Dépannage
CLOSED: [2022-04-09 Sat 14:25]
Pas de réparation possible avan fin avril
** DONE Appel garage Yamaha Besançon pour commencer réparation
SCHEDULED: <2022-04-29 Fri>
** DONE Aller chercher moto
* DONE Signer contrat moto
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-12 Sun 11:19
:ARCHIVE_OLPATH: Moto
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: moto
:END:
* DONE Notes <2022-04-10 Sun>
CLOSED: [2022-04-17 Sun 11:14] SCHEDULED: <2022-04-10 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-12 Sun 15:20
:ARCHIVE_OLPATH: Japonais/Leçon Aya
:ARCHIVE_CATEGORY: aya
:ARCHIVE_TODO: DONE
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_TODO: DONE
:END:
* DONE Organiser enterrement vie de garçon :joris:
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-06 Mon 21:47
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: ???
:ARCHIVE_TODO: DONE
:END:
** DONE Inviter + programme
** DONE Confirmer date avec Joris
CLOSED: [2022-04-23 Sat 17:14]
** DONE Réserver
* DONE Appeler pour demander carte médecin internat
DEADLINE: <2022-05-22 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-06 Mon 21:47
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: ???
:ARCHIVE_TODO: DONE
:END:
Attente code par courrier puis rappeler ANS
* DONE Billet de trains
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-06 Mon 21:49
:ARCHIVE_OLPATH: Inbox/Mariage Florian
:ARCHIVE_CATEGORY: ???
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: florian
:END:
* DONE Hébergement
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-06 Mon 21:49
:ARCHIVE_OLPATH: Inbox/Mariage Florian
:ARCHIVE_CATEGORY: ???
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: florian
:END:
* DONE Location voiture
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-06 Mon 21:49
:ARCHIVE_OLPATH: Inbox/Mariage Florian
:ARCHIVE_CATEGORY: ???
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: florian
:END:
* DONE Voir avec Miva pour hébergement Paris
:PROPERTIES:
:ARCHIVE_TIME: 2022-06-06 Mon 21:49
:ARCHIVE_OLPATH: Inbox/Mariage Florian
:ARCHIVE_CATEGORY: ???
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:END:
* DONE Vérifier réception carte médecin
DEADLINE: <2000-05-20 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-30 Mon 22:05
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Devrait arriver<2022-05-27 Fri>
* DONE Alimentation PC portable
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-30 Mon 22:05
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
** DONE Échanger
Envoyé<2022-05-07 Sat>
** DONE Nouvelle commande
* DONE Minoxidil
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-30 Mon 22:06
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Mail envoyé <2022-05-19 Thu>
* DONE Rendre le Coran
DEADLINE: <2022-05-22 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-30 Mon 22:06
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
* DONE Changer disque dur PC portable laure
DEADLINE: <2022-05-23 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-30 Mon 22:06
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
Commandé
* DONE Déclaration de revenus
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-30 Mon 22:07
:ARCHIVE_OLPATH: Impôts
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
a priori, rien à déclarer en plus value selon Aurélien.
Va demander au notaire. Mot mis sur la déclaration.
SCHEDULED: <2022-04-24 Sun>
* DONE Utiliser chèque énergie
CLOSED: [2022-04-10 Sun 17:20] SCHEDULED: <2022-04-10 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-05-30 Mon 22:07
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:END:
* DONE Utiliser chèque Chuullanka
CLOSED: [2022-04-17 Sun 18:20] SCHEDULED: <2022-04-17 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-23 Sat 17:14
:ARCHIVE_OLPATH: Inbox
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_TODO: DONE
:END:
* DONE Contester majoration
DEADLINE: <2022-03-26 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2022-04-09 Sat 14:26
:ARCHIVE_CATEGORY: todo
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
:ARCHIVE_FILE: /usr/home/alex/org/projects.org
Archived entries from file /home/alex/org/projects.org
# -*- mode: org -*-
Archived entries from file /home/alex/roam/personal/projects.org
* DONE Nettoyer public
CLOSED: [2023-09-30 Sat 17:36] SCHEDULED: <2023-09-30 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-10-01 Sun 21:51
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Backups
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-09-30 Sat 16:21]
* DONE Nettoyer private
CLOSED: [2023-09-30 Sat 17:57] SCHEDULED: <2023-09-30 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-10-01 Sun 21:52
:END:
* DONE Compléter dossier
CLOSED: [2023-08-30 Wed 16:38]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat/Logement trevenans
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: trevenans cs
:END:
* DONE Louer camionette
CLOSED: [2023-09-16 Sat 18:19] SCHEDULED: <2023-09-16 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat/Logement trevenans
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: trevenans cs
:END:
/Entered on/ [2023-09-13 Wed 22:57]
* DONE Mail DSI pour conservation compte (attente)
CLOSED: [2023-11-02 Thu 22:29] SCHEDULED: <2023-10-27 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Relancer DAM pour conservation compte
CLOSED: [2023-11-02 Thu 22:29] SCHEDULED: <2023-10-27 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Demande de conservation de compte
CLOSED: [2023-10-22 Sun 21:06] SCHEDULED: <2023-10-20 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-19 Thu 18:27]
Nécessite UF (demandé)
* DONE Envoyer choix d'option précoce
CLOSED: [2023-10-10 Tue 23:12] SCHEDULED: <2023-10-10 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-10 Tue 23:12]
* DONE Dossier admnistratatif Trevenans
CLOSED: [2023-10-09 Mon 22:30] SCHEDULED: <2023-10-09 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-09 Mon 22:08]
* DONE Présentation dépistage hémato :presentation:
CLOSED: [2023-10-19 Thu 18:29]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:END:
** DONE Refaire analyse bouche
CLOSED: [2023-10-07 Sat 17:49] SCHEDULED: <2023-10-07 Sat>
** DONE Traitement patients bouches
CLOSED: [2023-10-07 Sat 18:01] SCHEDULED: <2023-10-07 Sat>
** DONE Faire analyse selles
CLOSED: [2023-10-07 Sat 19:30] SCHEDULED: <2023-10-07 Sat>
:LOGBOOK:
CLOCK: [2023-10-07 Sat 18:02]--[2023-10-07 Sat 19:30] => 1:28
:END:
** DONE Revoir avec Audrey pour différence (bleu et jaune)
CLOSED: [2023-10-16 Mon 19:39] SCHEDULED: <2023-10-16 Mon>
** DONE Réunion audrey
CLOSED: [2023-10-16 Mon 19:39] SCHEDULED: <2023-10-16 Mon>
** DONE Traitement patients selles
CLOSED: [2023-10-10 Tue 22:52] SCHEDULED: <2023-10-09 Mon>
** DONE [#A] Résumer Torres 2022
CLOSED: [2023-10-08 Sun 12:42] SCHEDULED: <2023-10-07 Sat>
<[Pdf]> - "~/papers/bacterio/torres2022.pdf"
<[Notes]> - "~/roam/research/biblio.org#** Multi-body-site colonization screening cultures for predicting multi-drug resistant Gram-negative and Gram-positive bacteremia in hematological patients"
** DONE Première version avec contexte, Torres et nos résultats
CLOSED: [2023-10-11 Wed 21:47] SCHEDULED: <2023-10-08 Sun>
"~/roam/research/presentations/bacterio/depistage hemato/notes.org#* Présentation"
** KILL Présenter Santibiez 2023
CLOSED: [2023-10-19 Thu 18:29]
** DONE Corriger présentation
CLOSED: [2023-10-17 Tue 23:19] SCHEDULED: <2023-10-16 Mon>
/Entered on/ [2023-10-16 Mon 22:01]
* DONE Cas clinique H.influenza :hinfluenzae:
CLOSED: [2023-09-28 Thu 11:43]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:END:
** DONE Finir bibliographie H. influenza
CLOSED: [2023-09-09 Sat 20:19] SCHEDULED: <2023-09-09 Sat>
/Entered on/ [2023-09-09 Sat 16:40]
** DONE Envoyer biblio initiale à Xavier
CLOSED: [2023-09-10 Sun 22:51] SCHEDULED: <2023-09-10 Sun>
** DONE Résumé article PCR
CLOSED: [2023-09-28 Thu 11:43]
/Entered on/ [2023-09-17 Sun 16:08]
** DONE Envoyer première version à Xavier
CLOSED: [2023-09-17 Sun 22:31] SCHEDULED: <2023-09-17 Sun>
/Entered on/ [2023-09-17 Sun 16:08]
* DONE Copie carte d'identié + mutuelle accueil hôpital
CLOSED: [2023-08-19 Sat 20:09] SCHEDULED: <2023-08-17 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-05 Sun 14:54
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-08-08 Tue 21:18]
* DONE Cas clinique H.influenza :hinfluenzae:
CLOSED: [2023-09-28 Thu 11:43]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: bacterio
:ARCHIVE_TODO: DONE
:END:
** DONE Finir bibliographie H. influenza
CLOSED: [2023-09-09 Sat 20:19] SCHEDULED: <2023-09-09 Sat>
/Entered on/ [2023-09-09 Sat 16:40]
** DONE Envoyer biblio initiale à Xavier
CLOSED: [2023-09-10 Sun 22:51] SCHEDULED: <2023-09-10 Sun>
** DONE Résumé article PCR
CLOSED: [2023-09-28 Thu 11:43]
/Entered on/ [2023-09-17 Sun 16:08]
** DONE Envoyer première version à Xavier
CLOSED: [2023-09-17 Sun 22:31] SCHEDULED: <2023-09-17 Sun>
/Entered on/ [2023-09-17 Sun 16:08]
* DONE Examen bactério :partiel:
CLOSED: [2023-10-18 Wed 22:52]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: bacterio
:ARCHIVE_TODO: DONE
:END:
** DONE Passe 1: tous [37/37]
CLOSED: [2023-10-05 Thu 16:58] DEADLINE: <2023-10-06 Fri> SCHEDULED: <2023-10-06 Fri>
- [X] <(Angines bacteriennes)>
- [X] <(Antibiogramme - Enterobacteries)>
- [X] <(Antibiogramme - Staphylocoques)>
- [X] <(Antibiogramme - Streptococoque, enterocoque, Listeria)>
- [X] <(Antibiogramme)>
- [X] <(Cambylobacter)>
- [X] <(Chlamydia - mycoplasmes)>
- [X] <(Clostridium difficile)>
- [X] <(Concentrations critiques)>
- [X] <(Conseil anti-infectieux)>
- [X] <(Declaration obligatoire)>
- [X] <(Diagnostic moleculaire - Bacteriologie)>
- [X] <(EBCU etiologies)>
- [X] <(ECBU interpretation)>
- [X] <(ECBU pre-analytique)>
- [X] <(EEQ, CIQ)>
- [X] <(Examen microscopique)>
- [X] <(Gonocoque)>
- [X] <(Hemocultures 1)>
- [X] <(Hemocultures 2)>
- [X] <(Hygiène)>
- [X] <(Infections cutanees)>
- [X] <(Legionelle)>
- [X] <(MALDI - TOF)>
- [X] <(Meningites bacteriennes )>
- [X] <(Pre-analytique bacteriologie)>
- [X] <(Qualité)>
- [X] <(Salmonelle - shigelle)>
- [X] <(Securite Transfusionnelle)>
- [X] <(Serologie bacterienne)>
- [X] <(Syphilis)>
- [X] <(Tests rapides antigeniques et moleculaires)>
- [X] <(Tuberculose)>
- [X] <(Typage moleculaire bacterien)>
- [X] <(Vaccination personnel)>
- [X] https://scut.srht.site/notes/medecine/20230528235124-culture.html
- [X] A. agalactiae
** DONE Passe 2: cours non tobmé avec interro + révision + interro [33/35]
CLOSED: [2023-10-15 Sun 12:59] DEADLINE: <2023-10-11 Wed> SCHEDULED: <2023-10-07 Sat>
- [X] <(Angines bacteriennes)>
- [X] <(Antibiogramme - Enterobacteries)>
- [X] <(Antibiogramme - Staphylocoques)>
- [X] <(Antibiogramme - Streptococoque, enterocoque, Listeria)>
- [X] <(Antibiogramme)>
- [X] <(Cambylobacter)>
- [-] Mécanisme résistance antibio
- [X] <(Chlamydia - mycoplasmes)>
- [X] <(Clostridium difficile)>
- [X] <(Concentrations critiques)>
- [X] <(Conseil anti-infectieux)>
- [X] <(Declaration obligatoire)>
- [X] <(Diagnostic moleculaire - Bacteriologie)>
- [X] <(EBCU etiologies)>
- [X] <(ECBU interpretation)>
- [X] <(ECBU pre-analytique)>
- [X] <(Examen microscopique)>
- [X] <(Gonocoque)>
- [X] <(Hemocultures 1)>
- [X] <(Hemocultures 2)>
- [X] <(Infections cutanees)>
- [X] <(Legionelle)>
- [X] <(MALDI - TOF)>
- [X] <(Meningites bacteriennes)>
- [X] <(Pre-analytique bacteriologie)>
- [-] BMR (cours ? définition a minima)
- [X] <(Qualite)>
- [X] <(Salmonelle - shigelle)>
- [X] <(Serologie bacterienne)>
- [X] <(Syphilis)>
- [X] <(Tests rapides antigeniques et moleculaires)>
- [X] <(Tuberculose)>
- [X] <(Typage moleculaire bacterien)>
- [X] <(Culture)>
- [X] A. agalactiae
** DONE Passe 3 [27/36]
CLOSED: [2023-10-18 Wed 00:10] DEADLINE: <2023-10-16 Mon> SCHEDULED: <2023-10-22 Sun>
- [X] <(Angines bacteriennes)>
- [X] <(Antibiogramme - Enterobacteries)>
- [X] <(Antibiogramme - Staphylocoques)>
- [X] <(Antibiogramme - Streptococoque, enterocoque, Listeria)>
- [X] <(Antibiogramme)>
- [X] <(Cambylobacter)>
- [ ] Mécanisme résistance antibio
- [X] <(Chlamydia - mycoplasmes)>
- [X] <(Clostridium difficile)>
- [X] <(Concentrations critiques)>
- [X] <(Conseil anti-infectieux)>
- [X] <(Declaration obligatoire )>
- [X] <(Diagnostic moleculaire - Bacteriologie)>
- [ ] <(EBCU etiologies)>
- [ ] <(ECBU interpretation)>
- [ ] <(ECBU pre-analytique)>
- [X] <(Examen microscopique)>
- [X] <(Gonocoque)>
- [X] <(Hemocultures 1)>
- [X] <(Hemocultures 2)>
- [X] <(Infections cutanees)>
- [X] <(Legionelle)>
- [X] <(MALDI - TOF)>
- [X] <(Meningites bacteriennes)>
- [X] <(Pre-analytique bacteriologie)>
- [ ] BMR (cours ? définition a minima)
- [X] <(Qualite)>
- [X] <(Salmonelle - shigelle)>
- [X] <(Serologie bacterienne)>
- [X] <(Syphilis)>
- [X] <(Tests rapides antigeniques et moleculaires)>
- [ ] <(Tuberculose)>
- [X] <(Typage moleculaire bacterien)>
- [ ] <(Culture)>
- [ ] A. agalactiae
- [ ] Bactérie (refaire un tour)
* DONE Présentation dépistage hémato :presentation:
CLOSED: [2023-10-19 Thu 18:29]
:PROPERTIES:
:CATEGORY: bacterio
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: bacterio
:ARCHIVE_TODO: DONE
:END:
** DONE Refaire analyse bouche
CLOSED: [2023-10-07 Sat 17:49] SCHEDULED: <2023-10-07 Sat>
** DONE Traitement patients bouches
CLOSED: [2023-10-07 Sat 18:01] SCHEDULED: <2023-10-07 Sat>
** DONE Faire analyse selles
CLOSED: [2023-10-07 Sat 19:30] SCHEDULED: <2023-10-07 Sat>
:LOGBOOK:
CLOCK: [2023-10-07 Sat 18:02]--[2023-10-07 Sat 19:30] => 1:28
:END:
** DONE Revoir avec Audrey pour différence (bleu et jaune)
CLOSED: [2023-10-16 Mon 19:39] SCHEDULED: <2023-10-16 Mon>
** DONE Réunion audrey
CLOSED: [2023-10-16 Mon 19:39] SCHEDULED: <2023-10-16 Mon>
** DONE Traitement patients selles
CLOSED: [2023-10-10 Tue 22:52] SCHEDULED: <2023-10-09 Mon>
** DONE [#A] Résumer Torres 2022
CLOSED: [2023-10-08 Sun 12:42] SCHEDULED: <2023-10-07 Sat>
<[Pdf]> - "~/papers/bacterio/torres2022.pdf"
<[Notes]> - "~/roam/research/biblio.org#** Multi-body-site colonization screening cultures for predicting multi-drug resistant Gram-negative and Gram-positive bacteremia in hematological patients"
** DONE Première version avec contexte, Torres et nos résultats
CLOSED: [2023-10-11 Wed 21:47] SCHEDULED: <2023-10-08 Sun>
"~/roam/research/presentations/bacterio/depistage hemato/notes.org#* Présentation"
** KILL Présenter Santibiez 2023
CLOSED: [2023-10-19 Thu 18:29]
** DONE Corriger présentation
CLOSED: [2023-10-17 Tue 23:19] SCHEDULED: <2023-10-16 Mon>
/Entered on/ [2023-10-16 Mon 22:01]
* DONE Déclaration stage hémato UNESS
CLOSED: [2023-11-14 Tue 22:21] SCHEDULED: <2023-11-13 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Internat
:ARCHIVE_CATEGORY: internat
:ARCHIVE_TODO: DONE
:END:
* DONE Envoyer devis dentiste à mutuelle
CLOSED: [2023-09-21 Thu 23:03] SCHEDULED: <2023-09-19 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Santé
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-09-19 Tue 12:18]
* DONE Mail Juliette + Paul pour resoumission
CLOSED: [2023-09-10 Sun 22:36] SCHEDULED: <2023-09-10 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-09-10 Sun 22:21]
* DONE Mail Dr Laithier
CLOSED: [2023-09-18 Mon 19:36] SCHEDULED: <2023-09-17 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-09-17 Sun 16:06]
* DONE Avis paul sur ACPA non
CLOSED: [2023-10-02 Mon 21:58]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
* DONE Corriger article
CLOSED: [2023-11-08 Wed 19:03] SCHEDULED: <2023-11-05 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
** DONE Ajouter images Dr Vidaud
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
** DONE Comprendre score LRR pour gain
CLOSED: [2023-09-21 Thu 23:03] SCHEDULED: <2023-09-21 Thu>
** DONE Corriger discussion: remaniement complexe
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
** DONE Phénotype "mild" chez le père + détailler moléculaire
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
** DONE Traitement FBXW7 ?
CLOSED: [2023-10-11 Wed 16:08] SCHEDULED: <2023-10-15 Sun>
Lié à NF1 et non FBXW7 (voir mail V. Laithier)
* DONE Réponse reviewer
CLOSED: [2023-11-05 Sun 18:46] SCHEDULED: <2023-11-05 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
* DONE Correction Juliette
CLOSED: [2023-11-18 Sat 11:55] SCHEDULED: <2023-11-19 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:55
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Recherche/NF1
:ARCHIVE_CATEGORY: nf1
:ARCHIVE_TODO: DONE
:END:
* DONE Remplacer clavier SK :clavier:
CLOSED: [2023-10-28 Sat 21:36]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-07 Sat 22:58]
** DONE Demande à Cooler Master un remplacement
CLOSED: [2023-10-15 Sun 12:43] SCHEDULED: <2023-10-15 Sun>
Envoyée <2023-10-07 Sat>
Sera probablement refusée car via Amazon
** DONE Retour Amazon
CLOSED: [2023-10-28 Sat 21:36] SCHEDULED: <2023-10-28 Sat>
Renvoie vers le constructeur ...
* DONE Coudre fermeture éclair pantalon
CLOSED: [2023-10-11 Wed 12:48] SCHEDULED: <2023-10-11 Wed>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-09 Mon 22:09]
* DONE Réclamation train Paris - Besancon
CLOSED: [2023-10-19 Thu 18:31] SCHEDULED: <2023-10-22 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-16 Mon 22:01]
** KILL TER
CLOSED: [2023-10-16 Mon 22:05]
"Par ailleurs, en cas de retard ou de suppression de train, il n'existe pas de garantie ponctualité sur TER, aucun remboursement ne sera effectué."
** DONE Allianz
CLOSED: [2023-10-19 Thu 18:31] SCHEDULED: <2023-10-23 Mon>
Manque justificatif de retard mais le site ne trouve pas le trajet...
https://www.ter.sncf.com/bourgogne-franche-comte/services-contacts/bulletin-retard-resultats?search=N4IgJgpgDghgTgFwK5wgZQQeygBQDYwDGEIAXKAHYwC2JpIO8AlgM4C0AQhHIQJ4AEHTCgDmmERQj82-Rrxb8wAcgCCSAG7cJJADQhWGbPiJ0EcJBD1MwZEAA4A7ADY7Ttw5B6EvKHRAALViw4JkIQAF89eBD1GDxDXAJiMkoaPy4WGAoAc8wKNgA1JkwEBF19FgTjZNIzCysbekcHAEY7AAZ2jy8fP0CWYNCIqLgYuIARGDLbACZ2mYBmNhb25YBWABVO0m3OgGp5nfbPEGimWLwNplpbFqdSABYPcKA
* DONE Rendre livres BU
CLOSED: [2023-10-28 Sat 21:36] SCHEDULED: <2023-10-27 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-27 Fri 21:14]
* DONE Changer courroie distribution :courroie:
CLOSED: [2023-09-30 Sat 18:53] SCHEDULED: <2023-09-29 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
À faire au bout de 10ans, on attend l’an prochain
** DONE [#B] Commander pièce
CLOSED: [2023-09-11 Mon 19:18] SCHEDULED: <2023-09-11 Mon>
/Entered on/ [2023-09-11 Mon 19:12]
** DONE Prendre rendez vous
CLOSED: [2023-09-14 Thu 22:44] SCHEDULED: <2023-09-11 Mon>
* DONE Commander pièce courroie de distribution
CLOSED: [2023-09-14 Thu 22:44] SCHEDULED: <2023-09-11 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
/Entered on/ [2023-09-11 Mon 19:12]
* DONE Prendre rendez vous courroie distribution
CLOSED: [2023-10-07 Sat 17:48]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:56
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
* DONE Changer phare arrière droit
CLOSED: [2023-10-08 Sun 13:24] SCHEDULED: <2023-10-08 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
* DONE Changer ampoule clignotant arrière droit
CLOSED: [2023-10-19 Thu 17:18] SCHEDULED: <2023-10-19 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Voiture/Mazda 5
:ARCHIVE_CATEGORY: mazda5
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: voiture
:END:
Ampoule commandée
* DONE Saisie administrative taxe d'habitation
CLOSED: [2023-07-30 Sun 15:02]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-07-02 Sun 18:20]
Découverte <2023-07-02 Sun>. Virement 100.50€ fait.
Mail envoyé ce jour
* DONE Vendre
CLOSED: [2023-11-02 Thu 22:31]
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
** DONE Envoyer Dimensions frigo et machine à laver
CLOSED: [2023-10-17 Tue 23:20] SCHEDULED: <2023-10-17 Wed>
* DONE Photo à Éric pour lit
CLOSED: [2023-07-30 Sun 19:07] SCHEDULED: <2023-07-30 Sun>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
* DONE SMS annonce déménagement
CLOSED: [2023-07-29 Sat 10:57] SCHEDULED: <2023-07-29 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-07-29 Sat 10:25]
* DONE Lettre recommandée annonce déménagement
CLOSED: [2023-07-29 Sat 10:57] SCHEDULED: <2023-07-29 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
#+category: maison
* DONE Résilier box
CLOSED: [2023-10-26 Thu 09:21] SCHEDULED: <2023-10-26 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-03 Tue 23:11]
Envoyé le mail + règlement intérieur. Ce n'est pas une vrai attestation...
Soit raison impérative (pas de frais), soit logement avec déménagement
* DONE Résilier eau
CLOSED: [2023-11-05 Sun 14:51] SCHEDULED: <2023-11-03 Fri>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
:ARCHIVE_OLPATH: Maison
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
À faire après avoir quitté le logement (rétroactif)
* DONE Résilier électricité
CLOSED: [2023-10-26 Thu 09:26] SCHEDULED: <2023-10-26 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-18 Sat 11:57
:ARCHIVE_FILE: ~/roam/personal/projects.org
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:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: DONE
:END:
* DONE Résilier ordures ménagères
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:END:
Mail envoyé
* DONE Payer ordures ménagères
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:END:
/Entered on/ [2023-10-03 Tue 23:12]
Envoyé TIP. RIB déjà envoyé ? Sinon à repaer <2023-10-07 Sat>
* DONE Course
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/Entered on/ [2023-10-09 Mon 22:09]
* DONE Renvoyer clavier corsair SK
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:ARCHIVE_OLPATH: Maison
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:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-10-26 Thu 09:27]
* DONE Payer facture eau Gennes: à vérifier
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:ARCHIVE_TODO: DONE
:END:
Payé 2023-11-08, à vérifier
/Entered on/ [2023-11-05 Sun 15:28]
* DONE Déposer chèque caution
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/Entered on/ [2023-11-06 Mon 21:00]
* KILL Vendre vélo
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:ARCHIVE_TODO: KILL
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/Entered on/ [2023-07-29 Sat 10:23]
* DONE Demande remboursement frais compte bancaire
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:ARCHIVE_OLPATH: Banque
:ARCHIVE_CATEGORY: banque
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-08-13 Sun 11:16]
À surveiller
Relancé 2023-10-15 Sun: relance la directrice d'agence
* KILL Gentoo package diagrams-graphviz :gentoo:haskell:
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:ARCHIVE_OLPATH: Programmation/Gentoo
:ARCHIVE_CATEGORY: maison
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: cs
:END:
/Entered on/ [2023-05-27 Sat 22:28]
* KILL Comprendre pourquoi git-annex ne lit pas home
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:ARCHIVE_TIME: 2023-11-23 Thu 21:45
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:ARCHIVE_OLPATH: Backups
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: KILL
:END:
/Entered on/ [2023-10-01 Sun 21:31]
Unable to parse git config
cannot find git-annex
* KILL Comprendre pourquoi git-annex ne lit pas home
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:PROPERTIES:
:ARCHIVE_TIME: 2023-11-23 Thu 21:45
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:ARCHIVE_OLPATH: Backups
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: KILL
:END:
/Entered on/ [2023-10-01 Sun 21:31]
Unable to parse git config
cannot find git-annex
* DONE Location (blackfriday)
CLOSED: [2023-11-20 Mon 19:32] SCHEDULED: <2023-11-20 Mon>
:PROPERTIES:
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:ARCHIVE_OLPATH: Maison/Serveur/Seedbox
:ARCHIVE_CATEGORY: seedbox
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-11-20 Mon 18:29]
* DONE Configurer rtorrent
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:ARCHIVE_TODO: DONE
:END:
* DONE Tester 1 livres :mam:
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:ARCHIVE_TIME: 2023-11-26 Sun 18:55
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison/Serveur/Seedbox
:ARCHIVE_CATEGORY: seedbox
:ARCHIVE_TODO: DONE
:END:
* DONE Ouvrir IP :mam:
CLOSED: [2023-11-20 Mon 22:22] SCHEDULED: <2023-11-21 Tue>
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:ARCHIVE_TIME: 2023-11-26 Sun 18:55
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison/Serveur/Seedbox
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:ARCHIVE_TODO: DONE
:END:
* DONE Vérifier connectivity :mam:
CLOSED: [2023-11-20 Mon 22:22] SCHEDULED: <2023-11-21 Tue>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-26 Sun 18:55
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Maison/Serveur/Seedbox
:ARCHIVE_CATEGORY: seedbox
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2023-11-20 Mon 22:04]
* KILL depuis raspberry:/media/annex
CLOSED: [2023-11-23 Thu 21:44] SCHEDULED: <2023-11-23 Thu>
:PROPERTIES:
:ARCHIVE_TIME: 2023-11-23 Thu 21:45
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Backups/Git-annex en local
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: KILL
:END:
À vérifier
- [X] public
- [X] private
- [ ] data
* KILL depuis laptop:~/annex
CLOSED: [2023-11-23 Thu 21:44] SCHEDULED: <2023-11-23 Thu>
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:ARCHIVE_TIME: 2023-11-23 Thu 21:45
:ARCHIVE_FILE: ~/org/projects.org
:ARCHIVE_OLPATH: Backups/Git-annex en local
:ARCHIVE_CATEGORY: backup
:ARCHIVE_TODO: KILL
:END:
- [ ] public
- [ ] private
- [ ] data
```{=latex}
\def\dec{$\searrow{}$}
```
```{=latex}
\def\inc{$\nearrow{}$}
```
```{=latex}
\newcommand{\tabitem}{~~\llap{\textbullet}~~}
```
```{=latex}
\newcommand{\ttabitem}{~~~~~~\llap{$\square$}~~}
```
```{=latex}
\newcommand{\tttabitem}{~~~~~~~~\llap{-}~~}
```
::: table
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
Accès simple
----------------------------- ----------------------------- --------------------------------- ---------------------------- ---------------------------------
Adulte Femme enceinte Enfants Remarques
Combinaison d\'artémisinine 1 intention au choix Hospitalisation 1re intention
-- artémether -- 3 jours -- CI 1er trimestre -- ATCD d\'atteintes cardiaques
-luméfantrine Avec un repas gras et allaitement, congénitales
(malabsorption -- ATCD de QT long
-- (arténimol À jeun depuis 3 heures \- CI pendant
pipéraquine) la grossesse -- Pas plus de 2 traitements/an
et allaitement -- 2 mois au moins
entre 2 traitements
Atovaquone- 2e intention Alternative pour le 2e intention IR sévère
proguanil -- Si CI aux CTA 1er trimestre
-- 3 j avec un repas gras
(mauvaise biodisponibilité)
Méfloquine Non recommandée Non recommandée 3e intention
Chloroquine : 3 jours 3 jours 3 jours
espèce autre que
P. falciparum
Quinine 3e intention si IV 2e intention 3e intention si IV
nécessaire : Utilisable tout au nécessaire
Relais PO dès que possible long de la grossesse
Accès grave
Artésunate 7 jours Balance bénéfice/embryotoxicité
Quinine Si artésunate indisponible Si artésunate indisponible
```{=latex}
}
```
:::
# Corps étranger
## Toux : ne rien faire
## Asphyxie :
- conscient : Heimlichx5 - tapesx5 jusque i
- inconscient : retirer avec doigt si gros obstacle, puis massage
cardiaque
## Inconscience
Respire ?
- oui : PLS
- non : massage cardiaque immédiat ! Demander défibrillateur, $O_2$ et
rea ! *30 massage - 2 air*. Préparer 10mg adrénaline
NB : si bébé : 5 insuff + 15 massage - 2 air NB : si enfant \> 1an : 5
insuff - 30 massage - 2 air
% Printing bacteria with biocon package
\newbact{cereus}{genus=Bacillus, epithet=cereus}
\newbact{jejuni}{genus=Campylobacter, epithet=jejuni}
\newbact{chlamydia}{genus=Chlamydia, epithet=trachomatis}
\newbact{cpneumoniae}{genus=Chlamydia, epithet=pneumoniae}
\newbact{psitacci}{genus=Chlamydia, epithet=psitacci}
%
\newbact{botulisme}{genus=Clostridium, epithet=botulinum}
\newbact{difficile}{genus=Clostridium, epithet=difficile}
\newbact{perfringens}{genus=Clostridium, epithet=perfringens}
\newbact{diphterie}{genus=Corynebacterium, epithet=diphteria}
%
\newbact{burnetii}{genus=Coxiella, epithet=burnetii}
\newbact{charbon}{genus=Bacillus, epithet=anthracis}
%
\newbact{tranchees}{genus=Bartonella, epithet=quintana}
%
\newbact{recurrente}{genus=Borreila, epithet=recurrentis}
\newbact{ecoli}{genus=Escherichia, epithet=coli}
%
\newbact{faecalis}{genus=Enteroccocus, epithet=faecalis}
%
\newbact{gardnerella}{genus=Gardnerella, epithet=vaginalis}
\newbact{ducreyi}{genus=Haemophilus, epithet=ducreyi}
\newbact{influenzae}{genus=Haemophilus, epithet=influenzae}
\newbact{helicobacter}{genus=Helicobacter, epithet=pylori}
\newbact{granulomatis}{genus=Klebsiella, epithet=granulomatis}
\newbact{oxytoca}{genus=Klebsiella, epithet=oxytoca}
\newbact{listeria}{genus=Listeria, epithet=monocytogenes}
\newbact{catarrhalis}{genus=Moraxella, epithet=catarrhalis}
\newbact{tuberculose}{genus=Mycobacterium, epithet=tuberculosis}
\newbact{mpneumoniae}{genus=Mycoplasma, epithet=pneumoniae}
\newbact{genitalium}{genus=Mycoplasma, epithet=genitalium}
\newbact{gonocoque}{genus=Neisseria, epithet=gonorrhoeae}
\newbact{meningocoque}{genus=Neisseria, epithet=meningitidis}
\newbact{aeruginosa}{genus=Pseudomonas, epithet=aeruginosa}
\newbact{jirovecii}{genus=Pneumocystis, epithet=jirovecii}
\newbact{typhus}{genus=Rickettsia, epithet=prowazekii}
\newbact{conorii}{genus=Rickettsia, epithet=conorii}
%
\newbact{salmonelle}{genus=Salmonella, epithet=enterica}
\newbact{dore}{genus=Staphylococcus, epithet=aureus}
\newbact{gallolyticus}{genus=Staphylococcus, epithet=gallolyticus}
\newbact{saprophyte}{genus=Staphylococcus, epithet=saprophyticus}
%
\newbact{pneumocoque}{genus=Streptococcus, epithet=pneumoniae}
\newbact{pyogenes}{genus=Streptococcus, epithet=pyogenes}
\newbact{toxoplasmose}{genus=Toxoplasma, epithet=gondii}
\newbact{syphilis}{genus=Treponema, epithet=pallidum}
\newbact{trichomonose}{genus=Trichomonas, epithet=vaginalis}
\newbact{whipplei}{genus=Tropheryma, epithet=whipplei}
%-------------------------------------------------------------------------------
%% Parasits
%-------------------------------------------------------------------------------
\newbact{saginata}{genus=Taenia, epithet=saginata}
\newbact{solium}{genus=Taenia, epithet=solium}
\section{Bactéries}%
\label{sec:bacteries}
Aérobies
\begin{longtable}[]{@{}lll@{}}
\toprule
\begin{minipage}[b]{0.08\columnwidth}\raggedright
\strut
\end{minipage} & \begin{minipage}[b]{0.41\columnwidth}\raggedright
Gram +\strut
\end{minipage} & \begin{minipage}[b]{0.42\columnwidth}\raggedright
Gram -\strut
\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.08\columnwidth}\raggedright
Cocci\strut
\end{minipage} & \begin{minipage}[t]{0.41\columnwidth}\raggedright
En amas :\\
\begin{itemize}
\tightlist
\item
\emph{Staphylococcus aureus}\\
\item
Staphylocoques coagulase negative\\
\end{itemize}
En chaînettes :\\
\begin{itemize}
\tightlist
\item
streptocoques bêta-hémolytiques :\\
S. \emph{pyogenes}, \emph{agalactiae}, \emph{dysgalactiae}\\
\item
S. \emph{pneumoniae}\\
\item
autres : S. \emph{salivarius}, \emph{sanguis}, \emph{oralis},\\
\emph{mutans},complexe ``milleri''\\
(S. \emph{constellatus}, \emph{intermedius}, \emph{anginosus}),\\
S. \emph{gallolyticus}\\
\end{itemize}
Entérocoques : E. \emph{faecalis}, \emph{faecium}\strut
\end{minipage} & \begin{minipage}[t]{0.42\columnwidth}\raggedright
\emph{Neisseria}
\begin{itemize}
\tightlist
\item
N. \emph{meningitidis}
\item
N. \emph{gonorrhoeae}
\end{itemize}
Cocco-baccilles
\begin{itemize}
\tightlist
\item
\emph{Moraxella} spp
\end{itemize}\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.08\columnwidth}\raggedright
Bacilles\strut
\end{minipage} & \begin{minipage}[t]{0.41\columnwidth}\raggedright
\emph{Listeria} spp.\\
\emph{Corynebacterium} spp.\\
\emph{Bacillus} spp.\\
\emph{Erysipelothrix} spp.\\
\emph{Nocardia} spp.\strut
\end{minipage} & \begin{minipage}[t]{0.42\columnwidth}\raggedright
Entérobactéries :
\begin{itemize}
\tightlist
\item
\emph{Escherichia coli}, \emph{Klebsiella} spp.,\\
\emph{Enterobacter} spp., \emph{Serratia}, spp.,\\
\emph{Proteus} spp., \emph{Salmonella} spp.\\
\emph{Shigella} spp., \emph{Yersinia} spp., \emph{Citrobacter} spp.
\end{itemize}
Autres :
\begin{itemize}
\tightlist
\item
\emph{Pseudomonas} spp.\\
\item
\emph{Stenotrophomonas} spp.\\
\item
\emph{Acinetobacter} spp.\\
\item
\emph{Campylobacter} spp.\\
\item
\emph{Helicobacter} spp.\\
\item
\emph{Vibrio} spp.\\
\item
\emph{Bordetella} spp.\\
\item
\emph{Haemophilus} spp.\\
\item
\emph{Brucella} spp. (cocco-bacille)\\
\item
\emph{Pasteurella} spp.\\
\item
\emph{Legionella} spp.\\
\item
\emph{Aeromonas} spp.\\
\item
\emph{Burkholderia} spp.\\
\item
\emph{Kingella} spp.\\
\item
\emph{Francisella} spp\\
\end{itemize}\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}
\subsection{Anaérobies}
\begin{longtable}[]{@{}ll@{}}
\toprule
\begin{minipage}[b]{0.71\columnwidth}\raggedright
Gram +\strut
\end{minipage} & \begin{minipage}[b]{0.23\columnwidth}\raggedright
Gram -\strut
\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.71\columnwidth}\raggedright
\emph{Clostridium}: \emph{tetani}, \emph{botulinum}, \emph{perfringens},
\emph{difficile}\\
\emph{Peptococcus} spp.\\
\emph{Propionibacterium acnes}\\
\emph{Actinomyces} spp.\strut
\end{minipage} & \begin{minipage}[t]{0.23\columnwidth}\raggedright
\emph{Bacteroides} spp. \emph{Fusobacterium} \emph{Prevotella} spp.
\emph{Porphyromonas} spp.\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}
\subsection{Autres}
\begin{longtable}[]{@{}ll@{}}
\toprule
\begin{minipage}[b]{0.71\columnwidth}\raggedright
Atypiques\strut
\end{minipage} & \begin{minipage}[b]{0.23\columnwidth}\raggedright
Spirochètes\strut
\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.71\columnwidth}\raggedright
Intracellulaires :\\
\begin{itemize}
\tightlist
\item
\emph{Chlamydia} spp.\\
\item
\emph{Rickettsiales} :~\emph{Rickettsia} spp, \emph{Bartonella} spp.,
~\\
\item
\emph{Anaplasma} spp., \emph{Coxiella} spp\\
\end{itemize}
Sans paroi (mollicutes) : \emph{Mycoplasma} spp., \emph{Ureaplasma}
spp.\\
\strut
\end{minipage} & \begin{minipage}[t]{0.23\columnwidth}\raggedright
\emph{Treponema} spp.\\
\emph{Borrelia} spp.\\
\emph{Leptospira} spp.\\
\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}
\begin{longtable}[]{@{}ll@{}}
\toprule
\begin{minipage}[b]{0.66\columnwidth}\raggedright
Mycobactéries\strut
\end{minipage} & \begin{minipage}[b]{0.28\columnwidth}\raggedright
Autres\strut
\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.66\columnwidth}\raggedright
\emph{Mycobacterium tuberculosis}\\
\emph{M. leprae}\\
Mycobactéries atypiques (\emph{M. avium} intracellulaire)\\
~\\
\strut
\end{minipage} & \begin{minipage}[t]{0.28\columnwidth}\raggedright
\emph{Tropheryma whipplei}\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}
\subsection{Bonus : Etymologie}
\emph{Acinetobacter} : \emph{acineto} (qui ne bouge pas) + \emph{bacter}
(bâton)\\
\emph{Actinomyces} : \emph{actis} (rayon) + \emph{myces} (champignon)\\
\emph{Aeromonas} : \emph{aeros} (air) + \emph{monas} (unité) = une unité
qui produit du gaz\\
\emph{Anaplasma} : \emph{an} (sans) + \emph{plasma} (forme)\\
\emph{Bacteroides} : \emph{bacter} (bâton) + \emph{oides} (qui
ressemble)\\
\emph{Bartonella} : d'après Alberto Leonard Barton Thompson\\
\hspace*{0.333em} - \emph{henselae} : d'après D. M. Hensel\\
\emph{Bordetella} : d'après Jules Bordet\\
\emph{Borellia} : d'après A. Borrel\\
\emph{Brucella} : d'après Sir David Bruce\\
\emph{Burkholderia} : d'après W. H. Burkholder\\
\emph{Campylobacter} : \emph{campylo} (courbé) + \emph{bacter} (bâton)\\
\emph{Chlamydia} : \emph{chlamus} (manteau)\\
\emph{Clostridium} : \emph{kloster} (fuseau)\\
\hspace*{0.333em} - \emph{botulinum} : \emph{botulus} (saucisse) =
d'après les premiers aliments mis en cause\\
\hspace*{0.333em} - \emph{difficile} : difficile à étudier\\
\hspace*{0.333em} - \emph{perfringens} (qui casse en morceaux)\\
\hspace*{0.333em} - \emph{tetani} : \emph{tetanus} (tension)\\
\emph{Corynebacterium} : \emph{korune} (gourdin) + \emph{bakteria}
(bâton) = bactérie en forme de gourdin\\
\emph{Coxiella} : d'après Harold R. Cox\\
\emph{Citrobacter} : \emph{citrus} (citron) + \emph{bacter} (bâton) =
bactérie utilisant du citrate\\
\emph{Enterobacter} : \emph{enteron} (intestin) + \emph{bacter}
(bâton)\\
\emph{Erysipelothrix} : erysipelas (erysipèle) + \emph{thrix} (cheveux)
= fil d'erysipèle\\
\emph{Escherichia} : d'après Theodor Escherich\\
\emph{Francisella} : d'après Edward Francis\\
\emph{Fusobacterium} : \emph{fusus} (fuseau) + \emph{bacterium}
(bâton)\\
\emph{Haemophilus} : \emph{haema} (sang) + \emph{philus} (qui aime)\\
\emph{Helicobacter} : \emph{helix} (tordu) + \emph{bacter} (bâton)\\
\emph{Kingella} : d'après Elizabeth King\\
\emph{Klebsiella} : d'après Edwin Klebs\\
\emph{Legionella} (une petite légion/armée)\\
\emph{Leptospira} : \emph{leptos} (fin) + \emph{spira} (spire, hélice) =
en forme d'hélice fine\\
\emph{Listeria} : d'après Joseph Lister\\
\emph{Moraxella} : d'après Victor Morax\\
\emph{Mycobacterium} : \emph{mycos} (champignon) + \emph{bacter}
(bâton)\\
\hspace*{0.333em} - \emph{leprae} : \emph{lepra} (lèpre)petite
protubérance)\\
\hspace*{0.333em} - \emph{tuberculosis} : \emph{tuberculum} (petite
protubérance)\\
\emph{Mycoplasma} : \emph{mycos} (champignon) + \emph{plasma} (forme)\\
\emph{Neisseria} : d'après Albert Neisser\\
\hspace*{0.333em} - \emph{gonorrhea} : \emph{gonos} (semence) +
\emph{rhein} (flux) = écoulement de pus\\
\hspace*{0.333em} - \emph{meningitidis} : \emph{meninx} (membrane) +
\emph{itis} (inflammation)\\
\emph{Nocardia} : d'après Endmon Nocard\\
\emph{Pasteurella} : d'après Louis Pasteur\\
\emph{Peptococcus} : \emph{pepto} (digérer) + \emph{coccus} (baie) = le
coccus qui digère\\
\emph{Prophyromonas} : \emph{porphyro} (violet) + \emph{monas} (unité)\\
\emph{Prevotella} : d'après A. R. Prévot\\
\emph{Pseudomonas} : \emph{pseudo} (faux) + \emph{monas} (unité)\\
\emph{Propionibacterium} : de l'acide propionique\\
\emph{Proteus} : cf le dieu grec Proteus des rivières et oceans\\
\emph{Rickettsia} : d'après H. T. Ricketts\\
\emph{Salmonella} : d'après D.E Salmon\\
\emph{Serratia} : d'après Serafino Serrati\\
\emph{Shigella} : d'après K. Shiga\\
\emph{Staphylococcus} : \emph{staphyle} (grappe) + \emph{coccus}
(baie)\\
\hspace*{0.333em} - \emph{aureus} (doré)\\
\emph{Stenotrophomonas} : \emph{stenos} (étroit) + \emph{trophos}
(nourisseur) + \emph{monas} (``unité'') = une unité qui se nourrit de
peu\\
\emph{Streptococcus} : \emph{streptos} (chaîne) + \emph{kokkos} (baie)\\
\hspace*{0.333em} - \emph{agalactiae} (sans lait)\\
\hspace*{0.333em} - \emph{dygalactiae} (mauvais lait)\\
\hspace*{0.333em} - \emph{pneumoniae} (poumon)\\
\hspace*{0.333em} - \emph{pyogenes} : \emph{pyon} (pus) + \emph{genes}
(egendré)\\
\emph{Treponema} : \emph{trepo} (tourner) + \emph{nema} (fil) = un fil
qui tourne\\
\emph{Tropheryma} : \emph{trophe} (nourriture) + \emph{eruma} (barrière)
= car cause malabsorption\\
\hspace*{0.333em} - \emph{Whipplei} : d'après George Whipple\\
\emph{Ureaplasma} : \emph{urea} (urée) + \emph{plasma} (forme)\\
\emph{Vibrio} (qui vibre)\\
\emph{Yersinia} : d'après A.J.E Yersin
----------- -----------------
pH 7.38 - 7.42
PaO~2~ 70 - 100 mmHg
SpO~2~ 95 - 100 %
PaCO~2~ 38 - 42 mmHg
HCO~3~\^- 23 - 28 mmol/L/
----------- -----------------
---------------------------- --------------------------------------
$Ca^{2+}$ 2.1 - 2.6 mmol/L
Créatinémie femme : 50 - 90 μmol/L
homme : 80 - 115 μmol/L
enfant \< 44 μmol/L
Clairance créat IRC : ≤ 60 mL/min/1.73 m^2^
Glycémie jeun 0.60 - 0.90 g/L ( 3.3 - 5.0 mmol/L )
Glycémie repas 1.20 - 1.30g/L ( 6.7 - 7.2 mmol/L)
$K^{+}$ 3.5 - 5 mmol/L
$Na^{+}$ 135 - 145 mmol/L
LDH (sang) $\approx$ 140 - 180 U/L
Phosphore (sang) $\approx$ 0.96 - 1.3 mmol/L
Urée (sang) $\approx$ 2.5 - 8.3 mmol/L
---------------------------- --------------------------------------
\begin{multicols}{2}
* Général
:UNNUMBERED: t
- Trouble psy sévère, chronique et fréquent
- Humeur, activité, énergie augmentées (manie) ou diminuées (dépression).
- Souvent associé à d'autres troubles psy (troubles anxieux, addictifs) et non psy (CV, syndrome métabolique, etc.).
- Origine multifactorielle (FR génétiques (60 à 70%), environnementaux.
Épidémio :
- 1-4 % population,
- 2e cause de suicide parmis troubles psy
- enfant : 0,1 %, ado> 1 %)
- Début à 15 et 25 ans, sex-ratio = 1 (type I) mais prédominance féminine pour type II
* Sémiologie psychiatrique
:PROPERTIES:
:UNNUMBERED: t
:END:
** Syndrome maniaque
- augmentation pathologique de l'humeur et de l'énergie ou de l'activité \ge 1 semaine ("pile électrique chez qui tout va trop vite)
- *urgence diagnostique et thérapeutique* \Rightarrow hospitalisation !
- 3 composantes (cf tableau)
- symptômes psychotique possible !
- idée délirantes
- hallucinations (40 à 50 %)
- comportements à risque, recherche de sensations fortes, substances psychoactives, achats pathologiques
** Syndrome hypomaniaque
- >\ge 4 jours consécutifs
- semblable au syndrome maniaque mais moins intense, rententissement moindre. rupture totale avec l'état antérieur
- hospitalisation non nécessaire
** Syndrome dépressif
Y penser si
- EDC avant 25 ans/en post-partum/début rbutal
- ATCD \ge 3 EDC
- ATCD familial de trouble de l'humeur
- non réponse ttt antidépresseur
- mélancolique et saisonnier.
* Diagnostic
:PROPERTIES:
:UNNUMBERED: t
:END:
** Épisode maniaque
#+ATTR_LATEX: :environment enumerate :options [label=\Alph*.]
A. \ge 1 semaine presque tous les jours avec humeur est élevée/expansive/irritable de façon anormale et persistante
B. \ge 3 symptômes (intensité significative + changement notable du comportement):
- augmentation de l'estime de soi ou idées de grandeur
- réduction du besoin de sommeil
- désir constant de parler
- fuite des idées
- distractibilité
- augmentation de l'activité orientée vers un but ou agitation psychomotrice
- engagement excessif dans des activités à potentiel élevé de conséquences dommageables (achats inconsidérés)
- altération marquée professionnel/social ou nécessitant hospitalisation
C. Pas imputable à une substance / autre affection médicale générale.
** Épisode hypomaniaque
#+ATTR_LATEX: :environment enumerate :options [label=\Alph*.]
A. Idem A. de la manie mais \ge 4 jours consécutifs.
B. Idem B. épisode maniaque
C. Modifications indiscutables du fonctionnement
D. Manifestes pour les autres.
E. *Pas* d'altération marquée du fonctionnement professionnel ou social ou nécessitant une hospitalisation. S'il existe des caractéristiques psycho-
F. Idem épisode maniaque
** Épisode dépressif caractérisé
#+ATTR_LATEX: :environment enumerate :options [label=\Alph*.]
A. \ge 5 des symptômes pendant \ge 2 semaines, + changement par rapport au fonctionnement antérieur et\ge 1 symptomes parmis {humeur dépressive, perte d'intérêt ou de plaisir} :
- humeur dépressive présente pratiquement toute la journée, PTLJ
- diminution marquée de l'intérêt/plaisir pour presque toutes les activités pratiquement toute la journée, PTLJ
- modification significative du poids sans régime ou modification de l'appétit PTLJ.
- insomnie ou hypersomnie PTLJ
- agitation ou ralentissement psychomoteur PTLJ
- fatigue ou perte d'énergie tous les jours
- sentiment de dévalorisation ou de culpabilité excessive ou inappropriée PTLJ
- diminution de l'aptitude à penser ou à se concentrer ou indécision PTLJ
- pensées de mort récurrentes, idées suicidaires récurrentes sans plan précis
B. Détresse cliniquement significative/altération du fonctionnement social, professionnel ou dans d'autres domaines importants.
C. Pas due aux effets physiologiques directs d'une substance ou d'une autre affection médicale générale.
** Caractéristiques cliniques de l'épisode
- *psychotiques* : idées délirantes, d'hallucinations. /Congruentes ou non/ à l'humeur (consistant avec les thèmes, ex : maniaque + thème mégalomaniaque)
- *mixtes* : symptômes dépressifs pendant épisode maniaque.
(l'inverse s'appelle un épisode dépressif caractérisé avec caractéristique mixte \Rightarrow _risque suicidaire_ élevé !)
- *anxieuses* \Rightarrow _risque suicidaire_ élevé !
- avec *début en péri-partum* : pendant la grossesse et jusqu'à 4 semaines après l'accouchement
- *catatoniques* = catalepsie (flexibilité cireuse), négativisme, stéréotypies, impulsions, écholalie, écho praxie. /NB: trouble bipolaire = cause la plus fréquente du syndrome catatonique/
** Selon l'évolution des épisodes récurrents
- Avec caractère *saisonnier* : épisodes maniaques, hypomaniaques ou dépressifs) à une période particulière de l'année avec épisode / rémission /virage
- Avec *cycles rapides* : \ge 4 épisodes de l'humeur sur les 12 derniers mois
** Types
#+ATTR_LATEX: :environment enumerate :options [label=\Roman*.]
- \ge 1 épisode(s) maniaque(s)
- \ge 1 épisode(s) hypomaniaque(s) et \ge 1 épisodes dépressifs caractérisés.
** Diagnostics différentiels
_Non psy_ :
- substances psychoactives++ (alcool, cannabis, amphétamines et cocaïne, hallucinogènes).
- neuro: tumeur cérébrale, SEP, AVC, pathologie neuro- dégénérative, épilepsie focale (rare)
- endoc: hypo/hyper-thyroïdie, maladie de Cushing
- métaboliques : hypoglycémie, troubles ioniques, maladie de Wilson, etc.
- médicamenteuses (corticoïdes, antidépresseurs, interféron-alpha, bêta-bloquants, L-Dopa, etc.).
Bilan:
- Sanguin :
- glycémie, ionogramme, calcémie. urée, créatinémie.
- NFS, plaquettes, CRP, TSH US, hépatique.
- Toxiques urinaires : cannabis, cocaïne, opiacés, amphétamines.
- Imagerie :
- Cérébrale : IRM + EEG si c'est un premier épisode
- ECG (bilan pré-thérapeutique des antipsychotiques et du lithium).
- trouble dépressif récurrent
_Psy_: trouble de personnalité, déficit de l'attention, schizophrénie, trouble anxieux, TOC, trouble délirant persistant, troubles addictifs
** Complications
- cycles rapideh
- trouble psychiatriques : addictifs, anxieux, troubles du sommeil et des rythmes, etc.
- non-psy : CV, syndromes métaboliquesx..
- suicide (15 % des bipolaires décèdent par suicide)
- délits/crimes
- désinsertion familiale professionnelle et sociale
* Prise en charge
:PROPERTIES:
:UNNUMBERED: t
:END:
** Hospitalisation en psychiatrie
- Si *épisode maniaque* = hospitalisation en urgence +/- sans consentement.
- Si *EPDC + critères de gravité* (caractéristique mélancolique, psychotique, mixte, etc.)
- Autres : risque suicidaire élevé, conséquences délétères pour le patient et pour l'entourage et les soignants risque hétéro agressif, ou complications médico-légales.
** Phase aiguë : général
- Symptomatique : agitation, risque suicidaire, réhydratation et troubles hydro-électrolytiques, perturbation du sommeil, comportements à risque (grossesse, MST)
- Surveillance efficacité du traitement
** Traitement d'attaque (6-8 semaines)
Épisode maniaque :
- *Arrêt antidépresseur* (peuvent induire le virage maniaque),
- *Lithium* /valproate (Depakote)/carbamazépine
- *Antipsychotique de 2e génération* (Olanzapine, Risperidone, Quetiapine, Aripiprazole).
- *Protection juridique* : sauvegarde de justice en cas de dépenses ou achats excessifs
EDC
+ Lithium /Lamotrigine /Quetiapine monothérapie
+ au moins 2 semaines de traitement à dose efficace.
+ Prévention et surveillance des idées suicidaires.
** Consolidation (4-6 mois)
Idem si bonne tolérance, arrête anxiolytique e hypnotique si possible
** Long cours (prophylaxie)
Selon patient
** Autres
- *électroconvulsivothérapie* (ECT) = si pronostic vital engagé et après échec des autres ttt. Curatif pour les épisodes. Indications :
- EDC sévère/caractéristiques mélancoliques/résistant aux ttt
- épisode maniaque sévère et prolongé/résistant aux tt
- syndrome catatonique
- trouble bipolaire avec cycles rapides
- mauvaise tolérance des psychotropes, risque de décompensation
- CI aux autres traitements (femme enceinte, personne âgée, etc.).
- *Psychothérapie* : TCC, thérapie interpersonnelles
- *Éducation thérapeutique*
- Réhabilitation psychosociale: remédiation cognitive, réadaptation psychosociale
#+LaTeX: \end{multicols}
```
PSYCHOAFFECTIVES PHYSIOLOGIQUE
-------------------------------------------------------- ---------------------------------------------------------
**Perturbations de l\'humeur** : **Perturbations du sommeil**
\- humeur élevée, expansive, exaltée, euphorique \- insomnie partielle/totale,
\- ou irritabilité \- réduction du temps de sommeil
**Perturbations des émotions** : \+ à une absence de sensation de fatigue.
\- labilité émotionnelle **Perturbations des conduites alimentaires** :
\- hyperréactivité ou hyperesthésie \- anorexie (partielle ou totale) ou hyperphagie,
(réponses émotionnelles disproportionnées par \- amaigrissement
rapport aux stimuli émotionnels), \- possible déshydratation.
\- hypersyntonie (participation spontanée et **Perturbations de la sexualité** :
adhésion très rapide à l\'ambiance affective) \- augmentation du désir et excitation sexuelle
**Altérations du contenu de la pensée** : , hypersexualité
\- augmentation de l\'estime de soi,
\- idées de grandeur, sentiment de
toute-puissance, idées mégalomaniaques,
\- altérations ou absence de la conscience du trouble.
PSYCHOMOTRICE
**Accélération du cours de la pensée** **Accélération motrice et comportemental** :
\- tachypsychie (accélération des idées), \- agitation motrice, hyperactivité souvent stérile,
\- fuites des idées (impression que les idées fusent), \- augmentation de l\'énergie,
\- coq-à-l\'âne (changement rapide d\'une idée \- augmentation des activités à but dirigé
à l\'autre sans lien apparent), (professionnelles, sociales ou sexuelles),
\- jeux de mots, ludisme, associations par assonances. \- logorrhée (augmentation du débit de parole)
**Altérations cognitives** \- tachyphémie (augmentation de la vitesse de parole),
\- hypervigilance, \- hypermimie (augmentation des expressions du visage),
\- distractibilité, \- désinhibition (contact familier).
\- altérations attention et concentration.
```{=latex}
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::: table
```{=latex}
\adjustbox{max width=\linewidth}{
```
TNM CCR Prosate Poumon Sein Mélanome
----------- ---------------------- --------------------------- ---------------------- --------------------------- ----------------------------------
T1 muqueuse non visible 1-3cm 0.01-2cm 0.01-1mm
T2 sous-muqueuse a: \< 1/2 lobe 3-5cm 2.01-5cm 1.01-2mm
b: \> 1/2 lobe
C: 2 lobes
T3 musculeuse vésicules séminales **5**-7cm \> **5** cm 2.01-4mm
T4 séreuse autres structures \> 7cm thorax/peau \> 4mm
Extension **scan TAP et colo** *Si risque \> faible* **scan TAP** *Si ≥ T3, ≥ N1,* **clinique**
± echo-endo rectale **scinti os** et **IRM cérébrale** *grade III, RH-, HER2+++* ± echo si ≥ T2 ulcéré ou T3
et IRM pelvienne ± IRM prostate + pelvis et **TEP** **scan TAP + scinti** ± scan TAP cérébral si T4 ulcéré
(si K rectum) (risque intermédiaire) ou ± BRAF si métastase
ou scan TAP (risque haut) **TEP**
```{=latex}
}
```
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```
Enfant, adolescent Adulte
------------------ ---------------------------------------------------- -------------------------------------------------------
Anamnestiques \- Perte de poids \> 2 kg/semaine. \- perte de 20 % du poids en 3 mois.
\- Refus de manger/boire \- Malaises et/ou chutes ou pertes de connaissance.
\- Lipothymies ou malaises d'allure orthostatique. \- Vomissements incoercibles.
\- Fatigabilité/ épuisement \- Échec de la renutrition ambulatoire.
Cliniques \- IMC \< 14 kg/m2 si \> 17 ans \- IMC \< 14 kg/m2.
\- (13.2 si 16-16 et 12.7 si 13-14)
\- Pouls \< 40/min \- Bradycardie sinusale FC \< 40/min.
\- Tachycardie. \- FC \> 60/min si IMC \< 13 kg/m2.
\- PAs \< 80 mmHg
\- PA \< 80/50 mmHg, hypoTA OS \- PA \< 90/60 mmHg.
\- Hypothermie \< 35,5 °C. \- Hypothermie \< 35 °C.
\- Hyperthermie.
\- Ralentissement idéique et verbal, confusion. \- Signes cliniques de déshydratation.
\- Syndrome occlusif. \- Amyotrophie importante avec hypotonie axiale.
Paracliniques \- Acétonurie (BU), hypoglycémie \< 0,6 g/L. \- Hypoglycémie sympto \< 0,6 g/L (\< 0,3 g/L sinon).
\- Hypokaliémie \- Hypokaliémie \< 3 mEq/L .
\- Hypophosphorémie \- Hypophosphorémie \< 0,5 mmol/L.
\- Hyponatrémie \- Natrémie \< 125 mmol/L (potomanie,
\- [Hypomagnésémie]{.underline} \- Natrémie \> 150 mmol/L (déshydratation)
\- Anomalies de l'ECG
\- Créatinine \> 100 µmol/L. \- Clairance de la créatinine \< 40 mL/min.
\- Cytolyse (\> 4 x N). \- Cytolyse hépatique \> 10 x N..
\- Leuconeutropénie (\< 1 000 /mm3). \- Leucopénie \< 1 000 /mm3 (ou PNN \< 500 /mm3).
\- Thrombopénie (\< 60 000 /mm3).
Psychiatriques Risque suicidaire \- TS réalisée ou avortée.
\- Plan suicidaire précis.
\- Automutilations répétées.
Comorbidités \- Trouble psy intense justifiant hospit
\- Dépression.
\- Abus de substances.
\- Anxiété.
\- Symptômes psychotiques.
\- Troubles obsessionnels compulsifs.
Anorexie mentale \- Idéations obsédantes intrusives et permanentes
\- Renutrition nécessaire (SNG...)
\- Exercice physique excessif et compulsif
\- Conduites de purge
Coopération \- Échec antérieur d'une PEC ambulatoire
\- Patient peu coopérant
\- Motivation trop insuffisante
Environnementaux Disponibilité de l'entourage \- Épuisement familial.
\- Problèmes familiaux
Stress environnemental \- Conflits sfamiliaux sévères.
\- Critiques parentales élevées.
\- Isolement social sévère.
Disponibilité des soins \- PEC ambulatoire impossible
Traitements antérieurs \- Échec des soins ambulatoires
::: table
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=0.8\linewidth}{
```
----------------- ------------------------- ----------------------- ------------------------ -----------------------------
Retard de résorption Inhalation Infection Maladie des
du liquide méconiale néonatale membranes hyalines
pulmonaire (MMH)
Contexte Césarienne (surtout Nouveau-né à terme Facteurs de risque Prématurité (\< 32 SA)
avant travail) ou post-terme d\'INBP Absence de
Liquide amniotique corticothérapie
méconial anténatale
Asphyxie périnatale Parfois diabète
maternel
Clinique Détresse respiratoire Détresse respiratoire Non spécifique Détresse respiratoire
immédiate s\'améliorant immédiate, apparue très
progressivement en d\'évolution rapidement après
quelques heures potentiellement grave la naissance et
Polypnée prédominante d\'aggravation
progressive
Radio du thorax Syndrome interstitiel Opacités alvéolaires ± Opacités alvéolaires Syndrome alvéolaire
modéré grossières, irrégulières bilatéral
Scissurite asymétriques
Épanchement Troubles de
interlobaire ventilation
Gaz du sang Normaux Hypoxie, hypercapnie Variables Hypoxie, hypercapnie
Traitement PEP par canules nasales Ventilation mécanique Antibiothérapie Surfactant exogène
Rarement ventilation avec PEP Soutien ventilatoire Ventilation mécanique
mécanique avec PEP adapté avec PEP
Pronostic Excellent Celui de l\'asphyxie Celui de l\'infection Celui de la prématurité
périnatale Dysplasie bronchopulmonaire
----------------- ------------------------- ----------------------- ------------------------ -----------------------------
```{=latex}
}
```
:::
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\begin{table}
\centering
\adjustbox{max width=0.8\linewidth}{
\begin{tabular}{lllll}
& Retard de résorption & Inhalation & Infection & Maladie des\\
& du liquide & méconiale & néonatale & membranes hyalines\\
& pulmonaire & & & (MMH)\\
\hline
Contexte & Césarienne (surtout & Nouveau-né à terme & Facteurs de risque & Prématurité (< 32 SA)\\
& avant travail) & ou post-terme & d'INBP & Absence de\\
& & Liquide amniotique & & corticothérapie\\
& & méconial & & anténatale\\
& & Asphyxie périnatale & & Parfois diabète\\
& & & & maternel\\
\hline
Clinique & Détresse respiratoire & Détresse respiratoire & Non spécifique & Détresse respiratoire\\
& immédiate s'améliorant & immédiate, & & apparue très\\
& progressivement en & d'évolution & & rapidement après\\
& quelques heures & potentiellement grave & & la naissance et\\
& Polypnée prédominante & & & d'aggravation\\
& & & & progressive\\
\hline
Radio du thorax & Syndrome interstitiel & Opacités alvéolaires & ± Opacités alvéolaires & Syndrome alvéolaire\\
& modéré & grossières, & irrégulières & bilatéral\\
& Scissurite & asymétriques & & \\
& Épanchement & Troubles de & & \\
& interlobaire & ventilation & & \\
\hline
Gaz du sang & Normaux & Hypoxie, hypercapnie & Variables & Hypoxie, hypercapnie\\
\hline
Traitement & PEP par canules nasales & Ventilation mécanique & Antibiothérapie & Surfactant exogène\\
& Rarement ventilation & avec PEP & Soutien ventilatoire & Ventilation mécanique\\
& mécanique avec PEP & & adapté & avec PEP\\
\hline
Pronostic & Excellent & Celui de l'asphyxie & Celui de l'infection & Celui de la prématurité\\
& & périnatale & & Dysplasie bronchopulmonaire\\
\end{tabular}
}
\end{table}
\end{document}
# Douleur
:CUSTOM~ID~: sec:orgc3e2804
## Divers {#sec:org377567d}
- Douleurs par excès de nociception : anti-inflammatoires, opioïdes en
pratique
- Douleurs chez personne âgée : interaction douleur, dépression et
démence
- Douleur chez l\'enfant : anesthésique locaux topique (EMLA), mélange
oxygène-protoxyde d\'azote (MEOPA)
- Santé mentale : anxiété pour douleur aigüe, dépression pour douleur
chronique
- anesthésie : hypnotique (CS) + morphinique (analgésie) curare
(relâchement musc). Médullaire ou périphérique
- douleurs neuro : antidépresseurs tricycliques et mixet et
antiépileptiques = efficaces sur douleurs continues et paroxystiques
## Autres médicaments {#sec:org475373b}
- anesthésiques locaux :
- EMLA : douleurs provoquées par les soins)
- techniques de bloc : prévenir douleurs post-op
- capsaïcine :
- faible concentration : douleurs musc, arthrose, neuro (immédiat)
- forte concentration : 3 mois sur douleurs neuro (neurotoxique !)
- corticoïdes : anti-inflammatoire, et (+ anesthésiques locaux) sur
lésion/irritation nerf
- kétamine : anesthésie seulement
## Évaluation de la douleur chez l\'adulte {#sec:org452c6a5}
--------------------- ----------------------
Quantitative EVS
EVA
EN
Qualitative DN4
Retentissement HAD
QDSA
QCD
Âgé non communicant Doloplus (chronique)
Algoplus (aigüe)
--------------------- ----------------------
## 132 : Antalgiques {#sec:org4a2e159}
### Palier 1 et AINS {#sec:orgf617733}
1. Paracétamol
1ere intention, surtout douleur chronique
Prescription : 3-4g/24h (adulte) avec délai 4-6h. Délai 1h, dure
4-6h. Enfant : 60mg/kg/24g espacée de 6h
Seul pour douleurs faibles/modérées, avec opioïdes sinon
Tolérance :
- si surdosage :
- hépatotoxique urgence N-acétylcysténine
- insuf rénale aigüe et nécrose tubulaire
- thrombocytopénie
- sinon bonne tolérance. Surveiller HTA, hypersensibilité
2. AINS
COX-1 : protège muqueuse gastro-duodénale et pro-agrégant. COX-2 :
inflammation, effet anti-agrégant
Antalgique à faible dose. Pour douleurs {ostéo-articulaire, trauma,
post-op, néplasiques}, coliques néphrétiques, dysménorrhées
essentielles, migraines.
OS, injectable (limiter à 48h !) ou pommade/gel
Effets indésirables :
- digestif [^1]:
- mineur : nausées, vomissements, gastralgies, douleurs abdo
- grave : ulcère, perforation digestive, hémorragie
- autres : ulcère oesophagien[^2], aggravation diverticulose,
anorectites/brûlures anales
- FR : { \> 65 ans, ATCD ulcère/hémorragie dig, infection ,
maladie générale sévère}, {+ AINS, + corticoïdes,
+anticoag/agrégants, +aspirine} FR $\ge$ 3 ou aspirine :
éviter !
- rein :
- risque hypovolémie, néphropathie, âgé, association
(diurétique, IEC, ARAII)
- insuf rénale fonctionnel (créat !), rétention hydrosodée,
hyperkaliémie, néphropathie intestitielle, (nécrose
papillaire)
- cutanés/muqueus fréquents : bénin, urticaire (sd
Lyelle/Stevens-johnson)
- allergiques (rhinite, conjonctivite, oedème de Quincke, asthme)
ou respiratoire
- si anémie, chercher saignement digestif
- hépatite (souvent silencieuse)
- sd confusionnel (âgé)
- CV : rétention hydrosodée, risque thrombotique artériel
Éviter interactions : AINSE aspirine, {anticoag, ticlopidine},
{diurétiques, IEC}, lithium, corticoïdes, méthotrexate
### Palier II {#sec:org164bdeb}
60mg codéine = 50mg tramadol = 10mg morphine
Douleurs aigües (courte) ou chronique (courte/long)
Codéine :
- agoniste opioïde naturel métabolite \* morphine
- seul (sirop, dihydrocodéine) ou avec paracétamol.
- 1-2 comprimés toutes 6-8h
Tramadol :
- seul, libération prolongée (LP) sur 12h [^3] ou immédiate (LI)[^4]
- max 400mg/j.
- IV lente seulement en hôpital
Poudre d\'opium avec paracétamol : 1-2 gélules toutes 4h (max 10/j)
Contre-indications : insuf respiratoire, asthme grave, insuf
hépatocellulaire sévère, enfants \< 12 ans \[codéine\] ou 3 ans
\[tramadol\], allaitement, épilepsie non contrôlé \[tramadol\],
+(ant)agoniste morphinique, +IMAO[^5] \[tramadol\].
Effets indésirables :
- ceux des opioïdes = sédation, vertige, {constipation, nausées,
vomissements}, {bronchospasme (dépression respiratoire)}, rétention
d\'urine
- sécheresse buccale, douleurs abdo, troubles visuels, convulsion (si
facteurs)
Éviter codéine si enceinte. posologie si âgé
### Palier III {#sec:org98d3e49}
AMM :
- douleurs *non* cancéreuse = morphine, oxycodone, fentanyl
(transdermique)
- douleurs cancéreuse = idem et fentanyyl transmuqueus, hydromorphone
1. Formes
Catégorie Molécule Note forme Action
----------------------- --------------- -------------------- --------------- ------------------------
Agonistes purs Morphine référence. Chlorhydrate
Sulfate LP (12-24h) ou LI (4h)
Hydromorphone K (2eme intention) 12h (délai 2h)
Oxycodone) morphine x2 LP (12h) ou LI (4h)
Fentanyl morphine x50-150 Transdermique 72h (délai 12-18h)
Transmuqueuse 1-2h (délai 10min)
Méthadone dpdance opiacés
Agonistes partiels buprénorphine morphine x30.
Effet plafond
Agoniste-antagonistes nalbuphine pédiatrie++
Antagonistes naloxone Effet plafond
2. CI
Insuf respi décompensée, insuf hépatocellulaire sévère, insuf rénale
sévère, épilepsie non contrôlée, trauma crânier et HTIC, intox
alcoolique aigüe, +IMAO, associer agonistes avec a. partiel ou
a-antagonistes
3. EI
- Constipation (fréquent !):
- préventif = laxatif oral systématique, hygiéno-diététique,
oxycodone et naloxone
- curatif : laxatif, fécalome ?, ttt rectal.[^6]
- Nausées, vomisseements(fréquent !):
- préventif : anti-émétique
- curatif : neuroleptique action centrale, corticoïdes,
sétrons, droperidol
- Somnolence : dose ou rotation
- Dépression respi (FR \< 10min) : réa et naloxone
- Trouble s confusionnels, cognitifs : doses, rotation
- Dysurie, rétention :[^7] doses, sondage, chercher médicaments
favorisants
- Prurit : antihsistaminique, rotation
Dépendance : pyschologique (recherche compulsvie), physique (sd
sevrage)
4. Surdosage
Somnolence, respi irrégulière, FR \< 10/min Échelle de sédation (0 à
3)[^8], de qualité de respiration (R0 à R3)[^9]
Réat et injection narcan (naloxone) : 0.4mg par dose de 0.04mg/2min
jusque R1/R0
5. Indications :
Privilégier formale orale et LP
- Douleurs aigüe : très intenses ou (modéré/sévère ne répondant
pas au palier
II). Oral (parentéral si urgence)
- Douleurs chroniques cancéreuses ou (non cancéreuses après échec
étiologique, palier 1, II et techniques). Oral et LP.
Équivalence :
- morphine : 1 oral = 1/2 SC = 1/3 IV
- 1 morphine Iv = 1 oxycodone IV/SC
- oxycodone : 1 oral = 1/2 IV/SC
Prescription : ordonnance sécurisée, $\le$ 28j
## Antiépileptiques {#sec:org97d7952}
Douleur neuropathique :
1. Gabapentinoïdes
2. tricycliques/opioïdes (2eme intention)
## Antidépresseur {#sec:orgf21ce39}
Classes :
- tricyclique : amitriptyline
- inhibiteurs de la recapture de la noradrénaline et sérotonie :
venlafaxine, duloxétine, milnacipran
Douleurs chroniques :
- neuropathiques, lombalgie, céphalée : amitriptyline
- fibromyalgie : duloxétine, milnacipran
## Grands syndromes {#sec:org99fc91d}
Pneumo
- Dyspnée : morphinique, benzodiazepine O$_{\text{2}}$ (en phase
terminale ?)
- Encombrements bronchiques : demi-assis, soins de bouches, éviter
aspirations, anticholinergiques
Digestifs :
- nausées, vomissements : alimentation, soins de bouche,
neuroleptiques, corticoïdes, agonistes récepteurs 5-HT3 (si chimio)
benzodiazepine
- occlusion intestinale : origine mécanique ou fonctionnelle
(motricité). Fréquent si carcinose péritonéale
- à jeûn + réhydratation IV/SC
- antiémétique (neuroleptique), antisécrétoires
anti-cholinergique, antisécrétoire analogue somatostatine, IPP,
corticothérapie, antalgique SNG
- constipation : hygiéno-diététique, laxatif osmotique/stimulation (3e
jour : suppositoire de glycérine)
Neuropsy :
- confusion : neuroleptique (éviter benzodiazepine !)
- anxiété : benzodiazepine, hydroxine. Si échec neuroleptique
[^1]: NB : coxibs probabilité de développer un ulcère simple/compliqué
mais retard circatrisation d\'un ulcère gastrique ...
[^2]: Donc toujours prendre avec de l\'eau, debout et sans être à jeun !
[^3]: 1 prise/j, 24h si 2 prises/j
[^4]: Toutes 4-6h
[^5]: Inhibiteurs de la monoamine oxydase
[^6]: Si 0 selles : bithérapie laxative, lavement rectal, antagoniste
morphinique périph
[^7]: Y enser si HTA, douleurs abdo, agitation inhabituelle
[^8]: 0 = éveillé, 3 = très somnolent, éveillable par stimulation
tactile.
[^9]: R0 = normale, R3 = pauses/apnée
% Created 2021-02-23 Tue 23:37
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\author{Alexis}
\date{\today}
\title{Dyslipidémies}
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\tableofcontents
Risque CV athéromateux : LDL haut, HDL bas et selon hyperTG (facteurs associés: surpois, diabète, HDL bas)
Bila lipidique (EAL) selon formule de Friedwal : LDL = CT - HDL - TG/5 (en g/L) ou TG/2.2 si mmol/L
Normal = \textbf{LDL < 1.6g/L, HDL < 0.4g/L, TG > 1.5g/L}
Hyperlipidémies secondaires.
\begin{center}
\begin{tabular}{lll}
Étiologies & Diagnostique & Type d'hyperlipidémie\\
\hline
Hypothyroïdie & TSH & HCH/HLM\\
Cholestase & Bilirubine, phosphatase alcaline & HCH\\
Syndrome néphrotique & Protéinurie, œdèmes & HLM\\
Insuffisance rénale chronique & Créatinine & HTG/HLM\\
Alcoolisme & Interrogatoire & HTG\\
Diabète & Glycémie, HbA1c & HTG\\
Hyperlipidémie iatrogène & Interrogatoire & \\
Œstrogènes & `` & HTG\\
Corticoïdes & `` & HLM/HTG\\
Rétinoïdes & `` & HTG\\
Antirétroviraux & `` & HTG\\
Ciclosporine & `` & HCH/HLM\\
Diurétiques, bêtabloquants & `` & HTG modérée\\
\end{tabular}
\end{center}
\begin{center}
\begin{tabular}{ll}
Hypercholestérolémies familiales & \emph{mutation du gène du LDL-récepteur} (fréquent++)\\
monogéniques & - hétérozygote : fréquente (1/500), LDL-C : 2 - 4 g/L,\\
& \textbf{xanthomes tendineux, arc cornéen prématuré}, risque CV élevé\\
& - homozygote : \textbf{exceptionnelle} (1/1 000 000), LDL-C : > 5 g/L\\
& , xanthomes dès l'enfance, \textbf{grave} (RA\ldots{} dès la 1re décennie)\\
& \emph{Mutation gène de l'apolipoprotéine B} (apoB), gène proétine \emph{PCSK9} (rare)\\
\hline
Hypercholestérolémies polygéniques & \textbf{Très fréquente}, LDL augmenté +/- hyperTG. Risque CV selon LDL et autres fR\\
\hline
Hyperlipidémie familiale combinée & fréquente (1 à 2 \% )\\
& hypercholestérolémie/hyperTG/mixte, risque CV variable\\
\hline
Dysbêtalipoprotéinémie ( III) & rare, prédisposition génétique + surpoids, diabète, hypothyroïdie, ttt\\
& LDL et TG élevé\\
& \textbf{xanthomes plans palmaires, xanthomes tubéreux jaune orangé} = caractéristiques\\
& risque CV élevé\\
\hline
Hypertriglycéridémie familiale & rare, risque athérogène incertain.\\
Hyperchylomicronémies primitives & très rares. TG > 10 g/L voire 100 Risque de pancréatite aiguë++\\
\end{tabular}
\end{center}
\begin{center}
\begin{tabular}{llll}
Risque & Critère & Objectif LDL & TTT\\
\hline
Faible & SCORE < 1\%< & < 1.15g/L & Diététique\\
\hline
Modéré & 1\% ≤ SCORE < 5\%< & < 1.15g/L (3 mmol/L) & Diététique\\
& Diabète de type 1/2 avant 40 ans sans atteinte d’organe cible & & \\
\hline
Elevé & 5\% ≤ SCORE < 10\%< & < 1g/L (2.6 mmol/L) & + médic\\
& Diabète de type 1 ou 2: & & \\
& Avant 40 ans avec au moins un FdRCVou atteinte d’organe & & \\
& Après 40 ans sans atteinte d’organe cible ou FdRCV & & \\
& IRC modérée & & \\
& PA ≥ 180/110mmHg & & \\
\hline
Très élevé & SCORE ≥ 10\% & & \\
& Diabète de type 1 ou 2 ≥ 40 ans avec au moins un FdRCV & < 0.7g/L (1.8 mmol/L) & + médic\\
& IRC sévère & & \\
& Maladie CV documentée & & \\
\end{tabular}
\end{center}
\section{Diététique :}
\label{sec:orgfc6fdd5}
\begin{itemize}
\item diminuer acides gras saturés, augmenter mono/poly-insaturés
\item augmenter fruits, légumes céréales
\item diminuer cholestérol alimentaire
\item huile d'olive, fruits à coque
\item + limiter alcool, controle poids, sédentarité
\end{itemize}
Pour hyperTG modérée : diminuer poids, alcool et sucres simples
\section{C Traitement médicamenteux}
\label{sec:orgdd4964a}
\begin{itemize}
\item Risque faible/modéré : diététique 3 mois puis médic si échec
\item Sinon médic d'emblée
\item statines contre-indiquées en cas de grossesse.
\end{itemize}
\begin{center}
\begin{tabular}{ll}
Hypercholestérolémies pures & \textbf{statine} -> - echec: augmenter dose -> echec : ajout ézétimibe\\
et hyperlipidémies mixtes & si intolérance statine: ézétimibe\\
\hline
Hypertriglycéridémies pures & TG < 5 g/L: diététique seul. sinon ajout fibrate\\
hypercholestérolémie familiale hétérozygote & dépistage (1er degré). Cf hypercholestérolémie pure\\
\end{tabular}
\end{center}
Surveillance:
\begin{itemize}
\item EAL à 12 semaine puis à 8-12 après chaque changement.
\item \textbf{myalgies} (statines++) => surveillance musculaire clinique (dosage CPK si risque)
\item hépatique: avant puis à 8-12 semaines. Si ALAT > 3 N, arrêter/diminuer statine
\end{itemize}
Nouveautés thérapeutiques: immunoglobuline monoclonales humaines = Ac anti-PCSK9, alirocumab, évolocumab
\end{document}
1. V=25mm/s (1 carreau = 40ms). Étalonnage : 1mV = 1cm
2. Rythme (sinusal ? : un P avant QRS, FC
3. Dépolarisation atriale : P
- Positive en DI, DII, DIII, aVF et négatives en aVR
- HAG si durée \> 100ms (2.5mm), HAD si amplitude \> 0.25 mV
(2.5mm)
- Absente : bloc sinoauriculaire
4. Conduction atrio-ventriculaire : PR
- normal si 120-200ms, BAV si \> 200ms
5. Dépolarisation ventriculaire : QRS
- Hémibloc : antérieur G si déviation gauche, postérieur G si
déviation droite
- R croît de V1 à V6
- Amplitude: microvoltage si \< 5mm, HVG si S1 + RV5 \> 35mm
- Durée \> 120ms : BdD = droit si RR\' en V6 et rS en V1, gauche
si RsR\' en V1 et Rs en V6 \[incomplet si QRS \< 120ms mais \>
80ms\]
6. Repolarisation ventriculaire : ST, T, QT
- ST isoélectrique ?
- T faible amplitude, de même sens que QRS
# Syndrome de Turner
Rare (1 cas pour 2 500 filles), (45, X) chez la fille Clinique:
- RCIU
- retard de croissance prédominant sur la taille
- hypertélorisme avec orientation en bas et dehors des fentes
palpébrales, cou court et large avec implantation basse des cheveux,
écartement mamelonnaire,
cubitus valgus
- insuffisance ovarienne =\> absence de développement pubertaire,
infertilité
- cardiopathie (coarctation de l\'aorte, bicuspidie aortique) et
uropathie (rein en « fer à cheval ») parfois ;
- infections ORL à répétition ;
- pas de déficience intellectuelle habituellement.
⚠ Caryotype systématique chez les filles de petite taille même en
l\'absence de signes cliniques (formes en mosaïques)
# Syndrome de Kallmann
Hypogonadisme hypogonadotrophique ( déficit en GnRH) et d\'une anosmie
(défaut du développement du système olfactif et de la migration
embryonnaire des neurones synthétisant la GnRH.) Multiples modes de
transmission 1/8 000 garçons et 1/40 000 filles. Clinique :
- micro pénis, cryptorchidie
- absence de puberté spontanée
- anosmie
- autres: syncinésies controlatérales d\'imitation, aplasie rénale,
fente labiale ou palatine, agénésie dentaire, surdité.
% Created 2019-01-22 Tue 22:02
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\newglossaryentry{SHBG}{name=SHBG,description={Sex Hormone-Binding Globulin. Diminue avec des androgènes, augmente avec les oestrogènes}}
\newacronym{SOPK}{SOPK}{Syndrome des ovaires polymicrokystiques}
\newacronym{OGE}{OGE}{Organes génitaux externes}
\newacronym{CAIS}{CAIS}{Complete Androgen Insensitivity Syndrome}
\newacronym{IOP}{IOP}{Insuffisance ovarienne primitive}
\newglossaryentry{Leydigcell}{name={cellule de Leydig},description={Produit de la testostérone. Localisé près des tubules séminifères (testicules)}. Activé par LH}
\newglossaryentry{Sertolicell}{name={cellule de Sertoli},description={Participe à la production du sperme. Localisé dans un tubule séminifère. Activé par FSH}}
\newacronym{HVG}{HVG}{Hypertrophie ventriculaire gauche}
\newglossaryentry{NF1}{name=NF1, description={Neurofibromatose 1. Tâches café au lait, neurofibromes (cutanées, nodulaires [le long d'un trajet d'un nerf] ou plexiformes [K possible]), nodules de Lisch sur l'iris.}}
\newacronym{NEM2}{NEM2}{Néoplasie endocrinienne multiple 2}
\newglossaryentry{VHL}{name={von Hippel-Lindau}, description={Hémangioblastome du cervelet/moelle épinière, de la rétine, phéochromocytome}}
\newglossaryentry{PCC}{name={Phéochromocytomes}, description={Tumeur de la médullo-surrénale}}
\newacronym{PGG}{PGG}{Paragangliomes}
\newacronym{ADP}{ADP}{Adénopathie}
\newglossaryentry{TPO}{name={Thyroid peroxydase (TPO)},description={Enzyme de la thyroïde servant à générer la thyroxine (T4) et triiodothyroine (T3)}}
\newacronym{ATS}{ATS}{Antithyroïdiens de synthèse}
\newacronym{GH}{GH}{Hormone de croissance (Growth hormone)}
\newacronym{CLU}{CLU}{Cortisol libre urinaire}
\newacronym{IS}{IS}{Insuffisance surrénale}
\newglossaryentry{PTH}{name={Parathyroide Hormone (PTH)},description={Stimule la résorbtion osseuse (ostéoclastes) pour libérer plus de calcium}}
\newglossaryentry{sdMetabolique}{name={Syndrome métabolique},
description={IMC > 28 kg/$m^2$, HTA,
(HDL < 0.35g/L ou TG > 2g/L ou dyslipidémie traitée),
ATCD diabète familial/gestionnel, temporairement induit.
Autre définition (NCEP III) : (\diameter abdo > 100cm \male ou 88cm \female),
hyperglycémie (glycémie à jeun > 1g/L),
dyslipidémie (TG > 1.5g/L et (HDL < 0.4g/L \male ou 0.5g/L \female)),
HTA (> 130mmHg systole ou > 85mmHg diastole)}}
\author{Alexis Praga}
\date{\today}
\title{Endocrinologie}
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\begin{document}
\maketitle
\tableofcontents
\section{35 : Contraception}
\label{sec:org539cd44}
\subsection{Contraception hormonale}
\label{sec:org3581d98}
Oestroprogestatifs
\begin{itemize}
\item Contient \{oestrogène, progestatif (gen 1,2 ou 3), autres progestatif\}
\item Administration orale, transdermique ou vaginale
\item Action : \{pas d'ovulation, endomètre peu à apte à la nidation, glaire
cervicale imperméable aux spermatozoïdes\}
\end{itemize}
Progestatifs seuls
\begin{itemize}
\item Microprogestatifs : action sur glaire cervicale, endomètre
\item Macroprogestatifs : si CI oestroprogestatifs
\item Administration : orale, injection, implant, intra-utérin (stérilet)
\end{itemize}
\subsection{Pratique}
\label{sec:orgddf1a45}
Oestroprogestatifs : le premier jour des règles pendant 21j puis 7 j
d'arrêt. \emph{Tjrs au même moment}. Si oubli < 12h, ASAP sinon contraception mécanique \(\ge 7\) jours
Microprogestatifs : toujours à la même heure. Si oubli < 3h, ASAP, sinon
contraception mécanique \(\ge 7\) jours
Macroprogestatifs : commencer le 5eme jour du cycle
\subsection{Contre-indications}
\label{sec:org62bf106}
Oestroprogestatifs : absolues =
\begin{itemize}
\item thromboemboliques veineux/artériels, prédisposition thromboses
\item lupus évolutif, connectivites, porphyries
\item vasc, cardiaque, cérébrales, oculaires
\item valvulopathie, troubles rythmes thrombogènes
\item HTA non contrôlée
\item diabète et micro/macroangiopathie
\item tumeur hormono-dépendantes (sein, utérus\ldots{})
\item hépatiques sévères
\item hémorragies génitales non diagnostiquées
\item (tumeurs hypophysaires)
\end{itemize}
Macro/microprogestatifs : cancers \{sein, endomètre\}, insuf hépatique, accident
TEV récents
\subsection{Recommandation}
\label{sec:orgb8fb7eb}
Sans CI, oestroprogestatif minidosé et progestatif 2eme génération monophasique
(Minidril)
\subsection{Efficacité}
\label{sec:org83842d2}
Indice de Pearl\footnote{\(\frac{N}{N_e/10}\times 100\) avec N = nb grossesses
accidentelles, \(N_e\) nombres de mois d'exposition} < 0.07\% pour oestroprogestatif
(< 2\% pour les microprogestatifs)
Attention : certains inducteurs enzymatiques réduisens l'efficacité (ou
millepertuis).
Ado : sous- ou mal utilisée
\subsection{Tolérance}
\label{sec:org73cd727}
Oestroprogestatifs :
\begin{itemize}
\item bien tolérée, pas de perte de poids
\item surveiller métabolisme
\item active coagulation mais \inc fibrinolyse. Légère augmentation du risque
d'accident TEV
\item vasc : faible \inc PA
\item cancer : ovaire = risque -50\%, idem pour l'endomètre, faible \inc pour sein
\end{itemize}
Microprogestatifs : troubles des règles (spotting, aménorrhées), grossesse
extra-utérine
Macroprogestatifs : hypoestrogénie, aménorrhées, spotting
\subsection{Surveillance}
\label{sec:orgb475377}
Consulter si céphalée, déficit sensitivomoteur, (douleur ou oedème) MI, dyspnée,
douleur thoracique
Examen clinique :
\begin{itemize}
\item préthérapeutique : gynéco, frottis cervico-vaginal dès 25 ans si
asymptomatique.
\item PA à +3mois puis tous 6 mois
\item hyperoestrogénie (tension mammaire), hypoestrogénie (sécheresse vaginale)
\end{itemize}
Biologie : cholestérol total, triglycérides, glycémie à jeun à +3mois. Si FR, le
faire avant (!) prescription
Gynéco : métrorragies, spottings.
Frottis cervico-utérin dès 25 ans (+1 an puis tous 3 ans) indépendamment contraception
\subsection{Femmes à risques}
\label{sec:org9d30589}
Diabétique :
\begin{itemize}
\item non hormonale : si diabète 1 > 15 ans ou micro/macroangiopathie \thus locale
(nullipare, peu de rapports) ou intra-utérin (multipare, diabète équilibré)
\item hormonale :pas d'oestropregestatifs si \{tabac, non équilibré, HTA, surpoids,
diabète compliqué\} \thus progestatif
\end{itemize}
Dyslipidémie : oestroprogestatif si < 3g/L cholestérol total, triglycérides <
2g/L
Thrombose veineuse
\begin{itemize}
\item prédisposant : anomalies de l'hémostase (génétique, acquises), ATCD familiaux
\item dépistage : thrombose, multiples fausses couches, ATCD thrombose < 45 ans
\item CI oestrogène, acétate de chlormadinone à la place
\end{itemize}
Autres :
\begin{itemize}
\item HTA : oestroprogestatifs si 0 FR
\item tabac = CI
\item si migraine et vascularite, voir spécialiste
\end{itemize}
\subsection{Contraception d'urgence}
\label{sec:org07f96a6}
\begin{itemize}
\item lévonorgestrel ASAP < 72h
\item ulipristal acétate ASAP < 120h mais 3x plus cher
\end{itemize}
\section{37 : Stérilité du couple}
\label{sec:orgec86955}
Infertile : 0 grossesse après 1 an de rapports non protégés. Stérilité si
définitif.
Stérilité = partagée !!
\subsection{Interrogatoire}
\label{sec:org29b9515}
\begin{itemize}
\item Couple
\item Femme : âge++ (détérioration après 35 ans), \{grossesses antérieure,
avortements\}, infections/curetages++, ATCD chir/infectieux, douleurs
pelviennes (rapports, règles), conditions de vie, radio/chimio
\item Homme : trouble libido/érection, ATCD cryptorchidie/trauma testiculaire, ATCD
chir pelvienne/scrotale, ATCD médicaux (orchite ourlienne++), tabac/anabolisants\ldots{}
\end{itemize}
\subsection{Examen clinique}
\label{sec:org99f06ad}
\begin{itemize}
\item \female : âge++, obésité/maigreur, tour taille et hanche, pilosité, PA,
galactorrhé provoqué, gynéco.
\begin{itemize}
\item Si anovulation (a/oligo-ménorrhée) : hyperprolactinémie, hyperandrogénie,
troubles comportement alimentaire, bouffées chaleur
\end{itemize}
\item \male : IMC, pilosité, hypoandrisme, cicatrice chir, varicocèle\footnote{Dilatation variqueuse des veines du cordon spermatique},
gynécomastie, gynoïde/enuchoïde
\begin{itemize}
\item volume testiculaire++, palpation cordospermatiques
\end{itemize}
\end{itemize}
\subsection{Examens complémentaires}
\label{sec:orgf6ad85f}
Premiere intention, femme
\begin{itemize}
\item Hormonale++ : oestradiol, LH, FSH, prolactine plasmatique. Puis progestérone plasmatique (si cycle réguliers)
\item Écho ovarienne++
\item Hystérographie++
\end{itemize}
Première intention, homme :
\begin{itemize}
\item spermogramme++ (concentration, mobilité, morphologie). Attention aux variabilités !
\item hormonale++ si oligo-/azoo-spermie : testostérone, LH, FSH puis \gls{SHBG}
\end{itemize}
Test poist-coïtal (discuté)
\subsection{Étiologie}
\label{sec:org65dbbb6}
Femme :
\begin{itemize}
\item \emph{anovulation} : très fréquent ! Souvent aménorrhées ou irrégularités. Causes :
\gls{SOPK}, hyperprolactinémie, insuf ovarienne primitive, déficit gonadotrope, psycho-nutritionnel
\item \emph{obstacle mécanique} :
\begin{itemize}
\item anomalie du col utérin et insuf glaire cervicale : post-conisation/curetage
\item obstacle, anomalie utérine : manoeuvres post-partum, polypes muqueux\ldots{} \thus
echographie
\item obstacle tubaire : cause majeure++. Souvent salpingite (Chlamydia++)
\end{itemize}
\item \emph{endométriose} : rarement en cause si modérée. hystérosalpingographie puis coelioscopie
\end{itemize}
Homme :
\begin{itemize}
\item \emph{azoospermie}
\begin{itemize}
\item \emph{sécrétoire} : diagnostic = volume testiculaire < 10ml, concentration FSH
faible
\end{itemize}
\thus caryotype, analyse bras long Y, écho testiculaire (élimine K), déficit gonadotrope (rare)
\begin{itemize}
\item \emph{obstructive} : volume et concentration ormale, volume séminal \dec \thus
examen clinique
\begin{itemize}
\item cause congénitale : agénésie bilat des canaux déférent++ (soit anomalie
biallélique gène CFTR, soit isolée)
\item acquis : infectieux (gonocoque, tuberculose, Chlamydia) \thus échographie
\end{itemize}
\item exploration chir testiculaire et des voies excrétrices : si azoospermie
confirmée par plusieurs spermogrammes, bilan génétique
\end{itemize}
\item \emph{oligo-asthéno-térato-spermie} : \dec nombre et mobilité, \inc formes anormales
\thus caryotype, brang long Y. Traitement = assistance médicale procréation
\end{itemize}
\section{40 : Aménorrhée}
\label{sec:org8f66a65}
Déf: absence de cycle menstruel après 16 ans (primaire) ou interruption chez
femme réglée (secondaire). Physiologique : grossesse, lactation, ménopause
Tout arrêt > 1 mois \thus enquête étiologique \danger
Atteinte de l'axe hypothalamo-hypophysio-ovarien ou anomalie tractus utérin
\begin{tcolorbox}
Pas de traitement oestrogénique sans enquête étiologique
\end{tcolorbox}
\subsection{Conduite}
\label{sec:org9d522b0}
\subsubsection{Primaire}
\label{sec:org26a95f9}
Forte proba de cause génétique/chromosomique. Chercher carences nutritionnelle
\begin{itemize}
\item Si absence de dév. pubertaire : doser FSH, LH
\begin{itemize}
\item Si basses, tumeur hypothalamo-hypophysaire, dénutrition ou génétique : \{sd
de Kalmann (anosmie), mutation récepteur GnRH (rare), atteinte
gonadotrophines (exceptionnels), mutation LH\}
\item Si hautes : sd de Turner (caryotipe 45, X0),
\end{itemize}
\item Examen gynéco, écho pelvienne
\begin{itemize}
\item Pas d'utérus : sd de Rokitanski, tissu testiculaire dans les canaux
inguinaux (ex: \acrshort{CAIS})
\item ambiguité \acrshort{OGE} : dysgénésie gonadique, hyperplasie congénitale surrénales,
anomalies sensibilité/biosynthèse androgènes
\end{itemize}
\end{itemize}
\subsubsection{Secondaire}
\label{sec:orgd87fb01}
Souvent acquises.
Interrogatoire : médic, maladie endoc/chronique,
gynoc/obstétriques, insuf ovarienne (bouffées de chaleur). Douleurs pelviennes
cycliques : cause utérine
Examen clinique :
\begin{itemize}
\item poids et taille (carence nutritionnelle)
\item hyperandrogénie : \gls{SOPK}, déficit 21-hydroxylase, (sd Cushing)
\item carence oestrogénique : pas de glaire +2 semainesa après saignement \thus
anovulation
\item pas de signe d'appel : enquête nutritionnelle
\end{itemize}
Dosages hormonaux : cf Table \ref{tab:amenorrhe_second}
\begin{table}
\begin{tabular}{llllll}
\toprule
hCG & prolactine \inc & FSH \inc & estradiol& testostérone \inc & sinon\\
& & & LH, FSH àdec & & \\
\midrule
grossesse & médicaments & \acrshort{IOP} & tumeur H-H & tumeur surrénales & \gls{SOPK}\\
& adénome à prolactine & & nutrition & tumeur ovarienne sécrét. & \\
& tumeur H-H & & & & \\
\bottomrule
\end{tabular}
\caption{Évaluation hormonale d'une aménorrhée secondaire. H-H = hypothalamo-hypophysaire}
\label{tab:amenorrhe_second}
\end{table}
\subsection{Causes}
\label{sec:org7e48c5f}
\subsubsection{1. Déficit gonadotrope organique/fonctionnel}
\label{sec:org90903d3}
\paragraph{Prolactine normale \footnote{Hypothalamus n'arrive pas à libérer la GnRH au bon rythme.}}
\label{sec:org7fc803c}
\begin{itemize}
\item Atteintes organiques : tumeur/infiltration \thus IRM
\begin{itemize}
\item macroadénomes hypophysaires, craniopharyngiomes
\item chercher hyperprolactinémie, insuf antéhypophysaire associé
\end{itemize}
\item Atteintes fonctionnelles : apports nutritionnels insufisants par rapport à l'activité physique intense+++
\end{itemize}
\paragraph{Hyperprolactinémie}
\label{sec:orgd8599e5}
Atteinte hypothalamo-hypophysaire (majeure++)
Médicaments ou tumeurs \thus pas de traitement dopaminergique sans imagerie \danger
\paragraph{Autres}
\label{sec:org5efba9e}
\begin{itemize}
\item Endocrinopathies : sd de Cushing, dysthyroïdes déficits 21-hydroxylase
\item Hypophysaire (rare) : auto-immune (majorité), sd de Sheehan (très rare, nécrose hypophysaire post-partum)
\end{itemize}
\subsubsection{2. Anovulation non hypothalamique}
\label{sec:org180cde2}
\paragraph{SOPK (majorité)}
\label{sec:org85338b5}
Pas de pic de LH, ni de progestérone. Oestradiol mais non cycliques
Irrégularité menstruelles, puis aménorrhées avec acné, hirsutisme
Diagnostic :
\begin{itemize}
\item 2 parmi : \{hyperandrogénie clinique\footnote{Séborrhéee, acné, hirsutisme, \inc testostérone}, oligo-/a-novulation, hypertrophie
ovarienne (écho)\}
\item exclure bloc 21-hydroxylase, tumeur de l'ovaire, sd Cushing
\item exclure hyperprolactinémie
\end{itemize}
Diagnostic parfois difficile :
\begin{itemize}
\item sans hyperandrogénie \thus écho
\item \{atteinte partielle axe gonadotrope, macroprolactinémie\} peuvent y ressembler
\end{itemize}
Acné : cherche hyperandrogénie, régularité cycle menstruel \thus éliminer
hyperplasie congénitale des surrénales
2 causes :
\begin{itemize}
\item tumeur ovarienne ou résistance insuline
\begin{itemize}
\item virilisation si tumeur
\item imagerie si testostérone > 1.5ng/mL. Si normale, cherche hypothécose
(obésité morbide androïde, acanthosis nigricans, insulino-résistance)
\end{itemize}
\item pathologie surrénale :
\begin{itemize}
\item sd de Cushing si signes hypercortisolisme \thus cortisol libre urinaire et
freinage minute
\item tumeur surrénale \thus scanner des surrénales
\item déficit enzymatique en 21-hydroxylase (\danger formes tardives qui peuvent
mimer SOPK)
\end{itemize}
\end{itemize}
\subsubsection{3. Insuf ovarienne primitive}
\label{sec:org6aa8f88}
\inc FSH
Causes :
\begin{itemize}
\item chir, chimio, radiothérapie
\item anomalie caryotype (sd Turner)
\item anomalie gènes \emph{FMR1} (sd X fragile)\footnote{Transmission mère-fils. Expansion instable des triplets CGG jusqu'à
l'absence de transcript de FMR1 (Fragile X Mental Retardation 1). \\
\danger Risque d'IOP pour la pré-mutation seulement \thus dépister chez
\female + IOP < 40 ans par PCR et Southern Blot}
\item auto-immune
\end{itemize}
\subsubsection{4. Anomalie utérine}
\label{sec:org3256169}
\paragraph{Congénitales}
\label{sec:orgf95baaf}
Si dév pubertaire normal :
\begin{itemize}
\item et douleurs pelviennes cycliques : imperforation hyménéale/malformation vaginale \thus examen gynéco.\\
\item ou sans douleurs \thus agénésie utérus ?
\end{itemize}
Difficulté : différence agénésie mullérienne isolée (46,XX)- anomalies androgènes
(46,XY) \thus testostérone
\paragraph{Secondaires}
\label{sec:orgfd85482}
Synéchies utérines (trauma de l'utérus), tuberculose utérine
\section{47 : Puberté}
\label{sec:orga842b34}
\subsection{Normale}
\label{sec:orgaf1f3b6}
\textasciitilde{}4 ans, acquisition de la taille définitive, fonction de
reproduction. Classification de Tanner (5 stades)
\begin{table}[htbp]
\caption{Puberté normale}
\centering
\begin{tabular}{llll}
\toprule
\female & & \male & \\
\midrule
seins & 11 ans [8,13] & volume testiculaire & 11.5 ans [9.5,14]\\
règles & 13 ans [10,15] & \inc taille verge & 12.5 ans\\
croissance & 5 \(\rightarrow\) 8cm/an & croissance & 5 \(\rightarrow\) 10cm/an\\
taille & 163cm & taille & 175cm\\
\bottomrule
\end{tabular}
\end{table}
\subsection{Retards}
\label{sec:orga820eb2}
\begin{tcolorbox}
\male : volume testiculaire < 4mL après 14 ans \footnotemark\\
\female : pas de seins à 13 ans, pas de règles à 15 ans
\end{tcolorbox}
\footnotetext{ou longueur < 25mm}
\begin{tcolorbox}
Hypogonadisme\footnotemark central ou périphérique ?
\begin{itemize}
\item FSH, LH \inc : pour compenser le manque des gonades (hypergonadotrope = primaire)
\item FSH, LH N ou \dec : problème hypothalamo-hypophysaire\footnotemark (hypogonadotrope = secondaire)
\end{itemize}
\end{tcolorbox}
\footnotetext\{Chez \male{}, manque de testostérone\}
\footnotetext{Rappel : LH entraîne la production de testostérone}
\begin{itemize}
\item centrale : congénital (pas de cassure de croissance, micropénis,
cryptorchidie), acquis (tumeur ?), "fonctionnel" (maladie générale, trouble
comportement alimentaire), isolé
\item périphérique : sd de Turner chez \female, sd Klinefelter \male
\item retard simple (élimination)
\end{itemize}
Clinique :
\begin{itemize}
\item parents, grossesse, courbe de croissance. Chercher trbles digestifs, polyuro-polydispsie, céphalée, anomalies champ visuel
\item pathologie acquise, OGE, testicules, anosmie (Kallmann)
\end{itemize}
Âge osseux : 13 ans \male, 11 ans \female
Biologie : stéroïdes sexuels
\begin{itemize}
\item FSH, LH basses \thus hypothalamo-hypophysaire
\item testostérone chez \male, oestradial/écho chez \female
\end{itemize}
IRM indispensable si déficit gonadotrope (tumeur) \danger
Caryotype si :
\begin{itemize}
\item FSH élevé
\item toujours chez \female{} de taille < -2DS avec retard pubertaire/gonadotrophine \inc
\end{itemize}
\subsubsection{Étiologies}
\label{sec:org984c09b}
Hypogonadotropes
\begin{itemize}
\item congénitaux : isolés, sd de Kallman, autres déficits hypophysaires, sd
polymalformatifs
\item acquis : tumeurs hypophysaires, post-radiothérapie
\end{itemize}
Hypogonadotropes fonctionnels
\begin{itemize}
\item maladies chroniques digestives/cardiaques/respi
\item sport intense
\item maladies endocriniennes
\end{itemize}
Hypergonadotropes
\begin{itemize}
\item congénitaux : sd Turner, sd Klinefelter, autres atteintes primitevs
\item acquis : castration, trauma, oreillons, chimio/radio
\end{itemize}
\subsubsection{Traitement}
\label{sec:org9fc62d5}
Cause si possible. Sinon doses \inc de testostérone (\male) ou oestrogènes puis
oestroprogestatif (\female)
\subsection{Précoces}
\label{sec:org42abb44}
Avant 8ans \female ou 9.5 ans \male
\subsubsection{Centrales}
\label{sec:org4fd68ef}
8x plus fréquent chez \female{} que \male{}. Chez \female{}, causes
idiopathiques. Chez \male{}, causes tumorales à 50\%
Clinique :
\begin{itemize}
\item dév prématuré harmonieux (pas de règles chez \female)
\item crises de rires (harmatome hypothalamique), tâches cutanées (neurofibromatose
I ou sd McCune-Albright)
\end{itemize}
Biologie :
\begin{itemize}
\item testostérone élevée chez \male{} mais variabilité d'oestradiol chez \female{}
\end{itemize}
IRM hypothalamo-hypophysaire indispensable \danger (petite taille
définitive). Écho pelvienne pour \female{}
Traitement si risque de petite taille adulte : analogues GnRH jusque âge normal
de puberté
\subsubsection{Périphériques}
\label{sec:org445207b}
Clinique : \inc vitesse de croissance, avance maturation osseusse
Stéroïdes élevées, LH et FSH bas. Écho pelvienne chez fille
Étiologie :
\begin{itemize}
\item tumeurs ovarienne (rares) : écho puis histologies
\item kystes folliculaires : bénins, régression spontanée possible
\item sd McCune-Albright :
\begin{itemize}
\item \{puberté précoce ovarienne, taches cutanées "café-au-lait", dysplasie fibreuses os\}. \danger tableau pas toujours complet !
\item oestradiol élevé, gonadotrophines basses, écho = utérus stimulé, kystes ovariens. Dominance \female
\end{itemize}
\item médicaments
\item testotoxicose (rare, cellule de Leydig activé et LH basses), adénome leydigien
(très rare)
\item tumeurs à hCG (\male)
\end{itemize}
\subsubsection{Avances dissociées}
\label{sec:orgeb93510}
\begin{itemize}
\item Isolé des seins : beaucoup de filles ( de 3 mois à 3 ans)
\item Métrorragies isolées : chercher vulvite, vulvovaginite, prolapsus urétrale,
corps étranger. Éliminter kyste ovarien, sd McCune-Albright par l'absence des
sein
\end{itemize}
\thus écho pelvienne
\begin{itemize}
\item Pilosité pubienne isolée : chercher forme d'hyperplasie congénitale des
surrénales (\inc 17-hydroxyprogestérone, stimulation ACTH), prémature pubarche
(élimination !)
\end{itemize}
\section{48 : Cryptorchidie}
\label{sec:orga7fd930}
\subsection{Enfant}
\label{sec:orgfef3a1b}
Localisation anormale et inaboutie du testicule. Très fréquente : 3\%
nouveaux-nés, 20\% préma. 2/3 descendent spontanément à 1 an de vie
Clinique : checher micropénis (< 2cm, hypospadias, autres)
Explorations : endocrinienne pour toute cryptorchidie \danger
\begin{itemize}
\item bilatérale : doser 17-hydroxyprogestérone chez \female{} virilisée pour éliminer hyperplasie
congénitale des surrénales
\item testostérone, \gls{Leydigcell} (INSL3), \gls{Sertolicell} (AMH, inhibine B sérique), FSH, LH mesurée jusque 4-6mois\footnote{\danger Testostérone, FSH, LH interprétables [6mois, puberté]}
\item si bilatéral, écho (vérifier l'absence de dérivés mülleriens)
\end{itemize}
Étiologie
\begin{itemize}
\item hypogonadisme hypogonadotrope congénital
\item anorchidie rare
\item si hypospade en plus, chercher dysgénésie testiculaire
\item sd polymalformatif
\end{itemize}
Suivre l'âge de l'apparition de la puberté !
Traitement : chir dès 2 ans, indispensable ! (risque de cancer)
\subsection{Adulte}
\label{sec:orgc11ba55}
\begin{itemize}
\item Risque : hypogonadisme, infertilité, cancer testicule
\item Examen clinique : scrotum, gynécomastie, signes d'hypogonadisme
\item Complémentaire : \{FSH, LH, testostérone\}, hCG si tumeur à la palpation, écho
scrotale, spermogramme
\end{itemize}
\section{51 : Retard de croissance}
\label{sec:org9884db2}
\danger Ne pas passer à côté de pathologies sévères
Phases :
\begin{itemize}
\item foetale (rapide, \{nutrition, insuline, IGF-2\})
\item précoce 0-3ans (rapide, \{insuline, IGF, hormones thyroïdiennes\})
\item prépubertaire (plus lente, décroît, \{génétique, GH/IGF, hormones thyroïdiennes\})
\item pubertaire (\{stéroïdes sexuels, GH, nutrition\})
\end{itemize}
Retard statural = \{taille < -2DS, ralentissements croissance, croissance \(\le\) parents\}
Prise de poids, obésité, ralentissement croissance \thus chercher
hypercorticisme, tumeux craniopharyngiome sur l'hypothalamus, hypopituitarisme
Examen :
\begin{itemize}
\item ATCD : taille, parents, néonatale, médicaux/chir, contexte social
\item morphotype, dév. pubertaire, tous les système, psychoaffectif
\end{itemize}
\subsection{Principales causes}
\label{sec:org26d07d3}
\begin{itemize}
\item Si poids < poids idéal : cf table \ref{tab:org55b5dc0}
\item Si poids \(\ge\) poids idéal : cf table \ref{tab:orgc3f8b0d}. Précisions :
\begin{itemize}
\item Test de stimulation de l'hormone de croissance (\danger si doute, IRM)
\item Ralentissement sévère \thus bilan en urgence (craniopharyngiome, thyroïdite de
Hashimoto)
\item\relax [0, 3] ans : digestives pédiatrique (coeliaque, mucoviscidose), [3,puberté] :
endoc constitutionnelle, à la puberté : déficit hormone, patho osseuse
\item Savoir différencier retard pubertaire simple d'un vrai retard
\end{itemize}
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:org55b5dc0}
Causes de retard pondéral}
\centering
\begin{tabular}{ll}
\toprule
Maladie coeliaque & IgA totales, IgA anti-transglutamase, fibro\\
Crohn & VS, écho anse grêle\\
Mucoviscidose & Test sueur\\
Anorexie mentale & Courbe de poids\\
Insuf rénale chroniques & Créat, iono, explo fonctionnelles\\
Anémie chroniques & NFS\\
Rachitisme hypophosphatémique & Bilan phosphocalcique\\
Patho mitochondriales & lactate/pyruvate, génétique, biopsie musc, fond d'oeil\\
Nanisme psychosocial & \\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htbp]
\caption{\label{tab:orgc3f8b0d}
Causes de retard statural}
\centering
\begin{tabular}{lll}
\toprule
Endocrino & Déficit GH (congénital, acquis [tumeur]) & IRM\\
& Hypothyroïdie & T4L, TSH, Ac anti-TPO\\
& Hypercorticisme (iatrogène) & Cortisol libre urinaire/à 23h, ACTH\\
& Déficit hormones sex. & Testostérone, GnRH, IRM\\
\midrule
Constitutionelles & Sd Turner & Caryotype\\
& Sd Noonan & Gène PTPN11\\
\midrule
Autres & Osseuses (a-/hypo-chondroplasie) & Radio\\
& RCIU & Taille naissance\\
& Petite taille idiopathique & Élimination\\
\bottomrule
\end{tabular}
\end{table}
\subsection{Exploration :}
\label{sec:org15cda80}
\begin{itemize}
\item Caryotype : fille taille < -2DS ou < -1.5DS sous taille parentale moyenne
\item NFS, VS, foie, rein
\item IgA totales, anti-transglutaminase
\item GF-1, T4L, TSH
\item Radio
\end{itemize}
\section{78 : Dopage}
\label{sec:org77e8421}
\subsection{Substances augmentant la testostérone}
\label{sec:orgafce8a1}
\begin{itemize}
\item Stéroïdes anabolisant, testostérone : \inc masse musc, puissance
\item Risque : thrombotique, rupture musculo-tendineuse, trouble personnalité, foie, trouble libido, adénome/cancer de la prostate
\item Femmes : masculinisation, hirsutisme, acné, aménorrhée, anovulation, hypertrophie clitoridienne, libido exacerbée
\end{itemize}
\vspace*{0.5cm}
\begin{itemize}
\item \emph{Testostérone} : test chromatographique + spectrométrie de masse (très sensible
et spécifique)
\item \emph{Dihydrotestostérone} (DHT) : traitement gynécomastie
\item \emph{Anabolisants} : \inc tissu cellulaire (muscle).
\end{itemize}
ES : rétention hydrosodée, HTA, IDM, hépatite
\begin{itemize}
\item \emph{hCG} : diminuer épitestostérone/testostérone après dopage (IM, SC). Testée dans
le sang ou urine.
\item \emph{Anti-oestrogène} : stimule production testiculaire de stéroïdes
\end{itemize}
\subsection{Hormone de croissance (GH), IGF-1}
\label{sec:orge7edf04}
\begin{itemize}
\item GH \inc masse musculaire, modifie architecture sequelette, acromégalie \emph{mais}
pas d'effet sur volume d'activité physique. Détection difficile : approche
indirecte (cascade biologique) et mesure des forme circulante et comparaison à r-hGH
\item IGF-1 mime certains effet GH
\end{itemize}
\subsection{Glucocorticoïdes, ACTH}
\label{sec:orgd2c082f}
\begin{itemize}
\item Glucocorticoïdes : antalgiques, psychostimulants, combativité. ES : HTA,
oedème, rupture ligament/tendon
\end{itemize}
\danger arrêt brutal = dangereux
\section{120 : Ménopause et andropause}
\label{sec:org7e6e969}
\label{sec:120}
\subsection{Ménopause}
\label{sec:org0be1514}
Déf: plus de règle > 1 an \textpm{} sd climatérique, lié à une carence
oestrogénique. Vers 51 ans.
Pré-ménopause : irrégularités cycles puis dysovulation puis anovulation \textasciitilde{}5 ans
avants.
\subsubsection{Diagnostic}
\label{sec:orgc75c3f1}
Clinique seulement \danger : bouffées de chaleur, \female > 50 ans. Bio
seulement si hystérectomie \thus \dec oestradiol et \inc FSH
En pratique : progestatif seul 10j/mois x3 \thus pas de saignement à l'arrêt =
diagnostic
Aménorrhée < 40 ans = pathologique !
\subsubsection{Conséquences}
\label{sec:orgf8d5614}
Court terme : bouffées de chaleur, trouble sommeil/humeur, \dec sécrétions
vaginales
Moyen terme : douleurs ostéoarticulaires, \inc perte osseuse (selon ATCD d'insuf
ovarienne prématurée, fractures non traumatiques, médicaments, calcium/vit D)
Long terme : \inc risque CV. Incertitude sur SNC
\subsubsection{Traitement}
\label{sec:orgec81c6c}
Bénéfices
\begin{itemize}
\item court terme : qualité de vie à +5-10 ans
\item long terme :
\begin{itemize}
\item prévention ostéoporose
\item cardiovasculaire et neuro = incertain
\item cancer du côlon
\end{itemize}
\end{itemize}
Risques :
\begin{itemize}
\item \inc cancer du sein, accident veineux thromboemboliques (mais chiffres absolus
faibles)
\item \inc AVC ischémique, lithiase bilaires
\end{itemize}
\paragraph{Thérapeutique}
\label{sec:orgc5ffbac}
\begin{itemize}
\item oestrogène (17\(\beta\)-oestradiol) oral/percutané/transdermique\footnote{Percutané, transdermique : limite \inc facteur de coagulation.} 25 jours/mois
\item \textbf{et} progestatif (au moins les 12 derniers jours) per os/transdermique
\end{itemize}
\danger hémorragie de privation possible. Si pendant le traitement, faire écho
pelvienne, hystéroscopie
\paragraph{CI}
\label{sec:orgda06f84}
Cancer du sein, endomètre, ATCD thromboembolique artériel (ischémique,
cardiopathie embolinogène) ou veineux, hémorragie génitale sans diagnostic, hépatique
\paragraph{Mise en route}
\label{sec:orga6511dc}
\begin{itemize}
\item Interrogatoire : ATCD \{cancer, métabolique, vasculaire\}, carence oestrogénique
\item Examen physique : poids, PA, palpation seins, gynéco, frottis cervico-vaginal
\item Mammograhpie !
\item Cholestérol, triglycérides, glycémie
\end{itemize}
\paragraph{En pratique}
\label{sec:orgdd635e2}
1ere intention si trouble fonctionnels importants. 2eme si risque
d'ostéoporose. Sinon au cas par cas.
\paragraph{Surveillance}
\label{sec:org1b8c3ab}
3-6mois (surdosage = douleur, tension mammaire). Puis tous les 6-12 mois,
mammographie tous les 2 ans, frottis CV tous les 3 ans.
Traitement \(\ge\) 5 ans !!
\paragraph{Alternatives}
\label{sec:orgab4c595}
\begin{itemize}
\item Modulateurs spécifiques du récepteur des oestrogènes : raloxifène
\item tibolone
\item traitement local préserve tractus urogénital
\end{itemize}
NB : Dépister FR CV. Promouvoir exercice, calcium, vit D
\subsection{Andropause}
\label{sec:orgf2a226e}
Chez majorité des hommes mûrs/âgés en bonne santé non obèse, baisse de
testostérone inconstante (2\%).
\subsubsection{Démarche}
\label{sec:org2c825c8}
\begin{itemize}
\item Interrogatoire : libido, érection, énergie vitale, mobilité/activité physique
\item Examen clinique : IMC, virilisation, gynécomastie, palper testicules
\item Mesure de testostérone totale :
\begin{itemize}
\item > 3.2ng/mL = normale \thus étiologies non endocrino
\item \(\in\) [2.3, 3.2] : doser SHBG, calculer index de T libre, si bas, chercher cause
\item < 2.3 ng/mL : chercher cause
\end{itemize}
\end{itemize}
\subsubsection{Étiologie}
\label{sec:org3c66ac6}
Si FSH, LH élevée, \emph{insuf testiculaire primitive}
\begin{itemize}
\item lésionnelle : chimio, radiation, alcoolisme surtout. Autres : castration,
torsion, orchite ourlienne
\item cryptorchidie bilatérale
\item chromosomique : sd Klinefelter++
\item lié à sénescene, cause génétique (rare !)
\end{itemize}
Sinon \emph{hypogonadisme hypogonadotrope}
\begin{itemize}
\item tumeur région hypothalamo-hypophysaire : craniopharyngiome, adénome
hypophysaire++, autres
\item infiltratif : sarcoïdose, hémochromatose
\item chir, radiothérapie, traumau
\item hyperprolactinémie, carence nutritionnelle, Cushing, tumeur testiculaire
\end{itemize}
\section{122 : Troubles de l'érection}
\label{sec:org7edd3d4}
Nécessite : réseau vasculaire, appareil musculaire lisse, retour veineux, signal nerveux,
appareil hormonal et psychisme fonctionnels
Déf : incapacité persistante à obtenir/maintenir érection pour rapport sexuel satisfaisant
Âge = FR (car déficit neurosensoriel, \inc testostérone, comorbidités)
\subsection{Conduite diagnostique}
\label{sec:org29a8cb9}
\subsubsection{Interrogatoire}
\label{sec:org72da416}
\begin{itemize}
\item DD avec perte désir, trouble éjaculation, douleurs pendant, anomalies morphologiques
\item Caractérisation : primaire/secondaire, brutal/progressif,
permanent/situationnel, sévérité (délai trouble-consult, capacité résiduelle,
masturbation)
\item Pathologies, facteur :
\begin{itemize}
\item primaire : trouble psychogène perso, complexe identitaire, trouble
relationnel, conflit socioprof, anomalie génitale
\item secondaire : ATCD abdo-pelvien, diabète, FR CV, patho CV, neuro, trouble
miction, endocrinopathie, troubles sommeil, traitement, déficit
androgénique, sd dépressif, troubles addictifs
\end{itemize}
\end{itemize}
\subsubsection{Clinique}
\label{sec:org5d73eaa}
\begin{itemize}
\item Gynécomastie, hypoandrisme, petits testicules, anomalies du pénis (La Peyronie)
\item CV : HTA, pouls, souffle
\item neuro : sensibilités périnée, MI
\item endoc : anomalie CV
\end{itemize}
\subsubsection{Bio}
\label{sec:org78afc0a}
Glycémie, lipidique (si > 1 an), \{NFS, iono, créat\}, foie (si > 5 ans), déficit
androgénique
Doser prolactine, hormones thyroïdiennes
\subsection{Bilan secondaire et approfondi}
\label{sec:org3f1b94a}
Secondaire : sexo/psychologique, épreuve pharmacologique (prostaglandine,
inhibiteur de la phospohdiestérase 5)
\subsection{Étiologies}
\label{sec:org479a3f8}
Plus fréquentes :
\begin{itemize}
\item vasculaire : FR = HTA
\item endocrino++ : diabète
\item génito-pelvien : chir pelvienne
\item trauma médullaire
\item neuro dégénératif
\item iatrogène : antihypertenseur
\end{itemize}
\subsection{Aspects endocriniens}
\label{sec:org26d4fa4}
\subsubsection{Androgènes circulants}
\label{sec:orgb5e4b67}
Influe libido, intérêt sexuel, érection (seulement spontanée!)
Hypogonadisme (diag difficile) :
\begin{itemize}
\item asthénie, gynécomastie, dépilation, perte force musculaire, adiposité androïde
\item doser testostérone totale \textpm{} SHBG, prolactine. FSH, LH pour l'origin
\end{itemize}
\subsubsection{Hyperprolactinémie}
\label{sec:orga7a359e}
Tumeur hypophysaire (IRM), champ visuel si tumeur
supra-sellaire, \{T4L, cortisol, IGF-1, testostérone\}
\thus correction par agoniste dopaminergique
\subsubsection{Diabète}
\label{sec:org18f41c4}
sucré = 1ere cause de trouble érectile (TE). TE fréquents chez diabètique.
Facteurs : mal équilibré, complications, âge, ancienneté diabète
Physiopatho : neuropathie autonomie, microangiopathie \thus défaut relaxation
musculaire. Macroangiopathie \thus ischémie organes érectiles
\danger facteurs psychogènes hyportants !
Diabète et TE \thus mesure testostérone systématique (hypogonadisme ?)
Clinique :
\begin{itemize}
\item TE peut révéler diabète.
\item diabète et TE : cherche trouble endoc, vasc, neuro, médicament, dépression
\item TE = FR d'ischémie myocardite silencieuse \danger
\end{itemize}
\subsection{PEC}
\label{sec:orga08f20d}
Ttt étiologie seulement pour : trouble psychogène pur, chir possible, endocrino
\subsubsection{Trouble endocrinien}
\label{sec:orgb78a2a6}
\begin{itemize}
\item Si hypogonadisme confirmé par bio\footnote{Baisse libido, testostérone totale < 3 ng/mL} : androgène oraux/intramusc/transderm
\item CI : nodule prostatique palpable, PSA > 3ng/mL
\item Surveiller prostate, foie, hématocrite
\end{itemize}
\subsubsection{Pharmacologique}
\label{sec:orged89f3d}
\begin{itemize}
\item FR, Hb glyquée < 7\%, psycho/sexologique
\item 1ere intention
\begin{itemize}
\item inhibiteurs des phosphodiésterases type 5\footnote{Efficace si stimulation sexuelle (même chez diabétique)}
\item Sinon apomorphine, yohimbine = peu efficace
\item "Pompe" = efficace mais résistance psycho
\end{itemize}
\item 2eme intention : drogue vasoactive = efficace mais douleurs peniennes, priapisme
\item Prothèses péniennes = dernier recours, par chirurgien spécialisé
\end{itemize}
\section{124 : Ostéopathies}
\label{sec:orgc997287}
Ostéoporose : fragilité excessive du squelette (\dec minéraux osseux, modif
microarchitecture). T-score < -2.5 DS valeur moyenne par DXA
Dominance \female. Primaire ou secondaire :
\begin{itemize}
\item endocrino : hypogonadisme, sd Cushing, hyperthyroïdie, hyperparathyroïdie, diabète
\item digestives, générale, génétique, médicaments, autres
\end{itemize}
\subsection{Hypogonadisme}
\label{sec:org170d3b2}
Carence oestrogénique \inc ostéoclastogénèse. Aggravé par la précocité,
déminéralisation
\subsubsection{Anorexie mentale}
\label{sec:org1ef689d}
Biochimie : marqueurs de formation \dec (isoenzyme des phosphastales alcalines,
ostéocalcine), marqueurs de résorption normaux (CTx, NTx)
Aggravé par troubles nutritionnels. Hypercortisolisme hypothalamique réversible
Ostéoporose fréquente, risque de fractures \(\times 7\)
Traitement
\begin{itemize}
\item multidisciplinaire
\item pilule oestroprégestative en pratique (limite perte osseuse)
\end{itemize}
\subsubsection{Activité physique intensive}
\label{sec:orgb28d2bb}
Hypoestrogénie hypothalamique
Facteur : activité\footnote{Marathon, danse classique, demi-fond, triathlon, gymnastique, cyclisme}, troubles menstruels, apports alimentaires
Résorption généralisée (rachis++), \inc fractures de fatigue
Traitement : si aménorrhées, \dec activité ou oestroprogestatifs
\subsubsection{Pathologies hypophysaires}
\label{sec:org07a22e6}
Prolactinomes, adénome corticotrope influent remodelage osseux
Perte osseuse rapide (8\% par an), récupération variable.
Traitement : \female{} non ménopausée : oestrogénothérapie
\subsubsection{Iatrogènes}
\label{sec:org6fb2346}
Agonistes GnRH (patho utérines), inhibiteurs aromatase (cancer sein)
Réversible à l'arrêt (moins bien si âgée)
Traitement : bisphosphonates, denosumab
\subsubsection{Dysgénésies gonadique}
\label{sec:orge0efb7b}
Sd Turner = plus fréquent (1/2500 à naissance)
\dec masses osseuse, continue à l'adolescence. \inc risque fracture chez
l'adulte.
Traitement : oestrogénisation (hypogonadisme) et hormone de croissance. Adulte :
oestroprogestatif
\subsection{Hyperthyroïdie, traitement par hormones thyroïdiennes}
\label{sec:orgcd803a8}
Cause fréquente d'ostéoporose secondaire \thus dosage systématique TSH
Hormones thyroïdiennes \inc remodelage : résorption sur l'os cortical++ et trabéculaire
En pratique, rarement évolution jusque l'atteinte osseuse (ttt
rapide). Adapter posologie hormones thyroïdiennes au cancer thyroïdien.
Prévention :
\begin{itemize}
\item densitométrie
\item bisphosphonates sujet âgé ou risque extrémité supérieure du fémur
\item surveillance si ttt suppressif de fonction thyroïdienne
\end{itemize}
\subsection{Hypercortisolisme, corticothérapie}
\label{sec:org289dbfe}
\dec ostéoblastes, \inc activité ostéoclaste. \dec absorption intestinale
calcium, \inc pertes urinaires calcium, hyperparathyroïdisme
Surtout trabéculaire (vertèbres, côtes, radius). Aggravé si prépubertaire, hypogonadisme
Fractures vertébrales fréquentes, surtout sd Cushing avec adénome corticotrope/surrénalien
Traitement :
\begin{itemize}
\item pré-corticothérapie : status osseux, FR
\item supplément vitaminocalcique
\item bisphosphonates, tériparatide si corticothérapie > 3 mois, prednisone > 7.5mg/j
et T-score \(\ge -1.5\)
\end{itemize}
\subsection{Hyperparathyroïdie primitive}
\label{sec:org56e85c0}
Fréquent, notamment chez femme ménopausée. Ostéoporose fréquente \thus dépistage
systématique par DXA
Production continue PTH : \inc résorption os cortical (tiers proximal radius,
fémur)\footnote{Souvent aussi extr supérieure du fémur et vertèbres.}
Diminution limitée (10\%). Souvent favorable post-parathyroïdectomie.
Traitement : chir si T-score < -2:5. Sinon anti-ostéoclastiques\footnote{Oestrogènes, raloxifène, bisphosphonates}, calcimimétique\footnote{Cinacalcet}
\subsection{Chez l'homme}
\label{sec:org1edd6c2}
Pas de T-score reconnu.
Fracture radius distal plus rares.
Ostéoporoses secondaires plus fréquentes chez l'homme : hypercorticisme,
hypogonadisme congénital/acquis/iatrogène, alcoolisme, hypercalciurie
idiopathiques, génétique
\section{207 : Sarcoidose}
\label{sec:org2f52bf6}
Atteinte hypothalamo-hypophysaire exceptionnelle. Conséquences : diabète
inspide central, insufisance gonadotrope
Radio : IRM centrée sur hypothalamo-hypophyse = référence (T1,T2 injecté) \thus
infiltration plancher 3eme venticule, infundibulum, tige hypophysaire épaissie
\textpm{} hypophyse augmente de volume
DD : tuberculose, histiocytose, lymphome, autres tumeurs de la région
Si patient avec sarcoïdose connue : diagnostic = déficit endocrinien et imagerie\footnote{Faire bilan hormonal : natrémie, testostérone totale et libre/ostradiol,
FSH, LH, T4L, TSH, prolactine}
Sinon : atteinte rare\footnote{adénome hypophysaire 90\%, méningiome, craniopharyngiome, patho
inflammatoires infiltratives}, diag = radio et arguments sarcoïdose\footnote{Atteinte poumon évocatrice, \inc{} ACE, pas de tuberculose, granulome
non caséeux (histologie)}.
Traitement : sarcoïdose et déficits hormonaux
\section{215 : Hémochromatose}
\label{sec:orgd0cdf97}
Hémochromatose primitive : génétique, surcharge en fer. 5 pour 1 000 !
Physiopatho :
\begin{itemize}
\item Absorption intestinale régule stockage de fer
\item Fer entre dans l'entérocyte (DMT1), puis stocké via ferritine ou relargé par ferroportine
\item Hepcidine \dec quand besoins fer \inc (!)
\item Hémochromatose : hepcidine effondrée, DMT1 et ferroportine \inc
\end{itemize}
Génétique : gène HFE à 95\% et mutation C282Y/C282Y ou C282Y/H63D
\subsection{Clinique}
\label{sec:org0600d82}
En pratique, suspicion aux "3 A" : asthénie, arthralgies, \inc ALAT
\subsubsection{Atteintes :}
\label{sec:org5f45c0c}
\begin{itemize}
\item foie : \inc ALAT ou hépatomégalie. Cirrhose \(\approx\) 90\% décès
\item coeur : cardiopathie dilatée, troubles rythme
\item endocrino :
\begin{itemize}
\item diabète++ (accumulation pancréatique de fer) insulino-pénie/-résistance
\item hypogonadisme+ : impuissance \male, aménorrhée \female, \dec libdio,
ostéoporose
\item insuf thyriodienne exceptionnelle
\end{itemize}
\item articulaire : arthrite chronique ("poignée de main"), chrondocalcinose
\item cutané : mélanodermie (tardive)
\end{itemize}
\subsection{Diagnostic}
\label{sec:org4482947}
\begin{itemize}
\item Si CS-Tf\footnote{Coefficient de saturation de la transferrine} < 45\% : si ferritine \inc, cherche hépatosidérose dysmétabolique,
acéruléoplasminémie, mutation gène de la ferroportine 1
\item Sinon, CS-Tf > 45\% :
\begin{itemize}
\item si C282Y/C282Y ou C282Y/H63D : diagnostic
\item sinon, si ferritine \inc, test génétique de 2eme intention, biopsie
hépatique
\end{itemize}
\end{itemize}
Examen complémentaires : pancréas (glycémie), foie (transaminases, écho abdo), ECG \textpm{} écho
cardiaque, radio articulation, bilan testostérone
Dépistage chez parents (1er degré) : bilan martial \textpm{} dépistage génétique. \danger mutation \(\neq\) maladie
\subsection{Stades}
\label{sec:org3a36a76}
\begin{enumerate}
\item Asymptomatique, CS-Tf, ferritinémie normaux
\item CS-Tf \inc
\item CS-Tf \inc et ferritine \inc
\item Idem et expression clinique affectant qualité de vie
\item Idem et expression clinique affectant pronostic vital
\end{enumerate}
\subsection{Traitement}
\label{sec:org28dfb59}
À partir du stade 2
\subsubsection{Saignées = référence}
\label{sec:org63b4091}
Objectif : ferritine < 50 g/L (hebdomadaire) puis entretien tous les
2-4 mois. Ne pas dépasser 550mL !
CI : anémie sidéroblastique, thalassémie majeure, cardiopathies sévères
\subsubsection{Autres}
\label{sec:org818b6c2}
\begin{itemize}
\item Érythraphérèse : coûteuse, plus difficile
\item Chelation du fer : 2eme intention (coût, effets indésirable)
\item diététique : pas d'alcool, éviter vitamine C mais \textbf{conserver} apports en fer !
\item Symptomatique
\end{itemize}
\subsection{Suivi}
\label{sec:org0033037}
Résultats en 3-6 mois sur été générale.
Bilan ferrique (stade 0,1) ferritinémie, hémoglobine (stade 2 à 4)
\section{219, 220 : Facteurs de risque CV, dyslipidémies}
\label{sec:org5813199}
Rappel : FR = causalité et \{relation forte, \(\propto\) dose, indépendant des autres
FR, plusieurs étude, exposition précède maladie, plausible, réversible++\}
Risque absolu = un individu. Relatif = \(\frac{R_{\text{exposé}}}{R_{\text{non exposé}}}\)
Prévention : primaire (avant accident), secondaire (éviter nouvel), tertaire
(traiter séquelles\}
\subsection{FR}
\label{sec:orgfb1d3b0}
\begin{itemize}
\item Non modifiable : âgé (> 50A \male, > 60A \female), ATCD familiaux IDM/mort
subite < 55A \male, 65A \female)
\item Modifiable : tabagisme, LDL \inc, HDL < 0.40g/L, diabète, insuf rénale
chronique
\end{itemize}
Estimation : Étude Framingham, SCORE. En pratique :
\begin{itemize}
\item interrogatoire : ATCD familiaux CV, personnels, FR
\item examen : athérome asymptomatique (pouls périphérique, souffle vasculaire),
symptomatique (ECG)
\end{itemize}
\subsection{Tabac}
\label{sec:orge9eb099}
30\% adulte, 25\% femmes enceintes
\inc rapide du risque après sevrage (mécanisme prothrombotique du tabac).
RR = 3 de maladie coronarienne, = 5 d'IDM/mort subite, = 2-7 d'AOMI, = 2 d'AVC.
\danger tabac - contraception oestroprogestative
\subsection{Hyperlipidémie}
\label{sec:org4d8d9c5}
\hyphenation{hyper-cho-lesté-ro-lé-mie}
\showhyphens{hyperholestérolémie}
\subsubsection{Étiologies}
\label{sec:orga9b2083}
Secondaire
\begin{itemize}
\item Bilan selon contexte : TSH, glycémie, créat, protéinurie, BU
\item Comorbidité :
\begin{itemize}
\item hypocholestérolémie : hypothyroïdie, (cholestase, anorexie mentale)
\item mixtes : sd néphrotique, grossesse
\item hypertriglycéridémie : insuf rénale chronique, alcoolisme, (obésité, diabète
avec sd métabolique)
\end{itemize}
\item Iatrogène : ciclosporine, corticoïdes, oestrogènes oraux, rétinoïdes,
IFN-\(\alpha\), certains antétroviraux, neuroleptiques, diurétiques thiazidiques, betabloquant
\end{itemize}
Primaire
\begin{itemize}
\item Hypercholestérolémies familiales monogéniques
\begin{itemize}
\item mutation du gène du récepteur LDL++ : hétérozygote (xanthomes tendineux,
complications CV précoces) ou homozygote (rare, DC vers 20 ans)
\item mutation du gène de l'apoliporotéine B
\item mutation du gène PCSK9
\end{itemize}
\item Hypercholestérolémies polygéniques : fréquent, complications CV tardives
\item Hyperlipidémies combinées familiales : fréquent++, pas de xanthèmes,
complicastions CV suivant intensité
\item Dysbetalipoprotéinémie : xanthomes pathognomoniques
\item Hypertriglycéridémie familiale : rare, pas de xanthomes
\item Hyperchylomicronémie primitive : souvent hypertriglycéridémies majeurs
\end{itemize}
\subsection{HTA et risque CV}
\label{sec:org2ad68bf}
PAs \(\ge\) 140, PAd \(\ge\) 90mmHg (3 consultations à 3 mois)\footnote{-5mmHg si automesure. -10mmHg si MAPA sur 14h}
40\% adulte. Proba \inc si sd métabolique. Aggravé par \acrshort{HVG}, glomérulopathie
Clinique, bio, ECG
\subsection{Diabète et risque CV}
\label{sec:orgd0689da}
Complications coronariennes ischémique : RR \female{} > \male.
AOMI : RR \texttimes{} 5, AVC RR \texttimes{} 2.
Diabète 2 : maladie coronarienne peut précéder diabète ! \thus dépistage
\subsection{PEC}
\label{sec:orgc88cc22}
Dépistage familial si pathologie métaboblique \inc risque vasc
\subsubsection{Sevrage tabac}
\label{sec:orgd00b878}
Évaluer dépendance nicotine
Poids + 5kg en moyenne
Substituts nicotinique (6sem-6mois) : n'aggrave pas maladie
coronarienne/troubles rythmes
Varéniclide, bupropion = dernière ligne (8 semaines)
\subsubsection{Activité physique}
\label{sec:org48b60c8}
\begin{itemize}
\item \dec insulino-résistance, \dec triglycéridémie, \inc HDL
\item \dec PA repos, \inc périmètre marche AOMI, \inc pronostic complications coronariennes ischémiques
\end{itemize}
3x45min à 75\% \(O_2\)
\subsubsection{Diététique}
\label{sec:org46ed7e5}
\begin{itemize}
\item Lipides : graisses < 35\%, \dec gras saturés, \inc mono-insaturés, \{poisson gras, noix, \(\Omega_{\text{3}}\)\}, \dec cholestérol
\item Autres : \inc fruits, légumes, \{noix, noisettes, amandes\}, sel < 6g/j, alcool
< 3 verres vin, \dec sucres simples, -20\% calories
\end{itemize}
Hypertriglycéridémie :
\begin{itemize}
\item modérées : -20\% calories ++, \inc activité physique
\item majeur : arrêt alcool, régime hypo- (si obèse) ou iso-calorique avec < 30g
lipides (si obèse) ou 20g
\end{itemize}
\subsubsection{Hypolipémiants :}
\label{sec:org3a464aa}
Statines :
\begin{itemize}
\item \dec LDL, \dec TG \inc HDL
\item ES : myalgies, \inc CPK, \inc transaminases, \inc risque diabète 2
\item CI : HS, grossesse, allaitement
\end{itemize}
\subsubsection{Traitement hypercholestérolémies}
\label{sec:org5aa2e59}
En primaire si LDL reste élèvé à +6 mois traitement. En secondaire si complication ischémique
Objectifs :
\begin{itemize}
\item primaire :
\begin{itemize}
\item LDL < 1.3g/L si risque CV faible (pop générale, diabète ou hypercholestérolémie familale)
\item LDL < 1g/L sinon
\end{itemize}
\item secondaire : systématique
\end{itemize}
Molécules
\begin{itemize}
\item hypercholestérolémies : statines
\item hypertriglycéridémies : diététique si TG > 2g/L, statines si TG < 4g/L et HDL
bas, fibrate sinon
\end{itemize}
Augmenter doses progressivtement puis suivi : 2-3 mois tant que objectifs non
atteints puis 1-2/an
\subsection{Antihypertenseurs}
\label{sec:org3508162}
Diurétiques, betabloquant, inhibiteurs calcique, IEC, ARA II\footnote{Antagonistes des récepteurs de l'angiotensine II}
Monoprise, monothérapie en 1ere intention
Objectif : [130, 139] et < 90mmHg. Visites mensuelles jusque l'objectif
Suivi : pas d'hypotension orthostatique, \{iono, créat, DFG\} +15j après
chaquement changement, suspension diurétiques et ARA si déshydratation
\subsection{Antiagrégants plaquettaire}
\label{sec:org0566af7}
Prévention secondaire : systématique. Clipodigrel-aspirine systématique à +1 mois
après stent, +1 ans après stent actif
\section{221 : HTA, causes endocriniennes}
\label{sec:org366db22}
Déf: \(\ge\) 140/90 mmHg.
Dépistage d'une HTA secondaire : doit être systématique mais économe\ldots{}
Enquête :
\begin{itemize}
\item initiale : ATCD familiaux HTA, souffle para-ombilical, rein/masse abdo à la
palpation, signe d'hypercortisolisme/acromégalie, bio \thus
protéinurie/hématurie, imagerie, hormonale (selon signes)
\item si résistance malgré 3 antihypertenseurs (dont 1 diurétique), chercher toutes
les cause d'HTA
\end{itemize}
HTA curables : 3-5\%. Cf les catégories ci-dessous !
\subsection{Hyperminéralocorticisme primaire (HAP)}
\label{sec:org6dbe58d}
Physiopatho : aldostérone, cortisol, désoxycorticostérone \thus rétention sodée
\thus HTA et inhibe sécrétion de rénine.
Penser à HAP si hypokaliémie (< 3.5mmol/L) ou HTA résistante
\begin{tcolorbox}
Si la surrénale produit plus d'aldostérone : régulation négative par la rénine (en théorie)
\end{tcolorbox}
\begin{algorithm}
\caption{Explorations des HAP}
Arrêt diurétiques\;
Vérifier natriurèse+, kaliurèse > 20mmol/j\;
\If{aldostérine/rénine \times 2}{
Si aldo \inc et rénine \dec : HAP\;
Si aldo \inc et rénine \inc : hyperaldo. secondaire\;
Sinon aldo \dec et rénine \dec : autre minéralocorticisme\;
}
\end{algorithm}
Tests dynamiques possibles : stimulation (recherche un défaut de), freination
(recherche une freination)
\subsubsection{Adénome de Conn}
\label{sec:orge29f34f}
Forme généralement curable
\begin{itemize}
\item imagerie : nodule unilatéral > 10mm au scanner.
\end{itemize}
\danger il faut prouver une sécrétion unilatérale d'aldostérone \thus
cathétérisme si scanner douteux/patient jeune/HTA résistante
\begin{itemize}
\item chir possible (mais tumeur bénigne, risque récidive)
\item si autre HAP : médicaments en continus
\end{itemize}
\subsubsection{Hyperminéralocorticismes familiaux}
\label{sec:org69b0526}
Lié à l'aldostérone, désoxycorticostérone, cortisol
\subsection{HTA endocrines iatrogènes}
\label{sec:orga1892d6}
Contraception oestroprogestative, corticostéroides, réglisse
\subsection{Phéochromocytomes, paragangliomes fonctionnels}
\label{sec:org5b891dc}
\gls{PCC} : médullosurrénale. \gls{PGG} fonctionnels : autres ganglions sympathiques
PCC : spontanément mortel. Dépistage :
\begin{itemize}
\item HTA avec céphalées, sueurs, palpitations, HTA paroxystiques/diabète sans
surpoids
\item sd familial : \gls{NF1}, \gls{VHL}, \gls{NEM2}, sd phéochromocytomes-paragangliomes familiaux
\end{itemize}
Diagnostic : métanéphrines \inc.
Puis imagerie :
\begin{itemize}
\item PCC : uniques, \textasciitilde{}5cm.
\item PGG siègent dans l'organe de Zuckerkandl, vessie, hiles rénaux, médiastin postérieur, péricarde, cou.
\end{itemize}
Puis médecine nucléaire
Toujours dépistage :
\begin{itemize}
\item clinique : taches "café-au-lait", neurofibromatomes, nodules de Lish (NF1),
hémangioblastomes (VHL)
\item génétique : NEM2, VHL
\end{itemize}
Toujours traitement chir mais surveillance long terme
\subsection{Sd de Cushing}
\label{sec:org8674552}
Correspond hypersécrétion de cortisol
Signes : acné, ecchymoses, faiblesse musc, hirsutisme, oedèmes, ostéoporose, PAd
> 105mmHg, vergetures pourpres
Étiologies :
\begin{itemize}
\item maladie de Cushing (adénome corticotrope) à 66\%
\item tumeur non hypophysaire (15\%) : adénome sécrétant surrénalien ou
corticosurrénalome
\end{itemize}
\subsubsection{Démarche}
\label{sec:org98f0c9e}
\begin{tcolorbox}
CRH (hypothalamus) stimule ACTH (hypophyse) qui stimule la production de
glucocorticoïdes (surrénale)
\end{tcolorbox}
\begin{itemize}
\item Diagnostic positif : cortisol plasmatique \footnote{Physiologique = minimal à minuit, donc mesure à minuit. Mesure salivaire possible.}, cortisolurie (sur 24h), test de freinage rapide\footnote{1mg de dexaméthasone à minuit. Action de rétrocontrôle négative du
cortisol donc on vérifie le cortisol plasmatique le lendemain à 8h.}
\item Diagnostic étiologique selon ACTH :
\begin{itemize}
\item ATCH diminuée \thus adénome, corticosurrénalome, hyperplasie bilatérale
\item ATCH normale ou \inc \thus test CRH. si positif : tumeur ectopique ou
maladie de Cushing
\end{itemize}
\end{itemize}
\subsection{Causes rare}
\label{sec:orgf11df1c}
Tumeurs à rénine, acromégalie
\section{238 : Hypoglycémie}
\label{sec:org67be7d1}
Diagnostic : neuroglucopénie et glycémie < 0.50g/L (0.60 chez diabétique) et correction symptômes
à normalisation (triade de Whipple)
Causes :
\begin{itemize}
\item sécrétion inappropriée d'insuline (hypoglycémiante)
\item (rare) : défaut de sécrétion d'hormones hyperglycémiantes (GH, glucagon,
catécholamine, cortisol), déficit néoglucogénèse, défaut substrat
\end{itemize}
\subsection{Symptômes}
\label{sec:org527ad85}
Neuroglucopénie : faim brutale, troubles concentration, troubles moteurs,
troubles sensitifs, troubles visuels, convulsions focales/généralisése,
confusion
Coma hypoglycémique : début brutal, agité (sueurs), irritation pyramidale, hypothermie
\begin{itemize}
\item souvent signes adrénergiques : anxiété, tremblements, nausées, sueurs,
pâleur, tachycardie
\end{itemize}
\subsection{Causes}
\label{sec:org0012513}
Diabétique : traité par insulines, hypoglycémiants oraux
\subsubsection{Insulinome}
\label{sec:orgc7d5067}
1ere cause tumorale (mais rare). Maligne dans 10\%, < 2cm (90\%)
Clinique : manif. adrénergiques surtout
Diagnostic : épreuve de jeûne, cf table \ref{tab:org03790d7}
\begin{table}[htbp]
\caption{\label{tab:org03790d7}
Diagnostic d'hypoglycémie (jeûne) avec DD}
\centering
\begin{tabular}{llll}
\toprule
& Diagnostic positif & Insuline cachée & Sulfonylurée cachée\\
\midrule
Glycémie & basse & basse & basse\\
Signes & neuroglucopénie & & \\
Insulinémie & normale mais inadaptée & dosable & dosable\\
Peptide C & bas & dosable & indosable\\
Sulfamides & 0 & & \\
pro-insuline & élevée & & indosable\\
\bottomrule
\end{tabular}
\end{table}
Scanner en coupe fine du pancréas et écho-endoscopie si médecin habitué
Traitement : chir
\begin{tcolorbox}
Hypoglycémie par sécrétion inaproppriée d'insuline : triade de Whipple, glycémie \le 0.45g/L\footnotemark avec
insulinémie \ge 3 mUL/L, peptide C \ge 0.6ng/mL
\end{tcolorbox}
\footnotetext{Spontanément/jeûne}
\section{239 : Goitre, nodules thyroïdiens, cancers thyroïdiens}
\label{sec:org91d435b}
Besoins en iode quotidiens (synthèse hormones thyroïdiennes) : \(\approx\) 150 \(\mu\)g/jour (ado,
adulte, \texttimes{} 2 chez enceinte)
Goitre = hypertrophie de la thyroïde :
\begin{itemize}
\item palpation > dernière phalange du pouce
\item écho : volume > 20 \(cm^3\) (18 femme adulte, 16 ado)
\end{itemize}
\subsection{Évaluation}
\label{sec:org23701f9}
Clinique : mobile déglutition/visible cou en extension/visible à
distance. Chercher : gene fonctionelle, signes de compression, signes de
dysfonction thyroïdienne, \acrshort{ADP}
Bio :
\begin{itemize}
\item TSH++ : \inc, déficit production, si \dec, imprégnation excessive en hormones thyroïdiennes.
\item compléter par T4, et si TSH \inc : Ac anti-TPO, anti-Tg
\end{itemize}
Échographie
\subsection{Goitre simple}
\label{sec:orgf4ad1a7}
Hypertrophies normo-fonctionnelles non inflammatoires non cancéreuses
Facteurs : \female, tabac, déficience iodée
\subsubsection{Évolution}
\label{sec:org6e13add}
Constitution à l'adolescence (cliniquement latente) puis plurirondulaire : gêne
cervicale \thus TSH, écho, ponction, scintigraphie
\danger cherche caractère plongeant sur radio !
À ce stade, complications : hématocèle, strumite, hyperthyroïdie, compression
organes de voisinages, cancerisation (5\%)
\subsubsection{PEC}
\label{sec:org2393fd0}
\begin{itemize}
\item Ado : levothyroxine (1 à 1.5 \$\(\mu\)\$g/kg/j) jusque V normal. Vérifier TSH
\item Adulte/agé : si multinodulaire non malin, surveillance. Si symptomatique,
thyroïdectomie totale
\item Goitre ancien, négligé : iode 131
\end{itemize}
\inc iode, notamment grossesse
\subsubsection{Autres pathologies responsables}
\label{sec:org8363432}
\begin{itemize}
\item Maladie de Basedow
\item Thyroïdites :
\begin{itemize}
\item Hashimoto = hypertrophique. Goitre très ferme, expose à l'hypothyroïdie. Ac Ant-TPO\inc\inc{}, écho : goitre diffus, hypoéchogène
\item autres thyroïdites
\end{itemize}
\item Troubles de l'hormonosynthèse
\end{itemize}
\subsection{Nodules thyroïdes}
\label{sec:org1382bef}
Déf : toute hypertrophie localisée de la gande thyroïde. Majorité = bénin (5\%
cancers, de très bon pronostic)
Prévalence \(\approx\) décennie du sujet. \texttimes{} 2 chez \female. \inc si grossesse,
déficience iode, irradiation cervicale
\subsubsection{Évaluation :}
\label{sec:org00a8d0e}
Si signe d'accompagnement :
\begin{itemize}
\item nodule douloureux brutal : hématocèle
\item nodule douloureux + fièvre : thyroïdite subaigüe
\item nodule compressif + ADP : cancer
\item nodule + hyperthyroïdie : nodule toxique
\item nodule + hypothyroïdie : thyroïdite lymphocytaire
\end{itemize}
Si isolé :
\begin{itemize}
\item TSH \dec : nodule hyperfonctionnel ? \thus scintigraphie
\item TSH N : tumeur \thus écho, cytologie
\item TSH \inc : thyroïdite lymphocytaire ? \thus Ac anti-TPO
\end{itemize}
Pronostic plutôt suspect :
\begin{itemize}
\item homme, enfant/âgé, ATCD irradiation cervicale, > 3cm, ovalaire, dur, irrégulier, > 20\% en un an
\item écho : hypoéchogène, contour irrégulier, microcalcifications, ADP
\end{itemize}
Bio : TSH surtout.
\begin{itemize}
\item si nodule, calcitonine > 100pg/mL = argument solide pour cancer médullaire thyroïde.
\item calcitonine \(\in\) [20,50]pg/mL : idem ou hyperplasise des cellules C ou insuffisant rénal
\end{itemize}
Examens :
\begin{itemize}
\item Échographie (classification TI-RAD de 1 à 6)
\item Cytologie si nodule suspect (classification Bethesda de 1 à 6)
\item Scinti si cytologie ininterprétable 2 fois ou indéterminée
\end{itemize}
\subsubsection{Thérapeutique}
\label{sec:orge3df9ce}
\begin{itemize}
\item Chir si suspect clinique/écho/cyto/calcitonine \inc\inc{} : thyroïdectomie si dystrophie controlatérale
\item Surveillance sinon
\item Hormonal si bénin dans familles avec goitres plurinodulaire, < 50 ans.
\end{itemize}
Kystes, hématocèles : anéchogène \thus ponction \textpm{} hormonothérapie , alcoolisation.
Grossesse : chir possible 2e trimestre ou après accouchement
Nodule oculte : < 1cm. Risque de cancer 5\%, faible pouvoir agressif
\begin{itemize}
\item \danger si ADP, hérédité cancer médullaire thyroïde, fixation au TEP
\item ponction seulement si hypoéchogène et > 8mm
\end{itemize}
\subsection{Cancers thyroïdiens}
\label{sec:orga5007f2}
1.5\% cancers, 4eme chez la femme
Découverte : fortuite++, ADP cervicale, signes de compression, flushes/diarrhée,
localisation métastatique
Anatomie :
\begin{itemize}
\item carcinomes différenciés d'origine vésiculaire : papillaire (85\%, excellent
pronostic), vésiculaires (5\%), peu différenciés (2\%)
\item carcinomes anaplasiques (1\%)
\item carcinomes médullaires au dépens des cellules C
\item autres
\end{itemize}
Risque de rechute/décès :
\begin{itemize}
\item taille tumeur, effraction capsule thyroïdienne, métastase (clasif TNM de I à IV)
\item mortalité \(\propto\) âge, dépend de l'histologie, exérèse
\end{itemize}
\subsubsection{Thérapeutique}
\label{sec:orgc3cee28}
\begin{itemize}
\item Plan cancer
\item Chir en 1ere intention (anatomopatho pendant = certitude) : thyroïdectomie
totale. Curage ganglionnaire si besoin (systémique si carcinome médullaire,
si enfant/ado). \\
Complications : hémorragie postopératoire , hypoparathyroïdie (calcium + vit D), paralysie transitoire/définitive nerfs récurrents
\end{itemize}
\vspace*{10pt}
\emph{Cancers différenciés d'origine vésiculaire}
\begin{itemize}
\item iode 131 : seulement post-thyroïdectomie totale (haut risque). Nécéssite
stimulation par L-T4 ou injection TSH. Puis hospit après en chambre 2-5 j
et contraception 6-12 mois. \\
ES : \{nausées, oedèmes\}, \{agueusie, sialadénite\}. \\
Scinti obligatoire à +2-8j : fixation extracervicale à distance = métastases
\item hormonal : L-T4 si haut risque ou échec traitement initial. Puis mesurer TSH à
+6sem-2mois (pas avant !)
\item surveillance : 80\% des récidives à 5 ans \thus écho cervicale, rhTSH,
Tg\footnote{Thyroglobuline} à 6-12mois : cytoponction puis imagerie si Tg > seuil. Sinon \dec LT4
\item traitement récidives : chir si cervicale. Plus compliqué si métastates
(iode131 si fixant sinon ttt local ou molécules ciblées). Maintenir LT4
\end{itemize}
\emph{Cancers anaplasiques}\\
Tuméfaction cervicale rapidement progressive, dure, adhérente, sujet âgé \thus radio-chimio. Pronostic très péjoratif
\emph{Cancers médullaires}
\begin{itemize}
\item TTT : chir \textpm{} curage ganglionnaire
\item Surveillance : calcitonine > 150\(\mu\)g/L \thus bilan de localisation.
\item Temps doublement : 6 mois = pronostic très mauvais.
\item Traitement métastases = local.
\end{itemize}
Étude génétique dans tous les cas : positif \thus chercher phéochromocytome,
hyperparathyroïdie + enquêtes apparentés
\section{240 : Hyperthyroïdie}
\label{sec:orgcf5659f}
\begin{tcolorbox}
Examen en 1ere intention : TSHus (puis T4L !)
\end{tcolorbox}
Déf : hyperfonctionnement de la glande thyroïdienne. Sd de thyrotoxicose =
conséquence sur les tissus.
Prévalence élevée, 7\texttimes{} femme
Physiopatho :
\begin{itemize}
\item TSH, \gls{TPO} et Tg peuvent être des auto-antigènes
\item thyroïde produit surtout thyroxine (T4\footnote{[T4] n'est à l'équilibre que +5 semaines après modification de T4}), convertie en T3 par foie, muscle
squelette.
\item effet :
\begin{itemize}
\item \inc production chaleur, \inc production énergie, \inc consommation \(O_2\)
\item \inc débit cardiaque, système nerveux, \inc ostéclasie, \inc lipolyse, \inc
glycémie, rétrocontrole négatif hypophysaire
\end{itemize}
\end{itemize}
\subsection{Sd de thyrotoxicose}
\label{sec:org957a38e}
Clinique (par fréquence \dec) :
\begin{itemize}
\item CV : tachycardie (régulière, repos, \inc effort), \inc intensité bruits
coeurs, \inc PAs
\item neuropsy : nervosité, tremblement fin régulier des extrémités, fatigue
générale, troubles sommeil
\item thermophobie, hypersudation,
\item amaigrissement rapide, important, avec appétit conservé
\item autre : polydipsie, amyotrophie, \inc frequence selles, rétraction paupière
supérieure (gynécomastie, troubles règle)
\end{itemize}
Examen complémentaire : TSH effondrée. T4 ou T3 libre pour l'importance
Complications :
\begin{itemize}
\item cardiaque (surtout personnes fragiles) : troubles rythme supraV (FA), insuf
cardiaque (droite, avec débit N ou \inc), aggravation insuf coronaire
\item crise aigüe thyrotoxique (exceptionnelle)
\item musculaire (âgé)
\item ostéoporose (\female ménopausée) : rachis
\end{itemize}
\subsection{Étiologies (fréquence \dec)}
\label{sec:org7653659}
\subsubsection{Auto-immunes}
\label{sec:org25523d7}
\emph{Maladie de Basedow}\\
1\% population. Auto-immune, sur terrai génétique. Poussées puis rémissions
Clinique :
\begin{itemize}
\item goitre diffus homogène, élastique, souffle
\item oculaire (spécifique, inconstant) : rétraction et asynérgie palpébrale,
inflammation, exophtalmie, oedème paupières, inflammation conjonctive,
limitation mouvement regard
\thus examen ophtalmo ! (acuité visuel, cornée, papille, oculomotricité, tonus
intraoculaire)\\
Mauvais pronostic : exophtalmie importante, paralysie complète, neuropathie
optique, hypertonie oculaire avec souffrance papillaire
\item dermopathie (exceptionnelle) placard rouge, surélevé, induré, face ant jambes
\end{itemize}
Diagnostic : manif oculaire suffit. sinon : écho (hypoéchogène, vascularisé),
(scinti), Ac anti-récepteur TSH
\emph{Autres auto-immune}\\
\begin{itemize}
\item Thyroïdite post-partum (5\%) : hyperthyroïdie transitoire puis hypothyroïdie. Ac
anti-TPO mais pas Ac anti-récepteur TSH
\item Thyroïdite d'Hashimoto : goitre irrégulier, très ferme. Écho :
hypoéchogène. Ac anti-TPO mais pas anti-récepteur TSH
\end{itemize}
\subsubsection{Nodules thyroïdiens hypersécrétans}
\label{sec:org523121b}
Âge plus avancé, sd de thyrotoxicose pur (pas de manif oculaire)
\begin{itemize}
\item Goitre multinodulaire toxique : à la clinique, puis écho. Scinti : "en damier"
\item Adénome toxique : palpation nodule unique, écho : tissulaire/partiellement
kystique. Scinti nécessaire : reste du parenchyme "froid"
\end{itemize}
\subsubsection{Iatrogènes}
\label{sec:org0fe40a2}
\begin{itemize}
\item Iode : produits contraste, amiodarone. 2 formes : fonctionnelle ou lésionnelle
(lyse des cellules)
\end{itemize}
\danger sous amiodarone : T4L \inc mais T3L, TSH N
\begin{itemize}
\item Hormones thyroïdiennes : pour maigrir. Diag : scinti (pas de fixation), Tg
effondrée
\item Interféron (fréq++)
\end{itemize}
\subsubsection{Thyroïdite subaigüe de De Quervain}
\label{sec:org29b804a}
Affection banale virale. Diagnostic clinique (goitre dur et douleureux). Hyper-
puis hypo-thyroïdie. Echo = hypoéchogène
\subsubsection{Thyrotoxicose gestionnelle transitoire}
\label{sec:org15147f4}
Fréquent (2\% grossesse). 1er trimestre : nervosité, tachycardie, pas de prise de
poids
DD : Basedow (pas Ac anti-récepteur TSH)
\subsubsection{Rares}
\label{sec:org239154f}
Mutations activatrices du récepteur TSH, métastase massives sécrétantes (K
thyroïdiens vésiculaire différencié), tumeurs placentaires/testiculaires, \{sd
résistance hormones thyroïdiennes, adénome hypophysaire\}
\subsection{Forme clinique}
\label{sec:org8bdc929}
\begin{itemize}
\item Enfant : généralement Basedow (néonatale/acquise) : avance staturale et
osseuses, hyperactivité \textpm{} signes oculaires
\item Femme enceinte : passage d'Ac \thus hyper- ou hypo-thyroïde. Passage
d'antithyroïdiens de synthèse \thus goitre, hypothyroïdie possible. Contraception !
\item Âgé : évolution discrète (AEG, fonte musculaire, cachexie, insuf
cardiaque). Penser thyrotoxicose si troubles rythme/insuf cardiaque
\end{itemize}
\subsection{Traitement}
\label{sec:org07c73c0}
{} Urgence : crise aigüe thyrotoxicose, cardiothyréose chez âgé/cardiqaue,
orbitopathie maligne, cachexie vieillard, Basedow chez \female{} enceinte
Repos, sédatifs, bêtabloquant, contraception
\gls{ATS} :
\begin{itemize}
\item -mazole (30-60mg/j), -thiouracile (300-600mg/j) : bloque TPO
\item ES : allergies cut, \inc enzymes hépatiques, neutropénie, agranulocytose++
( !!)
\item surveillance : T4 libre jusque N puis T4L et TSH. NFS 10jours pendant 2 mois (agranulocytose)
\end{itemize}
Chir : thyroidectomie totale sauf si adénome toxique (lobectomie)
Radio-iode : simple, sans risque génétique/cancérisation secondaire (\danger{} orbitopathie\ldots{}). CI : femme enceinte.
\subsubsection{Résultats}
\label{sec:org9e5efda}
\begin{itemize}
\item Basedow : thyroïdectomie \thus hypothyroïdie définitive. Radio-iode \thus
hypothyroïdie 50\%, risque aggravation orbitopathie. Donc ttt médical (1-2
ans) puis chir/iode si récidive
\item Adénome/goitre multinodulaire toxique : chir, iode
\item Induite par l'iode : arrêt si possible
\item Thyroïdite subaigüe : anti-inflammatoire (AINS/corticoïde)
\end{itemize}
\subsubsection{Formes particulières}
\label{sec:org2c10ecf}
\begin{itemize}
\item Cardiothyréose : propanolol et anticoag. Si insuf cardiaque : tonicardiaque,
diurétiques, vasodilatateurs, betabloquant, anticoag. Pour thyrotoxicose : ATS
puis chir/iode 131
\item Crise aigüe thyrotoxique : soins intensifs, réa, ATS, propanolol, corticoïdes,
iode131 après 24h ATS
\item Orbitopathie : pas d'effet ATS, iode peut aggraver !! Si simple, collyre. Si maligne : cf spécialiste
\item Femme enceinte : si transitoire, repos. Si Basedow : repos si mineur. Si forme
importante : ATS faible dose. Si formes grave, chir (2eme trimestre) possible)
\end{itemize}
\thus surveillance avant et après accouchement
\section{241 : Hypothyroïdie}
\label{sec:org3612558}
\begin{tcolorbox}
Rappel : TRH (hypothalamus) stimule la production de TSH (hypophyse) qui stimule la thyroïde
\end{tcolorbox}
\begin{itemize}
\item Atteinte de la glande thyroïde : \inc TSH et
\begin{itemize}
\item soit T4L N : hypothyroïdie frustre
\item soit T4L \dec : hypothyroïdie patente
\end{itemize}
\item Ou hypothalamo-hypophysaire : T4L \dec et
\begin{itemize}
\item soit TSH \dec ou N : hypophysaire
\item soit TSH légèrement /inc : hypothalamus
\end{itemize}
\end{itemize}
\subsection{Sémiologie}
\label{sec:orga272108}
Général :
\begin{itemize}
\item sd d'hypométabolisme\footnote{Asthénie, somnolence, hypothermie, frilosité, constipation, bradycardie,
prise poids modeste}
\item peau pâle/jaune, sèche, squameuse, dépilée; cheveux secs cassants
\item myxoedeme cutanéomuqueux : faciès "lunaire", voix rauque, hypoacousie,
macroglossie
\item neuromusc : crampes, myalgies
\item endocrinien : (galactorrhée), troubles règles, troubles libido
\end{itemize}
Cliniques (rare, diag fait avant) :
\begin{itemize}
\item CV : bradycardie sinusale, \dec contractilité, (insuf cardiaques, troubles
rythme V), épanchement péricardique, favorise athérome coronarien
\item neuromusc, neuropsy : dépressif, sd confusionnel, démence, myopathie prox,
apnée sommeil
\item coma myxoedemateux : si hypothyroïdie primaire profonde et
aggression. Convulsion, EEG non spécifique. Hyponatrémie. Pronostic sévère
\end{itemize}
Palpation : glande ferme hétérogène, pseudonodulaire
Grossesse :
\begin{itemize}
\item complication mère : HTA, prééclampsie, fausse couche, hémorragie post-partum
\item complications foetus : troubles developpement neuro-intellectuel, hypotrophie
\item 1er trimestre : TSH \dec, T4L limite sup. Puis TSH normale, T4L basses
(physiologique !)
\end{itemize}
Anomalies bio :
\begin{itemize}
\item hémato : anémie normocytaire normochrome (si macrocytose, penser anémie de
Biermer) troubles de coagulation,hémostase
\item hypercholestérolémie, \inc CPK, hyponatrémie dilution
\end{itemize}
\subsection{Étiologies}
\label{sec:org34c65fc}
\subsubsection{Hypothyroïdie primaire}
\label{sec:org97a7e33}
Auto-immunes :
\begin{itemize}
\item Thyroïdite d'Hashimoto :
\begin{itemize}
\item goitre ferme, irégulier, Ac anti-TPO.
\item infiltration lymphocytaire du parenchyme thyroïdien. Facteurs environnementaux,
terrain génétique.
\item penser à lymphome si \inc rapide du goitre
\item écho thyroïdiennes : hypoéchogène, hétérogène, vasc hétérogène (scint
inutile)
\end{itemize}
\item Thyroïdite atrophique : pas de goitre, Ac anti-thyroidiens moins
élevés. Souvent une évolution d'Hashimoto, > 50 ans.
\item Thyroïdite du post-partum : idem, petit goitre. Normalement résolutif dans
l'année. 5\% des grossesses
\end{itemize}
Non auto-immune :
\begin{itemize}
\item thyroïdite subaigüe de De Quervain : inflammation du parenchyme. Phase de
thyrotoxicose puis hypothyroïdie
\item thyroïdite sans Ac
\item thyroïdite iatrogène : interferon++, amiodarone, ATS, iode131, radiothérapie
cervicale, lithium, ttt anti-tyrosine kinase (cancéro)
\end{itemize}
Autres : carences iodées (endémie++), hypothyroïdie congénitale (dépistage à
naissance + 72h\footnote{Clinique discrète : ictère prolongé, constipation, hypotonie, pleurs
rauques, difficulté succin, fontanelles larges, hypothermie})
\subsubsection{Démarche diagnostique}
\label{sec:org3d87a54}
TSH puis (T4L (profondeur) et Ac anti-TPO, échographie pour étiologie)
\subsubsection{Insuffisance thyréotrope}
\label{sec:org83434d0}
\begin{itemize}
\item compression région hypothalamo-hypophysaire (HH) par tumeur (adénome hypophysaire
souvent)
\item séquelle post-chir, post-radio des tumeurs de la région HH
\item séquelles méningite, trauma crânien, hémorragie méningée
\item génétiques (rare)
\end{itemize}
IRM systématique !
\subsection{Traitement}
\label{sec:org1c731ba}
Lévothyroxine (T4)
\begin{itemize}
\item hypothyroïdie patente : L-T4 50 à 150 \(\mu\)g/j. Si coronarien : \inc progressivement
de 12.5 à 25\(\mu\)g/j. \danger Surveillance ! (ECG hebdo si grave, hospit si coronarien
récent, sinon patient doit consulter si douleurs thoraciques)
\item hypothyroïdie frustre : 3 cas
\begin{itemize}
\item TSH > 10mUI/L ou Ac anti-TPO : ttt
\item TSH < 10mUI/L et pas d'Ac anti-TPO : surveillance
\item si grossesse : dès TSH \(\ge\) 3mUI/L
\item à discuter sinon
\end{itemize}
\end{itemize}
Suivi
\begin{itemize}
\item hypothyroïdie primaire : objectif : TSH \(\in [0.5, 2.5]\) mUI/L (\(\approx\) 10mUI/L pour âgé, et < 2.5mUI/L pour femme eceinte)
\item insuf thyréotrope : suivi sur T4L seulement
\end{itemize}
Situations particulières:
\begin{itemize}
\item grossesse : \inc posologie dès diagnostic grossesse
\item \inc si interférence avec l'absorption intestinale\{sulfate de fer, carbonate de calcium, hydroxyde
d'alimunie, cholestyramine\}, la clairance \{phénobabrital, carbamazépinex, rifampicine,
phénytoïne, sertraline, chlooriqune\}, oestrogenes
\item néonatale : L-T4 à vie
\end{itemize}
\subsection{Dépistage ?}
\label{sec:orgc91734e}
\begin{itemize}
\item Adulte : si risque : signes clinique, goitre, hypercholestérolémie, ATCD
thyroïdiens, auto-immunité thyroïdienne, irradiation cervicale, \{amiodarone,
lithium, interféron, cytokines\}
\item Femme enceinte : si signes, contexte thyroïdien (perso/familial), auto-immunité
\end{itemize}
\section{242 : Adénome hypophysaire}
\label{sec:org2f9cadb}
\subsection{Sd tumoral}
\label{sec:org117b991}
Clinique :
\begin{itemize}
\item céphalées : rétro-orbitaire, localisése
\item trouble visuels : "voile", par compression des voies optiques. Fond d'oeil,
acuité visuelle OK. Quadra-/hémi-anopsie temporale (sup si quadra)
\item apoplexie hypophysaire (rare) brutal : céphalées violentes, sd méningé sd
confusionnel, troubles visuel.\\
Imagerie en urgence \danger : adénome en nécrose/hémorragie
\end{itemize}
IRM = examen de référence :
\begin{itemize}
\item microadénome : arrondi, homogène, hypo-T1, hypointense après injection,
signes indirects
\item macroadénome : > 10mm, iso-T1 et hyperintension après injection. Regarder
expansion vers chiasma optique et sinus (sphénoïdal, cavernux)
\item DD : craniopharyngiome intra-sellaire (hétérogène, hyperT2), méningiome
intra-sellaire (dure-mère spiculée)
\end{itemize}
\subsection{Sd d'hypersécrétion}
\label{sec:org6b7dd71}
\subsubsection{Hyperprolactinémie\footnote{Prolactine est sécrétée par l'hypophyse}}
\label{sec:org54f32ec}
Fréquente \thus cherche adénome hypophysaire (même si majorité = médicament)
Signes :
\begin{itemize}
\item \female : galactorrhée (pas forcément causée par prolactine ! mais chercher
quand même), troubles du cycle menstruel (doser !)
\item \male : galactorrhée, gynécomastie (rare), troubles sexuels. Hypogonadisme
\thus doser prolactine
\item 2 sexes : risque d'ostéoporose
\end{itemize}
\begin{tcolorbox}
Diagnostique d'hyperprolactinémie
\begin{enumerate}
\item Vérifier hyperprolactinémie (kits, agrégats)
\item Écarter grossesse, médicaments, hypothyroïdie périphérique, insuf rénale
\item IRM :
\begin{itemize}
\item microadénome ?
\item sinon différentier macroadénome à prolactine VS autre tumeur associée à
hyperprolactinémie : régression sous agoniste dopaminergique si macrodénome
\end{itemize}
\end{enumerate}
\end{tcolorbox}
\subsubsection{Acromégalie (excès de \gls{GH})}
\label{sec:org35b98f5}
Clinique :
\begin{itemize}
\item Sd dysmorphique : extrémités élargies, visage (nez élargi, front bombé, lèvres épaisses, tendance prognathisme\}
\item Signes fonctionnels : sueurs, céphalées, paresthésies des mains, douleurs articulaires, asthénie fréquente, HTA (50\%)
\end{itemize}
Complications :
\begin{itemize}
\item CV : hypertrophie myocardite (écho), débit \inc. Puis insuf cardiaque
congestive
\item arthropathie périphérique : grosses articulations, radio (interligne \inc,
ostéophite), rachis (spondylose d'Erdheim)
\item diabète/intolérance glucose, SAS, goitre, polypes du colons
\end{itemize}
\begin{tcolorbox}
Diagnostic d'acromégalie : absence de freinage de la GH pendant hyperglycémie provoquée
orale (GH > 0.4ng/mL), \inc IGF-1\footnotemark
\end{tcolorbox}
\footnotetext{La GH stimule la production d'IGF-1.}
Puis bilan tumoral, retentissement fonctionnel hypophysaire, retentissement
acromégalie
\subsubsection{Sd de Cushing (excès de glucocorticoïdes)}
\label{sec:orgd0cdee3}
Excès de glucocorticoïdes : causes iatrogènes ou adénomes hypophysaires
corticotropes
Clinique :
\begin{itemize}
\item anomalies acquises. Amyotrophie ceinture et abdomen, lenteur cicatrisation,
peu amincie (mains), ecchymoses au moindre choc, vergétures cutanée (flancs,
racine des membres, mammaire, péri-ombilic), visage érythrosique, congestif,
varicosité
\item moins spécifique : +10kg, graisse facio-tronculaire (visage arrondi), bosse de
bison, hyperandrogénie, OMI
\item autres : ostéoporose (asymptomatique), spanioménorrhée, \dec libido, HTA,
troubles psy
\end{itemize}
Bio : intolérance glucide
\begin{tcolorbox}
Diagnostic d'hypercorticisme :\\
Si (\acrshort{CLU} \inc, réponse anormale au freinage minute\footnotemark, cortisol minuit > 72ng/mL) :
\begin{enumerate}
\item Confirmation par freinage standard\footnotemark
\item Dosage ACTH :
\begin{itemize}
\item Si bas, scanner surrénales pour adénome\footnotemark
\item Sinon IRM hypophysaire, freinage fort, test CRH,
test métopirone \thus sécrétion ectopique (normal) ou maladie de Cushing
\end{itemize}
\end{enumerate}
\end{tcolorbox}
\footnotetext{Freinage minute = cortisolémie matin après 1mg dexaméthasone à 23h (rétrocontrole négatif en théorie des glucocorticoïdes sur cortisol)}
\footnotetext{Freinage standard/faible : urines sur 48h puis idem après 0.5mg dexméthasone. On vérifie également le rétrocontrôle négatif}
\footnotetext{ACTH stimule la production de glucocorticoïdes (via surrénales). Un excès de cortisol est censé diminuer la production d'ACTH. Si oui, atteinte surrénale !}
DD : stress intense, dépression sévère, psychose, alcoolisme (CLU modéré,
freinage minute anormal) \thus épreuve du temps
\subsection{Insuffisance antéhypophysaire}
\label{sec:org49dce73}
Clinique : face pâle, "veillot", dépigmentation aréole mammaire et OGE,
dépilation complète aisselles pubis
Signes des déficits hypophysaires :
\begin{itemize}
\item gonadotrope : \male = \{\dec libido, pilosité visage \dec, petits
testicules mou, infertile\}, \female = \{aménorrhée, dyspareunie\}, ostéoporose,
(retard pubertaire)
\item corticotrope : asthénie, hypotension, amaigrissement, pas de déficit
aldostérone ! (hyponatrémie de dilution). Risque de collapsus CV
\item hypothyroïdie modérée
\item somatotrope : adulte = \{\dec masse et force musc, adiposité abdo\}, enfant =
retard croissance, accidents hypoglycémiques
\end{itemize}
\subsubsection{Bilan hypophysaire}
\label{sec:org411850d}
\begin{itemize}
\item Déficit corticotrope : test Métopirone, cortisol < 200ng/mL si hypoglycémie (<
0.49g/L), autres test (cortisolémie, synacthone, CRH)
\item Déficit thyréotrope : \dec{} T4L sans augmentation de TSH
\item Déficit gonadotrope :
\begin{itemize}
\item \female{} préménopause : aménorrhée, oestradiol \dec, gonadotrophines
normales
\item \female{} postménopause : gonadotrophines basses\footnote{Ou dans les valeurs des femmes jeunes}
\item \male{} : troubles sexuels \dec testostérone
\end{itemize}
\item Déficit somatotrope : déficit GH enfant++ (retard croissance, pas de réponse
à stimulation GH) ou adulte (faire au moins 2 tests stimulation)
\item Prolactine normale/élevée
\end{itemize}
IRM si déficit hypophysaire
\section{243 : Insuffisance surrénale}
\label{sec:org15901ed}
\subsection{Insuffisance surrénale lente}
\label{sec:org2c8ea27}
Rare mais grave
Physiopatho :
\begin{itemize}
\item cortisol \footnote{Stimulé par ACTH, rétrocontrole nég. sur ACTH}) : hyperglycémiant, stimule = \{catabolisme protidique, lipogenèse, SNC, tonus vasculaire\}, inhibe
= \{hormone antidiurétique\}, anti-inflammatoire et antipyrétique,
minéralocorticoïde\\
Minimum 0-2h, maximum 7-9h
\item aldostérone : réabsportion Na+ et Cl-, excrète K+
\item androgènes surrénalien (stimulé par ACTH)
\end{itemize}
\begin{table}[htbp]
\caption{Insuffisance surrénale primaire (maladie d'Addison)/secondaire : clinique}
\centering
\begin{tabular}{ll}
\toprule
Primaire (surrénale) & Secondaire (hypophysaire)\\
\midrule
Fatigue, dépression, anorexie, nausées & \\
\dec poids, hypotension, hypotension orthostatique & \\
Hyperpigmentation & Pâleur\\
HyperK, hypoNa (manque sel) & HypoNa (dilution)\\
\bottomrule
\end{tabular}
\end{table}
\subsubsection{Diagnostic}
\label{sec:orgf9cc5df}
\danger ne pas attendre résultats pour commencer traitment
\begin{table}[htbp]
\caption{Insuffisance surrénale : diagnostic}
\centering
\begin{tabular}{lll}
\toprule
& Primaire & Secondaire\\
\midrule
cortisolémie à 8h & basse & basse\\
ACTH & haute & basse\\
aldostérone & basse & N\\
rénine & haute & N\\
Synacthène & réponse insuffisante du cortisol & réponse insuffisante\\
\bottomrule
\end{tabular}
\end{table}
Positif
\begin{itemize}
\item cortisolémie : à compléter avec tests dynamiques si valeurs "intermédiaires"
\item primaire ou secondaire ? ACTH \inc{} si primairei, rénine \inc si primaire
\item test Synacthène (+ Métopirone ou hypoglycémie insulinique si doute)
\end{itemize}
NB : femme enceinte = \{\inc seuil, faisceau d'args\}, enfant : répéter dosages
voire ttt probabiliste
\subsubsection{Étiologies de l' \acrshort{IS} primaire}
\label{sec:org2cec53b}
\begin{itemize}
\item Auto-immune (80\% adulte, 20\% enfant) :
\begin{itemize}
\item \emph{polyendocrinopathie de type 1} (mutation facteur de transcription AIRE)
\item ou \emph{type 2} (IS + 1 parmi \{thyroïdite d'Hashimoto+++, Basedow, diabète 1\}
\item \thus autoAc anti-21-hydroxylase, scanner (surrénales atrophiques)
\end{itemize}
\item \emph{tuberculose bilatérale surrénale} (10\%) : transplanté ou ID avec TCD tuberculose
\thus scanner surrénales (\inc puis atrophie et calcification). Bilan des
localisation tuberculose
\item \emph{VIH} (stade avancé) : iatrogène, infection opportuniste (CMV++), atteinte de
l'hypophyse (lymphome, CMV), corticoïde anti-inflammatoire et ritonavir
\end{itemize}
\danger dénutrition \thus spécialiste
\begin{itemize}
\item autres : \emph{iatrogènes}\footnote{Surrénalectomie bilatére, anticortisolique de synthèse, nécrose hémorragique}, \emph{métastases bilatérales}\footnote{\danger éliminer phéochromocytomes avant biopsie surrénale}, lymphomes, maladies
infiltratives, causes vasculaires
\item enfant : génétiques surtout = bloc enzymatique++ (dépistage obligatoire), adrénoleucodystrophie
\end{itemize}
\subsubsection{Étiologies de l'IS secondaire}
\label{sec:orgc0a82c9}
\begin{itemize}
\item \emph{interruption corticothérapie prolongée} surtout (> 7mg prednisone)
\item autres\footnote{S'associe souvent à d'autres insuffisances de l'axe hypothalamo-hypophysaire} : tumeur région hypothalamo-hypophysaire, hypophysite (auto-immune),
granulomatose, trauma, chir hypophysaire, radiothérapie, sd de Sheehan
\end{itemize}
\subsubsection{Prise en charge}
\label{sec:org5f94948}
Ttt substitutif :
\begin{itemize}
\item glucocorticoïdes (hydrocortisone) 15-25mg/j
\item minéralocorticoïde (fludrocortisone) 50-150\(\mu\)g/j si IS primaire
\end{itemize}
TTT cause
Éducation du patient :
\begin{itemize}
\item avoir carte, hydrocortisone (comprimés et injection), régime normosodé
\item pas de laxatifs, diurétiques, millepertuis, réglisse, jus de pamplemousse
\item ttt à vie
\item hydrocortisone en SC si > 2 vomissement/diarrhées en < 1/2 journée
\item adapter à chaleur, exercice, voyage
\end{itemize}
Surveillance clinique :
\begin{itemize}
\item fatigue, poids, PA
\item surdosage en hydrocortisone (gonflement/rougeur visage, \inc poids, HTA, os,
métabolisme, CV)
\item surdosage en fludrocortisone
\item cortisolémie et ACTH inutile !!
\end{itemize}
\subsection{Insuffisance surrénale aigüe}
\label{sec:org93c2f0f}
\subsubsection{Y penser}
\label{sec:orge500a5e}
\begin{itemize}
\item déshydratation extracellullaire avec pli cutané, hypotension
\item confusion, crises convulsives
\item troubles digestifs
\item douleurs (musc, céphalées)
\item fièvre
\end{itemize}
Biologie :
\begin{itemize}
\item hémoconcentration, insuf rénale fonctionnelle++
\item hypoNa, hyperK++
\item hypoglycémie, acidose métabolique, anémie, hyperlymphocytose,
hyperéosinophilie, natriurèse conservée
\end{itemize}
\subsubsection{Confirmation}
\label{sec:org8d0fa74}
Si diagnostic \textbf{non} posé : dosage cortisol (\dec\dec), ATCH (\inc si primitive, N ou \dec
si secondaire).
Ne pas attendre les résultats
\subsubsection{Causes}
\label{sec:orgb4ed3a0}
\begin{itemize}
\item Insuf surrénale chronique décompensée++
\item D'emblée si bloc enzymatique surrénalien (21-hydroxylase) complet (néonatale)
ou hémorragie bilat surrénale ou apoplexie hypophysaire
\item Décompensation par n'importe quelle patho intercurrente
\end{itemize}
\subsubsection{PEC}
\label{sec:org20b6be1}
\danger Urgence extrème
\begin{itemize}
\item Domicile : 100mg hydrocortisone (IV, IM, SC) puis transport
\item Hopital : réa puis
\begin{itemize}
\item perfusion NaCL (et G30\% si hypoglycémie)
\item ttt facteur déclenchant
\item surveiller : PA, FC, FR, oxymétrie de pouls, diurèse, T, glycémie, CS, ECG
si hyperK
\end{itemize}
\end{itemize}
Ttt préventif : patient doit \inc ses doses, médecin traitant au courant
\subsection{Arrêt d'une corticothérapie}
\label{sec:org93113a2}
Expose au rebond de la maladie causale, insuf surrénale secondaire
(corticotrope), sd de sevrage
À risque : (ttt \(\ge\) 3 semaines par \(\ge\) 20mg prednisone) ou (corticoïdes et inhib enzymatique du
cytochromie P450 (ritonavir)) ou sd Cushing iatrogène
\section{244 : Gynécomastie}
\label{sec:org3e8e77e}
Hyperplasie tissue glandulaire mammaire, fréquente. Dû à oestrogène \inc{} et testostérone \dec{}. Regarder aussi TeBG,
SHBG
\subsection{Démarche}
\label{sec:org79c5d17}
\begin{itemize}
\item Clinique : palpation = ferme/rugueux, mobile arrondi, centré par le mamelon (rien si adipomastie)
\item Mammographie si doute : opacité nodulaire/triangulaire (rien si adipomastie). Élimine cancer du sein (rare)
\item Physiologique ?
\begin{itemize}
\item 2/3 des nouveaux-nés
\item pubertaire : de 13 jusque 20 ans, rétrocède . Palper testicule pour atrophie testiculaire/tumeur
\item fréquente > 65 ans. Palpation testiculaire
\end{itemize}
\end{itemize}
\subsection{Étiologie}
\label{sec:org43c4c4b}
\begin{tcolorbox}
Causes fréquentes : médic, idiopathique, cirrhose, insuf testiculaire/gonadotrope, (tumoral)
\end{tcolorbox}
Évidente :
\begin{itemize}
\item insuf rénale chronique, cirrhose, médicaments (surtout spironolactone,
antiandrogène, kétoconazole, neuroleptiques, ATB antirétroviraux, antiulcéreux)
\end{itemize}
Sinon exploration hormonale : T4L, TSH, hCG, testostérone totale, LH, FSH,
prolactine, oestradiol
Causes endocriniennes :
\begin{itemize}
\item hyperthyroïdie
\item insuffisance testiculaire/hypogonadisme périphérique (8\%) : sd de Klinefelter
le plus fréquent
\item hypogonadisme d'origine hypothalamique/hypophysaire: testostérone basse, LH,
FSH normales/abaissées \thus imagerie hypophysaire, dosage
prolactine. Hyperprolactinémie ou tumorale
\item tumeur sécrétant oestrogène : oestradiol \inc, testostérone \dec \thus tumeur
testiculaire (ou surrénalienne rarement) \thus echo testiculaire ou scanner
abdo
\item tumeur sécrétant hCG : \inc hCG \thus écho testiculaire, scanner
cérébrales. Dans les bronches ou le foie parfois. Chimio.
\item Résistance androgènes (exceptionnelle) : testostérone \inc, LH \inc
\item idiopathique (25\%)
\end{itemize}
\subsection{Traitement}
\label{sec:orgd7f2568}
Traiter la cause. Sinon
\begin{itemize}
\item Pubertaire : ne rien faire
\item Idiopathique : androgènes non aromatisables 3 mois. Si inefficace, chir
plastique possible
\end{itemize}
\section{245 : Diabète}
\label{sec:org8399064}
\begin{tcolorbox}
Définition : glycémie à jeun \ge 1.26g/L (2 reprises) ou aléatoire \ge 2g/L \footnotemark
\end{tcolorbox}
\footnotetext{Normale à jeûn < 1.10g/L}
Caractéristiques diabète 1 (le diabète 2 s'y oppose) :
\begin{itemize}
\item ATCD familiaux rares
\item < 25 ans
\item début rapide explosif
\item symptomatologie bruyante
\item poids normal ou \dec
\item hyperglycémie majeure > 23g/L
\item souvent cétose
\item pas de complications dégénératives
\item mortalité par insuf rénale (CV pour diabète 2)
\end{itemize}
\subsection{Diabète 1}
\label{sec:org7a4c0f5}
Prévalence : 1/200 000 (10\% des diabétiques). Peut survenir à tout âge. \inc
incidence. Sex-ratio = 1
\subsubsection{Physiopathologie}
\label{sec:org047339e}
Carence en insuline par destruction cellules beta du pancréas. Soit auto-immun
(fréquent), soit idiopathique
Prédisposition génétique (Ag HLA, VNTR, CTLA-4, PTP-N22), facteurs
environnementaux.
Processus auto-immuns : au moins un Ac parmi les suivants dans 97\% : Ac
anti-\{ICA, GAD, IA2, insuline, ZnT8\}
Diabète \(\in\) sd polyendocrinien auto-immun : 10\% d'autres maladies auto-immunes =
thyroïdopathies (Basedow, thyroïdite), Addison, atrophie gastrique de Biermer,
maladie coeliaque, vitiligo
\begin{itemize}
\item doser Ac anti-TPO ou TSH (thyroïdite), anti-surrénale (Addison), anti-transglutaminase \textpm{} anti-endomysium (coeliaque), anti-paroi gastrique, anti-facteur intrinsèque (Biermer)
\item si positif : surveillance annuelle
\end{itemize}
\subsubsection{Clinique}
\label{sec:org19eb2ad}
\begin{tcolorbox}
Diabète 1 : \{polyuro-polydipsie, amaigrissement, polyphagie\}, glycémie $> 2g/L$ \pm cétonurie
\end{tcolorbox}
Habituel : début rapide/explosif, sd cardinal = polyuro-polydispsie,
amaigrissement, polyphagie, troubles visuels transitoires, examen pauvre (fonte
musc, signes d'acidose\footnote{Dyspnée de Kussmaul, haleine acétonique}, glycémie veineuse, cétonurie (acidocétose
inaugurale)
Formes
\begin{itemize}
\item Diabète 1 lent (LADA\footnote{Latent Autoimmune Diabetes in the Adult}) : début tardif, progessif, Ac positif. Insulinothérapie en 2-10 ans
\item Révélé par acidocétose : fréquente chez enfants, ne devrait plus être vues
\item Non insulinodépendantes : 3 auto-Ac positifs \thus 100\% d'avoir diabète 1 dans
5 ans. Rémission de quelques mois possibles.
\item cétosique du sujet noir d'origine africaine : mécanisme
auto-immun. Décompensation cétosique. Auto-Ac spécifique du diabète 1
nésgatifs.
\end{itemize}
Affirmer type 1 :
\begin{itemize}
\item clinique : triade maigreur/amaigrissement, cétose, < 35 ans
\item sinon auto-Ac
\item sinon :
\begin{itemize}
\item hérédité dominante : MODY, mutation SUR1/KIR6-2 (si diabète néonatal)
\item symptômes inhabituels : sd de Wolfram (atrophie optique, surdité, diabète
insipide < 20 ans), mitochondropathie (surdité, dystrophie maculaire,
cardiomyopathie transmission par la mère)
\item secondaire : cancer pancréas (amaigrissement), pancréatite chronique,
mucoviscidose, hémochromatose, médicaments
\end{itemize}
\end{itemize}
\subsubsection{Évolution}
\label{sec:orgf2909b7}
Schéma théorique : phase préclinique (destruction cellules beta), clinique (85\% détruites), clinique séquellaire
Diabète instable :
\begin{itemize}
\item itérations de cétoacidoses ou hypoglycémies sévères, psycho.
\item DD : gastroparésie, déficit systèmes contra-insuliniques, Ac anti-insuline
\end{itemize}
\subsubsection{PEC}
\label{sec:org808d1af}
Patient : contrôle glycémie, injection d'insuline, prévenir complications
métaboliques et vasculaires, adapter ttt, contrôle de l'alimentation \thus
éducation thérapeutiques
Objectifs : HbA1c < 7\% (enfants : entre 7.5 et 8.5, complication/sujet âgé : 8\%)
Autosurveillance : urinaire rare, glycémique 4/jour \footnote{De temps en temps 3h matin, postprandial}, (glucose en SC si
objectifs thérapeutiques non remplis) :
Surveillance :
\begin{itemize}
\item HbA1c : en pourcentage Hb totale, aucun sens si modif durée de vie moyenne des globules rouges\footnote{Hémoglobinopathie, anémie hémolytique, urémie, EPO, saignées}
\item diabétologue/pédiatre endocrinologue 3/an
\item \{lipides, créat, microalbuminurie\}
\item ophtalmo, cardiologie 1/an (sympto/âgé,compliqué), dentiste 1/an
\end{itemize}
Traitement insulinique (Table \ref{tab:orgae693a1} ): palliatif à vie
\begin{table}[htbp]
\caption{\label{tab:orgae693a1}
Traitement insulinique du diabète 1}
\centering
\begin{tabular}{llll}
\toprule
Type & Injection & Durée & Utilisation\\
\midrule
insuline humaine recombinante & IV, IM, SC & 7-8 & Prandiale, hyperglycémie\\
analogue rapide de l'insuline & IV, IM, SC & 4-6h & Pompe\\
forme lente & SC & 9-16h & \\
analogue lents & & 16-40h & \\
\bottomrule
\end{tabular}
\end{table}
Injection :
\begin{itemize}
\item Résorption SC \inc si injection dans muscle, chaleur, vasodilatition, selon zone et dose,
\item Stylo à insuline (pompe si échec)
\item Schéma : analogue lent (1-2/j) et analogue rapide (3-4)
\item dose "pour vivre", "pour manger", "pour traiter", activité physique \thus
éducation nutritionnelle
\end{itemize}
Effets secondaires : hypoglycémie, prise de poids légère, allergie rarissime,
lipoatrophie insulinique (immuno), lipohypertrophie si piqûres au même endroit
Non insulinique : accompagnement, alimentation variée sans interdits, exercice physique
\subsubsection{Cas particuliers}
\label{sec:org30604e5}
Enfant/ado :
\begin{itemize}
\item cétoacidoses fréquentes (risque d'oedème cérébral \inc si réa).
\item difficile à équilibrer et accepter chez l'ado
\item pompe chez très petit enfant
\end{itemize}
Femme :
\begin{itemize}
\item dépister diabète 1 pendant grossesse
\item contraception à discuter : pilule oestrogestative possible si \female{} jeune,
sans complication, non fumeuses, diabète bien équilibré
\item grossesse : pronostic quasi normal si équilibre dès conception
jusqu'accouchement et non compliqué. Analogue de l'insuline. \\
\danger{} HbA1c \dec , \inc besoin fin grossesse et \dec post-partum, aggravation rétinopathie
et néphropatie
\item CI absolue : insuf coronaire instable
\item HbA1c < 6.5\%, glycémie jeun < 0.9g/L
\end{itemize}
Ménopause : hormonothérapie seulement si médicalement indiqué
Jeûne :
\begin{itemize}
\item si intolérance gastrique : pas d'arrêt insuline, collations liquide/hospit. Vérifier cétonurie
\item pour examen à jeun : laisser agir analogue lent, surveiller glycémie
\item prolongé/stress : soluté glucosé et insuline en IV
\end{itemize}
\subsection{Diabète 2}
\label{sec:org048a072}
90\% de diabète. Prévalence 4\%. À risque : obèse, anomalie métabolisme
glucidique, ATCD familiaux diabète 2, ethnie noire/hispanique.
Age adulte.
\subsubsection{Physiopatho}
\label{sec:orgffd5cd7}
Insuline n'arrive pas à avoir une réponse amximale : défaut de captation
musculaire du glucose, \inc production hépatique du glucose, lipolyse \inc acides gras
libres circulants \thus (aggrave \dec insulinosécrétion et utilisation du glucose)
Insuf de sécrétion d'insuline, s'aggrave avec l'âge et la durée
Facteurs génétique. Hyperglycémie aggrave insulinosécrétion,
insulino-résistance. \dec sécrétion adiopkines
\subsubsection{Cliniques}
\label{sec:orged85310}
Signes secondaires hyperglycémie, souvent inaperçus. Décompression sévères \thus
polyurie, polydispie, amaigrissement, prurit vulvaire/balanite, infections
récidivantes
Dépistage : si
\begin{itemize}
\item glycémie veineuse à jeun pour : signes cliniques de diabètes, > 45 ans (tous les 3 ans), \(\ge\) 1 FR
\item non caucasien/migrant, \glslink{sdMetabolique}{sd métabolique}
\end{itemize}
DD : diabète 1 lent (LADA) (minceur, 0 ATCD, IA2 et GAD positifs), génétique
(MODY2, mitochondrial), secondaire (pancréatopathie, hémochromatose,
mucoviscidose, médicaments)
Évolution : insulinopénie -> insulinoréquerant. Pronostic selon complications.
\subsubsection{Traitement}
\label{sec:orgce73fc3}
Objectifs : normalisation HbA1c (< 6.5\%), améliorer glycémie, insulinosensibilité
Moyens : activité physique, régime (hypocalorique si surpoids) sans sucres
rapides, traitement oraux, analogues GLP-1, insuline
Ttt oral :
\begin{itemize}
\item biguanide (Metformine)+++ :
\begin{itemize}
\item ES = digestif.
\item CI = insuf rénale (?), hépatique, respiratoire
\end{itemize}
\item autres sulfamides, glinides, inhibiteurs DPP-4, inhibiteurs \(\alpha\)-glucosidase
\end{itemize}
Surveillance glycémique :
\begin{itemize}
\item HbA1c essentielle : < 7\% pour plupart des patients (8\% si comorbidité grave,
âgé fragile, ATCD complication macrovasc, insuf rénale chronique sévère, 9\% si
agé dépendante)
\item autosurveillance glycémique : pas systématique si ttt oral (1-3 cycles/j),
nécessaire si insuline
\end{itemize}
Hygiéno-diététique
\begin{itemize}
\item Activité physique
\begin{itemize}
\item avantages : \dec incidence diabète 2, \inc insulinorésistance, \inc TA
effort, \inc masse maigre, \dec masse grasse
\item intensité modérée \(\ge\) 30min et intense (> 60\% \(VO_{2max}\)) de 20min
\item 30min/jour, 3-5/semaine
\item CI : insuf coronarienne, rétinopathie proliférante non stabilisée
\item surveiller si risque hypoglycémie (reprise, intensité/durée
inhabituelle). \danger{} pieds !
\end{itemize}
\item Alimentation :
\begin{itemize}
\item hypocalorique si surpoids, équilibrée\footnote{50\% glucides, 30\% lipides, 20\% protides. Légumes et féculents pour \inc
absorption des glucides}, sans sucres rapides.
\item objectif : -5 à 10\% du poids
\end{itemize}
\end{itemize}
Traitement médicamenteux :
\begin{itemize}
\item oral : metformine (sinon sulfamide, puis inhibiteurs DPP-4 ou inhibiteurs
\(\alpha\)-glucosidase)
\item insulinothérapie
\begin{itemize}
\item quand : insulinorequérance (amaigrissement, asthénie, amyotrophie), observance thérapeutique, HbA1c > objectfis, CI oraux,
\end{itemize}
affections intercurrentes
\begin{itemize}
\item combiné = insuline intermédiaire/analogue lent + hypoglycémiant oraux si
insulinorequérance partielles. 0.2 U/kg/j à adapter
\item exclusive : autosurveillance glycémique quotidienne, même gestion que
diabète 1.
\item CI au renouvellement permis poids lourds
\end{itemize}
\end{itemize}
\subsection{Complications}
\label{sec:org8da55c1}
Souffrance vasculaire : micro- (rein, oeil, nef) et macro-angiopathie (\inc
athérosclérose). AOMI x6-10
\subsubsection{Physiopatho}
\label{sec:org4ed095d}
Excès de glucose entre dans les cellules endothéliales, musculaire lisses, péricytes.
Glycolyse : voies mineures \inc, systèmes de protection de la mitochondrie
débordés \\
\thus stress oxydant dans la cellule.
Autres causes d'agression: inflammation, activation rénine-angiotensine, voies profibrosantes,
induites par l'hypoxies. Systèmes de protection moins efficaces : antioxydants,
anti-inflammatoire, cellules progénitrices vasculaires, angio-, artério-genèse
Conséquences : épaississement des membranes basales, troubles perméabilité
vasculaire, spécifiques = \{profil vasculaire (rétine), fibrose (rein)\}
\subsubsection{Rétinopathie diabétique}
\label{sec:org3379bdb}
\paragraph{Déf}
\label{sec:org647d8fb}
diabète = risque d'une rétinopathie. Complications dont on peut éviter la
cécité ! \thus examen ophtalmo et surveillance annuelle, contrôler glycémie et
HTA, laser (si (pré-)proliférante), laser ou injection anti-VEGF (maculopathie
oedémateuse)
\paragraph{Épidémio}
\label{sec:orgb4de828}
90\% de rétinopathie après 30 ans de diabète, dont 30\% menaçant pronostic
visuel. Diabète = 1ere cause de cécité acquise en France chez < 50 ans. FR =
durée et intensité de l'hyperglycémie
\paragraph{Physiopatho}
\label{sec:orge6dc81d}
anomalie vasculaire (microanévrisme, trouble perméabilité capillaire) \thus soit
oedème (dangereux si maculaire), soit (ischémie puis angiogenèse\footnote{Risques : saignement entre rétine et vitré, traction sur rétine,
hypertonie oculaire} puis rétinopathie proliférante)
\paragraph{Examens}
\label{sec:orgd8bb7cb}
cécité possible du jour au lendemain \thus dépistage tous les 2 ans
(annuel si diabète/TA mal contrôlé, \{avant, trimestre, post-partum\} pour femme
enceinte)
Surveillance par examen ophtalmo, photo au rétinographe(dépistage seulement), tomographie de
cohérence optique
\paragraph{Gravité}
\label{sec:orgfcae8e9}
\begin{itemize}
\item au fond d'oeil :
\begin{itemize}
\item microanévrisme < exsudats < nodules blancs cotonneux, irrégularités \diameter{} veines, capillaires dilatés (préproliférante) < néovaisseaux (proliférante) < décollement rétine, hémorragies, glaucome néovasculaire
\item maculopathie : exsudat, oedème maculaire, ischémie
\end{itemize}
\item \dec acuité visuelle car hémorragie intravitréenne, décollementd rétine,
glaucome néovasculaire, maculopathie diabétique
\item complémentaire : angiographie fluorescéine, tomographie cohérence optique
(oedème maculaire), écho en mode B
\item risque d'évolution rapide : ado, puberté, grossesse, intensification de
l'insuline, chir cataracte, \inc TA, dégradation fonction rénale
\end{itemize}
\paragraph{Traitement}
\label{sec:org2d7b9a5}
équilibre glycémie et TA++, laser\footnote{\dec de 50\% risque de cécité, \dec néovascularisation dans 90\%. Danger
si oedème maculaire, traite seulement l'exsudat} (+ injection intraoculaire
d'inhibiteurs VEGF)
Autres complications : cataracte (+ freq), glaucome néovasculaire (redoutable),
paralysie oculomotrice (régresse spontanément qq mois)
\subsubsection{Néphropathie}
\label{sec:org471519b}
Diabète = 1ere cause d'insuf rénale terminale. Diabète 2 = \(\frac{3}{4}\)
diabétiques dyalisé. Risque CV x10 (D1), x3 (D2). Décès insuf rénale terminale
30\% (D1), 5\% (D2)
Physiopatho : \inc pression intra-glomérulaire \thus dilatation des
glomérules. Filtration améliorée puis décroît (sclérose) avec \inc
albumine\footnote{Microalbuminurie, macro quand détectable à la BU}. Et toxicité directe glucose.
\paragraph{Dépistage}
\label{sec:org9516b30}
1/an par BU (protéinurie, hématurie, infection urinaire),
rapport albuminurie/créatinurie (excrétion urinaire) et vérif à 6 mois
\paragraph{Diagnostic}
\label{sec:org8c0528e}
Signes cliniques tardifs (HTA si protéinurie, oedème si protéinurie et insuf
rénale)
\danger{} faux positifs pour microalbuminurie : orthostatisme prolongé, activité
physique intense, \(\Delta\) PA, tabac, fièvre, \inc insuf cardiaque, hyperglycémie,
infection urinaire
Signes associés :
\begin{itemize}
\item rétinopathie (surtout D1). FR CV : microalbuminurie, DFG \dec.
\item Penser sténose des artères rénale (surtout D2) si HTA résistante ou \dec\dec
rein.
\item Hyperkaliémie (\inc si IEC, sartans) \thus surveiller
\end{itemize}
Diagnostic histologique :
\begin{itemize}
\item pas besoin si \{rétinopathie (hyperglycémie prolongé), excrétion urinaire d'albumine \inc répétée et croissante\}
\item biopsie seulement si 0 rétinopathie, < 10 ans après diagnostic, aggravation rapide, hématurie HTA sévère, signes extra-rénaux
\item diabète 1 : hypertrophie mésangiale, glomérulaire < épaississement membrane basale, dépôts
mésangiaux < hyalinose artériolaire < glomérulosclérose nodulaire
\item diabète 2 : 1/3 typique, 1/3 vasculaire, 1/3 non néphropatie diabétique
\end{itemize}
Classification en 5 stades :
\begin{enumerate}
\setcounter{enumi}{3}
\item Néphropathie incipiens : microalbuminurie\footnote{30-300mg/24h ou 20-200mg/L}
\item Néphropathie : PA élevée, DFG \dec de 10mL/min/an, nodule de sclérose,
hyalinose artériolaire
\item Insuffisance rénale
\end{enumerate}
\paragraph{Traitement}
\label{sec:org7ffae2e}
Prévention
\begin{itemize}
\item primaire (diabète, FR HTA)
\item si microalbuminurie : HbA1c < 7\%, PA < 140/85, IEC ou sartans, FR, régime
hypoprotidique, sel < 6g/j
\item si macroalbuminurie : contrôle tension++ < 140/85mmHg. (IEC ou sartan) et
diurétique thiazidique. Protéinurie < 0.5g
\item si insuf rénale :
\begin{itemize}
\item si DFG < 30mL/min/1.73m\(^{\text{2}}\), HbA1c < 8\% et seuls autorisé : insuline, répaglinide, inhib \(\alpha\)-glucosidase,
\item surveiller glycémie (HbA1c souvent pertubrée si IR chronique)
\item PAs < 130mmHg
\item traiter anomalies phosphocalciques, anémie arégénérative, préparer suppléance rénale
\end{itemize}
\end{itemize}
Éviter AINS. Si nécessaire, pas d'IEC/sartan. Limiter produits contrastes iodés
Néphrologue si : doute diagnostique, DFG < 45mL/min/1.73m\(^{\text{2}}\), protéinurie brutale.
IEC, sartans : se méfier d'une sténose des artères rénales : doser kaliémie, créatininémie
Infections urinaires : \(\times 3\) dont 90\% asymptomatique (basses)
\begin{itemize}
\item Risque = contamination du haut appareil urinaire (pyélonéphrite, nécrose papillaire,
\end{itemize}
pyélonéphrite emphysémateuse), aggravation néphropathie glomérulaire.
\begin{itemize}
\item Ttt : oui si symptomatique. Sinon pas de consensus
\end{itemize}
\subsubsection{Neuropathie}
\label{sec:org9f56605}
\begin{itemize}
\item Autonome : tardive
\item Périphérique : 50\% des diabètes à 20 ans. FR : grande taille, tabac, âge,
AOMI, carences nutritionnelles/vitaminiques, alcool, insuf rénale
\end{itemize}
Atteinte métabolique et vasculaire.
Dépistage sur examen clinique et interrogatoire (+ examens complémentaires si
autonome)
Si débutante, souvent silencieuse ! Examen des pieds !
\paragraph{Sensorimotrice}
\label{sec:org581be5f}
Fibres les plus longues en premier ("chaussettes" puis "gants")\footnote{Exceptionnellement, douleurs abdominales}. Examen
clinique pour perte de sensibilité, interrogatoire pour douleur
\begin{itemize}
\item Polynévrite symétrique distale : fréquente (40\% diabétiques après 25 ans) avec
\begin{itemize}
\item hypoesthésie pression/tact/thermique/proprioceptique ignorée
\item parfois paresthésies distales, douleurs "arc électrique"
\item ROT achilléen aboli (puis rotulien)
\item voûte plantaire se creuse (tardivement)
\item complication : neuroarthropathie (pied "cubique" de Charcot)
\item rares : mononeuropathies avec signes moteurs déficitaires, douleurs à
exacerbation nocturne
\end{itemize}
\item Polynévrite asymétrique proximale : beaucoup plus rare. L2, L3
(L4). Fatigabilité et amyotrophie douloureuse proximale
\item Polyradiculopathie thoracique : rare, douleurs abdo aux niveaux T4-12
\item Mononévrite : 5-10\%, asymétrique. Souvent nerfs crâniens. Si MS
: compressive. Si MI : sensitif
\item Multinévrite : DD = vascularite
\end{itemize}
\paragraph{Autonome}
\label{sec:org8f04f4d}
Diabète ancien, mal équilibré \thus nerfs vagues, système sympathique
lésés. Régression rare
\begin{itemize}
\item CV : \{tachycardie sinusale quasi-permanente, (bradycardie permanente),
allongement QT\}
\item Vasomotrice : hypotension orthostatique \emph{sans} accélération du pouls, troubles
microcirculation périphérique\footnote{Hyperémie, rougeur, oedème}
\item Troubles sudation : sécheresse cutanée MI, parfois hypersudation partie
supérieure. Prurit possible
\item Digestive gastro-intestinale : \{parésie tractus digestif, dysphagie, gastroparésie (fréq), diarrhée banale/motrice capricieuse (diag d'élimination !\footnote{maladie coeliaque, pullulation microbienne, endocrine}, constipation, incontinence fécale (rare)\}
\item Vésicale : pas de perception de la vessie pleine, hypoactavité détrusor et
favorisé par polyurie de l'hyperglycémie. Résidu post-miction \thus
incontinence, rétention, infection urinaire \thus clinique, écho
(prostate, vessie)
\item Dysfonction érectile : psychogène, sd de Leriche\footnote{Thrombus bloquant l'aorte abdominale avant bifurcation} (rare). À rechercher
\emph{systématiquement}. \\
DD : examen génital, testostérone, prolactinémie. Traitement efficace presque toujours.
\end{itemize}
Examen
\begin{itemize}
\item clinique : interrogatoire (hypotension OS, diarrhée\ldots{}), inspection pieds, ROT abolis au niveau des troubles sensitifs, monofilament, sensibilité épicritique, thermoalgique, vibratoire\footnote{Grosses fibres\label{org8c6a3c8}}, proprioceptiques\textsuperscript{\ref{org8c6a3c8}}
\item ECG annuel, EMG si atypique
\item chercher dénervation cardiaque parasympathique : variation de la FC entre
inspiration et expiration\footnote{Sensible mais pas interprétable > 60 ans ou patho bronchorespiratoire}, rapport RR long/court pendant épreuve de
Valsalva, variation FC de couché à debout
\end{itemize}
DD : neuropathies métaboliques (insuf rénale, amylose, hypothyroïdie), toxiques
(alcool, tabac, iatrogène), paranéoplasiques, carentielles, inflammatoire,
infectieuse (Lyme, lèpre), autre (Charcot-Marie-Tooth, péri-artérite noueuse)
Traitement :
\begin{itemize}
\item préventif = glycémie. FR : alcool, tabac, insuf rénale, carence
vitamines B, médicaments.
\item Si installées, stabiliser et éviter les complications
(mal perforant plantaire++)
\item Antalgiques, hydratation peau
\end{itemize}
\subsubsection{Macroangiopathie}
\label{sec:org9d9ab3a}
\diameter > 200 \(\mu\)m. Plus fréquente et sévère. Artères visibles sur radio.
Prévention CV = \textbf{problème majeur} des diabétiques 2 : \(\frac{3}{4}\) DC d'une cause
CV.
Risque CV \texttimes{}2-3 (\texttimes{}3-4 chez \female). Risque coronarien \texttimes{}2-4, AV ischémique
\texttimes{}2, AOMI \texttimes{}5-10 !
\paragraph{Dépistage}
\label{sec:orgf6b7869}
Risque > 1\% = élevé\footnote{Calcul par les études UKPDS ou SCORE (mais \texttimes{}2-4 pour ce dernier)}
\emph{FR} :
\begin{itemize}
\item CV : > 50 ans \male (> 60 \female), diabète > 10 ans, ATCD IDM/mort subite (< 55
ans \male, < 65 ans \female) ATCD AVC constitué < 45 ans, tabac, HTA
permanente, HDLc < 0.4g/L, microalbuminurie > 30mg/24h
\item autres : obésité abdominale (> 102cm \male, > 88cm \female) ou IMC >
30k/m\(^{\text{2}}\), sédentarité, > 3 verres vin/j (2 si \female), pyschosociaux
\end{itemize}
Montrer atteinte artérielle :
\begin{itemize}
\item coronaropathie : ECG repos annuel, scinti avec épreuve d'effort ou coronarographie
\item carotides ? auscultation \thus écho si AIT possible
\item AOMI ? pieds, pouls, claudication, IPS cheville/bras < 0.7 ? Écho-doppler
\end{itemize}
\paragraph{Diagnostic}
\label{sec:org7cbb8fc}
Ischémie myocardique silencieuse fréquente ! Y penser si troubles digestifs,
asthénie à l'effort, troubles du rythme cardiaque, déséquilibre inexpliqué du
diabète, \dec PA \thus dépistage systématique si risque
Risque extrême : diabète et microangiopathie sévère (glomérulopathie et
protéinurie > 1g/L), atteinte vasculaire
AOMI : fréquemment avec neuropathie. 1/3 proximale (HTA), 1/3 distale sous
genou (glycémie, tabac), 1/3 proximale et distale. Pouls pédieux = bon pronostic
\paragraph{Traitement}
\label{sec:org3392675}
Revascularisation : stents par défaut (risque de resténose) et chir si atteinte
3 coronaires.
\begin{itemize}
\item Glycémie : Objectif 6.5\% si jeune et prévention primaire, 7\% si âgé ou plus à
risque. Metformine systématique
\item Activité physique systématique
\item Contrôle lipidique : LDL < 1.3g/L (1.0 si risque CV élevée ou
néphropatie). Statines (simvastatine, pravastatine, atorvastatine) ou fibrates\footnote{Pas en association !}
\item PAs \(\in\) [130, 139] et PAd < 90mmHg. Hygiéno-diététique et antihypertenseurs si
échec
\item Prévention thrombose si \(\ge\) 1 FR : aspirine 75-150mg
\item Poids : IMC < 25kg/m\(^{\text{2}}\), tour taille < 94cm \male, 80cm
\female. Hygiéno-diététique
\item Arrêt tabac : substituts nicotiniques (bupropion sinon). Anticiper polyphagie
réactionnelle et modification transitoire sensibilité insuline !
\end{itemize}
\subsubsection{Pied diabétique}
\label{sec:orgdea3ba8}
1 patient sur 10 à risque d'1 amputation d'orteils. Éviter les plaies pour prévenir l'amputation
Mal perforant plantaire, plaie ischémie d'orteil/membre
À risque : diabète et pouls faible, neuropathie et trouble statique pied,
troubles sensibilité \{algique, vibratoire, thermique, profonde\}, ulcération
pieds
\paragraph{Mal perforant plantaire (MPP)}
\label{sec:org15f1807}
Neuropathies entraîne hypoesthésie et déformations
ostéoarticulaires \thus durillons puis fissure et infection \thus
dermo-hypodermite.
Révélé par : pus, fonte purulente localisé tisseux adipeux
\paragraph{Autres}
\label{sec:org6bd46ac}
\begin{itemize}
\item Ischémie/nécrose : si oblitération/sténose artères de moyen-petit calibre. Peau
froide, fine, dépilée, livedo. \danger nécrose peut arriver en qq heures \thus
revasculariser en urgence
\item Combinaison nécrose et MPP
\item Dermo-hypodermite nécrosante : très rare, urgence vitale . \{Teinte gris,
hémodynamique altérée, plaie odeur fétide\} \thus débrider en urgence, ATB. \\
Cas particulier : gangrène gazeuse à \bact{perfringens} (crépitations à la
palpation, clartés parties moelles\} \thus urgence vitale \danger
\end{itemize}
\paragraph{CAT}
\label{sec:org46137df}
\begin{itemize}
\item Dater l'apparition, neuropathie ou artériopathie. Plaie : localisation, couleur,
signes de diffusion, \{fièvre, frisson, teint gris\}, douleur.
\item Contact : orthopédiste si drain d'une infection purulente. Chir vasculaire si
doute sur l'ischémie. Réanimateur si tableau sévère.
\item Radio pieds bilatérale (ostéite ?), si infection : NFS, iono, CRP
\item Surveillance si état clinique
\item TTT :
\begin{itemize}
\item décharge (chaussure, arrêt de travail), excision kératose à domicile : peut
suffire
\item anticoagulation si alitement, antalgique,
\item réhydratation, équilibrer glycémie si besoin
\item anti-escarre si ischémie, vaccin anti-tétanos !
\item si infection : parage et drainage, ATB (cocci G+ si récent, sinon bacille G-)
\item revascularisation si plaie artériopathique
\end{itemize}
\end{itemize}
Ostéite : grave mais pas une urgence. Basé sur radio. Ttt . résection
chirurgicale ou ATB 6-12semaine et sans l'appui
\subsubsection{Autres}
\label{sec:org83ea325}
Peau :
\begin{itemize}
\item nécrobiose lipoïdique (rare, ttt mal codifié)
\item dermopathie diabétique (fréquente, cicatrices brunâtre, régresse spontanément)
\item bullose diabétique (cicatrise spontanément)
\item lipodystrophie (hypertrophie le plus souvent, dû à des injections trop souvent
au même endroit)
\item acanthosis nigricans (placards cutanés brunâtres, cou/aisselles, plis inguinaux)
\item vitiligo (taches achromiques)
\item xanthomatose éruptives (nodules rouge/jeun si grande hypertriglycéridémies)
\end{itemize}
Infections : bactériennes plus nombreuses, fonction polynucléaires altérée
\begin{itemize}
\item otite nécrosante : écoulement auriculaire, douleur intense et insomniante,
inflammation conduit auditif externe avec granulome/nécrose du plancher du
conduit \thus \danger urgence, ORL spécialisé
\item mucormycose : rhino-cérébro-orbitale, destruction osseuse, nécrose muqueuse
paroi des sinus. Fièvre, obstruction et écoulement nasal, oedème jugal et
palpébral \thus urgence
\end{itemize}
Foie : hépatologue dès anomalie transaminases ou \(\gamma\)-GT
Articulations :
\begin{itemize}
\item capsulite rétractile : douleur diffuse des épaules, limitations
mouvements actifs et passifs, frequence \texttimes{}4. Ttt : antalgiques, corticoïdes locaux,
physiothérapie
\item Maladie de Dupuytren : sclérose réractile de l'aponévrose palmaire moyenne
\item Chéiroarthropathie : raideur des doigts, peau épaissie et cireuse, signe de la
prière
\item Arthrose : fréquente diabétique 2
\end{itemize}
Dents : maladie parodontale
\begin{itemize}
\item car \{plus de plaque dentaire, \inc production
toxine, matrice extracellullaire altérée, vasculairisation gencive aussi\}
\item contrôle diabète, brossage, fil dentaire, soins dentaires prévention
\item signes : dents branlantes, saignements gencive brossage/mastication
\thus dentiste tous 6 mois
\end{itemize}
\textbf{Suivi diabète} :
\begin{itemize}
\item complications oculaires, rénales, neuro, cv
\item fond d'oeil annuel, ECG repos annuel, bilan cardio approfondi si risque CV
\inc, écho-doppler MI (si > 40 ans, diabète > 20 ans) tous 5 ans
\item bio : HbA1c 4/an, glycémie veineuse, lipides 1/an, microalbuminurie 1/an,
créatininémie jeun, clairance créat 1/an, TSH
\end{itemize}
\subsubsection{Complications métaboliques}
\label{sec:org3c6d81a}
Coma cétoacidosique
\begin{itemize}
\item acétonurie, glycosurie, glycémie 2.5g/L, pH veineux < 7.25, bicarbonate <
15mEg/L
\item cause : déficit insuline absolu/relatif, inconnue
\item évolution : cétose puis cétoacidose (Kussmaul, stupeur, déshydratation mixte)
\item gravité : âgé, ph < 7, kaliémie 4-6 mmol/L, coma profond, TA instable, pas de
diurèse après 3h, vomissements incoercibles
\item DD : urgence abdo, coma hyperosmolaire
\item Régression sous ttt en 24-48h. Complication iatrogène : oedème cérébral,
surcharge hydrosodée
\item ttt :
\begin{itemize}
\item éducation : si cétose, maintenir injections, supplément insuline rapide,
acétonurie si glycémie > 2.5g/L
\item curatif : insuline rapide IV, recharge volumique, apport potassimu, glucose
si besoin, facteur déclenchant
\end{itemize}
\end{itemize}
Coma hyperosmolaire :
\begin{itemize}
\item glycémie > 6g/L, osmolalité > 350mmol/kg, natrémie corrigée > 155mmol/L, pas
de cétose ni d'acidose
\item FR : > 80 ans, infection aigüe, diurétique, pas d'accès aux boissons, corticothérapie
\item ttt : réhydratation prudente, lente, insuline IV, surveillance, héparine
préventive, ttt causal, soins yeux/bouche/aérosols/aspiration bronchique
\end{itemize}
Hypoglycémie : inévitable
\begin{itemize}
\item mais pas mortelle, pas séquelle au cerveaux, ne déclenche pas d'accident vasculaire/cardiaque.
\item peur chez diabiétique, déstabilise diabète, attention si âgé ou alcoolique
\item favorisé par : hypoglycémie mineure répétées ignorées, neuropathie végétative
\item cause : repas insuffisants, effort physique, erreur d'injection
\end{itemize}
\section{249 : Amaigrissement}
\label{sec:org28dd9c8}
Fréquent
\subsection{Interrogatoire}
\label{sec:org533ee74}
\begin{itemize}
\item Histoire pondérale, conditions, de vie, psychologique, activité physique excessive et apports alimentaires insuffisants
\item Anorexie, \{troubles digestifs, palpitations, sd polyuro-polydipsie\}, troubles
libido/érection, amnénorrhée (anorexie mentale ou hypothalamique
fonctionnelle), médicaments (nausée, anorexie), dépression masquée++
\end{itemize}
\subsection{Examens :}
\label{sec:org8de6a36}
Clinique : poids, taille, IMC, pli cutané, fonte musculaire, carences vitamines,
pâleur cutanéomuqueuse
Complémentaires :
\begin{itemize}
\item bio : NFS (anémie), VS/CRP (inflammatoire), iono (hyponatrémie \thus insuf
surrénale), BU (glycosurie), calcémie, \{transaminase, \(\gamma\)-GT\}(foie), TSH
(hyperthyroïdie), \{B12, folates, TP, albuminémie\}, graisses fécales ?
(pancréatite chronique calcifiante), dénutrition\footnote{(Pré-)Albumine, IGF-1, ferritine sérique}
\item Radio thoracique (tuberculose), écho abdo (abcès/tumeur), fibro (obstacle),
DEXA (composition corporelles)
\end{itemize}
\subsection{Étiologie}
\label{sec:org90bf74b}
\begin{itemize}
\item Poids stables, apports nutritionnels normaux, examens normaux : maigreur
constitutionnelle
\item Si perte de poids confirmée, éliminer anorexie mentale, maladies digestives,
iatrogène, cancer extradigestif, maladies infectieuses, neuro, grande
défaillance cardiaque/rénale/respi/hépatique, alcool
\item Sinon, causes endocrines :
\begin{itemize}
\item diabète 1 ou 2 : glycémie, HbA1C
\item hyperthyroïdie : TSH \dec\dec, hormones thyroïdiennes \inc
\item hypercalcémie : si \gls{PTH} inadaptée, hyperparathyroïdie primaire
\item insuf surrénalienne : cortisol, ACTH plasmatique
\item panhypopituitarisme\footnote{Insuffisance antéhypophysaire complète} : cortisol \dec
\item phéochromocytomes : (nor)métanéphrines dans urines 24h, imagerie surrénales
\end{itemize}
\end{itemize}
\section{251 : Obésité}
\label{sec:org0159ff1}
\subsection{Adulte}
\label{sec:org2e4818a}
Surpoids = IMC \(\in\) [25, 29.9]kg/m\(^{\text{2}}\). Obésité :
\begin{itemize}
\item grade 1 : IMC \(\in\) [30, 34.9]kg/m\(^{\text{2}}\).
\item grade 2 : IMC \(\in\) [35, 39.9]kg/m\(^{\text{2}}\).
\item grade 3 : IMC \(\ge\) 40kg/m\(^{\text{2}}\).
\end{itemize}
Limites : sous-estimé chez asiatiques. Seulement pour [18,65] ans
Phases : prise de poids, constituée, perte, rechutes
Localisation : viscéral (scanner, IRM), sous-cutanée, ectopique (muscle, foie)
Épidémio : +27.5\% 1980-2013 (monde). France : de plus en plus jeune, \inc chez >
65 ans
Étiologie :
\begin{itemize}
\item génétique: envisager si précoce (naissance +24 mois), troubles du
comportement alimentaire
\item obésités communes liées à des facteurs environementaux (majorité) : surtout
déséquilibre apport caloriques- dépense
\begin{itemize}
\item antipsychotiques, glucocorticoïdes, antidépresseurs,
antiépileptiques, antidiabétiques
\item arrêt du tabac, privation de sommeil (?), hypothalamique (rare)
\end{itemize}
\end{itemize}
Complications : \inc RR mortalité, métabolique, CV, respi, ostéoarticulaire,
digestive, rénale, gynéco, cutanée, néoplasiques, psychosociale
\subsubsection{Clinique}
\label{sec:org0c9a6c7}
\begin{itemize}
\item Interrogatoire :
\begin{itemize}
\item ATCD familiaux d'obésité, poids naissance, âge surpoids,
poids max et min, circonstances déclenchantes, tentatives antérieures, phases
\item Comportement alimentaire (carnet), évaluation dépense énergétique, pyscho-comportementale
\item Complications (SAS)
\end{itemize}
\item Examen : poids, taille, PA, tour de taille\footnote{Obésité abdominale : > 88cm \female, > 102cm \male}, obésité secondaire
\item Complémentaires : glycémie à jeune, lipides, hépatique, uricémie, ECG repos
\end{itemize}
\subsubsection{Traitement}
\label{sec:org0b89533}
\begin{itemize}
\item Diététique, activité physique (\(\forall\) IMC)
\item Psychologique
\item Médicaments (IMC \(\ge\) 30 ou (\(\ge\) 27 et comorbidités)) : orlistat
\item Chir bariatrique : \{anneau gastrique ajustable, sleeve gastrectomie\},
\{court-circuit gastrique, dérivation biliopancréatique\} : < 65 ans. Prise en
charge 6 mois avant et post-op à vie (carences vitaminiques)\footnote{CI : troubles cognitifs sévères, troubles sévères non stabilisés du
comportement alimentaire, dépendances à l'alcool / substances psychoactives, pas
de PEC médicale, pronostic vital mis en jeu, CI à l'anesthésie générale,
incapacité à faire un suivi médical prolongé}
\end{itemize}
\subsection{Enfant/ado}
\label{sec:org5316694}
\danger{} évolutivité. Surpoids : IMC > 25. Obésité
\begin{itemize}
\item grade 1 : > 30kg/m\(^{\text{2}}\)
\item grade 2 : > 35kg/m\(^{\text{2}}\)
\item grade 3: > 40kg/m\(^{\text{2}}\)
\end{itemize}
Épidémio : stabilisation mais obésités sévères \texttimes{}4
\subsubsection{Étiologies}
\label{sec:org3358ba5}
\begin{itemize}
\item génétiques : mutation sur récepteur de la mélanocortine type 4 = 2.5-5\%
\item communes (majorité) : facteurs environnementaux et prédisposition génétique
\begin{itemize}
\item repond d'adiposité à 6 ans. Risque d'obésité \(\propto\) précocité du rebond
\item tour de taille/taille > 0.62 = forte valeur prédictive
\item FR : surpoids parent, poids excessif/tabac pendant grossesse, anomalie de
croissance foetale, \inc\inc poids à naissance + 2ans, difficulté
socio-éoc, manque d'activité physique, troubles sommeil, psychopatho
\end{itemize}
\item secondaires (rare) : ralentissement de la vitesse de croissance naturelle
\end{itemize}
\subsubsection{Complications}
\label{sec:org4c0aa19}
\begin{itemize}
\item HTA : > 97e percentile + 10mmHg
\item Insulinorésistance avec glycémie normale fréquente
\item \inc TG et \dec HDL
\item Stéatose hépatique non alcoolique
\item Rachialgies, gonalgies, troubles statique vertébrales. Penser à l'épiphysiolyse
de la tête fémorale : garçons [10,15] ans avec douleur mécanique de hanche
\thus radio de profil
\item Psychologique
\end{itemize}
\subsubsection{Clinique}
\label{sec:org181761d}
Interrogatoire :
\begin{itemize}
\item ATCD familaux,
\item personnels : poids, taille naissance, âge d'appartition, changements environnementaux, tentatives antérieures, troubles des règles
\item comportement alimentaire (difficile)
\end{itemize}
Examen clinique :
\begin{itemize}
\item poids, taille, PA, tour de taille, pli-cutané (masse grasse < 20\% après 5 ans), courbes de
croissance (ralentissement = pathologique !), dermato (acanthosis nigricans =
insulinorésistance, vergétures= hypercorticisme, intertrigo, mycose)
\end{itemize}
Pas d'examens complémentaires !
\subsubsection{Traitement}
\label{sec:org6f29b11}
Prévention surtout. Modifier style de vie (efficacité faible). Chir possible
avec équipes spécialisées
\section{252 : Diabète gestationnel}
\label{sec:orgd87a74f}
Physio chez femme enceinte selon moitié:
\begin{itemize}
\item non diabétique : (\inc insulinéme, insulinosensibilité) puis (insulinorésistance
\thus hyperinsulinisme ou diabète gestationnel)
\item à risque de diabète : (hypoglycémie, cétose) puis (insulinosécrétion
postprandiale insuffisante)
\end{itemize}
\subsection{PEC du diabète pré-gestationnel}
\label{sec:org02b0895}
Grossesse à risque mais fécondité normale (sauf si sd ovaires polykystiques).
\danger{} Normalisation glycémie préconception \(\rightarrow\) accouchement
\begin{itemize}
\item HbA1c \(\le\) 6.5\%
\item glycémie à jeun \(\in\) [0.6, 0.9]g/L
\item glycémie repas + 1h < 1.40g/L et +2h 1.20g/L
\end{itemize}
\subsubsection{Risque foetus}
\label{sec:orge7056f9}
\begin{itemize}
\item Fausses couches spontanées \texttimes{}2, \(\propto\) hémoglobine glycquée
\item Malformation congénitales \texttimes{}2, constituée pendant 8 premières semaines :
cardiaque, neuro, rénale \thus \inc fausses couches spontanées, mortalité
foeatale/néonatale, malfomations
\item 2e trimestre : macrosomie, hypoxie tissulaire, retard maturation pulmonaire,
hypertrophie cardiaque septale
\item 3e trimestre : mort foetale
\item Accouchement : \inc prématurés, césariennes. Danger : trauma foetal,
hypoglycémie sévère, hypocalcémie, hyperbilirubinémie/polyglobulie, détresse
respi transitoire, maladie des membranes hyalines
\item Long terme : surpoids/obésité et diabète 2
\end{itemize}
\subsubsection{Risque mère}
\label{sec:org3b4a2f0}
\begin{itemize}
\item HTA (30\%) : si > 20 SAc, risque de toxémie gradivique. \texttimes{}5 si
diabète 1. Risque vital
\item Rétinopathie : ttt préalable si rétinopathie proliférative. CI : rétinopathie
proliférative floride non traitée
\item Néphropathie :
\begin{itemize}
\item FR = \{HTA, déséquilibre glycémique, rétinopathie évoluée dès
départ, diabète ancien, insuf rénale, hydramnios, correction trop rapide d'une
hyperglycémie chronique\}.
\item Insuf rénale \thus hypotrophie foetale, prééclampsie. Si IR préexistante : 50\%
mortalité foeatale \textbf{in utero}
\item dépistage : créat plasmatique, microalbuminurie, protéinurie
\item IEC contre-indiqués
\end{itemize}
\item Coronaropathie : exceptionnelle mais gravissime. Dépister si diabète ancien et
complications microvasculaire (ECG, effort)
\item Infection urinaire \inc, risque pyélonéphrite, décompensation diabétique
\item Diabète 1 : \inc risque dysfonction thyroïdiennes
\end{itemize}
\subsubsection{PEC}
\label{sec:orgfe3e3eb}
\begin{itemize}
\item Avant grossesse : glycémie \(\in\) [0.7, 1.20] préprandial, \(\in\) [1, 1.4]
postprandial et HbA1c < 7\%
\begin{itemize}
\item diabète 1 : \inc insuline
\item diabète 2 : insuline si régime ne suffit pas/arrêt ttt oral
\end{itemize}
\item Pendant
\begin{itemize}
\item équilibre glycémique++ (6 glycémies capillaires/jour)
\begin{itemize}
\item \danger variations physiologiques : insuline \dec puis \inc puis \dec\dec
\item cétonémie/cétonurie si glycémie > 2g/L
\end{itemize}
\item \(\ge\) 1600kcal/j 2eme et 3eme tri
\item surveiller poids, PA, créat plasmatique, microalbuminurie, protéinurie, FO,
BU, protéinurie
\item surveillance obstétricale : dater++ (12-14SA), malformations (22-24), placenta et liquide
amniotique (32-34SA), cardiomyopathie hypertrophique (32-34SA), bien-être
foetal
\item pas de bêtamimétique si prématuré
\end{itemize}
\end{itemize}
\subsubsection{(Post)partum}
\label{sec:org6bd13fb}
Accouchement programmé souvent, facilité si rétinopathie sévère, insuline
SC/IV et glucosé avec surveillance horaire
Puis : insuline selon besoin pré-grossesse (D1) ou arrêt (D2)
\subsection{Diabète gestationnel}
\label{sec:org29b17e7}
Si lié à la grossesse, apparait en 2eme partie. Risque : pré-éclampsie,
césarienne (\(\propto\) hyperglycémie matenrelle). FR : surpoids
Même complications liées à l'hyperinsulinisme que pré-gestationnel
\subsubsection{Dépistage}
\label{sec:orgf2eb18b}
Si FR seulement :
\begin{itemize}
\item \(\ge\) 35ans
\item IMC \(\ge\) 25kg/m\(^{\text{2}}\)
\item ATCD : diabète gestationnel, macrosomie, diabète chez parents 1er degré
\end{itemize}
Diagnostic :
\begin{itemize}
\item début de grossesse si glycémie jeun \(\ge\) 0.92g/L \thus PEC immédiate
\item sinon à 24-28SA et (glycémie jeun < 0.92g/L ou non faite) : hyperglycémie
provoquée oralement
\end{itemize}
\subsubsection{Traitement}
\label{sec:orgd152022}
\begin{itemize}
\item Diététique (30-35kcal/kg [25 si surpoids]), activité physique, antidiabétique
CI , insuline si régime ne suffit pas après 8 jours
\item Surveillance : glycémie (6/jour puis 4/jour), cétonurie (si glycémie > 2g/L),
HTA
\item Objectif : glycémie jeun < 0.95g/L et postprandiale +2h < 1.20g/L
\end{itemize}
Post-partum : arrêt insuline et surveillance glycémie (diabète antérieur
?). Vérifier glycorégulation à 3 mois. Risque de récidive si grossesse
\section{253 : Nutrition chez le sportif}
\label{sec:org49b1f6c}
\subsection{Examen d'aptitude}
\label{sec:org159f684}
Dépister les pathologies induisant un risque vital/fonctionnel grave : mort
subite (1-4/100 000 après 35 ans)
Obligation légale si compétition (licencié ou non)\footnote{Médecin qualifé pour : alpinisme, armes à feu, mécaniques, aériens, sous-marins, de combat
avec HS}
Examen :
\begin{itemize}
\item ATCD sportif, médicaux familiaux (CV, hypercholestérolémie familiale),
conduites à risque, alimentaire, ttt, toxiques
\item Clinique :
\begin{itemize}
\item poids, taille, IMC, (courbe de croissance)
\item maturation pubertaire
\item ostéoarticulaire, cardiorespiratoire, test dynamique sous-maximal
(Ruffier-Dickson)
\end{itemize}
\item Complémentaire : ECG repos\footnote{Pour 1er certificat puis tous les 3 ans puis tous les 5
ans jusque 35 ans}, CV
\end{itemize}
\subsection{Bénéfices/inconvénients}
\label{sec:org1d10f92}
Adulte :
\begin{itemize}
\item Bénéfices :
\begin{itemize}
\item maintien santé : \dec mortalité prématurée, \inc qualité de vie, \inc
autonomie (âgé), régule poids
\item prévention : cancers (colon, sein), CV, métabolique, ostéoporose \female
\item ttt : anxiété, cardiomyopathie ischémique, BPCO, obésité, diabète 2, neuro,
rhumatismales, dégénératives
\end{itemize}
\item Surveillance : dépistage d'insuf coronarienne > 40 ans, \danger nutrition et
hydratation si > 3h/semaine
\item Recommandation : 150min/semaine (modéré) ou 75min/semaine (soutenu). Idéal : x2
\end{itemize}
Enfant :
\begin{itemize}
\item Bénéfices :
\begin{itemize}
\item dev psychosocial : \dec stress, anxiété, \inc intégration sociale, \inc
confiance en soi
\item dev psychomoteur : concentration, coordination, équilibre
\item \inc masse maigre, \inc densité osseuse
\item prévention : sd métabolique, surpoids, CV
\end{itemize}
\item Surveillance : nutrition (éviter retards de croissance/pubertaire), attitude
alimentaires restrictives
\item Recommandation : 60min/jour (modéré-soutenu) et renforcement musculaire,
osseux 3x/semaine
\end{itemize}
\subsection{Besoins nutritionnels}
\label{sec:org4799504}
\begin{center}
\begin{tabular}{llll}
\toprule
Intensité & durée & Energie & Limitation\\
\midrule
Très intense & secondes & ATP, P-Cr & \\
Intense & minutes & Glycogène musculaire & Lactate\\
Faible-élevée & prolongée & glycogène musculaire/lipides & VO\(_{\text{2}}\) max\\
\bottomrule
\end{tabular}
\end{center}
Macronutriments :
\begin{itemize}
\item Glucides : détermine l'épuisement si endurance \thus index glycémique faible à
distance, IG élevé juste avant. Pendant : maintenir glycémie. Après :
reconstituer les stocks de glycogène
\item Lipides à limiter si intensité élevé/compétition
\item Protides : endurance 1.2-1.4g/kg/j, force : 1.3-1.5g/kg/j si maintien masse, sinon jusque 2.5g-kg/j
\end{itemize}
Hydrosodé : avant = 500ml en 2h (prévention). Pendant : NaCl si \(\ge\) 1h selon
intensité (jusque 1.5L/h). Après : 150\% perte pondérale.
Minéraux, vitamines:
\begin{itemize}
\item attention situation à risque : déficit en fer, contrainte de poids,
alimentation glucidiques mais faible densité nutritionnelle, exclusion de
groupes d'aliments
\item endurance : vit B énergétiques\footnote{Thiamine, riboflavine, niacine, B6} , vit. "antioxydantes"\footnote{Vit C, E, \(\beta\)\{xcarotène}
\item force : \inc vit B6, \inc "antioxydantes"
\end{itemize}
\subsubsection{Enfant}
\label{sec:orgda1e961}
Apport insuffisants \thus retard croissance staturo-pondéral ou pubertaire,
\dec masse musculaire, déminéralisation osseuse, déficit immunitaire.
Surveiller calcium, vit D, fer.
\section{265 : Hypocalcémie, dyskaliémie, hyponatrémie}
\label{sec:org95ee1f6}
\subsection{Hypocalcémie (hypoCa)}
\label{sec:orgc6de158}
Éliminer fausses hypoCa dues à l'hypoalbuminémie\footnote{Une partie du calcium est lié à l'albumine}.
Calcémie = équilibre absorption intenstinale, résorption osseuse, excrétion
rénale. Régulé par PTH, calcitriol
Clinique :
\begin{itemize}
\item hyperexcitabilité neuromusc : paresthésie main, pieds, péribuccales
(spontanées/effort), signe de Trousseau ("main d'accoucheur"), signe de
Chvosteck (peu spécifique), crises de tétanie (paresthésie, fasciculation
pouvant entraîner arrêt respi)
\item chronique : sd de Fahr\footnote{Cataracte sous-capsulaire, calcification des noyaux gris centraux} \thus signes extrapyramidaux, crises comitiales
\item \inc QTc \thus troubles du rythmes
\item dans l'enfance : musc, neuro, cardiaques
\end{itemize}
\subsubsection{Principales causes}
\label{sec:org819e265}
\begin{itemize}
\item Hypoparathyroïdes : anamnèse et \{hypoCa, PTH \dec, phosphatémie
normale/haute\}.
\begin{itemize}
\item post-chir++ : parathyroïdectomie totale
\item congénitale : sd Di George++\footnote{Hypoplasie des parathyroïdes et du thymus, dysmorphie faciale, anomalies cardiaques}
\end{itemize}
\item Pseudoparathyroïdies : génétiques : résistance à la PTH \thus PTH
\inc. Chondrodysplasie possible
\item Anomalie vitamine D
\begin{itemize}
\item carence vit D = 1ere cause hypoCa chez nourrisson \thus rachitisme
carentiel. Chez l'adulte, seulement si déficit prolongé et profond
\item malabsorption digestive, insuf rénale chronique, cirrhose
\end{itemize}
\end{itemize}
\subsubsection{TTt}
\label{sec:org851b0ed}
\begin{itemize}
\item Aigüe = urgence \thus calcium IV lente (2-3x10ml). Suspension des ttt qui \inc
QTc, réduction digoxine
\item Chronique : vit D (ou dérivés actifs) et calcium per os
\end{itemize}
\subsection{Hyper-/hypo-kaliémie,}
\label{sec:org7560470}
Retentissement cardiaque \thus vital
\subsubsection{HyperK}
\label{sec:orgcf364f1}
Principales causes
\begin{itemize}
\item Acidose (sort K+ de la cellule) et insulinopénie (réduit entrée K+) : ttt par
insuline à risque d'hypoK \danger \thus apport K+ dès normokaliémie
\item Hypoaldostéronisme
\begin{itemize}
\item insuf surrénale périphérique
\item secondaire : chez > 65 ans, diabétiques. Risque = aggravation si IEC ou ARA II
\end{itemize}
\item Pseudo-hypoaldostéronisme : résistance à l'aldostérone (génétique)
\end{itemize}
\subsubsection{HypoK}
\label{sec:org02883a1}
\begin{itemize}
\item Dénutrition sévère : anorexique, post-chir bariatrique sans suivi
\item Insulinothérapie : si cétoacidose et troubles digestifs majeurs \thus
insulinothérapie seulement après normokaliémie, sinon arrêt cardiocirculatoire
\item \inc activité \(\beta\)adrénergique
\item Paralysie périodique famililiale : exceptionnelle, paralysie brutale
transitoire des 4 membres
\item Hyperaldostéronisme ou hypercorticisme : y penser si HTA (non constante) et hypoK avec
kaliurèse \inc
\item Polyurie : hyperglycémie \inc
\item Hypomagnésémie : si Mg \dec, malabsorption, pertes digestives causées par
IPP. Sinon : pertes urinaires acquises/génétique
\item Bloc 11-\(\beta\)hydroxystéroïde déshydrogénase : tableau similaire à
hyperaldostéronisme primaire mais avec aldostérone \dec. Si HTA et hypoK,
vérifier réglisse et pastis (glycyrrhizine)
\end{itemize}
\subsection{Hyponatrémie endocrinienne}
\label{sec:org477c763}
HypoNa = anomalie électrolytique la plus commune chez hospitalisés
Osmolarité (mosm/L) : 2\texttimes{}([Na+] + [K+]) + glycémie + urée
\begin{figure}[htpb]
\centering
\resizebox{0.9\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
level distance=1.5cm,
edges={nodes={fill=white}},
layered layout]
{
Osmolalité -> {
Augmentée -> "Hyperglycémie";
Normale -> "HyperTG\\Hyperprotidémie";
Diminuée -> Volémie -> {
"Augmentée\\(hyperhydrat. extracell)" -> "Insuf cardiaque\\Cirrhose\\Sd néphrotique"
-> "Sérum salé\\isotonique";
"Normal\\(hyperhydrat intracell)" -> "Hypothyroïdie\\Insuf corticotrope\\SIADH"
-> "Sérum salé\\hypertonique";
"Diminué\\(déshydrat extracell)" -> "Perte digestives\\rénales, cérébrales\\Insuf corticosurrénales aigüe"
-> "Restriction hydrosodée";
};
};
};
}
\caption{Démarche diagnostique et ttt devant une hyponatrémie}
\end{figure}
Physiopatho : hormone anti-diurétique (ADH) : répond au stimulus osmotique,
volémique et stress etc. Action vasoconstrictive, corticotrope (stress),
antidiurétique
\subsubsection{SIADH}
\label{sec:org2bbb436}
PA et FC normale, pas de pli cutané, (déshydratation extra-cellulaire) ni
d'oedème (hyperhydratation extra-cellulaire)
DD : cf figure. Si hyponatrémie hypoosmolaire normovolémique :
\begin{itemize}
\item insuf corticotrope : cortisolémie et ACTH
\item insuf surrénale aigüe
\item hyporthyroïdie proto-thyroïdienne : TSH \inc
\item hypopituitarisme antérieure : cortisolémie, TSH, T4L
\end{itemize}
Étioliogies :
\begin{itemize}
\item iatrogènes : neuroleptiques, antidépresseurs, chimio, carbamazépine,
desmopressine
\item quasi toutes affections neuro, notament intervention trans-sphénoïdale
(adénome corticotrope)
\item pulmonaires
\item tumeurs malignes : cancer bronchique à petites cellules++
\item rares : mutation récepteur V2 ADH, marathonien, VIH
\item Intoxication aigüe à l'eau
\end{itemize}
\subsubsection{Traitement}
\label{sec:org23f3fb0}
Urgence si < 115mmol/L ou \{délire, coma, convulsion\} \thus sérum salé
hypertonique jusque Natrémie = 120mmol/L (puis restriction hydrique).
\danger{} < 12mmol/24h sinon tableau d'AVC (myélinolysie centropontine) !!
Thérapeutique :
\begin{itemize}
\item restriction hydrique : mal tolérée
\item déméclocycline : induit diabète inspidie néphrogénique
\item aquarétique (tolvaptan)
\end{itemize}
Indications :
\begin{itemize}
\item symptômes cliniques sévères/récent : sérum salé hypertonique
\item symptômes plus modérés : sérum et tolvaptan
\item sinon restriction hydrique et tolvaptan (ou déméclocycline)
\end{itemize}
\section{266 : Hypercalcémie}
\label{sec:org4abc6d2}
Diagnostic = double dosage calcémie. Étiologie selon parathormone (PTH)
Physio : calcémie régulée par PTH et calcitriol
\begin{itemize}
\item PTH: \inc absorption intestinale du calcium et phosphore, \inc résorption
osseuse, \dec réabsorption phoshpore et \inc absorption calcium (rein)
\item PTH régulée par récepteur sensible au calcium (CaSR)
\end{itemize}
Bio : calcémie totale = \{calcium ionisé, calcium lié = \{lié à l'albumine,
complexé aux anions\}\}. Calcium ionisé \(\approx\) 50\% calcium total\footnote{Sauf si acidose, hyperprotidémie, \inc phosphore/sulfate sériques}
Clinique : asthénie, \{polyuro-polydipsie, lithiases rénales\}, \{anorexie,
constipation, nausées\}, \{apathie, somnolence, confusion, psychose, coma\}, \{HTA,
\dec QT\}
\danger hyperglycémie maligne = urgence {} avec déshydratation, \{confusion,
coma, insuf rénale\} et risques de troubles du rythme cardiaque, bradycardie avec asystolie
\subsection{Étiologies}
\label{sec:org42dac98}
\subsubsection{Hypercalcémie PTH dépendante (PTH N ou \inc)}
\label{sec:org38d8ccb}
\begin{itemize}
\item \textbf{Hyperparathyroïdie\footnote{La PTH est produite par la parathyroïde\ldots{}} primaire} (55\%) : lésion parathyroïde.
\begin{itemize}
\item Signes cliniques précédents avec rénaux, osseux (clinique et radio\footnote{Ostéite fibrokystique de von Recklinhausen, exceptionnelle.}) \thus créatinine
plasmatique, scénal rénal non injecté
\item Surtout densité osseuse (tier distal du radius)
\item Bio : hypercalcémie et PTH non adaptée (N ou \inc).
\begin{itemize}
\item \danger corriger déficit vitamine D avant doser calcémie.
\item \danger DD : sd hypercalcémie-hypocalciurie familiale,
hyperparathormonémie avec ttt au lithium
\item calcémie et phosphorémie n'ont de sens qu'avec une fonction rénale normale
\item calciurie : si augmentée, enlève les DD précédents
\end{itemize}
\item imagerie : bio primaire mais sert si indication opératoire seulement (écho, scinti)
\item étiologie :
\begin{itemize}
\item majorité : sporadique, isolé
\item NEM1\footnote{Néoplasie endocirinienne multiple de type 1} (1\%) : hyperparathyroïdie primaire = 95\%. Recherche tumeurs
endocrines pancréas et duodenum, adénomes hypophysaires
\item NEM2 : cancer médullaire de thyroïde puis phéochromocytome bilat et
hyperparathyroïdie primaire avec atteinte multiglandulaire
\item \danger hyperparathyroïdie primaire chez jeune = suspicion transimission
génétiques
\item hyperparathyroïdie \emph{secondaire} : adaptation à hypocalcémie (chercher chez
insuf rénaux chronqiue)
\item hyperparathyroïdie \emph{tertaire} : insuf rénaux chronique
\end{itemize}
\end{itemize}
\item \textbf{hypercalcémie-hypocalciurie familiale bénigne} : hypercalcémie,
hypophosphorémie, (hypermagnésémie), calciurie \dec\dec{}, PTH inadaptées
(N ou \inc)
\item Lithium
\end{itemize}
\subsubsection{hypercalcémie PTH-indépendante}
\label{sec:orgc480281}
\begin{itemize}
\item \textbf{Hypercalcémie des affections malignes} (30\%) : PTH \dec\dec{}.
\begin{itemize}
\item Tumeurs : poumon, sein, rein, tractus digestif
\item Production tumorale de PTHrp (mime PTH)
\end{itemize}
\item Autres :
\begin{itemize}
\item granulomatose : hyperphosphorémie, PTH \dec
\item iatrogènes : vitamine D (hypercalcémie, hyperphosphorémie, PTH passe),
vitamine A (asthénie sévère, douleurs musc et osseuse, alopécie des
sourcils, chéilite fissuraire), diurétiques thiazidique, buveurs de laits
(plutôt fortes doses d'antiacide ou carbonate de calcium)
\end{itemize}
\end{itemize}
\subsection{Traitement}
\label{sec:org26fb781}
Hypoparathyroïdie primitive : guérison par ablation des adénome(s) par chir
conventionnelle ou mini-invasive (faire imagerie avant !)
Sinon, traitement palliatif : bisphosphonates (inhibe résorption osseuse),
calcimimétiques (\dec PTH),
\danger Hypercalcémie = urgence {} :
\begin{itemize}
\item sérum phy
\item bisphosphonate en perf lente ou corticothérapide IV (myélome/hémopathie) ou dialyse (maligne)
\end{itemize}
\section{303 : Tumeurs de l'ovaire (hormono-sécrétante)}
\label{sec:org78fc714}
\subsection{Sécrétant des oestrogènes}
\label{sec:orgf786305}
Tumeurs de la granulosa :
\begin{itemize}
\item malignes, les plus fréquentes des tumeurs des cordons sexuels et du stroma.
\item plutôt femmes [30,50] ans
\item jeune fille : pseudo-puberté précoce. Femme :
aménorrhées/ménométrorragie. Ménopausée : saignement vaginal dû à hyperplasie
endométriale\footnote{Tumeurs souvent > 10cm, kystique, multiloculaire, unlatérale}
\item ttt : ovariectomie unilatérale mais récidives 10-33\%
\end{itemize}
Thécomes :
\begin{itemize}
\item très rare, surtout péri-/post-ménopause
\item Tumeurs solides, bénignes \thus exérèse = guérison
\end{itemize}
Sd Peutz-Jeghers (très très rare)
\subsection{Sécrétant des androgènes}
\label{sec:orgbbd5609}
Tumeurs à cellules de Sertoli-Leydig
\begin{itemize}
\item sécrète testostérone
\item rare. Y penser si hirsutisme récent avec signes de virilisation
\item DD : corticosurrénalome (faire scanner surrénales), sd Cushing (faire freinage
minute), block 21-hydroxylase (doser 17-hydroxyprogestérone)
\item femme 30-40ans
\item détecté à l'écho ovarienne vaginale ou IRM pelvienne
\item si < 5 cm, bon pronostic \thus ttt conservateur chez femme jeune
\end{itemize}
Tumeurs à cellules de Leydig
\begin{itemize}
\item cristaux de Reinke (caractéristique)
\item typiquement : virilisantes chez ménopausée
\item petite taille, bénigne \thus ovariectomie bilatérale
\end{itemize}
Tumeurs germinales sécrétantes
\begin{itemize}
\item tumeur ovarienne sécrétant de l'hCG : chez femme jeune, aménorrhée, douleurs
abdo/métrorragie. Tttt : conservateur si jeune, chimio si étendu
\item gonadoblastome : chez sd de Turner avec mosaïque et chromosome Y (risque
7-20\%) \thus gonadectomie préventive
\item autres : sécrétant hCG, T4, sérotonine
\end{itemize}
\section{305 Tumeurs du pancréas (endocrine)}
\label{sec:org9762786}
Rare, concerne pancréas et duodénome. Diagnostic histologique, compléteté par
immunohistochimie
Pronostic péjoratif : > 2 cm, invasion vasculaire, dissémination métastase
\begin{table}[htbp]
\caption{Caractéristiques des tumeurs endocrines duodéno-pancréatiques}
\centering
\begin{tabular}{ll}
\toprule
Sécrétion & Clinique\\
\midrule
Insuline & Hypoglycémie organiques\\
Gastrine & Ulcère oestro-gastro-duodénaux, diarrhées\\
ACTH & Cushing\\
Glucagon & Diabète, érythème migrateur, diarrhée, amaigrissement, thromboses\\
VIP & Diarrhée hydroélectrolytique profuse, hypokaliémie\\
GHRH & Acromégalie\\
\bottomrule
\end{tabular}
\end{table}
Imagerie : scanner spiralé TAP \textpm{} IRM abdo
Formes familiales : NEM1, neurofibromatose 1, von Hippel-Lindau
\section{310 : Tumeurs du testicule (aspects endocriniens)}
\label{sec:orge1d449a}
Prévalence : 9/100 000, ado/adulte jeune
\subsection{Tumeurs stromales}
\label{sec:orgf829d90}
Cellules de Leydig. Unilatérales, bénignes
\begin{itemize}
\item Garçon < 9 ans : pseudo-puberté précoce \thus testostérone plasmatique, écho
testiculaire
\item Adulte : féminisation, infertilité \thus oestradiol \inc, testostérone N ou \dec
\end{itemize}
Cellules de Sertoli : rares (enfant) ou exceptionnelles
(adulte). Féminisation/pseudo-puberté précoce à 50\%. Testostérone/oestradial
\inc, LH et FSH \dec, inhibine B \inc.\footnote{Peut appartenir à : complexe Carney, sd Petuz-Jeghers}
\subsection{Autres}
\label{sec:org8847683}
\begin{itemize}
\item Tumeurs germinales : fréquentes, écho testiculaire
\begin{itemize}
\item séminomateuses : fréquentes, pronostic bon
\item non séminomateuses : pronostic réservé
\end{itemize}
\item Inclusion surrénaliennes : par excès ACTSH. Marqueur : 17-hydroxyprogestérone
\end{itemize}
\subsection{PEC}
\label{sec:orgba232d4}
Glucocorticoïdes si inclusion surrénaliennes. Sinon chir 1ere intention. Chimio si métastases pulmonaires/ganglionnaires.
\printglossaries
\section{Annexes}
\label{sec:org9e029f8}
\subsection{Hormones}
\label{sec:orgae7ef15}
\begin{figure}[htpb]
\centering
\resizebox{!}{5cm}{
\tikz \graph [decision]
{
ht/hypothalamus[organ] -> ["CRH"] hh/hypophyse[organ] -> ["ACTH"] cs/corticosurrénale[organ];
cs -> cort/cortisol;
cort ->[bend left=60, "-"] ht;
cs -- ["+"] hh;
hh --["+"] ht;
};
}
\resizebox{0.4\linewidth}{!}{
\tikz \graph [decision]
{
ht/hypothalamus[organ] -> ["GnRH"] hh/hypophyse[organ] -> "FSH, LH" -> {
testicules[organ] -> test/testosterone;
ovaires[organ] -> est/estrogène;
};
test -> [bend left=70, "-"] ht;
test -> [bend left=60, "-"] hh;
est -> [bend right=70, "-"] ht;
};
}
\resizebox{!}{5cm}{
\tikz \graph [decision, layer distance=1.5cm]
{
ht/hypothalamus[organ] -> ["TRH"] hh/antéhypophyse[organ]
->["TSH"] th/thyroide[organ] -> "T4, T3";
th -> [bend left=60, "-"] hh;
th -> [bend left=70, "-"] ht;
};
}
\resizebox{!}{5cm}{
\tikz \graph [decision, layer distance=1.5cm]
{
ht/hypothalamus[organ] -> ["GHRH"] hh/hypophyse[organ] -> Foie[organ] -> "IGF-1" -> {
os;
muscle;
graisse..;
}
};
}
\end{figure}
\begin{table}[htbp]
\caption{Hormones produite par les surrénales (du moins au plus profond)}
\centering
\begin{tabular}{ll}
\toprule
Zone de la surrénale & Hormones\\
\midrule
corticale (glomerusa) & minéralocorticoïdes (aldostérone)\\
corticale (fasciculata) & glucocorticoïdes (cortisol)\\
corticale (reticularis) & androgènes\\
médullaire & épinephrine, norepinéphrine\\
\bottomrule
\end{tabular}
\end{table}
\subsection{Syndromes génétiques}
\label{sec:orga811095}
\begin{center}
\begin{tabular}{llll}
\toprule
& Klinefelter & Turner & Kallmann\\
\midrule
Sexe & \male & \female & \male{}, \female\\
Frequence & 1/500 & 1/2000 \female & 1/30 000 \male{}, 1/250 000 \female{}\\
Caryotype & 46 XX,Y & genes manquants & \\
& & sur bras court d'un chr. X & \\
Caractéristiques & Hypogonadisme, infertilité & Petite taille & Anosmie\\
& gynécomastie & Aménorrhée & \male : Micropénis, cryptorchidie\\
& trouble apprentissage, comm. & Pas de seins ? & Pas de dev. sexuel secondaire\\
& & & \\
\bottomrule
\end{tabular}
\end{center}
\printglossaries
\end{document}
\documentclass[a5paper,12pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[francais]{babel}
\usepackage{fouriernc,parskip,booktabs,array}
\usepackage[margin=7mm,portrait]{geometry}
\usepackage{enumitem}
\usepackage{pgfpages} % <— load the package
\pgfpagesuselayout{4 on 1}[a4paper,border shrink=3mm] % <— set options
\pagestyle{empty} % No page number
\setlist{nolistsep}
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\begin{document}
\begin{center}
\Large{\textbf{Examen clinique}} \\
\end{center}
\subsection{ATCD}
\label{sec:org32b2aff}
chir, med, gynéco ($G_{X}P_{Y}$), familial
\subsection{Ttt}
\label{sec:orge6567b5}
habituel, allergies (dernier repas)
\subsection{MDV}
profession, main dominante, sport\\
toxiques, alcool, tabac, viral\\
conditions de vie, autonome
\subsection{HDLM}
\label{sec:org13306b7}
anamnèse: déclenché par ? favorisé par ?\\
clinique : quantifier, signes\\
complications, retentissement, fièvre, AEG
\subsection{Signes généraux}
SF: asthénie, anorexie, amaigrissement, sueurs, frissons, prurit, soif\\
Fièvre, hypothermie\\
Hydratation
\subsection{Urgences}
\underline{Choc} : Confusion, Hypertension, Oligurie, Cutané (TRC), TAchycardie,
POlypnée, Marbrures, Pouls\\
+ extrémités froides/cyanosées, collapsus, pouls paradoxal\\
\underline{SDRA} : \textit{hypoxémie} (cyanose, tachycardie, trouble CS), \textit{hypercapnie}
(Sueurs, Asterixis, Cephalées, HTA, Agitation)
\textit{épuisement ventilatoire} (respi > 30 ou < 10, tirage, respi paradoxale, encombrement bronchique), IC droite\\
Confusion, coma (glasgow, sd méningé, glycémie)
\subsection{Vasculaire}
Terrain : âge, ATCD familiaux IDM, diabète, HTA, tabac, dyslipidémie, obésité\\
SF: douleur thoracique (coronale, pleural, péricardite, dissection aortique), dyspnée, lipothymie/syncope, palpitation\\
Reflux abdomino-jugulaire
Turgescence jug, oedème périph\\
Palpation
Auscultation
\subsection{Vasculaire artériel}
SF: AIT (troubles paroles transitoire, déficit M/S, cécité transitoire), HTA
(céphalées, acouphènes, vertiges, épistaxis), claudication d'effort, ischémie
(douleur, froideur, déficit M, paresthésies)\\
PA, FC, IPS\\
TRC, pouls, auscult vasc.
\subsection{Veino-lymphatique}
SF: douleur, membre rouge chaud tuméfié ($\rightarrow$ score Wells, tour
mollet, cordon veineux)\\
Troubles trophiques, \oe{}dème, pincement dorsal 2eme orteil (lymph\oe{}dème)
\subsection{Pulmonaire}
SF: douleur thoracique (pleurale, EP), dyspnée, expectoration, toux, hémoptysie, hoquet, ronflement\\
FR, régularité\\
Distention thoracique, sd cave supérieure (CVC, \oe{}dème en pelerine, TJ),, cyanose, hippocratisme digital\\
Palpation, auscultation
\subsection{Digestif}
SF: douleur (ulcère, bilaiaire, pancrétatique, intestinale), transit (nausée,
vomissement, occlusif, diarrhée, constipation), hémorragie digestive
(haute/basse), sd \oe{}sophagien, sd rectal (épreinte, faux-besoins, tenesme)\\
Cicatrice, éventration, hernie, ictère, IHC (angiome stellaire, ongles,
astérixis, érythrose palmaire, \oe{}dème périph)\\
Palpation (point Mc Burney, sd péritonéal, HMG, SMG, masse )\\
Percussion, auscultation\\
TR
\subsection{Uro}
SF : douleur (rénale, vésicale, prostate, bourse), sd
irritatif/obstructif/brûlures, couleurs, écoulement, érection\\
Palpation (abdo, flanc, globe, bourse)\\
Percussion (fosse, globe)\\
TR/TV
\newpage
\subsection{Locomoteur}
\emph{SF}: douleur (articulation, méca/infla), raideur, gonflement, craquement,
blocage, marche (boîterie, claudication)\\
\emph{Rachis} : courbures, épineuses (palpation, percussion), paravértébraux
(sonnette) [NCB = sonnette, étirement bras, sciatique/cruralgie = sonnette,
lasègue, Léri]\\
\emph{Sacroiliaque} : interligne, écartement/rapportement, cisaillement H, V, trépied\\
\emph{Articulation périph} : inflammation, palpation, déformation, mobilité passiv./act.\\
Genou :
\begin{itemize}
\item épanchement (choc rotulien), palpé rotulien, rabot, Zohlen, ressaut rotulien
\item méniscal : palpation, grinding test, Thessaly (monopoday + RI-RE)
\item ligaments : LCA (Lachman , tiroir 60$^{\circ}$), LCP (60$^{\circ}$),
capsule (valg/valr ext.), coque (valg/valr 30$^{\circ}$)
\end{itemize}
Épaule : conflit sous-acromial (Neer, Hawkins, Yocum), coiffe (Jobe = supra,
Patte = infra, belly-press= sous-scap)\\
Poignet : Finkelsten (tendinop. de De Quervain)
Pied : interligne Chopart, Lisfranc, éversion/inversion
Cheville : Ottawa (5eme métatarsien/naviculaire ; malléole +/6cm; appui)
\subsection{Neuro}
SF: céphalée, douleur neuro, confusion/mémoire, 5 sens, équilibre, vertiges,
déficit S/M, mouvements anormaux,, dificultés marche\\
Droitier/gaucher\\
Tremblements, dyskinésie, myoclonie, dystonie\\
Testing musculaire (Barré, Migazzini, court abd. pouce, interosse, ext. doigts,
relevurs pied, fléchisseurs orteils)\\
RCP\\
Tonus musculaire, ROT\\
Sensibilité (tact, thermique + talon-genou, doigt-nez)\\
Nerf crâniens (II [AV, RPM], oculomotricité, V [trijumeau], VII [occlusion palpébrale, grimace], VII [Romberg, nystagmus], IX et X [déglutition], XI [sterno-cléido-mastoïdien] XII [langue])\\
Signe méningé (nuque, Brudzinksi, Kernig)\\
Doigts-nez, marionnettes\\
Romberg, marche, ordres\\
Fonction sup : langage, articulation, mémoire
\subsection{Gynéco}
SF: douleur (dyspareunie, cyclique), écoulement, aménorrhée, SFU, prurit, , mammaire\\
Abdo (inspection, palpation)\\
Sein (gangliona axillaire, sus-claviculaire)\\
Périnée (vulve, glandes, prolapsus)\\
Spéculum, TV (col, vagin, utérius)
\subsection{Hémato}
Sd anémique : asthénie, dyspnée, pâleur, tachycardie, acouphènes, céphalées,
palpitation
+ pâleur conjonctives, cut-muqueuse, souffle cardiaque\\
Sd tumoral : fièvre, sueurs, -10\% poids, aire ganglionnaire (tête, cou,
axillaier, coude, inguinales, poplitées), SMG, HMG\\
Sd hémorragique : épistaxis, gingivorragie, méno-MTR, hémorragie digestive,
épistaxis, hémarthrose, IC, purpuras\\
Sd infectieux
\subsection{Endocrino}
Thyroïde\\
Diabéte : SF (angor, AIT, vision), pied : cutané, pouls, TRC, réflexe, monofilament
\subsection{ORL}
Audition:
hypoacousie, cophose, acouphène, otodynie/algie, otorrhée
otoscopie, Rinne, Weber
Équilibre\\
Larynx: dysphonie, dyspnée laryngée (rauque expi), dysphagie, toux\\
Oropharynx: hernie/colique, odynophagie, trismus, xérostomie + palpation\\
Fosses nasales: rhinorrhée, épistaxis, obstruction rhinolalie, anosmie, douleur,
céphalie\\
\subsection{Ophtalmo}
SF: BAV, phosphène, métamorphopsie, ptosis, diplopie, rougeur, prurit, larmoiement,\\
Paupière, glande, cornée (cercle PK, hémorragie, conjonctivite), conjonctives (pâleur, ictère), globe (tonus,
exo/endo), pupille (mydriasie, myosis, leucocorie)\\
AV
\end{document}
# Cardiologie
`\def\arrow{$\rightarrow$}`{=latex}
## 220 Dyslipidémies
##### Diagnostic
Clinique :
- hypercholestérolémie : arc cornéen (\< 50A), xanthélasmas, xanthomes
tendineux/fesses ou mains/coudes
- hyperTG : HMG stéatosique, SMG, xanthomes cutanés éruptifs
Bio
- lipides = hypercholestérolémie : CT/TG \> 2.5, hyperTG : TG/CT \>
2.5, mixte sinon
- sérum clair/limpide si hypercholestérolémie, lactescent sinon
Bilan normal : LDL \< 1.6g/L, HDL \> 0.4g/L, TG \< 1.5g/L
##### Classification
Tab [tab:hyperlipidémies_primaire](tab:hyperlipidémies_primaire),
[tab:hyperlipidémies_secondaire](tab:hyperlipidémies_secondaire)
Impact Classif Type Fréquence Dépôts Risque
------------- --------- -------------------------------- ----------- ------------ -------------------
Cholestérol IIa familale monogénique oui CV
\- hétérozygote freq parfois
\- homozygote très rare fréquents
\- mutation apoB freq
polygénique freq++ rare
TG IV familiale rare rare
I, V hypercholymicronémie primitive très rare inconstant ☡ TG \> 10g/L !
pancréatite aigüe
Mixte IIb familiale combinée freq rares
III dysβlipoprotéinémie rare inconstant
: Hyperlipidémies primaires
Cause Diagnostic Impact
--------------------------------------- ---------------------------------- --------------------------------------
Hypothyroïdie TSH cholestérol, mixte
Sd néphrotique, grossesse protéinurie, œdème cholestérol
Cholestase Bilirubine, phosphatase alcaline cholestérol
IR chronique, créatinine TG, mixte
Alcoolisme interrogatoire TG
Diabète glycémie TG
Iatrogène : ciclosporine, corticoïdes oestrogènes oraux, rétinoïdes, IFN-α, antétroviraux, neuroleptiques
diurétiques thiazidiques, βbloquant
: Hyperlipidémies secondaire
#### Risque faible (0 FR), intermédiaire ( ≥ 1 FR), haut (ATCD)
FR semblables au\~*s**c**o**r**e**p**r**é**c**é**d**e**n**t* : tabac
≤ 3 ans, HTA, diabète, HDL \< 0.40g/L, âge \> 50 (♂) ou 60 (♀), ATCD
familiaux IDM ou mort subite
##### Traitement
Hypercholestérolémies : primaire si LDL élèvé à ttt+6 mois, secondaire
si complication ischémique
- Objectifs LDL \< 0.7g/L si risque très élevé, \< 1g/L si élevé, \<
1.15g/L sinon
- hypercholestérolémies : [statines]{.underline}[^1] (sinon ézétimibe)
- hypertriglycéridémies : [diététique]{.underline} ± statines si TG \>
2g/L (fibrates si échec)
Diététique
- lipides \< 40%, graisses : mono- et polyinsaturées, cholestérol
alimentaire \< 300mg/j
- 5 fruits ou légumes/j, sodium \< 6g/j, `\dec`{=latex} poids
- HyperTG :
- modérées : -20% calories ++, `\inc`{=latex} activité physique
- majeur : arrêt alcool, régime hypocalorique avec \< 30g lipides
(obèse)
# Endocrinologie
## 32 † Allaitement maternel
## 35 † Contraception
### Contraception hormonale
Oestroprogestatifs
- Contient {oestrogène, progestatif (gen 1,2 ou 3), autres
progestatif}
- Administration orale, transdermique ou vaginale
- Action : {pas d\'ovulation, endomètre peu à apte à la nidation,
glaire cervicale imperméable aux spermatozoïdes}
Progestatifs seuls
- Microprogestatifs : action sur glaire cervicale, endomètre
- Macroprogestatifs : si CI oestroprogestatifs
- Administration : orale, injection, implant, intra-utérin (stérilet)
### Pratique
Oestroprogestatifs : le premier jour des règles pendant 21j puis 7 j
d\'arrêt. *Tjrs au même moment*. Si oubli \< 12h, ASAP sinon
contraception mécanique $\ge 7$ jours
Microprogestatifs : toujours à la même heure. Si oubli \< 3h, ASAP,
sinon contraception mécanique $\ge 7$ jours
Macroprogestatifs : commencer le 5eme jour du cycle
### Contre-indications
Oestroprogestatifs : absolues =
- thromboemboliques veineux/artériels, prédisposition thromboses
- lupus évolutif, connectivites, porphyries
- vasc, cardiaque, cérébrales, oculaires
- valvulopathie, troubles rythmes thrombogènes
- HTA non contrôlée
- diabète et micro/macroangiopathie
- tumeur hormono-dépendantes (sein, utérus...)
- hépatiques sévères
- hémorragies génitales non diagnostiquées
- (tumeurs hypophysaires)
Macro/microprogestatifs : cancers {sein, endomètre}, insuf hépatique,
accident TEV récents
### Recommandation
Sans CI, oestroprogestatif minidosé et progestatif 2eme génération
monophasique (Minidril)
### Efficacité
Indice de Pearl[^2] \< 0.07% pour oestroprogestatif (\< 2% pour les
microprogestatifs)
Attention : certains inducteurs enzymatiques réduisens l\'efficacité (ou
millepertuis).
Ado : sous- ou mal utilisée
### Tolérance
Oestroprogestatifs :
- bien tolérée, pas de perte de poids
- surveiller métabolisme
- active coagulation mais `\inc`{=latex} fibrinolyse. Légère
augmentation du risque d\'accident TEV
- vasc : faible `\inc`{=latex} PA
- cancer : ovaire = risque -50%, idem pour l\'endomètre, faible
`\inc`{=latex} pour sein
Microprogestatifs : troubles des règles (spotting, aménorrhées),
grossesse extra-utérine
Macroprogestatifs : hypoestrogénie, aménorrhées, spotting
### Surveillance
Consulter si céphalée, déficit sensitivomoteur, (douleur ou oedème) MI,
dyspnée, douleur thoracique
Examen clinique :
- préthérapeutique : gynéco, frottis cervico-vaginal dès 25 ans si
asymptomatique.
- PA à +3mois puis tous 6 mois
- hyperoestrogénie (tension mammaire), hypoestrogénie (sécheresse
vaginale)
Biologie : cholestérol total, triglycérides, glycémie à jeun à +3mois.
Si FR, le faire avant (!) prescription
Gynéco : métrorragies, spottings.
Frottis cervico-utérin dès 25 ans (+1 an puis tous 3 ans) indépendamment
contraception
### Femmes à risques
Diabétique :
- non hormonale : si diabète 1 \> 15 ans ou micro/macroangiopathie
`\thus`{=latex} locale (nullipare, peu de rapports) ou intra-utérin
(multipare, diabète équilibré)
- hormonale :pas d\'oestropregestatifs si {tabac, non équilibré, HTA,
surpoids, diabète compliqué} `\thus`{=latex} progestatif
Dyslipidémie : oestroprogestatif si \< 3g/L cholestérol total,
triglycérides \< 2g/L
Thrombose veineuse
- prédisposant : anomalies de l\'hémostase (génétique, acquises), ATCD
familiaux
- dépistage : thrombose, multiples fausses couches, ATCD thrombose \<
45 ans
- CI oestrogène, acétate de chlormadinone à la place
Autres :
- HTA : oestroprogestatifs si 0 FR
- tabac = CI
- si migraine et vascularite, voir spécialiste
### Contraception d\'urgence
- lévonorgestrel ASAP \< 72h
- ulipristal acétate ASAP \< 120h mais 3x plus cher
## 37 † Stérilité du couple
Infertile : 0 grossesse après 1 an de rapports non protégés. Stérilité
si définitif.
Stérilité = partagée !!
### Interrogatoire
- Couple
- Femme : âge++ (détérioration après 35 ans), {grossesses antérieure,
avortements}, infections/curetages++, ATCD chir/infectieux, douleurs
pelviennes (rapports, règles), conditions de vie, radio/chimio
- Homme : trouble libido/érection, ATCD cryptorchidie/trauma
testiculaire, ATCD chir pelvienne/scrotale, ATCD médicaux (orchite
ourlienne++), tabac/anabolisants...
### Examen clinique
- ♀ : âge++, obésité/maigreur, tour taille et hanche, pilosité, PA,
galactorrhé provoqué, gynéco.
- Si anovulation (a/oligo-ménorrhée) : hyperprolactinémie,
hyperandrogénie, troubles comportement alimentaire, bouffées
chaleur
- ♂ : IMC, pilosité, hypoandrisme, cicatrice chir, varicocèle[^3],
gynécomastie, gynoïde/enuchoïde
- volume testiculaire++, palpation cordospermatiques
### Examens complémentaires
Premiere intention, femme
- Hormonale++ : oestradiol, LH, FSH, prolactine plasmatique. Puis
progestérone plasmatique (si cycle réguliers)
- Écho ovarienne++
- Hystérographie++
Première intention, homme :
- spermogramme++ (concentration, mobilité, morphologie). Attention aux
variabilités !
- hormonale++ si oligo-/azoo-spermie : testostérone, LH, FSH puis
gls:SHBG
Test poist-coïtal (discuté)
### Étiologie
Femme :
- *anovulation* : très fréquent ! Souvent aménorrhées ou
irrégularités. Causes : gls:SOPK, hyperprolactinémie, insuf
ovarienne primitive, déficit gonadotrope, psycho-nutritionnel
- *obstacle mécanique* :
- anomalie du col utérin et insuf glaire cervicale :
post-conisation/curetage
- obstacle, anomalie utérine : manoeuvres post-partum, polypes
muqueux... `\thus`{=latex} echographie
- obstacle tubaire : cause majeure++. Souvent salpingite
(Chlamydia++)
- *endométriose* : rarement en cause si modérée.
hystérosalpingographie puis coelioscopie
Homme :
- *azoospermie*
- *sécrétoire* : diagnostic = volume testiculaire \< 10ml,
concentration FSH faible
`\thus`{=latex} caryotype, analyse bras long Y, écho testiculaire
(élimine K), déficit gonadotrope (rare)
- *obstructive* : volume et concentration ormale, volume séminal
`\dec`{=latex} `\thus`{=latex} examen clinique
- cause congénitale : agénésie bilat des canaux déférent++
(soit anomalie biallélique gène CFTR, soit isolée)
- acquis : infectieux (gonocoque, tuberculose, Chlamydia)
`\thus`{=latex} échographie
- exploration chir testiculaire et des voies excrétrices : si
azoospermie confirmée par plusieurs spermogrammes, bilan
génétique
- *oligo-asthéno-térato-spermie* : `\dec`{=latex} nombre et mobilité,
`\inc`{=latex} formes anormales `\thus`{=latex} caryotype, brang
long Y. Traitement = assistance médicale procréation
## 40 † Aménorrhée
Déf: absence de cycle menstruel après 16 ans (primaire) ou interruption
chez femme réglée (secondaire). Physiologique : grossesse, lactation,
ménopause
Tout arrêt \> 1 mois `\thus`{=latex} enquête étiologique ☡
Atteinte de l\'axe hypothalamo-hypophysio-ovarien ou anomalie tractus
utérin
```{=latex}
\begin{tcolorbox}
Pas de traitement oestrogénique sans enquête étiologique
\end{tcolorbox}
```
### Conduite
#### Primaire
Forte proba de cause génétique/chromosomique. Chercher carences
nutritionnelle
- Si absence de dév. pubertaire : doser FSH, LH
- Si basses, tumeur hypothalamo-hypophysaire, dénutrition ou
génétique : {sd de Kalmann (anosmie), mutation récepteur GnRH
(rare), atteinte gonadotrophines (exceptionnels), mutation LH}
- Si hautes : sd de Turner (caryotype 45, X0),
- Examen gynéco, écho pelvienne
- Pas d\'utérus : sd de Rokitanski, tissu testiculaire dans les
canaux inguinaux (ex: acrshort:CAIS)
- ambiguité acrshort:OGE : dysgénésie gonadique, hyperplasie
congénitale surrénales, anomalies sensibilité/biosynthèse
androgènes
#### Secondaire
Souvent acquises.
Interrogatoire : médic, maladie endoc/chronique, gynoc/obstétriques,
insuf ovarienne (bouffées de chaleur). Douleurs pelviennes cycliques :
cause utérine
Examen clinique :
- poids et taille (carence nutritionnelle)
- hyperandrogénie : gls:SOPK, déficit 21-hydroxylase, (sd Cushing)
- carence oestrogénique : pas de glaire +2 semaines après saignement
`\thus`{=latex} anovulation
- pas de signe d\'appel : enquête nutritionnelle
Dosages hormonaux : cf Table `\ref{tab:amenorrhe_second}`{=latex}
```{=latex}
\begin{table}
\begin{tabular}{llllll}
\toprule
hCG & prolactine \inc & FSH \inc & estradiol& testostérone > 1.5ng/mL & sinon\\
& & & LH, FSH \dec & & \\
\midrule
grossesse & médicaments & \acrshort{IOP} & tumeur H-H & tumeur surrénales & \gls{SOPK}\\
& adénome à prolactine & & nutrition & tumeur ovarienne sécrét. & \\
& tumeur H-H & & & & \\
\bottomrule
\end{tabular}
\caption{Évaluation hormonale d'une aménorrhée secondaire. H-H = hypothalamo-hypophysaire}
\label{tab:amenorrhe_second}
\end{table}
```
### Causes
#### 1. Déficit gonadotrope organique/fonctionnel
##### Prolactine normale [^4]
- Atteintes organiques : tumeur/infiltration `\thus`{=latex} IRM
- macroadénomes hypophysaires, craniopharyngiomes
- chercher hyperprolactinémie, insuf antéhypophysaire associé
- Atteintes fonctionnelles : apports nutritionnels insufisants par
rapport à l\'activité physique intense+++
##### Hyperprolactinémie
Atteinte hypothalamo-hypophysaire (majeure++)
Médicaments ou tumeurs `\thus`{=latex} pas de traitement dopaminergique
sans imagerie ☡
##### Autres
- Endocrinopathies : sd de Cushing, dysthyroïdes déficits
21-hydroxylase
- Hypophysaire (rare) : auto-immune (majorité), sd de Sheehan (très
rare, nécrose hypophysaire post-partum)
#### 2. Anovulation non hypothalamique
##### SOPK (majorité)
Pas de pic de LH, ni de progestérone. Oestradiol mais non cycliques
Irrégularité menstruelles, puis aménorrhées avec acné, hirsutisme
Diagnostic :
- 2 parmi : {hyperandrogénie clinique[^5], oligo-/a-novulation,
hypertrophie ovarienne/folliculaire[^6] (écho)}
- exclure bloc 21-hydroxylase, tumeur de l\'ovaire, sd Cushing
- exclure hyperprolactinémie
Diagnostic parfois difficile :
- sans hyperandrogénie `\thus`{=latex} écho
- {atteinte partielle axe gonadotrope, macroprolactinémie} peuvent y
ressembler
Acné : cherche hyperandrogénie, régularité cycle menstruel
`\thus`{=latex} éliminer hyperplasie congénitale des surrénales
2 causes :
- tumeur ovarienne ou résistance insuline
- virilisation si tumeur
- imagerie si testostérone \> 1.5ng/mL. Si normale, cherche
hypothécose (obésité morbide androïde, acanthosis nigricans,
insulino-résistance)
- pathologie surrénale :
- sd de Cushing si signes hypercortisolisme `\thus`{=latex}
cortisol libre urinaire et freinage minute
- tumeur surrénale `\thus`{=latex} scanner des surrénales
- déficit enzymatique en 21-hydroxylase (☡ formes tardives qui
peuvent mimer SOPK)
#### 3. Insuf ovarienne primitive
`\inc`{=latex} FSH
Causes :
- chir, chimio, radiothérapie
- anomalie caryotype (sd Turner)
- anomalie gènes *FMR1* (sd X fragile)[^7]
- auto-immune
#### 4. Anomalie utérine
##### Congénitales
Si dév pubertaire normal :
- et douleurs pelviennes cycliques : imperforation
hyménéale/malformation vaginale `\thus`{=latex} examen gynéco.
- ou sans douleurs `\thus`{=latex} agénésie utérus ?
Difficulté : différence agénésie mullérienne isolée (46,XX)- anomalies
androgènes (46,XY) `\thus`{=latex} testostérone
##### Secondaires
Synéchies utérines (trauma de l\'utérus), tuberculose utérine
## 47 † Puberté
### Normale
\~4 ans, acquisition de la taille définitive, fonction de reproduction.
Classification de Tanner (5 stades)
♀ ♂
------------ ------------------------ ----------------------------- -------------------------
seins 11 ans \[8,13\] volume testiculaire 11.5 ans \[9.5,14\]
règles 13 ans \[10,15\] `\inc`{=latex} taille verge 12.5 ans
croissance 5 $\rightarrow$ 8cm/an croissance 5 $\rightarrow$ 10cm/an
taille 163cm taille 175cm
: Puberté normale
### Retards
```{=latex}
\begin{tcolorbox}
\male : volume testiculaire < 4mL après 14 ans \footnotemark\\
\female : pas de seins à 13 ans, pas de règles à 15 ans
\end{tcolorbox}
```
`\footnotetext{ou longueur < 25mm}`{=latex}
```{=latex}
\begin{tcolorbox}
Hypogonadisme\footnotemark central ou périphérique ?
\begin{itemize}
\item FSH, LH \inc : pour compenser le manque des gonades (hypergonadotrope = primaire)
\item FSH, LH N ou \dec : problème hypothalamo-hypophysaire\footnotemark (hypogonadotrope = secondaire)
\end{itemize}
\end{tcolorbox}
```
`\footnotetext{Chez \male, manque de testostérone}`{=latex}
`\footnotetext{Rappel : LH entraîne la production de testostérone}`{=latex}
- centrale : congénital (pas de cassure de croissance, ni micropénis,
ni cryptorchidie), acquis (tumeur ?), \"fonctionnel\" (maladie
générale, trouble comportement alimentaire), isolé
- périphérique : sd de Turner chez ♀, sd Klinefelter ♂
- retard simple (élimination)
Clinique :
- parents, grossesse, courbe de croissance. Chercher trbles digestifs,
polyuro-polydispsie, céphalée, anomalies champ visuel
- pathologie acquise, OGE, testicules, anosmie (Kallmann)
Âge osseux : 13 ans ♂, 11 ans ♀
Biologie : stéroïdes sexuels
- FSH, LH basses `\thus`{=latex} hypothalamo-hypophysaire
- testostérone chez ♂, oestradial/écho chez ♀
IRM indispensable si déficit gonadotrope (tumeur) ☡
Caryotype si :
- FSH élevé
- toujours chez ♀ de taille \< -2DS avec retard
pubertaire/gonadotrophine `\inc`{=latex}
#### Étiologies
Hypogonadotropes
- congénitaux : isolés, sd de Kallman, autres déficits hypophysaires,
sd polymalformatifs
- acquis : tumeurs hypophysaires, post-radiothérapie
Hypogonadotropes fonctionnels
- maladies chroniques digestives/cardiaques/respi
- sport intense
- maladies endocriniennes
Hypergonadotropes
- congénitaux : sd Turner, sd Klinefelter, autres atteintes primitives
- acquis : castration, trauma, oreillons, chimio/radio
#### Traitement
Cause si possible. Sinon doses `\inc`{=latex} de testostérone (♂) ou
oestrogènes puis oestroprogestatif (♀)
### Précoces
Avant 8ans ♀ ou 9.5 ans ♂
#### Centrales
8x plus fréquent chez ♀ que ♂. Chez ♀, causes idiopathiques. Chez ♂,
causes tumorales à 50%
Clinique :
- dév prématuré harmonieux (pas de règles chez ♀)
- crises de rires (harmatome hypothalamique), tâches cutanées
(neurofibromatose I ou sd McCune-Albright)
Biologie :
- testostérone élevée chez ♂ mais variabilité d\'oestradiol chez ♀
IRM hypothalamo-hypophysaire indispensable ☡ (petite taille définitive).
Écho pelvienne pour ♀
Traitement si risque de petite taille adulte : analogues GnRH jusque âge
normal de puberté
#### Périphériques
Clinique : `\inc`{=latex} vitesse de croissance, avance maturation
osseusse
Stéroïdes élevées, LH et FSH bas. Écho pelvienne chez fille
Étiologie :
- tumeurs ovarienne (rares) : écho puis histologies
- kystes folliculaires : bénins, régression spontanée possible
- sd McCune-Albright :
- {puberté précoce ovarienne, taches cutanées \"café-au-lait\",
dysplasie fibreuses os}. ☡ tableau pas toujours complet !
- oestradiol élevé, gonadotrophines basses, écho = utérus stimulé,
kystes ovariens. Dominance ♀
- médicaments
- testotoxicose (rare, cellule de Leydig activé et LH basses), adénome
leydigien (très rare)
- tumeurs à hCG (♂)
#### Avances dissociées
- Isolé des seins : beaucoup de filles ( de 3 mois à 3 ans)
- Métrorragies isolées : chercher vulvite, vulvovaginite, prolapsus
urétrale, corps étranger. Éliminter kyste ovarien, sd
McCune-Albright par l\'absence des sein
`\thus`{=latex} écho pelvienne
- Pilosité pubienne isolée : chercher forme d\'hyperplasie congénitale
des surrénales (`\inc 17`{=latex}-hydroxyprogestérone, stimulation
ACTH), prémature pubarche (élimination !)
## 48 † Cryptorchidie
### Enfant
Localisation anormale et inaboutie du testicule. Très fréquente : 3%
nouveaux-nés, 20% préma. 2/3 descendent spontanément à 1 an de vie
Clinique : chercher micropénis (\< 2cm, hypospadias, autres)
Explorations : endocrinienne pour toute cryptorchidie ☡
- bilatérale : doser 17-hydroxyprogestérone chez ♀ virilisée pour
éliminer hyperplasie congénitale des surrénales
- testostérone, gls:Leydigcell (INSL3), gls:Sertolicell (AMH, inhibine
B sérique), FSH, LH mesurée jusque 4-6mois[^8]
- si bilatéral, écho (vérifier l\'absence de dérivés mülleriens)
Étiologie
- hypogonadisme hypogonadotrope congénital
- anorchidie rare
- si hypospade en plus, chercher dysgénésie testiculaire
- sd polymalformatif
Suivre l\'âge de l\'apparition de la puberté !
Traitement : chir dès 2 ans, indispensable ! (risque de cancer)
### Adulte
- Risque : hypogonadisme, infertilité, cancer testicule
- Examen clinique : scrotum, gynécomastie, signes d\'hypogonadisme
- Complémentaire : {FSH, LH, testostérone}, hCG si tumeur à la
palpation, écho scrotale, spermogramme
## 51 † Retard de croissance
☡ Ne pas passer à côté de pathologies sévères
Phases :
- foetale (rapide, {nutrition, insuline, IGF-2})
- précoce 0-3ans (rapide, {insuline, IGF, hormones thyroïdiennes})
- prépubertaire (plus lente, décroît, {génétique, GH/IGF, hormones
thyroïdiennes})
- pubertaire ({stéroïdes sexuels, GH, nutrition})
Retard statural = {taille \< -2DS, ralentissements croissance,
croissance $\le$ parents}
Prise de poids, obésité, ralentissement croissance `\thus`{=latex}
chercher hypercorticisme, tumeux craniopharyngiome sur l\'hypothalamus,
hypopituitarisme
Examen :
- ATCD : taille, parents, néonatale, médicaux/chir, contexte social
- morphotype, dév. pubertaire, tous les système, psychoaffectif
### Principales causes
- Si poids \< poids idéal : cf table
[*retard pondéral*]{.spurious-link target="retard pondéral"}
- Si poids $\ge$ poids idéal : cf table
[*retard statural*]{.spurious-link target="retard statural"}.
Précisions :
- Test de stimulation de l\'hormone de croissance (☡ si doute,
IRM)
- Ralentissement sévère `\thus`{=latex} bilan en urgence
(craniopharyngiome, thyroïdite de Hashimoto)
- \[0, 3\] ans : digestives pédiatrique (coeliaque,
mucoviscidose), \[3,puberté\] : endoc constitutionnelle, à la
puberté : déficit hormone, patho osseuse
- Savoir différencier retard pubertaire simple d\'un vrai retard
------------------------------- ---------------------------------------------------------
Maladie coeliaque IgA totales, IgA anti-transglutamase, fibro
Crohn VS, écho anse grêle
Mucoviscidose Test sueur
Anorexie mentale Courbe de poids
Insuf rénale chroniques Créat, iono, explo fonctionnelles
Anémie chroniques NFS
Rachitisme hypophosphatémique Bilan phosphocalcique
Patho mitochondriales lactate/pyruvate, génétique, biopsie musc, fond d\'oeil
Nanisme psychosocial
------------------------------- ---------------------------------------------------------
: Causes de retard pondéral
------------------- -------------------------------------------- -------------------------------------
Endocrino Déficit GH (congénital, acquis \[tumeur\]) IRM
Hypothyroïdie T4L, TSH, Ac anti-TPO
Hypercorticisme (iatrogène) Cortisol libre urinaire/à 23h, ACTH
Déficit hormones sex. Testostérone, GnRH, IRM
Constitutionelles Sd Turner Caryotype
Sd Noonan Gène PTPN11
Autres Osseuses (a-/hypo-chondroplasie) Radio
RCIU Taille naissance
Petite taille idiopathique Élimination
------------------- -------------------------------------------- -------------------------------------
: Causes de retard statural
### Exploration :
- Caryotype : fille taille \< -2DS ou \< -1.5DS sous taille parentale
moyenne
- NFS, VS, foie, rein
- IgA totales, anti-transglutaminase
- GF-1, T4L, TSH
- Radio
## 69 † Troubles des conduites alimentaires (à compléter)
## 78 † Dopage
### Substances augmentant la testostérone
- Stéroïdes anabolisant, testostérone : `\inc`{=latex} masse musc,
puissance
- Risque : thrombotique, rupture musculo-tendineuse, trouble
personnalité, foie, trouble libido, adénome/cancer de la prostate
- Femmes : masculinisation, hirsutisme, acné, aménorrhée, anovulation,
hypertrophie clitoridienne, libido exacerbée
`\vspace*{0.5cm}`{=latex}
- *Testostérone* : test chromatographique + spectrométrie de masse
(très sensible et spécifique)
- *Dihydrotestostérone* (DHT) : traitement gynécomastie
- *Anabolisants* : `\inc`{=latex} tissu cellulaire (muscle).
ES : rétention hydrosodée, HTA, IDM, hépatite
- *hCG* : diminuer épitestostérone/testostérone après dopage (IM, SC).
Testée dans le sang ou urine.
- *Anti-oestrogène* : stimule production testiculaire de stéroïdes
### Hormone de croissance (GH), IGF-1
- GH `\inc`{=latex} masse musculaire, modifie architecture sequelette,
acromégalie *mais* pas d\'effet sur volume d\'activité physique.
Détection difficile : approche indirecte (cascade biologique) et
mesure des forme circulante et comparaison à r-hGH
- IGF-1 mime certains effet GH
### Glucocorticoïdes, ACTH
- Glucocorticoïdes : antalgiques, psychostimulants, combativité. ES :
HTA, oedème, rupture ligament/tendon
☡ arrêt brutal = dangereux
## 120 † Ménopause et andropause
### Ménopause
Déf: plus de règle \> 1 an ± sd climatérique, lié à une carence
oestrogénique. Vers 51 ans.
Pré-ménopause : irrégularités cycles puis dysovulation puis anovulation
\~5 ans avants.
#### Diagnostic
Clinique seulement !! : plus de règles ≥ 1 an, sd climatérique
(bouffées de chaleur, troubles du sommeil et humeur, sueurs nocturnes,
sécheresse vaginal), ♀ \> 50 ans.
Bio seulement si hystérectomie `\thus`{=latex} `\dec`{=latex} oestradiol
et `\inc`{=latex} FSH
En pratique : progestatif seul 10j/mois x3 `\thus`{=latex} pas de
saignement à l\'arrêt = diagnostic
Aménorrhée \< 40 ans = pathologique !
#### Conséquences
Court terme : sd climatérique
Moyen terme : douleurs ostéoarticulaires, `\inc`{=latex} perte osseuse
(selon ATCD d\'insuf ovarienne prématurée, fractures non traumatiques,
médicaments, calcium/vit D)
Long terme : `\inc`{=latex} risque CV. Incertitude sur SNC
#### Traitement
Bénéfices
- court terme : qualité de vie à +5-10 ans
- long terme :
- prévention ostéoporose
- cardiovasculaire et neuro = incertain
- cancer du côlon
Risques :
- `\inc`{=latex} cancer du sein, accident veineux thromboemboliques
(mais chiffres absolus faibles)
- `\inc`{=latex} AVC ischémique, lithiase bilaires
##### Thérapeutique
- oestrogène (17β-oestradiol) oral/percutané/transdermique[^9] 25
jours/mois
- **et** progestatif (au moins les 12 derniers jours) per
os/transdermique
☡ hémorragie de privation possible. Si pendant le traitement, faire écho
pelvienne, hystéroscopie
##### CI
Cancer du sein, endomètre, ATCD thromboembolique artériel (ischémique,
cardiopathie embolinogène) ou veineux, hémorragie génitale sans
diagnostic, hépatique
##### Mise en route
- Interrogatoire : ATCD {cancer, métabolique, vasculaire}, carence
oestrogénique
- Examen physique : poids, PA, palpation seins, gynéco, frottis
cervico-vaginal
- Mammographie !
- Cholestérol, triglycérides, glycémie
##### En pratique
1ere intention si trouble fonctionnels importants. 2eme si risque
d\'ostéoporose. Sinon au cas par cas.
##### Surveillance
3-6mois (surdosage = douleur, tension mammaire). Puis tous les 6-12
mois, mammographie tous les 2 ans, frottis CV tous les 3 ans.
Traitement ≥ 5 ans !!
##### Alternatives
- Modulateurs spécifiques du récepteur des oestrogènes : raloxifène
- tibolone
- traitement local préserve tractus urogénital
NB : Dépister FR CV. Promouvoir exercice, calcium, vit D
### Andropause
Chez majorité des hommes mûrs/âgés en bonne santé non obèse, baisse de
testostérone inconstante (2%).
#### Démarche
- Interrogatoire : libido, érection, énergie vitale, mobilité/activité
physique
- Examen clinique : IMC, virilisation, gynécomastie, palper testicules
- Mesure de testostérone totale :
- \> 3.2ng/mL = normale `\thus`{=latex} étiologies non endocrino
- ∈ \[2.3,3.2\] : doser SHBG[^10], calculer index de T libre, si
bas, chercher cause
- \< 2.3 ng/mL : chercher cause
#### Étiologie
Si FSH, LH élevée, *insuf testiculaire primitive*
- lésionnelle : chimio, radiation, alcoolisme surtout. Autres :
castration, torsion, orchite ourlienne
- cryptorchidie bilatérale
- chromosomique : sd Klinefelter++
- lié à sénescene, cause génétique (rare !)
Sinon *hypogonadisme hypogonadotrope*
- tumeur région hypothalamo-hypophysaire : craniopharyngiome, adénome
hypophysaire++, autres
- infiltratif : sarcoïdose, hémochromatose
- chir, radiothérapie, trauma
- hyperprolactinémie, carence nutritionnelle, Cushing, tumeur
testiculaire
## 122 † Troubles de l\'érection
Nécessite : réseau vasculaire, appareil musculaire lisse, retour
veineux, signal nerveux, appareil hormonal et psychisme fonctionnels
Déf : incapacité persistante à obtenir/maintenir érection pour rapport
sexuel satisfaisant
Âge = FR (car déficit neurosensoriel, `\inc`{=latex} testostérone,
comorbidités)
### Conduite diagnostique
#### Interrogatoire
- DD avec perte désir, trouble éjaculation, douleurs pendant,
anomalies morphologiques
- Caractérisation : primaire/secondaire, brutal/progressif,
permanent/situationnel, sévérité (délai trouble-consult, capacité
résiduelle, masturbation)
- Pathologies, facteur :
- primaire : trouble psychogène perso, complexe identitaire,
trouble relationnel, conflit socioprof, anomalie génitale
- secondaire : ATCD abdo-pelvien, diabète, FR CV, patho CV, neuro,
trouble miction, endocrinopathie, troubles sommeil, traitement,
déficit androgénique, sd dépressif, troubles addictifs
#### Clinique
- Gynécomastie, hypoandrisme, petits testicules, anomalies du pénis
(La Peyronie)
- CV : HTA, pouls, souffle
- neuro : sensibilités périnée, MI
- endoc : anomalie CV
#### Bio
Glycémie, lipidique (si \> 1 an), {NFS, iono, créat}, foie (si \> 5
ans), déficit androgénique
Doser prolactine, hormones thyroïdiennes
### Bilan secondaire et approfondi
Secondaire : sexo/psychologique, épreuve pharmacologique
(prostaglandine, inhibiteur de la phospohdiestérase 5)
### Étiologies
Plus fréquentes :
- vasculaire : FR = HTA
- endocrino++ : diabète
- génito-pelvien : chir pelvienne
- trauma médullaire
- neuro dégénératif
- iatrogène : antihypertenseur
### Aspects endocriniens
#### Androgènes circulants
Influe libido, intérêt sexuel, érection (seulement spontanée!)
Hypogonadisme (diag difficile) :
- asthénie, gynécomastie, dépilation, perte force musculaire,
adiposité androïde
- doser testostérone totale ± SHBG, prolactine. FSH, LH pour l\'origin
#### Hyperprolactinémie
Tumeur hypophysaire (IRM), champ visuel si tumeur supra-sellaire, {T4L,
cortisol, IGF-1, testostérone} `\thus`{=latex} correction par agoniste
dopaminergique
#### Diabète
sucré = 1ere cause de trouble érectile (TE). TE fréquents chez
diabètique.
Facteurs : mal équilibré, complications, âge, ancienneté diabète
Physiopatho : neuropathie autonomie, microangiopathie `\thus`{=latex}
défaut relaxation musculaire. Macroangiopathie `\thus`{=latex} ischémie
organes érectiles
☡ facteurs psychogènes prédominent !
Diabète et TE `\thus`{=latex} mesure testostérone systématique
(hypogonadisme ?)
Clinique :
- TE peut révéler diabète.
- diabète et TE : cherche trouble endoc, vasc, neuro, médicament,
dépression
- TE = FR d\'ischémie myocardite silencieuse ☡
### PEC
Ttt étiologie seulement pour : trouble psychogène pur, chir possible,
endocrino
#### Trouble endocrinien
- Si hypogonadisme confirmé par bio[^11] : androgène
oraux/intramusc/transderm
- CI : nodule prostatique palpable, PSA \> 3ng/mL
- Surveiller prostate, foie, hématocrite
#### Pharmacologique
- FR, Hb glyquée \< 7%, psycho/sexologique
- 1ere intention
- inhibiteurs des phosphodiésterases type 5[^12]
- Sinon apomorphine, yohimbine = peu efficace
- \"Pompe\" = efficace mais résistance psycho
- 2eme intention : drogue vasoactive = efficace mais douleurs
peniennes, priapisme
- Prothèses péniennes = dernier recours, par chirurgien spécialisé
## 124 Ostéopathies secondaires endocrines [^13]
Ostéoporose : -score \< -2.5 DS de la valeur moyenne par DXA
Marqueurs : résorption (Tx, NTx), formation osseuse : ostéocalcine,
phosphatases alcalines osseuses
##### Hypogonadisme
Carence oestrogénique `\inc`{=latex} ostéoclastogénèse. Tab
[tab:osteoporose_hypogonadisme](tab:osteoporose_hypogonadisme)
Type Conséquences Ttt
--------------------- ------------------------------------------------------------ ------------------------------------- -----------------------------------------------
Anorexie mentale Formation os `\dec`{=latex}, résorption N Risque de fractures $\times 7$ Multidisciplinaire
\+ oestroprégestatif
AP intensive Origine hypothalamique `\inc`{=latex} résorption os, `\dec`{=latex} activité ou oestroprogestatifs
`\inc`{=latex} fractures de fatigue
Lésion hypophysaire Doit impacter l\'axe gonadotrope Perte osseuse rapide œstrogènes
Iatrogène Agonistes GnRH`\tablefootnote{patho utérines}`{=latex}, Arrêt
inhibiteurs aromatase`\tablefootnote{cancer sein}`{=latex} ± isphosphonates, denosumab
Sd Turner `\dec`{=latex} ontinue à l\'adolescence `\inc`{=latex} fracture (adulte) Estrogénisation + GH
Oestroprogestatif
: Types d\'ostéoporose dûes à un hypogonadisme
##### Non hypogonadique
Tab [tab:osteoporose_autres](tab:osteoporose_autres)
Type Systématiquement Physio Atteinte PEC
------------------------ ------------------ ----------------------------------- ----------- ---------------------------------------------------------------------------------------------
Hyperthyroïdie *doser TSH* `\inc`{=latex} remodelage Cortical densitométrie ± bisphosphonates (âgé)
hormones thyroïdiennes surveillance (ttt suppressif)
Hypercortisolisme *Prévention* `\dec`{=latex} formation osseuse, Vertébres vitamine + calcium
corticothérapie `\inc`{=latex} résorbtion. ± bisphosphonates `\tablefootnote{si prednison > 7.5mg/j et T-score \le -1.5)}`{=latex}
Hyperparathyroïdie *Dépistage* DXA PTH `\inc`{=latex} résorption Cortical chir si T-score \< -2.5.
primitive (ménopausée++) Sinon anti-ostéoclastiques`\tablefootnote{oestrogènes,aloxifène, bisphosphonates}`{=latex},
calcimimétique`\tablefootnote{cinacalcet}`{=latex}
: Autres ostéoporoses secondaires endocrino
##### Chez l\'homme
Pas de T-score reconnu.
Surtout : hypercorticisme, hypogonadisme congénital/acquis/iatrogène,
alcoolisme, hypercalciurie idiopathiques, génétique
```{=latex}
\begin{tcolorbox}
\begin{itemize}
\item bisphosphonates (prévention ostéoporose cortisonique++) sinon dénosumbab
\item raloxifène (si faible risque fractures périphériques)
\item tériparatide (si \ge 2 fractures vertébrales)
\end{itemize}
\end{tcolorbox}
```
## 207 † Sarcoidose
Atteinte hypothalamo-hypophysaire exceptionnelle. Conséquences : diabète
inspide central, insufisance gonadotrope
Radio : IRM centrée sur hypothalamo-hypophyse = référence (T1,T2
injecté) `\thus`{=latex} infiltration plancher 3eme venticule,
infundibulum, tige hypophysaire épaissie ± hypophyse augmente de volume
DD : tuberculose, histiocytose, lymphome, autres tumeurs de la région
Si patient avec sarcoïdose connue : diagnostic = déficit endocrinien et
imagerie[^14]
Sinon : atteinte rare[^15], diag = radio et arguments sarcoïdose[^16].
Traitement : sarcoïdose et déficits hormonaux
## 215 † Hémochromatose
Hémochromatose primitive : génétique, surcharge en fer. 5 pour 1 000 !
Physiopatho :
- Absorption intestinale régule stockage de fer
- Fer entre dans l\'entérocyte (DMT1), puis stocké via ferritine ou
relargé par ferroportine
- Hepcidine `\dec`{=latex} quand besoins fer `\inc`{=latex} (!)
- Hémochromatose : hepcidine effondrée, DMT1 et ferroportine
`\inc`{=latex}
Génétique : gène HFE à 95% et mutation C282Y/C282Y ou C282Y/H63D
### Clinique
En pratique, suspicion aux \"3 A\" : asthénie, arthralgies,
`\inc`{=latex} ALAT
#### Atteintes :
- foie : `\inc`{=latex} ALAT ou hépatomégalie. Cirrhose ≈ 90% décès
- coeur : cardiopathie dilatée, troubles rythme
- endocrino :
- diabète++ (accumulation pancréatique de fer)
insulino-pénie/-résistance
- hypogonadisme+ : impuissance ♂, aménorrhée ♀, `\dec`{=latex}
libdio, ostéoporose
- insuf thyriodienne exceptionnelle
- articulaire : arthrite chronique (\"poignée de main douloureuse\"),
chrondocalcinose
- cutané : mélanodermie (tardive)
### Diagnostic
- Si CS-Tf[^17] \< 45% : si ferritine `\inc`{=latex}, cherche
hépatosidérose dysmétabolique, acéruléoplasminémie, mutation gène de
la ferroportine 1
- Sinon, CS-Tf \> 45% :
- si C282Y/C282Y ou C282Y/H63D : diagnostic
- sinon, si ferritine `\inc`{=latex}, test génétique de 2eme
intention, biopsie hépatique
Examen complémentaires : pancréas (glycémie), foie (transaminases, écho
abdo), ECG ± écho cardiaque, radio articulation, bilan testostérone
Dépistage chez parents (1er degré) : bilan martial ± dépistage
génétique. ☡ mutation ≠ maladie
### Stades
1. Asymptomatique, CS-Tf, ferritinémie normaux
2. CS-Tf `\inc`{=latex}
3. CS-Tf `\inc`{=latex} et ferritine `\inc`{=latex}
4. Idem et expression clinique affectant qualité de vie
5. Idem et expression clinique affectant pronostic vital
### Traitement
À partir du stade 2
#### Saignées = référence
Objectif : ferritine \< 50 g/L (hebdomadaire) puis entretien tous les
2-4 mois. Ne pas dépasser 550mL !
CI : anémie sidéroblastique, thalassémie majeure, cardiopathies sévères
#### Autres
- Érythraphérèse : coûteuse, plus difficile
- Chelation du fer : 2eme intention (coût, effets indésirable)
- diététique : pas d\'alcool, éviter vitamine C mais **conserver**
apports en fer !
- Symptomatique
### Suivi
Résultats en 3-6 mois sur état générale.
Bilan ferrique (stade 0,1) ferritinémie, hémoglobine (stade 2 à 4)
## 221 HTA, causes endocriniennes
Déf: ≥ 140/90 mmHg. Enquête :
- initiale : ATCD familiaux HTA, souffle para-ombilical, rein/masse
abdo à la palpation, signe d\'hypercortisolisme/acromégalie, bio
`\thus`{=latex} protéinurie/hématurie, imagerie, hormonale (selon
signes)
- si résistance malgré 3 antihypertenseurs (dont 1 diurétique),
chercher toutes les cause d\'HTA
##### Épidémiologie
10% des HTA sont secondaires et 5% sont guéries `\thus`{=latex}
hyperaldostéronisme primaire, phéochromocytomes, sd Cushing
### Hyperminéralocorticisme primaire (HAP)
Physiopatho : aldostérone, cortisol, désoxycorticostérone
`\thus`{=latex} rétention sodée `\thus`{=latex} HTA et inhibe sécrétion
de rénine[^18].
##### Diagnostic
Aldostérone `\inc`{=latex} (plasma/urine) et urine basse
- suspicion : hypokaliémie (\< 3.5mmol/L) ou HTA résistante
- confirmation : `\ref{algo:HAP}`{=latex}
```{=latex}
\begin{algorithm}
\caption{Explorations des HAP}
\label{algo:HAP}
Arrêt diurétiques\;
Vérifier natriurèse+, kaliurèse > 20mmol/j\;
\If{aldostérine/rénine \times 2}{
aldo \inc et rénine \dec : HAP\;
aldo \inc et rénine \inc : hyperaldo. secondaire\;
aldo \dec et rénine \dec : autre minéralocorticisme\;
}
\end{algorithm}
```
##### Ttt selon étiologie
Adénome de Conn : ndule unilatéral hypodense ∈ \[10,20\] mm au scanner
- prouver sécrétion aldostérone par cathétérisme si scanner
douteux/patient jeune/HTA résistante
- chir possible (mais tumeur bénigne, risque récidive)
Hyperplasies idiopathique: spironolactone à vie (hypoK) + contrôle PA
##### Hyperminéralocorticismes familiaux
Lié à l\'aldostérone, désoxycorticostérone, cortisol
### HTA endocrines iatrogènes
Contraception oestroprogestative, corticostéroides, réglisse
### Phéochromocytomes, paragangliomes fonctionnels
##### Physiopatho
gls:PCC : médullosurrénale. gls:PGG fonctionnels : autres ganglions
sympathiques {} PCC : spontanément mortel.
##### Dépistage :
- HTA avec céphalées, sueurs, palpitations (triade de Ménard), HTA
paroxystiques/diabète sans surpoids
- sd familial : gls:NF1, gls:VHL, gls:NEM2, sd
phéochromocytomes-paragangliomes familiaux
##### Diagnostic
`\inc`{=latex} métanéphrines
##### PEC
- Scanner/IRM/écho : PCC = uniques, \~5cm, PCC siègent dans l\'organe
de Zuckerkandl, vessie...
- Médicine nucléaire
- Traitement chir mais surveillance long terme
### Sd de Cushing (hypersécrétion de cortisol)
##### Diagnostic
Suspicion clinique + cortisol plasmatique [^19], cortisolurie 24h, test
de freinage rapide[^20]
- clinique: acné, ecchymoses, faiblesse musc, hirsutisme, oedèmes,
ostéoporose, PAd \> 105mmHg, vergetures pourpres
##### Étiologie
- ATCH diminuée `\thus`{=latex} adénome, corticosurrénalome,
hyperplasie bilatérale
- ATCH normale ou `\inc`{=latex} `\thus`{=latex} test CRH, test
freinage fort[^21]. si positif : tumeur ectopique ou maladie de
Cushing (adénome hypophysaire)
### Causes rare
Tumeurs à rénine, acromégalie
## 238 † Hypoglycémie
Diagnostic : neuroglucopénie et glycémie \< 0.50g/L (0.60 chez
diabétique) et correction symptômes à normalisation (triade de Whipple)
Causes :
- sécrétion inappropriée d\'insuline (hypoglycémiante)
- (rare) : défaut de sécrétion d\'hormones hyperglycémiantes (GH,
glucagon, catécholamine, cortisol), déficit néoglucogénèse, défaut
substrat
### Symptômes
Neuroglucopénie : faim brutale, troubles concentration, troubles
moteurs, troubles sensitifs, troubles visuels, convulsions
focales/généralisése, confusion
Coma hypoglycémique : début brutal, agité (sueurs), irritation
pyramidale, hypothermie
- souvent signes adrénergiques : anxiété, tremblements, nausées,
sueurs, pâleur, tachycardie
### Causes
#### Diabétique
Si traité par insulines, hypoglycémiants oraux
Ttt : sucre (3 morceaux) si CS, sinon glucagon 1mg par IM/SC (CI si
sulfonylurée : glucose en perfusion)
#### Insulinome
1ere cause tumorale (mais rare). Maligne dans 10%, \< 2cm (90%)
Clinique : manif. adrénergiques surtout
Diagnostic : épreuve de jeûne, cf table [*jeûne*]{.spurious-link
target="jeûne"}
Insulinome Insuline cachée Sulfonylurée cachée
-------------- ------------------------ ----------------- ---------------------
Glycémie basse basse basse
Signes neuroglucopénie
Insulinémie normale mais inadaptée dosable dosable
Peptide C augmenté *basse* augmenté
Sulfamides 0 0 *oui*
pro-insuline augmenté basse
: Diagnostic d\'hypoglycémie (jeûne) avec DD
Scanner en coupe fine du pancréas et écho-endoscopie si médecin habitué
Traitement : chir
```{=latex}
\begin{tcolorbox}
Hypoglycémie par sécrétion inaproppriée d'insuline : triade de Whipple, glycémie \le 0.45g/L\footnotemark avec
insulinémie \ge 3 mUL/L, peptide C \ge 0.6ng/mL
\end{tcolorbox}
```
`\footnotetext{Spontanément/jeûne}`{=latex}
## 239 † Goitre, nodules thyroïdiens, cancers thyroïdiens
Besoins en iode quotidiens (synthèse hormones thyroïdiennes) : ≈ 150
μg/jour (ado, adulte, × 2 chez enceinte)
Goitre = hypertrophie de la thyroïde :
- palpation \> dernière phalange du pouce
- écho : volume \> 20 $cm^3$ (18 femme adulte, 16 ado)
### Évaluation
Clinique : mobile déglutition/visible cou en extension/visible à
distance. Chercher : gene fonctionelle, signes de compression, signes de
dysfonction thyroïdienne, acrshort:ADP
Bio :
- TSH++ : `\inc`{=latex}, déficit production, si `\dec`{=latex},
imprégnation excessive en hormones thyroïdiennes.
- compléter par T4, et si TSH `\inc`{=latex} : Ac anti-TPO, anti-Tg
Échographie
### Goitre simple
Hypertrophies normo-fonctionnelles non inflammatoires non cancéreuses
Facteurs : ♀, tabac, déficience iodée
#### Évolution
Constitution à l\'adolescence (cliniquement latente) puis plurinodulaire
: gêne cervicale `\thus`{=latex} TSH, écho, ponction, scintigraphie ☡
cherche caractère plongeant sur radio !
À ce stade, complications : hématocèle, strumite, hyperthyroïdie,
compression organes de voisinages, cancerisation (5%)
#### PEC
- Ado : levothyroxine (1 à 1.5 μg/kg/j) jusque V normal. Vérifier TSH
- Adulte/agé : si multinodulaire non malin, surveillance. Si
symptomatique, thyroïdectomie totale
- Goitre ancien, négligé : iode 131
Dans tous les cas, `\inc`{=latex} iode (grossesse)
#### Autres pathologies responsables
- Maladie de Basedow
- Thyroïdites :
- Hashimoto = hypertrophique. Goitre très ferme, expose à
l\'hypothyroïdie. Ac Ant-TPO`\inc`{=latex}`\inc{}`{=latex}, écho
: goitre diffus, hypoéchogène
- autres thyroïdites
- Troubles de l\'hormonosynthèse
### Nodules thyroïdes
Déf : toute hypertrophie localisée de la gande thyroïde. Majorité =
bénin (5% cancers, de très bon pronostic)
Prévalence ≈ décennie du sujet. × 2 chez ♀. `\inc`{=latex} si
grossesse, déficience iode, irradiation cervicale
#### Évaluation :
Si signe d\'accompagnement :
- nodule douloureux brutal : hématocèle
- nodule douloureux + fièvre : thyroïdite subaigüe
- nodule compressif + ADP : cancer
- nodule + hyperthyroïdie : nodule toxique
- nodule + hypothyroïdie : thyroïdite lymphocytaire
Si isolé :
- TSH `\dec`{=latex} : nodule hyperfonctionnel ? `\thus`{=latex}
scintigraphie
- TSH N : tumeur `\thus`{=latex} écho, cytologie
- TSH `\inc`{=latex} : thyroïdite lymphocytaire ? `\thus`{=latex} Ac
anti-TPO
Pronostic plutôt suspect :
- homme, enfant/âgé, ATCD irradiation cervicale, \> 3cm, ovalaire,
dur, irrégulier, \> 20% en un an
- écho : hypoéchogène, contour irrégulier, microcalcifications, ADP
Bio : TSH surtout.
- si nodule, calcitonine \> 100pg/mL = argument solide pour cancer
médullaire thyroïde.
- calcitonine ∈ \[20,50\]pg/mL : idem ou hyperplasise des cellules C
ou insuffisant rénal
Examens :
- Échographie (classification TI-RAD de 1 à 6)
- Cytologie si nodule suspect (classification Bethesda de 1 à 6)
- Scinti si cytologie ininterprétable 2 fois ou indéterminée
#### Thérapeutique
- Chir si suspect clinique/écho/cyto/calcitonine
`\inc`{=latex}`\inc{}`{=latex} : thyroïdectomie si dystrophie
controlatérale
- Surveillance sinon
- Hormonal si bénin dans familles avec goitres plurinodulaire, \< 50
ans.
Kystes, hématocèles : anéchogène `\thus`{=latex} ponction ±
hormonothérapie , alcoolisation.
Grossesse : chir possible 2e trimestre ou après accouchement
Nodule oculte : \< 1cm. Risque de cancer 5%, faible pouvoir agressif
- ☡ si ADP, hérédité cancer médullaire thyroïde, fixation au TEP
- ponction seulement si hypoéchogène et \> 8mm
### Cancers thyroïdiens
1.5% cancers, 4eme chez la femme
Découverte : fortuite++, ADP cervicale, signes de compression,
flushes/diarrhée, localisation métastatique
Anatomie :
- carcinomes différenciés d\'origine vésiculaire : papillaire (85%,
excellent pronostic), vésiculaires (5%), peu différenciés (2%)
- carcinomes anaplasiques (1%)
- carcinomes médullaires au dépens des cellules C
- autres
Risque de rechute/décès :
- taille tumeur, effraction capsule thyroïdienne, métastase (clasif
TNM de I à IV)
- mortalité ∝ âge, dépend de l\'histologie, exérèse
#### Thérapeutique
- Plan cancer
- Chir en 1ere intention (anatomopatho pendant = certitude) :
thyroïdectomie totale. Curage ganglionnaire si besoin (systémique si
carcinome médullaire, si enfant/ado).\
Complications : hémorragie postopératoire , hypoparathyroïdie
(calcium + vit D), paralysie transitoire/définitive nerfs récurrents
`\vspace*{10pt}`{=latex}
*Cancers différenciés d\'origine vésiculaire*
- iode 131 : seulement post-thyroïdectomie totale (haut risque).
Nécéssite stimulation par L-T4 ou injection TSH. Puis hospit après
en chambre 2-5 j et contraception 6-12 mois.\
ES : {nausées, oedèmes}, {agueusie, sialadénite}.\
Scinti obligatoire à +2-8j : fixation extracervicale à distance =
métastases
- hormonal : L-T4 si haut risque ou échec traitement initial. Puis
mesurer TSH à +6sem-2mois (pas avant !)
- surveillance : 80% des récidives à 5 ans `\thus`{=latex} écho
cervicale, rhTSH, Tg[^22] à 6-12mois : cytoponction puis imagerie si
Tg \> seuil. Sinon `\dec`{=latex} LT4
- traitement récidives : chir si cervicale. Plus compliqué si
métastases (iode131 si fixant sinon ttt local ou molécules ciblées).
Maintenir LT4
/Cancers anaplasiques/\
Tuméfaction cervicale rapidement progressive, dure, adhérente, sujet âgé
`\thus`{=latex} radio-chimio. Pronostic très péjoratif
*Cancers médullaires*
- TTT : chir ± curage ganglionnaire
- Surveillance : calcitonine \> 150μg/L `\thus`{=latex} bilan de
localisation.
- Temps doublement : 6 mois = pronostic très mauvais.
- Traitement métastases = local.
Étude génétique dans tous les cas : positif `\thus`{=latex} chercher
phéochromocytome, hyperparathyroïdie + enquêtes apparentés
## 240 † Hyperthyroïdie
```{=latex}
\begin{tcolorbox}
Examen en 1ere intention : TSHus (puis T4L !)
\end{tcolorbox}
```
Déf : hyperfonctionnement de la glande thyroïdienne. Sd de thyrotoxicose
= conséquence sur les tissus.
Prévalence élevée, 7× femme
Physiopatho :
- TSH, gls:TPO et Tg peuvent être des auto-antigènes
- thyroïde produit surtout thyroxine (T4[^23]), convertie en T3 par
foie, muscle squelette.
- effet :
- `\inc`{=latex} production chaleur, `\inc`{=latex} production
énergie, `\inc`{=latex} consommation $O_2$
- `\inc`{=latex} débit cardiaque, système nerveux, `\inc`{=latex}
ostéclasie, `\inc`{=latex} lipolyse, `\inc`{=latex} glycémie,
rétrocontrole négatif hypophysaire
### Sd de thyrotoxicose
Clinique (par fréquence `\dec`{=latex}) :
- CV : tachycardie (régulière, repos, `\inc`{=latex} effort),
`\inc`{=latex} intensité bruits coeurs, `\inc`{=latex} PAs
- neuropsy : nervosité, tremblement fin régulier des extrémités,
fatigue générale, troubles sommeil
- thermophobie, hypersudation,
- amaigrissement rapide, important, avec appétit conservé
- autre : polydipsie, amyotrophie, `\inc`{=latex} frequence selles,
rétraction paupière supérieure (gynécomastie, troubles règle)
Examen complémentaire : TSH effondrée. T4 ou T3 libre pour l\'importance
Complications :
- cardiaque (surtout personnes fragiles) : troubles rythme supraV
(FA), insuf cardiaque (droite, avec débit N ou `\inc`{=latex}),
aggravation insuf coronaire
- crise aigüe thyrotoxique (exceptionnelle)
- musculaire (âgé)
- ostéoporose (♀ ménopausée) : rachis
### Étiologies (fréquence `\dec`{=latex})
#### Auto-immunes
/Maladie de Basedow/\
1% population. Auto-immune, sur terrain génétique. Poussées puis
rémissions
Clinique :
- goitre diffus homogène, élastique, souffle
- oculaire (spécifique, inconstant) : rétraction et asynérgie
palpébrale, inflammation, exophtalmie, oedème paupières,
inflammation conjonctive, limitation mouvement regard
`\thus`{=latex} examen ophtalmo ! (acuité visuel, cornée, papille,
oculomotricité, tonus intraoculaire)\
Mauvais pronostic : exophtalmie importante, paralysie complète,
neuropathie optique, hypertonie oculaire avec souffrance papillaire
- dermopathie (exceptionnelle) placard rouge, surélevé, induré, face
ant jambes
Diagnostic : manif oculaire suffit. sinon : écho (hypoéchogène,
vascularisé), (scinti), Ac anti-récepteur TSH\
*Autres auto-immune*
- Thyroïdite post-partum (5%) : hyperthyroïdie transitoire puis
hypothyroïdie. Ac anti-TPO mais pas Ac anti-récepteur TSH
- Thyroïdite d\'Hashimoto : goitre irrégulier, très ferme. Écho :
hypoéchogène. Ac anti-TPO mais pas anti-récepteur TSH
#### Nodules thyroïdiens hypersécrétans
Âge plus avancé, sd de thyrotoxicose pur (pas de manif oculaire)
- Goitre multinodulaire toxique : à la clinique, puis écho. Scinti :
\"en damier\"
- Adénome toxique : palpation nodule unique, écho :
tissulaire/partiellement kystique. Scinti nécessaire : reste du
parenchyme \"froid\"
#### Iatrogènes
- Iode : produits contraste, amiodarone. 2 formes : fonctionnelle ou
lésionnelle (lyse des cellules)
☡ sous amiodarone : T4L `\inc`{=latex} mais T3L, TSH N
- Hormones thyroïdiennes : pour maigrir. Diag : scinti (pas de
fixation), Tg effondrée
- Interféron (fréq++)
#### Thyroïdite subaigüe de De Quervain
Affection banale virale. Diagnostic clinique (goitre dur et douleureux).
Hyper- puis hypo-thyroïdie. Echo = hypoéchogène
#### Thyrotoxicose gestionnelle transitoire
Fréquent (2% grossesse). 1er trimestre : nervosité, tachycardie, pas de
prise de poids
DD : Basedow (pas Ac anti-récepteur TSH)
#### Rares
Mutations activatrices du récepteur TSH, métastase massives sécrétantes
(K thyroïdiens vésiculaire différencié), tumeurs
placentaires/testiculaires, {sd résistance hormones thyroïdiennes,
adénome hypophysaire}
### Forme clinique
- Enfant : généralement Basedow (néonatale/acquise) : avance staturale
et osseuses, hyperactivité ± signes oculaires
- Femme enceinte : passage d\'Ac `\thus`{=latex} hyper- ou
hypo-thyroïde. Passage d\'antithyroïdiens de synthèse
`\thus`{=latex} goitre, hypothyroïdie possible. Contraception !
- Âgé : évolution discrète (AEG, fonte musculaire, cachexie, insuf
cardiaque). Penser thyrotoxicose si troubles rythme/insuf cardiaque
### Traitement
{} Urgence : crise aigüe thyrotoxicose, cardiothyréose chez
âgé/cardiqaue, orbitopathie maligne, cachexie vieillard, Basedow chez ♀
enceinte
Repos, sédatifs, bêtabloquant, contraception
gls:ATS :
- -mazole (30-60mg/j), -thiouracile (300-600mg/j) : bloque TPO
- ES : allergies cut, `\inc`{=latex} enzymes hépatiques, neutropénie,
agranulocytose++ ( !!)
- surveillance : T4 libre jusque N puis T4L et TSH. NFS 10jours
pendant 2 mois (agranulocytose)
Chir : thyroidectomie totale sauf si adénome toxique (lobectomie)
Radio-iode : simple, sans risque génétique/cancérisation secondaire (☡
orbitopathie...). CI : femme enceinte.
#### Résultats
- Basedow : thyroïdectomie `\thus`{=latex} hypothyroïdie définitive.
Radio-iode `\thus`{=latex} hypothyroïdie 50%, risque aggravation
orbitopathie. Donc ttt médical (1-2 ans) puis chir/iode si récidive
- Adénome/goitre multinodulaire toxique : chir, iode
- Induite par l\'iode : arrêt si possible
- Thyroïdite subaigüe : anti-inflammatoire (AINS/corticoïde)
#### Formes particulières
- Cardiothyréose : propanolol et anticoag. Si insuf cardiaque :
tonicardiaque, diurétiques, vasodilatateurs, betabloquant, anticoag.
Pour thyrotoxicose : ATS puis chir/iode 131
- Crise aigüe thyrotoxique : soins intensifs, réa, ATS, propanolol,
corticoïdes, iode131 après 24h ATS
- Orbitopathie : pas d\'effet ATS, iode peut aggraver !! Si simple,
collyre. Si maligne : cf spécialiste
- Femme enceinte : si transitoire, repos. Si Basedow : repos si
mineur. Si forme importante : ATS faible dose. Si formes grave, chir
(2eme trimestre) possible)
`\thus`{=latex} surveillance avant et après accouchement
## 241 † Hypothyroïdie
```{=latex}
\begin{tcolorbox}
Rappel : TRH (hypothalamus) stimule la production de TSH (hypophyse) qui stimule la thyroïde
\end{tcolorbox}
```
- Atteinte de la glande thyroïde : `\inc`{=latex} TSH et
- soit T4L N : hypothyroïdie frustre
- soit T4L `\dec`{=latex} : hypothyroïdie patente
- Ou hypothalamo-hypophysaire : T4L `\dec`{=latex} et
- soit TSH légèrement `\inc`{=latex} : hypothalamus
- soit TSH `\dec`{=latex} ou N : hypophysaire
### Sémiologie
Général :
- sd d\'hypométabolisme[^24]
- peau pâle/jaune, sèche, squameuse, dépilée; cheveux secs cassants
- myxoedeme cutanéomuqueux : faciès \"lunaire\", voix rauque,
hypoacousie, macroglossie
- neuromusc : crampes, myalgies
- endocrinien : (galactorrhée), troubles règles, troubles libido
Cliniques (rare, diag fait avant) :
- CV : bradycardie sinusale, `\dec`{=latex} contractilité, (insuf
cardiaques, troubles rythme V), épanchement péricardique, favorise
athérome coronarien
- neuromusc, neuropsy : dépressif, sd confusionnel, démence, myopathie
prox, apnée sommeil
- coma myxoedemateux : si hypothyroïdie primaire profonde et
aggression. Convulsion, EEG non spécifique. Hyponatrémie. Pronostic
sévère
Palpation : glande ferme hétérogène, pseudonodulaire
Grossesse :
- complication mère : HTA, prééclampsie, fausse couche, hémorragie
post-partum
- complications foetus : troubles developpement neuro-intellectuel,
hypotrophie
- 1er trimestre : TSH `\dec`{=latex}, T4L limite sup. Puis TSH
normale, T4L basses (physiologique !)
Anomalies bio :
- hémato : anémie normocytaire normochrome (si macrocytose, penser
anémie de Biermer) troubles de coagulation,hémostase
- hypercholestérolémie, `\inc`{=latex} CPK, hyponatrémie dilution
### Étiologies
#### Hypothyroïdie primaire
Auto-immunes :
- Thyroïdite d\'Hashimoto :
- goitre ferme, irégulier, Ac anti-TPO.
- infiltration lymphocytaire du parenchyme thyroïdien. Facteurs
environnementaux, terrain génétique.
- penser à lymphome si `\inc`{=latex} rapide du goitre
- écho thyroïdiennes : hypoéchogène, hétérogène, vasc hétérogène
(scint inutile)
- Thyroïdite atrophique : pas de goitre, Ac anti-thyroidiens moins
élevés. Souvent une évolution d\'Hashimoto, \> 50 ans.
- Thyroïdite du post-partum : idem, petit goitre. Normalement
résolutif dans l\'année. 5% des grossesses
Non auto-immune :
- thyroïdite subaigüe de De Quervain : inflammation du parenchyme.
Phase de thyrotoxicose puis hypothyroïdie
- thyroïdite sans Ac
- thyroïdite iatrogène : interferon++, amiodarone, ATS, iode131,
radiothérapie cervicale, lithium, ttt anti-tyrosine kinase (cancéro)
Autres : carences iodées (endémie++), hypothyroïdie congénitale
(dépistage à naissance + 72h[^25])
#### Démarche diagnostique
TSH puis (T4L (profondeur) et Ac anti-TPO, échographie pour étiologie)
#### Insuffisance thyréotrope
- compression région hypothalamo-hypophysaire (HH) par tumeur (adénome
hypophysaire souvent)
- séquelle post-chir, post-radio des tumeurs de la région HH
- séquelles méningite, trauma crânien, hémorragie méningée
- génétiques (rare)
IRM systématique !
### Traitement
Lévothyroxine (T4)
- hypothyroïdie patente : L-T4 50 à 150 μg/j. Si coronarien :
`\inc`{=latex} progressivement de 12.5 à 25μg/j. ☡ Surveillance !
(ECG hebdo si grave, hospit si coronarien récent, sinon patient doit
consulter si douleurs thoraciques)
- hypothyroïdie frustre : 3 cas
- TSH \> 10mUI/L ou Ac anti-TPO : ttt
- TSH \< 10mUI/L et pas d\'Ac anti-TPO : surveillance
- si grossesse : dès TSH ≥ 3mUI/L
- à discuter sinon
Suivi
- hypothyroïdie primaire : objectif : TSH $\in [0.5, 2.5]$ mUI/L (≈
10mUI/L pour âgé, et \< 2.5mUI/L pour femme eceinte)
- insuf thyréotrope : suivi sur T4L seulement
Situations particulières:
- grossesse : `\inc`{=latex} posologie dès diagnostic grossesse
- `\inc`{=latex} si interférence avec l\'absorption
intestinale{sulfate de fer, carbonate de calcium, hydroxyde
d\'alimunie, cholestyramine}, la clairance {phénobabrital,
carbamazépinex, rifampicine, phénytoïne, sertraline, chlooriqune},
oestrogenes
- néonatale : L-T4 à vie
### Dépistage ?
- Adulte : si risque : signes clinique, goitre, hypercholestérolémie,
ATCD thyroïdiens, auto-immunité thyroïdienne, irradiation cervicale,
{amiodarone, lithium, interféron, cytokines}
- Femme enceinte : si signes, contexte thyroïdien (perso/familial),
auto-immunité
## 242 Adénome hypophysaire
##### Révélé par sd tumoral
Suspicion sur clinique, confirmé par IRM
- Clinique : céphalées, \"voile\" visuel [^26], quadra-/hémi-anopsie
temporale
- ☡ apoplexie hypophysaire [^27](rare) thus imagerie en urgence ☡
- IRM : microadénome (reste hypointense après injection) ou macro
adénome (\> 10mm, hyperintense après injection).
- DD : craniopharyngiome intra-sellaire , méningiome intra-sellaire
##### Révélé par sd d\'hypersécrétion (Tab [tab:sd_hypersecretion](tab:sd_hypersecretion))
Hypersécrétion Signes Diagnostic
-------------------- ---------------------------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Hyperprolactinémie galactorrhée et 1\. Confirmer
(prolactine) ♀: trouble cycle menstruel 2\. Éliminer grossesse, médicaments, hypothyroïdie
♂: gynécomastie, troubles sexuels. périphérique, IR
3\. IRM : microadénome
ou {macroadénome, tumeur non prolactinique}
Acromégalie Sd dysmorphique `\tablefootnote{Extrémités élargies, visage (nez élargi, front bombé, lèvres épaisses, tendance prognathisme}`{=latex} Pas de freinage à HGPO
(acrshort:GH) Signes fonctionnels `\tablefootnote{sueurs, céphalées, paresthésies mains, douleurs articulaires, asthénie fréquente, HTA}`{=latex} IGF-1 `\inc`{=latex}
Hypertrophie myocarde (IC `\thus`{=latex} DC )
Diabète, SAOS
Goitres, polypes côlon
Sd Cushing amyotrophie ceinture et abdomen, 1\. CLU `\inc`{=latex}, freinage minute`\tablefootnote{Cortisolémie matin après 1mg dexaméthasone à 23h (rétrocontrole négatif des glucocorticoïdes sur cortisol)}`{=latex} négatif
(glucocorticoïdes) peu amincie (mains), ecchymoses, vergétures 2\. Si ACTH `\dec`{=latex}: adénome surrénalien ou
corticosurrénalome malin
graisse facio-tronculaire, bosse de bison, 3\. Sinon freinage fort`\tablefootnote{Dexmathéasone toutes les 6h}`{=latex})
ostéoporose , hyperandrogénie \+ test stimulation ACTH (CRH, métopirone
spanioménorrhée ♀, impuissance ♂, `\dec`{=latex} libido, \- positif : Cushing (adénome hypophysaire)
HTA, troubles psy \- sinon sécrétion ectopique
DD : stress, dépression, psychose, alcoolisme
: Syndromes d\'hypersécrétion
##### Révélé par insuffisance antéhypophysaire (Tab [tab:insuf_antehypophysaire](tab:insuf_antehypophysaire))
Clinique : face pâle, \"veillot\", dépigmentation aréole mammaire et
OGE, dépilation complète aisselles pubis
IRM si déficit hypophysaire
Type Signes Diagnostic
-------------- --------------------------------------------------------------- ----------------------------------------------------------
Gonadotrope ♂ = {`\dec`{=latex} libido, pilosité visage `\dec`{=latex}, ♂ : troubles sexuels `\dec`{=latex} testostérone
petits testicules mou, infertile}
♀ = {aménorrhée, dyspareunie} ♀ préménopause : aménorrhée, oestradiol `\dec`{=latex},
gonadotrophines N
ostéoporose, (retard pubertaire) ♀ postménopause : gonadotrophines `\dec [fn:54]`{=latex}
Corticotrope asthénie, hypotension, amaigrissement test Métopirone,
pas de déficit en aldostérone ! cortisol \< 200ng/mL si hypoglycémie
Risque de collapsus CV (cortisolémie, synacthène, CRH)
Thyréotrope hypothyroïdie modérée `\dec{}`{=latex} T4L sans augmentation de TSH
Somatotrope adulte = {`\dec`{=latex} masse et force musc, adiposité abdo} stimulation GH $\times 2$
enfant = retard croissance, hypoglycémies stimulation GH
: Insuffisance antéhypophysaire
## 243 Insuffisance surrénale
### Insuffisance surrénale lente
Rare mais grave
Surrénales sécrètent :
- glucocorticoïdes ≈ cortisol [^28] : hyperglycémiant, `\inc`{=latex}
catabolisme protidique et tonus vasculaire, `\dec`{=latex} ADH,
anti-inflammatoire et antipyrétique, Minimum 0-2h, maximum 7-9h
- minéralocorticoïde ≈ aldostérone : réabsportion Na+ et Cl-, excrète
K+
- androgènes surrénalien (stimulé par ACTH)
Primaire (surrénale) Secondaire (hypophysaire)
-------------------------------------------------------------- ---------------------------
Fatigue, dépression, anorexie, nausées
`\dec`{=latex} poids, hypotension, hypotension orthostatique
Hyperpigmentation Pâleur
HyperK, hypoNa (manque sel) HypoNa (dilution)
: Insuffisance surrénale primaire (maladie d\'Addison)/secondaire :
clinique
##### Diagnostic
Cortisol + ACTH ☡ ne pas attendre résultats pour commencer traitment
- clinique :
[tab:insuf_surrenale_clinique](tab:insuf_surrenale_clinique)
Primaire Secondaire
------------------- ---------------------------------- ----------------------
cortisolémie à 8h basse basse
ACTH haute basse
aldostérone basse N
rénine haute N
Synacthène réponse insuffisante du cortisol réponse insuffisante
: Insuffisance surrénale : diagnostic
- cortisolémie (max = 8h) puis : ACTH `\inc{}`{=latex} si primaire,
rénine `\inc`{=latex} si primaire
- test Synacthène[^29] (+ Métopirone ou hypoglycémie insulinique si
doute)
NB : femme enceinte = {`\inc`{=latex} seuil, faisceau d\'args},
enfant : répéter dosages voire ttt probabiliste
##### Étiologies de l\' acrshort:IS primaire
- Auto-immune (80% adulte, 20% enfant) : gls:PET1, gls:PET2
`\thus`{=latex} autoAc anti-21-hydroxylase, scanner (surrénales
atrophiques)
- *tuberculose bilatérale surrénale* (10%) : transplanté ou ID avec
TCD tuberculose `\thus`{=latex} scanner surrénales
- *VIH* (stade avancé) : iatrogène, infection opportuniste (CMV++),
atteinte de l\'hypophyse (lymphome, CMV), corticoïde
anti-inflammatoire et ritonavir
☡ dénutrition `\thus`{=latex} spécialiste
- autres : *iatrogènes*[^30], *métastases bilatérales*[^31],
lymphomes, maladies infiltratives, causes vasculaires
- enfant : génétiques surtout = *bloc enzymatique* (dépistage
obligatoire), adrénoleucodystrophie
##### Étiologies de l\'IS secondaire
- *interruption corticothérapie prolongée* surtout (\> 7mg prednisone)
- autres[^32] : tumeur région hypothalamo-hypophysaire, hypophysite
(auto-immune), granulomatose, trauma, chir hypophysaire,
radiothérapie, sd de Sheehan
##### Prise en charge
Ttt cause et ttt substitutif :
- glucocorticoïdes (hydrocortisone) 15-25mg/j
- minéralocorticoïde (fludrocortisone) 50-150μg/j si IS primaire
Éducation du patient : régime normosodé, pas de laxatif, ttt à vie,
hydrocortisone en SC si \> 2 vomissement/diarrhées en \< 1/2 journée
Surveillance clinique : surdosage en hydrocortisone/fludocortisone,
cortisolémie et ACTH inutile !!
### Insuffisance surrénale aigüe
##### Diagnostic
Si diagnostic **non** posé : cortisol + ATCH. Ne pas attendre les
résultats
- clinique : déshydratation extracellullaire[^33] , confusion, trouble
dig, douleurs musc, fièvre
- biologie : IR, fonctionnelle++, hypoNa, hyperK++
##### Causes
- Insuf surrénale chronique décompensée++
- D\'emblée si bloc enzymatique surrénalien (21-hydroxylase) complet
(néonatale) ou hémorragie bilat surrénale ou apoplexie hypophysaire
- Décompensation par n\'importe quelle patho intercurrente
##### PEC
☡ Urgence extrème
- 100mg hydrocortisone (IV, IM, SC) `\thus`{=latex}
`\faHospital`{=latex} (réa)
- perfusion NaCL (et G30% si hypoglycémie)
- ttt facteur déclenchant
- surveiller : PA, FC, FR, oxymétrie de pouls, diurèse, T,
glycémie, CS, ECG si hyperK
Ttt préventif : patient doit `\inc`{=latex} ses doses, médecin traitant
au courant
### Arrêt d\'une corticothérapie
Risque = ebond de la maladie causale, insuf surrénale secondaire
(corticotrope), sd de sevrage
À risque : (ttt ≥ 3 semaines par ≥ 20mg prednisone) ou (corticoïdes et
inhib enzymatique du cytochromie P450 (ritonavir)) ou sd Cushing
iatrogène
## 244 † Gynécomastie
Hyperplasie tissue glandulaire mammaire, fréquente. Dû à oestrogène
`\inc{}`{=latex} et testostérone `\dec{}`{=latex}. Regarder aussi TeBG,
SHBG
### Démarche
- Clinique : palpation = ferme/rugueux, mobile arrondi, centré par le
mamelon (rien si adipomastie)
- Mammographie si doute : opacité nodulaire/triangulaire (rien si
adipomastie). Élimine cancer du sein (rare)
- Physiologique ?
- 2/3 des nouveaux-nés
- pubertaire : de 13 jusque 20 ans, rétrocède . Palper testicule
pour atrophie testiculaire/tumeur
- fréquente \> 65 ans. Palpation testiculaire
### Étiologie
```{=latex}
\begin{tcolorbox}
Causes fréquentes : médic, idiopathique, cirrhose, insuf testiculaire/gonadotrope, (tumoral)
\end{tcolorbox}
```
Évidente :
- insuf rénale chronique, cirrhose, médicaments (surtout
spironolactone, antiandrogène, kétoconazole, neuroleptiques, ATB
antirétroviraux, antiulcéreux)
Sinon exploration hormonale : T4L, TSH, hCG, testostérone totale, LH,
FSH, prolactine, oestradiol
Causes endocriniennes :
- hyperthyroïdie
- insuffisance testiculaire/hypogonadisme périphérique (8%) : sd de
Klinefelter le plus fréquent
- hypogonadisme d\'origine hypothalamique/hypophysaire: testostérone
basse, LH, FSH normales/abaissées `\thus`{=latex} imagerie
hypophysaire, dosage prolactine. Hyperprolactinémie ou tumorale
- tumeur sécrétant oestrogène : oestradiol `\inc`{=latex},
testostérone `\dec`{=latex} `\thus`{=latex} tumeur testiculaire (ou
surrénalienne rarement) `\thus`{=latex} echo testiculaire ou scanner
abdo
- tumeur sécrétant hCG : `\inc`{=latex} hCG `\thus`{=latex} écho
testiculaire, scanner cérébrales. Dans les bronches ou le foie
parfois. Chimio.
- Résistance androgènes (exceptionnelle) : testostérone
`\inc`{=latex}, LH `\inc`{=latex}
- idiopathique (25%)
### Traitement
Traiter la cause. Sinon
- Pubertaire : ne rien faire
- Idiopathique : androgènes non aromatisables 3 mois. Si inefficace,
chir plastique possible
## 245 Diabète
```{=latex}
\begin{tcolorbox}
Définition : glycémie à jeun \ge 1.26g/L (2 reprises) ou (aléatoire \ge 2g/L et signes hyperglycémie)\footnotemark
\end{tcolorbox}
```
`\footnotetext{Normale à jeûn < 1.10g/L}`{=latex}
Caractéristiques diabète 1 (le diabète 2 s\'y oppose) :
- ATCD familiaux rares, \< 25 ans, début rapide explosif avec
symptomatologie bruyante
- poids normal ou `\dec`{=latex}, hyperglycémie majeure \> 23g/L
- souvent cétose
- pas de complications dégénératives
- mortalité par insuf rénale (CV pour diabète 2)
### Diabète 1
Prévalence : 1/200 000 (10% des diabétiques). Peut survenir à tout âge.
`\inc`{=latex} incidence. Sex-ratio = 1
##### Physiopathologie
Carence en insuline par destruction cellules beta du pancréas.
Auto-immun++ ou idiopathique.
Prédisposition génétique, facteurs environnementaux.
☡10% d\'autres maladies auto-immunes `\thus`{=latex} doser Ac anti-TPO
(Basedow, thyroïdite), anti-surrénale (Addison), anti-transglutaminase ±
anti-endomysium (coeliaque), anti-paroi gastrique, anti-facteur
intrinsèque (Biermer)
##### Diagnostic
Clinique = glycémie $> 2g/L$, maigrissement, cétonurie ± acrshort:SPUPD
- NB : signes d\'acidose[^34] possibles
- *si doute* : Ac anti-GAD (± anti-ilôtsq anti-IA2, anti-insuline,
anti-ZnT8)
- *si négatif* :
- hérédité dominante : MODY, mutation SUR1/KIR6-2 (si diabète
néonatal)
- sd de Wolfram [^35], mitochondropathie[^36]
- secondaire : cancer pancréas, pancréatite chronique,
mucoviscidose, hémochromatose, médicaments
Formes : diabète 1 lent (LADA[^37]), (révélé par acidocétose), non
insulinodépendantes, cétosique du sujet noir d\'origine africaine :
mécanisme auto-immun
##### Évolution
Schéma théorique : estruction cellules β, clinique (85% détruites),
séquellaire
Diabète instable :
- itérations de cétoacidoses ou hypoglycémies sévères, psycho.
- DD : gastroparésie, déficit systèmes contra-insuliniques, Ac
anti-insuline
##### PEC
Insuline à vie (Table [*insuline*]{.spurious-link target="insuline"} ) +
alimentation variée sans interdits, exercice physique
- Stylo à insuline (pompe si échec) :analogue lent (1-2/j) et analogue
rapide (3-4) `\thus`{=latex} éducation nutritionnelle
- ES : hypoglycémie, lipoatrophie (immuno), lipohypertrophie (piqûres
au même endroit)
Objectifs : HbA1c \< 7% (enfants : entre 7.5 et 8.5, complication/sujet
âgé : 8%)
- 4 glycémies/jour, injection d\'insuline, adapter ttt, contrôle de
l\'alimentation `\thus`{=latex} éducation thérapeutiques
- Surveillance :
- HbA1c
- diabétologue/pédiatre endocrinologue 3/an
- {lipides, créat, microalbuminurie}
- ophtalmo, cardiologie 1/an (sympto/âgé,compliqué), dentiste 1/an
```{=org}
#+name: insuline
```
Type Injection Durée Utilisation
---------------------------------------------- ------------ -------- --------------------------
insuline humaine recombinante (Actrapid) IV, IM, SC 7-8 Prandiale, hyperglycémie
analogue rapide (Humalog, Novorapid, Apidra) IV, IM, SC 4-6h Pompe
forme lente (NPH) SC 9-16h
analogue lents (Lantus) 16-40h
: Traitement insulinique du diabète 1
##### Cas particuliers
- Enfant/ado : ☡ cétoacidoses
- Femme (cf Sec. [sec:diabete_gestationnel](sec:diabete_gestationnel)
- oestrogestatif à discuter
- grossesse : équilibre dès conception !! par analogue de
l\'insuline.
- CI absolue : insuf coronaire instable
- Pas d\'arrêt de l\'insuline (lent si examen à jeun)
### Diabète 2
90% de diabète. Prévalence 4%.
FR = obèse, anomalie métabolisme glucidique, ATCD familiaux diabète 2,
ethnie noire/hispanique.
##### Physiopatho
Insulinorésistance : causée par la génétique, sédentarité, excès
pondéral. Au niveau du muscle, foie, lipolyse
*Et* déficit insulinosécrétion.
##### Dépistage
Signes cliniques de diabètes, \> 45 ans (tous les 3 ans), ≥ 1 FR. Non
caucasien/migrant, `\glslink{sdMetabolique}{sd métabolique}`{=latex}
DD : diabète 1 lent, génétique (MODY2, mitochondrial), secondaire
(pancréatopathie, hémochromatose, mucoviscidose, médicaments)
##### Évolution
Insulinopénie `\thus`{=latex} insulinoréquerant. Pronostic selon
complications.
#### Traitement
- Activité physique 3-5/semaine: intensité modérée ≥ 30min/j et
intense (\> 60% $VO_{2max}$) de 20min
- CI : insuf coronarienne, rétinopathie proliférante non
stabilisée
- surveiller risque hypoglycémie, pieds !
- Alimentation : équilibrée, objectif = poids -5 à 10%
- Metformine++[^38] en oral ± sulfamide/glinides/inhibiteurs
DPP-4/inhibiteurs α-glucosidase/analogues GLP-1[^39]
- ± insulinothérapie quand insulinorequérance, mal équilibré(cf
diabète 1)
Objectifs : HbA1c \< 7%[^40] (8% si grave, 9% si agé dépendante)
- autosurveillance glycémique : pas systématique si ttt oral (1-3
cycles/j), nécessaire si insuline
### Complications
Souffrance vasculaire : micro- (rein, oeil, nef) et macro-angiopathie
(`\inc`{=latex} athérosclérose). AOMI x6-10
##### Physiopatho
Excès de glucose `\thus`{=latex} aggression des vaisseaux
(endothélial++), inhibition des mécanismes de défense cellulaires
Conséquences : épaississement des membranes basales, troubles
perméabilité vasculaire, prolif vasculaire (rétine), fibrose (rein)
##### Rétinopathie diabétique
Cf [chap 21 d\'ophtalmo](#retinopathie_diabetique)
#### Néphropathie
- Diabète = 1ere cause d\'IR terminale. Risque CV x10 chez DT1, 30% DC
IR terminale chez DT1 (5% chez DT2)
##### Physiopatho
`\inc`{=latex} pression intra-glomérulaire `\thus`{=latex} dilatation
des glomérules. Puis sclérose) avec `\inc`{=latex} albumine[^41].
##### Dépistage
1 BU/an protéinurie, hématurie, infection urinaire),
albuminurie/créatinurie
##### Diagnostic
Rétinopathie , plusieurs excrétions urinaire d\'albumine `\inc`{=latex}
- si doute : ponction-biopsie rénale :
- diabète 1 : hypertrophie mésangiale/glomérulaire \<
épaississement membrane basale, dépôts mésangiaux \< hyalinose
artériolaire \< glomérulosclérose nodulaire
- diabète 2 : 1/3 typique...
- 5 stades :
4. Néphropathie incipiens : microalbuminurie[^42]
5. Néphropathie : PA élevée, DFG `\dec`{=latex} de 10mL/min/an,
nodule de sclérose, hyalinose artériolaire
6. Insuffisance rénale
##### Traitement
Prévention
- primaire (diabète, FR HTA)
```{=html}
<!-- -->
```
- secondaire : Tab [tab:nephro_diabete](tab:nephro_diabete).
Surveiller glycémie !! Éviter AINS, produits contrastes iodés
Stade Objectifs Moyens
--------------------- ----------------------------- -----------------------------------------------------------------------------------------------
microalbuminurie : HbA1c \< 7%, PA \< 140/85 ~IEC~/sartans\_`\tablefootnote{\danger sténose artère rénales : doser K+, créat}`{=latex}, FR
*et* PEC tabac, régime hypoprotidique, sel \< 6g/j
macroalbuminurie PA \< 140/85mmHg IEC/sartan + diurétique thiazidique.
Protéinurie \< 0.5g
IR PAs \< 130mmHg
\- DFG ∈ \[30,60\] adapter poso
\- DFG \< 30mL/min HbA1c \< 8% autorisé : insuline, répaglinide, inhib α-glucosidase,
\- DFG \< 25 autorisé : inhib DPP4
: tab:nephro~diabete~
NB : infections urinaires : $\times 3$ dont 90% asymptomatique (basses)
`\thus`{=latex} ttt si symptomatique. Risque = contamination du haut
appareil urinaire aggravation néphropathie glomérulaire.
#### Neuropathie
- Autonome : tardive
- Périphérique : 50% des diabètes à 20 ans. FR : grande taille, tabac,
âge, AOMI, carences nutritionnelles/vitaminiques, alcool, insuf
rénale
Atteinte métabolique et vasculaire.
##### Diagnostic
Examen clinique et interrogatoire (+ complémentaires si autonome)
##### Sensorimotrice
En \"chaussettes\" puis en \"gants\")
- Polynévrite symétrique distale++ :
- hypoesthésie pression/tact/thermique/proprioceptique ignorée
- ± paresthésies distales, douleurs \"arc électrique\"
- ROT achilléen aboli (puis rotulien)
- voûte plantaire se creuse (tardivement)
- complication : pied \"cubique\" de Charcot
- Plus rare : polynévrite asymétrique proximale, polyradiculopathie
thoracique, mononévrite, multinévrite
##### Autonome
- CV : tachycardie sinusale, bradycardie, allongement QT
- Vasomotrice : hypotension orthostatique *sans* accélération du pouls
- Troubles sudation : sécheresse cutanée MI
- Digestive : parésie, dysphagie, gastroparésie (fréq), diarrhée,
constipation
- Vésicale : résidu post-miction `\thus`{=latex} IU `\thus`{=latex}
clinique, écho (prostate, vessie)
- Dysfonction érectile : psychogène, (sd de Leriche[^43]). DD : examen
génital, testostérone, prolactinémie.
Examen
- interrogatoire , inspection pieds, ROT abolis (niveau troubles
sensitifs), monofilament, sensibilité épicritique, thermoalgique,
vibratoire[^44], proprioceptiques[^45]
- ECG annuel, EMG si atypique
- Δ FC inspiration - expiration[^46], rapport RR long/court pendant
épreuve de Valsalva, Δ FC couché - debout
DD : neuropathies métaboliques (insuf rénale, amylose, hypothyroïdie),
toxiques (alcool, tabac, iatrogène), paranéoplasiques, carentielles,
inflammatoire, infectieuse (Lyme, lèpre), autre (Charcot-Marie-Tooth,
péri-artérite noueuse)
Traitement :
- préventif = glycémie. FR : alcool, tabac, insuf rénale, carence
vitamines B, médicaments.
- Si installées, stabiliser et éviter les complications (mal perforant
plantaire++)
- Antalgiques, hydratation peau
#### Macroangiopathie
⌀ \> 200 μm. Plus fréquente et sévère. Artères visibles sur radio.
Prévention CV = **problème majeur** des diabétiques 2 : $\frac{3}{4}$ DC
d\'une cause CV. Risque CV ×2-3 (×3-4 chez ♀).
##### Dépistage
Risque \> 1% = élevé[^47]
1. *FR* :
- CV : âge \> 50 ans ♂\[*f**n*:235\], diabète \> 10 ans, ATCD
IDM/mort subite[^48], ATCD AVC [^49], tabac, HTA permanente,
HDLc \< 0.4g/L, microalbuminurie \> 30mg/24h
- autres : obésité abdominale [^50], IMC \> 30k/m^2^, sédentarité,
\> 3 verres vin/j, pyschosociaux
2. Montrer atteinte artérielle :
- coronaropathie : ECG repos annuel, scinti avec épreuve d\'effort
ou coronarographie
- carotides ? auscultation `\thus`{=latex} écho si AIT possible
- AOMI ? pieds, pouls, claudication, IPS cheville/bras \< 0.7 ?
Écho-doppler
##### Diagnostic
- *Ischémie myocardique* silencieuse fréquente ! `\thus`{=latex}
dépistage systématique si trouble dig, asthénie effort...
- AOMI : 1/3 proximale (HTA), 1/3 distale sous genou (glycémie,
tabac), 1/3 proximale et distale
- : diabète + microangiopathie sévère, diabète + atteinte vasculaire
##### Traitement
Objectif HbA1c \< 6.5% (7% si âgé ou à risque.
- Activité physique
- LDL \< 1.3g/L (1.0 si risque CV élevée ou néphropatie) : statines
[ou]{.underline} fibrates
- PAs ∈ \[130,139\] et PAd \< 90mmHg.
- Poids : IMC \< 25kg/m^2^
- Arrêt tabac,
- Prévention thrombose si ≥ 1 FR : aspirine 75-150mg
Si revascularisation : stents par défaut et chir si atteinte 3
coronaires.
#### Pied diabétique
1 patient sur 10 à risque d\'1 amputation d\'orteils. Éviter les plaies
pour prévenir l\'amputation
##### Mal perforant plantaire (MPP)
Neuropathies `\thus`{=latex} hypoesthésie, déformations
ostéoarticulaires `\thus`{=latex} durillons puis fissure et infection
`\thus`{=latex} dermo-hypodermite.
Autres
- Ischémie/nécrose : peau froide, fine, dépilée, livedo.
`\thus`{=latex} revasculariser en urgence
- Nécrose + MPP
- Dermo-hypodermite nécrosante : très rare, `\thus`{=latex} débrider
en urgence, ATB. Cas particulier : gangrène gazeuse à
`\bact{perfringens}`{=latex} `\thus`{=latex} urgence vitale ☡
CAT
- Radio pieds bilatérale (ostéite ?), si infection : NFS, iono, CRP
- décharge, excision kératose à domicile si suffit
- réhydratation ± équilibre glycémie, anticoag, accin anti-tétanos !
- si infection : parage et drainage, ATB (cocci G+ si récent, sinon
bacille G-)
- si artério : revascularisation
- si ostéite : résection chirurgicale ou ATB 6-12semaine et sans
l\'appui
#### Autres
- Peau : nécrobiose lipoïdique (rare), dermopathie diabétique
(fréquente), lipodystrophie, acanthosis nigricans, vitiligo,
xanthomatose éruptives
- Infections : otite nécrosante (urgence !), mucormycose (urgence !)
- Foie : hépatologue dès anomalie transaminases ou γ-GT
- Articulations : capsulite rétractile, maladie de Dupuytren[^51],
Chéiroarthropathie, arthrose
- Dents : maladie parodontale `\thus`{=latex} dentiste tous 6 mois
```{=latex}
\begin{tcolorbox}
\begin{itemize}
\item annuel : FO, ECG repos
\item tous les 5 ans : écho-doppler MI (si > 40 ans, diabète > 20 ans) tous 5 ans
\item bio : HbA1c 4/an, glycémie veineuse, lipides 1/an, microalbuminurie 1/an,
créatininémie jeun, clairance créat 1/an, TSH
\end{itemize}
\end{tcolorbox}
```
#### Complications métaboliques
##### Coma cétoacidosique
- acétonurie, glycosurie, glycémie 2.5g/L, pH veineux \< 7.25,
bicarbonate \< 15mEg/L
- cause : déficit insuline absolu/relatif, inconnue
- évolution : cétose puis cétoacidose (Kussmaul, stupeur,
déshydratation mixte)
- gravité : âgé, ph \< 7, kaliémie 4-6 mmol/L, coma profond, TA
instable, pas de diurèse après 3h, vomissements incoercibles
- DD : urgence abdo, coma hyperosmolaire
- Régression sous ttt en 24-48h :
- éducation : si cétose, maintenir injections, supplément insuline
rapide, acétonurie si glycémie \> 2.5g/L
- curatif : insuline rapide IV, recharge volumique, K+, glucose si
besoin, facteur déclenchant
##### Coma hyperosmolaire :
- glycémie \> 6g/L, osmolalité \> 350mmol/kg, natrémie corrigée \>
155mmol/L, pas de cétose ni d\'acidose
- FR : \> 80 ans, infection aigüe, diurétique, [pas d\'accès aux
boissons]{.underline}, corticothérapie
- ttt : réhydratation prudente, lente, insuline IV, surveillance,
héparine préventive, ttt causal
##### Hypoglycémie
Inévitable mais pas mortelle
## 246 † Prévention par la nutrition
## 247 † Modifications thérapeutiques du mode de vie
## 248 † Dénutrition (à compléter)
## 249 † Amaigrissement
Fréquent
### Interrogatoire
- Histoire pondérale, conditions, de vie, psychologique, activité
physique excessive et apports alimentaires insuffisants
- Anorexie, {troubles digestifs, palpitations, sd polyuro-polydipsie},
troubles libido/érection, amnénorrhée (anorexie mentale ou
hypothalamique fonctionnelle), médicaments (nausée, anorexie),
dépression masquée++
### Examens :
Clinique : poids, taille, IMC, pli cutané, fonte musculaire, carences
vitamines, pâleur cutanéomuqueuse
Complémentaires :
- bio : NFS (anémie), VS/CRP (inflammatoire), iono (hyponatrémie
`\thus`{=latex} insuf surrénale), BU (glycosurie), calcémie,
{transaminase, γ-GT}(foie), TSH (hyperthyroïdie), {B12, folates, TP,
albuminémie}, graisses fécales ? (pancréatite chronique
calcifiante), dénutrition[^52]
- Radio thoracique (tuberculose), écho abdo (abcès/tumeur), fibro
(obstacle), DEXA (composition corporelles)
### Étiologie
- Poids stables, apports nutritionnels normaux, examens normaux :
maigreur constitutionnelle
- Si perte de poids confirmée, éliminer anorexie mentale, maladies
digestives, iatrogène, cancer extradigestif, maladies infectieuses,
neuro, grande défaillance cardiaque/rénale/respi/hépatique, alcool
- Sinon, causes endocrines :
- diabète 1 ou 2 : glycémie, HbA1C
- hyperthyroïdie : TSH `\dec`{=latex}`\dec`{=latex}, hormones
thyroïdiennes `\inc`{=latex}
- hypercalcémie : si gls:PTH inadaptée, hyperparathyroïdie
primaire
- insuf surrénalienne : cortisol, ACTH plasmatique
- panhypopituitarisme[^53] : cortisol `\dec`{=latex}
- phéochromocytomes : (nor)métanéphrines dans urines 24h, imagerie
surrénales
## 250 † Troubles nutritionnels chez sujet âgé (à compléter)
## 251 † Obésité(à compléter)
### Adulte
Surpoids = IMC ∈ \[25,29.9\]kg/m^2^. Obésité :
- grade 1 : IMC ∈ \[30,34.9\]kg/m^2^.
- grade 2 : IMC ∈ \[35,39.9\]kg/m^2^.
- grade 3 : IMC ≥ 40kg/m^2^.
Limites : sous-estimé chez asiatiques. Seulement pour \[18,65\] ans
Phases : prise de poids, constituée, perte, rechutes
Localisation : viscéral (scanner, IRM), sous-cutanée, ectopique (muscle,
foie)
Épidémio : +27.5% 1980-2013 (monde). France : de plus en plus jeune,
`\inc`{=latex} chez \> 65 ans
Étiologie :
- génétique: envisager si précoce (naissance +24 mois), troubles du
comportement alimentaire
- obésités communes liées à des facteurs environementaux (majorité) :
surtout déséquilibre apport caloriques- dépense
- antipsychotiques, glucocorticoïdes, antidépresseurs,
antiépileptiques, antidiabétiques
- arrêt du tabac, privation de sommeil (?), hypothalamique (rare)
Complications : `\inc`{=latex} RR mortalité, métabolique, CV, respi,
ostéoarticulaire, digestive, rénale, gynéco, cutanée, néoplasiques,
psychosociale
#### Clinique
- Interrogatoire :
- ATCD familiaux d\'obésité, poids naissance, âge surpoids, poids
max et min, circonstances déclenchantes, tentatives antérieures,
phases
- Comportement alimentaire (carnet), évaluation dépense
énergétique, pyscho-comportementale
- Complications (SAS)
- Examen : poids, taille, PA, tour de taille[^54], obésité secondaire
- Complémentaires : glycémie à jeune, lipides, hépatique, uricémie,
ECG repos
#### Traitement
- Diététique, activité physique (∀ IMC)
- Psychologique
- Médicaments (IMC ≥ 30 ou ( ≥ 27 et comorbidités)) : orlistat
- Chir bariatrique : {anneau gastrique ajustable, sleeve
gastrectomie}, {court-circuit gastrique, dérivation
biliopancréatique} : \< 65 ans. Prise en charge 6 mois avant et
post-op à vie (carences vitaminiques)[^55]
### Enfant/ado
☡ évolutivité. Surpoids : IMC \> 25. Obésité
- grade 1 : \> 30kg/m^2^
- grade 2 : \> 35kg/m^2^
- grade 3: \> 40kg/m^2^
Épidémio : stabilisation mais obésités sévères ×4
#### Étiologies
- génétiques : mutation sur récepteur de la mélanocortine type 4 =
2.5-5%
- communes (majorité) : facteurs environnementaux et prédisposition
génétique
- repond d\'adiposité à 6 ans. Risque d\'obésité ∝ précocité du
rebond
- tour de taille/taille \> 0.62 = forte valeur prédictive
- FR : surpoids parent, poids excessif/tabac pendant grossesse,
anomalie de croissance foetale, `\inc`{=latex}`\inc`{=latex}
poids à naissance + 2ans, difficulté socio-éoc, manque
d\'activité physique, troubles sommeil, psychopatho
- secondaires (rare) : ralentissement de la vitesse de croissance
naturelle
#### Complications
- HTA : \> 97e percentile + 10mmHg
- Insulinorésistance avec glycémie normale fréquente
- `\inc`{=latex} TG et `\dec`{=latex} HDL
- Stéatose hépatique non alcoolique
- Rachialgies, gonalgies, troubles statique vertébrales. Penser à
l\'épiphysiolyse de la tête fémorale : garçons \[10,15\] ans avec
douleur mécanique de hanche `\thus`{=latex} radio de profil
- Psychologique
#### Clinique
Interrogatoire :
- ATCD familaux,
- personnels : poids, taille naissance, âge d\'appartition,
changements environnementaux, tentatives antérieures, troubles des
règles
- comportement alimentaire (difficile)
Examen clinique :
- poids, taille, PA, tour de taille, pli-cutané (masse grasse \< 20%
après 5 ans), courbes de croissance (ralentissement = pathologique
!), dermato (acanthosis nigricans = insulinorésistance, vergétures=
hypercorticisme, intertrigo, mycose)
Pas d\'examens complémentaires !
#### Traitement
Prévention surtout. Modifier style de vie (efficacité faible). Chir
possible avec équipes spécialisées
## 252 † Diabète gestationnel + nutrition et grossesse (à compléter)
[]{#sec:diabete_gestationnel} Physio chez femme enceinte selon moitié:
- non diabétique : (`\inc`{=latex} insulinéme, insulinosensibilité)
puis (insulinorésistance `\thus`{=latex} hyperinsulinisme ou diabète
gestationnel)
- à risque de diabète : (hypoglycémie, cétose) puis (insulinosécrétion
postprandiale insuffisante)
### PEC du diabète pré-gestationnel
Grossesse à risque mais fécondité normale (sauf si sd ovaires
polykystiques).
☡ Normalisation glycémie préconception → accouchement
- HbA1c ≤ 6.5%
- glycémie à jeun ∈ \[0.6,0.9\]g/L
- glycémie repas + 1h \< 1.40g/L et +2h 1.20g/L
#### Risque foetus
- Fausses couches spontanées ×2, ∝ hémoglobine glycquée
- Malformation congénitales ×2, constituée pendant 8 premières
semaines : cardiaque, neuro, rénale `\thus`{=latex} `\inc`{=latex}
fausses couches spontanées, mortalité foeatale/néonatale,
malfomations
- 2e trimestre : macrosomie, hypoxie tissulaire, retard maturation
pulmonaire, hypertrophie cardiaque septale
- 3e trimestre : mort foetale
- Accouchement : `\inc`{=latex} prématurés, césariennes. Danger :
trauma foetal, hypoglycémie sévère, hypocalcémie,
hyperbilirubinémie/polyglobulie, détresse respi transitoire, maladie
des membranes hyalines
- Long terme : surpoids/obésité et diabète 2
#### Risque mère
- HTA (30%) : si \> 20 SAc, risque de toxémie gradivique. ×5 si
diabète 1. Risque vital
- Rétinopathie : ttt préalable si rétinopathie proliférative. CI :
rétinopathie proliférative floride non traitée
- Néphropathie :
- FR = {HTA, déséquilibre glycémique, rétinopathie évoluée dès
départ, diabète ancien, insuf rénale, hydramnios, correction
trop rapide d\'une hyperglycémie chronique}.
- Insuf rénale `\thus`{=latex} hypotrophie foetale, prééclampsie.
Si IR préexistante : 50% mortalité foeatale **in utero**
- dépistage : créat plasmatique, microalbuminurie, protéinurie
- IEC contre-indiqués
- Coronaropathie : exceptionnelle mais gravissime. Dépister si diabète
ancien et complications microvasculaire (ECG, effort)
- Infection urinaire `\inc`{=latex}, risque pyélonéphrite,
décompensation diabétique
- Diabète 1 : `\inc`{=latex} risque dysfonction thyroïdiennes
#### PEC
- Avant grossesse : glycémie ∈ \[0.7,1.20\] préprandial, ∈ \[1,1.4\]
postprandial et HbA1c \< 7%
- diabète 1 : `\inc`{=latex} insuline
- diabète 2 : insuline si régime ne suffit pas/arrêt ttt oral
- Pendant
- équilibre glycémique++ (6 glycémies capillaires/jour)
- ☡ variations physiologiques : insuline `\dec`{=latex} puis
`\inc`{=latex} puis `\dec`{=latex}`\dec`{=latex}
- cétonémie/cétonurie si glycémie \> 2g/L
- ≥ 1600kcal/j 2eme et 3eme tri
- surveiller poids, PA, créat plasmatique, microalbuminurie,
protéinurie, FO, BU, protéinurie
- surveillance obstétricale : dater++ (12-14SA), malformations
(22-24), placenta et liquide amniotique (32-34SA),
cardiomyopathie hypertrophique (32-34SA), bien-être foetal
- pas de bêtamimétique si prématuré
#### (Post)partum
Accouchement programmé souvent, facilité si rétinopathie sévère,
insuline SC/IV et glucosé avec surveillance horaire
Puis : insuline selon besoin pré-grossesse (D1) ou arrêt (D2)
### Diabète gestationnel
Si lié à la grossesse, apparait en 2eme partie. Risque : pré-éclampsie,
césarienne (∝ hyperglycémie matenrelle). FR : surpoids
Même complications liées à l\'hyperinsulinisme que pré-gestationnel
#### Dépistage
Si FR seulement :
- ≥ 35ans
- IMC ≥ 25kg/m^2^
- ATCD : diabète gestationnel, macrosomie, diabète chez parents 1er
degré
Diagnostic :
- début de grossesse si glycémie jeun ≥ 0.92g/L `\thus`{=latex} PEC
immédiate
- sinon à 24-28SA et (glycémie jeun \< 0.92g/L ou non faite) :
hyperglycémie provoquée oralement
#### Traitement
- Diététique (30-35kcal/kg \[25 si surpoids\]), activité physique,
antidiabétique CI , insuline si régime ne suffit pas après 8 jours
- Surveillance : glycémie (6/jour puis 4/jour), cétonurie (si glycémie
\> 2g/L), HTA
- Objectif : glycémie jeun \< 0.95g/L et postprandiale +2h \< 1.20g/L
Post-partum : arrêt insuline et surveillance glycémie (diabète antérieur
?). Vérifier glycorégulation à 3 mois. Risque de récidive si grossesse
## 253 † Nutrition chez le sportif
### Examen d\'aptitude
Dépister les pathologies induisant un risque vital/fonctionnel grave :
mort subite (1-4/100 000 après 35 ans) Obligation légale si compétition
(licencié ou non)[^56]
Examen :
- ATCD sportif, médicaux familiaux (CV, hypercholestérolémie
familiale), conduites à risque, alimentaire, ttt, toxiques
- Clinique :
- poids, taille, IMC, (courbe de croissance)
- maturation pubertaire
- ostéoarticulaire, cardiorespiratoire, test dynamique
sous-maximal (Ruffier-Dickson)
- Complémentaire : ECG repos[^57], CV
### Bénéfices/inconvénients
Adulte :
- Bénéfices :
- maintien santé : `\dec`{=latex} mortalité prématurée,
`\inc`{=latex} qualité de vie, `\inc`{=latex} autonomie (âgé),
régule poids
- prévention : cancers (colon, sein), CV, métabolique, ostéoporose
♀
- ttt : anxiété, cardiomyopathie ischémique, BPCO, obésité,
diabète 2, neuro, rhumatismales, dégénératives
- Surveillance : dépistage d\'insuf coronarienne \> 40 ans, ☡
nutrition et hydratation si \> 3h/semaine
- Recommandation : 150min/semaine (modéré) ou 75min/semaine (soutenu).
Idéal : x2
Enfant :
- Bénéfices :
- dev psychosocial : `\dec`{=latex} stress, anxiété,
`\inc`{=latex} intégration sociale, `\inc`{=latex} confiance en
soi
- dev psychomoteur : concentration, coordination, équilibre
- `\inc`{=latex} masse maigre, `\inc`{=latex} densité osseuse
- prévention : sd métabolique, surpoids, CV
- Surveillance : nutrition (éviter retards de croissance/pubertaire),
attitude alimentaires restrictives
- Recommandation : 60min/jour (modéré-soutenu) et renforcement
musculaire, osseux 3x/semaine
### Besoins nutritionnels
Intensité durée Energie Limitation
--------------- ----------- ------------------------------ ------------
Très intense secondes ATP, P-Cr
Intense minutes Glycogène musculaire Lactate
Faible-élevée prolongée glycogène musculaire/lipides VO~2~ max
Macronutriments :
- Glucides : détermine l\'épuisement si endurance `\thus`{=latex}
index glycémique faible à distance, IG élevé juste avant. Pendant :
maintenir glycémie. Après : reconstituer les stocks de glycogène
- Lipides à limiter si intensité élevé/compétition
- Protides : endurance 1.2-1.4g/kg/j, force : 1.3-1.5g/kg/j si
maintien masse, sinon jusque 2.5g-kg/j
Hydrosodé : avant = 500ml en 2h (prévention). Pendant : NaCl si ≥ 1h
selon intensité (jusque 1.5L/h). Après : 150% perte pondérale.
Minéraux, vitamines:
- attention situation à risque : déficit en fer, contrainte de poids,
alimentation glucidiques mais faible densité nutritionnelle,
exclusion de groupes d\'aliments
- endurance : vit B énergétiques[^58] , vit. \"antioxydantes\"[^59]
- force : `\inc`{=latex} vit B6, `\inc`{=latex} \"antioxydantes\"
#### Enfant
Apport insuffisants `\thus`{=latex} retard croissance staturo-pondéral
ou pubertaire, `\dec`{=latex} masse musculaire, déminéralisation
osseuse, déficit immunitaire.
Surveiller calcium, vit D, fer.
## 265 † Hypocalcémie, dyskaliémie, hyponatrémie
### Hypocalcémie (hypoCa)
Éliminer fausses hypoCa dues à l\'hypoalbuminémie[^60]. Calcémie =
équilibre absorption intenstinale, résorption osseuse, excrétion rénale.
Régulé par PTH, calcitriol
Clinique :
- hyperexcitabilité neuromusc : paresthésie main, pieds, péribuccales
(spontanées/effort), signe de Trousseau (\"main d\'accoucheur\"),
signe de Chvosteck (peu spécifique), crises de tétanie (paresthésie,
fasciculation pouvant entraîner arrêt respi)
- chronique : sd de Fahr[^61] `\thus`{=latex} signes extrapyramidaux,
crises comitiales
- `\inc`{=latex} QTc `\thus`{=latex} troubles du rythmes
- dans l\'enfance : musc, neuro, cardiaques
#### Principales causes
- Hypoparathyroïdes : anamnèse et {hypoCa, PTH `\dec`{=latex},
phosphatémie normale/haute}.
- post-chir++ : parathyroïdectomie totale
- congénitale : sd Di George++[^62]
- Pseudoparathyroïdies : génétiques : résistance à la PTH
`\thus`{=latex} PTH `\inc`{=latex}. Chondrodysplasie possible
- Anomalie vitamine D
- carence vit D = 1ere cause hypoCa chez nourrisson
`\thus`{=latex} rachitisme carentiel. Chez l\'adulte, seulement
si déficit prolongé et profond
- malabsorption digestive, insuf rénale chronique, cirrhose
#### TTt
- Aigüe = urgence `\thus`{=latex} calcium IV lente (2-3x10ml).
Suspension des ttt qui `\inc`{=latex} QTc, réduction digoxine
- Chronique : vit D (ou dérivés actifs) et calcium per os
### Hyper-/hypo-kaliémie,
Retentissement cardiaque `\thus`{=latex} vital
#### HyperK
Principales causes
- Acidose (sort K+ de la cellule) et insulinopénie (réduit entrée K+)
: ttt par insuline à risque d\'hypoK ☡ `\thus`{=latex} apport K+ dès
normokaliémie
- Hypoaldostéronisme
- insuf surrénale périphérique
- secondaire : chez \> 65 ans, diabétiques. Risque = aggravation
si IEC ou ARA II
- Pseudo-hypoaldostéronisme : résistance à l\'aldostérone (génétique)
#### HypoK
- Dénutrition sévère : anorexique, post-chir bariatrique sans suivi
- Insulinothérapie : si cétoacidose et troubles digestifs majeurs
`\thus`{=latex} insulinothérapie seulement après normokaliémie,
sinon arrêt cardiocirculatoire
- `\inc`{=latex} activité βadrénergique
- Paralysie périodique famililiale : exceptionnelle, paralysie brutale
transitoire des 4 membres
- Hyperaldostéronisme ou hypercorticisme : y penser si HTA (non
constante) et hypoK avec kaliurèse `\inc`{=latex}
- Polyurie : hyperglycémie `\inc`{=latex}
- Hypomagnésémie : si Mg `\dec`{=latex}, malabsorption, pertes
digestives causées par IPP. Sinon : pertes urinaires
acquises/génétique
- Bloc 11-βhydroxystéroïde déshydrogénase : tableau similaire à
hyperaldostéronisme primaire mais avec aldostérone `\dec`{=latex}.
Si HTA et hypoK, vérifier réglisse et pastis (glycyrrhizine)
### Hyponatrémie endocrinienne
HypoNa = anomalie électrolytique la plus commune chez hospitalisés
Osmolarité (mosm/L) : 2×(\[Na+\] + \[K+\]) + glycémie + urée
```{=latex}
\begin{figure}[htpb]
\centering
\resizebox{0.9\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
level distance=1.5cm,
edges={nodes={fill=white}},
layered layout]
{
Osmolalité -> {
Augmentée -> "Hyperglycémie";
Normale -> "HyperTG\\Hyperprotidémie";
Diminuée -> Volémie -> {
"Augmentée\\(hyperhydrat. extracell)" -> "Insuf cardiaque\\Cirrhose\\Sd néphrotique"
-> "Sérum salé\\isotonique";
"Normal\\(hyperhydrat intracell)" -> "Hypothyroïdie\\Insuf corticotrope\\SIADH"
-> "Sérum salé\\hypertonique";
"Diminué\\(déshydrat extracell)" -> "Perte digestives\\rénales, cérébrales\\Insuf corticosurrénales aigüe"
-> "Restriction hydrosodée";
};
};
};
}
\caption{Démarche diagnostique et ttt devant une hyponatrémie}
\end{figure}
```
Physiopatho : hormone anti-diurétique (ADH) : répond au stimulus
osmotique, volémique et stress etc. Action vasoconstrictive,
corticotrope (stress), antidiurétique
#### SIADH
PA et FC normale, pas de pli cutané, (déshydratation extra-cellulaire)
ni d\'oedème (hyperhydratation extra-cellulaire)
DD : cf figure. Si hyponatrémie hypoosmolaire normovolémique :
- insuf corticotrope : cortisolémie et ACTH
- insuf surrénale aigüe
- hyporthyroïdie proto-thyroïdienne : TSH `\inc`{=latex}
- hypopituitarisme antérieure : cortisolémie, TSH, T4L
Étioliogies :
- iatrogènes : neuroleptiques, antidépresseurs, chimio, carbamazépine,
desmopressine
- quasi toutes affections neuro, notament intervention
trans-sphénoïdale (adénome corticotrope)
- pulmonaires
- tumeurs malignes : cancer bronchique à petites cellules++
- rares : mutation récepteur V2 ADH, marathonien, VIH
- Intoxication aigüe à l\'eau
#### Traitement
Urgence si \< 115mmol/L ou {délire, coma, convulsion} `\thus`{=latex}
sérum salé hypertonique jusque Natrémie = 120mmol/L (puis restriction
hydrique).
☡ \< 12mmol/24h sinon tableau d\'AVC (myélinolysie centropontine) !!
Thérapeutique :
- restriction hydrique : mal tolérée
- déméclocycline : induit diabète inspidie néphrogénique
- aquarétique (tolvaptan)
Indications :
- symptômes cliniques sévères/récent : sérum salé hypertonique
- symptômes plus modérés : sérum et tolvaptan
- sinon restriction hydrique et tolvaptan (ou déméclocycline)
## 266 † Hypercalcémie
Diagnostic = double dosage calcémie. Étiologie selon parathormone (PTH)
Physio : calcémie régulée par PTH et calcitriol
- PTH: `\inc`{=latex} absorption intestinale du calcium et phosphore,
`\inc`{=latex} résorption osseuse, `\dec`{=latex} réabsorption
phoshpore et `\inc`{=latex} absorption calcium (rein)
- PTH régulée par récepteur sensible au calcium (CaSR)
Bio : calcémie totale = {calcium ionisé, calcium lié = {lié à
l\'albumine, complexé aux anions}}. Calcium ionisé ≈ 50% calcium
total[^63]
Clinique : asthénie, {polyuro-polydipsie, lithiases rénales}, {anorexie,
constipation, nausées}, {apathie, somnolence, confusion, psychose,
coma}, {HTA, `\dec`{=latex} QT}
☡ hyperglycémie maligne = urgence {} avec déshydratation, {confusion,
coma, insuf rénale} et risques de troubles du rythme cardiaque,
bradycardie avec asystolie
### Étiologies
#### Hypercalcémie PTH dépendante (PTH N ou `\inc`{=latex})
- **Hyperparathyroïdie[^64] primaire** (55%) : lésion parathyroïde.
- Signes cliniques précédents avec rénaux, osseux (clinique et
radio[^65]) `\thus`{=latex} créatinine plasmatique, scénal rénal
non injecté
- Surtout densité osseuse (tier distal du radius)
- Bio : hypercalcémie et PTH non adaptée (N ou `\inc`{=latex}).
- ☡ corriger déficit vitamine D avant doser calcémie.
- ☡ DD : sd hypercalcémie-hypocalciurie familiale,
hyperparathormonémie avec ttt au lithium
- calcémie et phosphorémie n\'ont de sens qu\'avec une
fonction rénale normale
- calciurie : si augmentée, enlève les DD précédents
- imagerie : bio primaire mais sert si indication opératoire
seulement (écho, scinti)
- étiologie :
- majorité : sporadique, isolé
- NEM1[^66] (1%) : hyperparathyroïdie primaire = 95%.
Recherche tumeurs endocrines pancréas et duodenum, adénomes
hypophysaires
- NEM2 : cancer médullaire de thyroïde puis phéochromocytome
bilat et hyperparathyroïdie primaire avec atteinte
multiglandulaire
- ☡ hyperparathyroïdie primaire chez jeune = suspicion
transimission génétiques
- hyperparathyroïdie *secondaire* : adaptation à hypocalcémie
(chercher chez insuf rénaux chronqiue)
- hyperparathyroïdie *tertaire* : insuf rénaux chronique
- **hypercalcémie-hypocalciurie familiale bénigne** : hypercalcémie,
hypophosphorémie, (hypermagnésémie), calciurie
`\dec`{=latex}`\dec{}`{=latex}, PTH inadaptées (N ou `\inc`{=latex})
- Lithium
#### hypercalcémie PTH-indépendante
- **Hypercalcémie des affections malignes** (30%) : PTH
`\dec`{=latex}`\dec{}`{=latex}.
- Tumeurs : poumon, sein, rein, tractus digestif
- Production tumorale de PTHrp (mime PTH)
- Autres :
- granulomatose : hyperphosphorémie, PTH `\dec`{=latex}
- iatrogènes : vitamine D (hypercalcémie, hyperphosphorémie, PTH
passe), vitamine A (asthénie sévère, douleurs musc et osseuse,
alopécie des sourcils, chéilite fissuraire), diurétiques
thiazidique, buveurs de laits (plutôt fortes doses d\'antiacide
ou carbonate de calcium)
### Traitement
Hyperparathyroïdie primitive : guérison par ablation des adénome(s) par
chir conventionnelle ou mini-invasive (faire imagerie avant !)
Sinon, traitement palliatif : bisphosphonates (inhibe résorption
osseuse), calcimimétiques (`\dec`{=latex} PTH),
☡ Hypercalcémie maligne = urgence {} :
- sérum phy
- bisphosphonate en perf lente ou corticothérapide IV
(myélome/hémopathie) ou dialyse (maligne)
## 303 † Tumeurs de l\'ovaire (hormono-sécrétante)
### Sécrétant des oestrogènes
Tumeurs de la granulosa :
- malignes, les plus fréquentes des tumeurs des cordons sexuels et du
stroma.
- plutôt femmes \[30,50\] ans
- jeune fille : pseudo-puberté précoce. Femme :
aménorrhées/ménométrorragie. Ménopausée : saignement vaginal dû à
hyperplasie endométriale[^67]
- ttt : ovariectomie unilatérale mais récidives 10-33%
Thécomes :
- très rare, surtout péri-/post-ménopause
- Tumeurs solides, bénignes `\thus`{=latex} exérèse = guérison
Sd Peutz-Jeghers (très très rare)
### Sécrétant des androgènes
Tumeurs à cellules de Sertoli-Leydig
- sécrète testostérone
- rare. Y penser si hirsutisme récent avec signes de virilisation
- DD : corticosurrénalome (faire scanner surrénales), sd Cushing
(faire freinage minute), block 21-hydroxylase (doser
17-hydroxyprogestérone)
- femme 30-40ans
- détecté à l\'écho ovarienne vaginale ou IRM pelvienne
- si \< 5 cm, bon pronostic `\thus`{=latex} ttt conservateur chez
femme jeune
Tumeurs à cellules de Leydig
- cristaux de Reinke (caractéristique)
- typiquement : virilisantes chez ménopausée
- petite taille, bénigne `\thus`{=latex} ovariectomie bilatérale
Tumeurs germinales sécrétantes
- tumeur ovarienne sécrétant de l\'hCG : chez femme jeune, aménorrhée,
douleurs abdo/métrorragie. Tttt : conservateur si jeune, chimio si
étendu
- gonadoblastome : chez sd de Turner avec mosaïque et chromosome Y
(risque 7-20%) `\thus`{=latex} gonadectomie préventive
- autres : sécrétant hCG, T4, sérotonine
## 305 † Tumeurs du pancréas (endocrine)
Rare, concerne pancréas et duodénome. Diagnostic histologique,
compléteté par immunohistochimie
Pronostic péjoratif : \> 2 cm, invasion vasculaire, dissémination
métastase
Sécrétion Clinique
----------- -------------------------------------------------------------------
Insuline Hypoglycémie organiques
Gastrine Ulcère oestro-gastro-duodénaux, diarrhées
ACTH Cushing
Glucagon Diabète, érythème migrateur, diarrhée, amaigrissement, thromboses
VIP Diarrhée hydroélectrolytique profuse, hypokaliémie
GHRH Acromégalie
: Caractéristiques des tumeurs endocrines duodéno-pancréatiques
Imagerie : scanner spiralé TAP ± IRM abdo
Formes familiales : NEM1, neurofibromatose 1, von Hippel-Lindau
## 310 † Tumeurs du testicule (aspects endocriniens)
Prévalence : 9/100 000, ado/adulte jeune
### Tumeurs stromales
Cellules de Leydig. Unilatérales, bénignes
- Garçon \< 9 ans : pseudo-puberté précoce `\thus`{=latex}
testostérone plasmatique, écho testiculaire
- Adulte : féminisation, infertilité `\thus`{=latex} oestradiol
`\inc`{=latex}, testostérone N ou `\dec`{=latex}
Cellules de Sertoli : rares (enfant) ou exceptionnelles (adulte).
Féminisation/pseudo-puberté précoce à 50%. Testostérone/oestradial
`\inc`{=latex}, LH et FSH `\dec`{=latex}, inhibine B
`\inc`{=latex}.[^68]
### Autres
- Tumeurs germinales : fréquentes, écho testiculaire
- séminomateuses : fréquentes, pronostic bon
- non séminomateuses : pronostic réservé
- Inclusion surrénaliennes : par excès ACTSH. Marqueur :
17-hydroxyprogestérone
### PEC
Glucocorticoïdes si inclusion surrénaliennes. Sinon chir 1ere intention.
Chimio si métastases pulmonaires/ganglionnaires.
## Annexes
### Hormones
```{=latex}
\begin{figure}[htpb]
\centering
\resizebox{!}{5cm}{
\tikz \graph [decision]
{
ht/hypothalamus[organ] -> ["CRH"] hh/hypophyse[organ] -> ["ACTH"] cs/corticosurrénale[organ];
cs -> cort/cortisol;
cort ->[bend left=60, "-"] ht;
cs -- ["+"] hh;
hh --["+"] ht;
};
}
\resizebox{!}{5cm}{
\tikz \graph [decision, layer distance=1.5cm]
{
ht/hypothalamus[organ] -> ["GnRH"] hh/hypophyse[organ] -> "FSH, LH" -> {
testicules[organ] -> test/testosterone;
ovaires[organ] -> est/estrogène;
};
test -> [bend left=70, "-"] ht;
test -> [bend left=60, "-"] hh;
est -> [bend right=70, "-"] ht;
};
}
\resizebox{!}{5cm}{
\tikz \graph [decision, layer distance=1.5cm]
{
ht/hypothalamus[organ] -> ["TRH"] hh/antéhypophyse[organ]
->["TSH"] th/thyroide[organ] -> ["T4"] "foie,muscles" -> "T3";
th -> [bend left=60, "-"] hh;
th -> [bend left=70, "-"] ht;
};
}
\resizebox{!}{5cm}{
\tikz \graph [decision, layer distance=1.5cm]
{
ht/hypothalamus[organ] -> ["GHRH"] hh/hypophyse[organ] -> ["GH"] Foie[organ] -> "IGF-1" -> {
os;
muscle;
graisse..;
}
};
}
\end{figure}
```
Zone de la surrénale Hormones
------------------------- -----------------------------------
corticale (glomerusa) minéralocorticoïdes (aldostérone)
corticale (fasciculata) glucocorticoïdes (cortisol)
corticale (reticularis) androgènes
médullaire épinephrine, norepinéphrine
: Hormones produite par les surrénales (du moins au plus profond)
### Syndromes génétiques
Klinefelter Turner Kallmann
------------------ ------------------------------ ----------------------------- -------------------------------
Sexe ♂ ♀ ♂, ♀
Frequence 1/500 1/2000 ♀ 1/30 000 ♂, 1/250 000 ♀
Caryotype 46 XX,Y genes manquants
sur bras court d\'un chr. X
Caractéristiques Hypogonadisme, infertilité Petite taille Anosmie
gynécomastie Aménorrhée ♂ : Micropénis, cryptorchidie
trouble apprentissage, comm. Pas de seins ? Pas de dev. sexuel secondaire
# Pneumologie
## 73 Addiction au tabac
Tabagisme : primaire (inspiré), secondaire (passif++), tertiaire
(exhalé) Produits : nicotine (dépendance), fumée de tabac (0.3 μm),
goudrons (cancérigène), CO (hypoxie, risque ischémie)
16 millions de fumeurs en 2013 (France). Éducation et cat. sociale
faible = plus tabagiques
##### Pathologies liées au tabac
- K : *broncho-pulmonaires* (90% dû à actif, 25% au passif). Voies
aérodigestives sup, vessie, pancréas, rein, col de l\'utérus
- Respiratoires : BPCO, asthme
- CV: cardiopathies ischémiques, artérite, HTA, cérébro-vasculaires,
athérome,
maladie coronaire
- Autres : digestives, kératites, retard consolidation os, agueusie,
anosmie
Passif :
- +25% risque cancer bronchique, +25% maladies CV, aggrave asthme,
BPCO
- nourrisson : RCIU[^69], $\nearrow$ risque infections respi,
mort-subite (1ere cause identifiée)
##### Prise en charge
Évaluer : consommation (paquets/années), dépendance, autres (alcool =
déclencheur, cannabis), motivation, comorbidités (psy, CV, respi)
##### Traitement
Conseil, motivationnel.
Substitut nicotinique, varénicline \[☡ suivi\], bupropion), TCC,
cigarette électronique
Sevrage : réussi si $\ge 1$ an
## 108 - Troubles du sommeil
##### Définitions
SAOS =
- somnolence diurne non expliquée
- *ou* 2 parmi {ronflements, étouffement, éveils répétés, sommeil non
réparateur, fatigue diurne, trble concentration, nycturie)}
- *et* IAH[^70] ≥ 5 [^71]
NB: Apnée obstructive (arrêt débit), centrale (idem, [sans]{.underline}
efforts ventilatoires) ou mixte
##### Épidémiologie
2% des ♀, 4% des ♂.
FR : obésité, homme, âge, anomalie voie aériennes supérieures.
Comorbidités : *somnolence diurne excessive*, HTA, AVC, maladie
coronaire, sd métabolique [^72], diabète, dylipidémie
##### Diagnostic
Suspicion clinique, confirmation par polygraphie
- clinique : nuit = {ronflements, pause respi, étouffement, nycturie},
journée = somnolence excessive (questionnaire d\'Epworth)
- examen : IMC, obésité abdo ($\ge$ 94 cm ♂, 80cm ♀), ORL[^73], CV,
respi
- polygraphie [^74] ou polysomnographie[^75] (cher++)
- faire aussi EFR (dépistage BPCO) et gaz du sang (complications
BPCO + SAOS)
DD : hypersomnie diurne (insomnie, sd dépressif, sédatif, hygiène de
sommeil, neuro)
##### Traitement
- Général : PEC[^76] surpoids, éviction {benzodiazépines,
myorelaxants, morphiniques}, PEC CV
- *Pression positive continue*[^77]. Sinon : orthèse d\'avancée
mandibulaire, voire chir
##### Autres
- Sd d\'apnée de type central : IC sévère, atteinte tronc cérébral,
séjour altitude, morphiniques
- Hypoventilation alvéolaire : Traitement = VNI
- Sd obésité hypoventilation[^78] : Traitement = VNI
## 151 † - Infections broncho-pulmonaires communautaires
### Bronchite aigue
Très fréquente, virale 90%.
Diagnostic clinique : épidémie, toux sèche $\to$ productive,
expectorations, [pas]{.underline} de crépitants.\
Ttt symptomatique seulement ! (pas d\'ATB, ni corticoïdes...)
### EBPCO (cf chap BPCO)
### Pneumonie aigue communautaire
##### Diagnostic
Radio
- Clinique : {toux, expect purulentes, dyspnée} + {fièvre, asthénie} +
crépitants
##### PEC
Si `\faHospital`{=latex} : hémocultures, ECBC, antigenurie pneumocoque
(± PCR, antigenurie légionelle)\
`\faHospital`{=latex} : signes de gravité (score CRB65[^79] ge ) /
incertitude / échec domicile / comorbidité / inobservance
##### Étiologies (Tab [tab:etio_pneumopathies](tab:etio_pneumopathies)
Pneumocoque Atypique Légionellose
----------- --------------------------------- ----------------------- -----------------------------
Début Brutal Progressif Rapidement progressif
Signes Thoraciques Extra-thoraciques Myalgie, digestif
Biologie Anémie hémolytique Hyponatrémie, rhabdomyolyse
Microbio CG+ chainettes/Ag pneumocoque + Ag légionelle +
RX thorax condensation systématisée Opacités multifocales CS ou OM
: Orientation clinique (non discriminant !)
- Pneumocoque : fréquent+++. Pas de transmission interhumaine
- Atypique : `\bact{mpneumoniae}`{=latex},
`\bact{cpneumoniae}`{=latex}, `\bact{psitacci}`{=latex}
- Legionnella : pas d\'isolement. DO
- Pneumonie virale : signes respi + sd grippal. Grippale = diagnostic
PCR, traitement = inihbiteur neuramidase ☡ `\bact{dore}`{=latex}
##### Traitement
Urgent, probabiliste. Oral, 7j[^80] Réévalué 48-72h
- Ambulatoire : *Amoxicilline* ou *macrolide* $\to$ switch
- `\faHospital`{=latex} *Amoxicilline* $\to$ réévaluation
- Réa : *C3G IV + macrolide IV* / *FQ* pour pneumocoque
Échecs :
- épanchement pleural, abcès, obstacle
- observance, pharmacocinétique, hors spectre
- diagnostic (EP, PID aigǜes, K, tuberculose pulmonaires, infarctus
pulmonaire, vascularite...)
##### Prévention
Vaccin : 2 doses + rappel enfant, 2 doses adulte (ID, comorbidité)
##### Immunodéprimé
Pneumocystose pulmonaire :
- RX : sd interstitiel diffus bilatéral symétrique.
- ATB cotrimoxazole 21j
## 180 † - Accidents du travail
Maladie professionnelle = lente, prolongée ($\neq$ accident du travail)
### Maladies
#### Asthmes
10-15% des asthmes. On a
- asthme professionnel : (avec latence \[immunologique\]) ou (sans
latence \[exposition unique\])
- asthme aggravé par le travail
Métiers : boulangers, santé, coiffeurs, peintres pistolets, bois,
nettoyage\
Diagnostic : de novo, profession, rythme
#### BPCO
[TVO]{acronym-label="TVO" acronym-form="singular+short"} lente
progressive + inflammation poumons. Facteurs professionnels = 10-20%
BPCO\
Métiers : mines, BTP, fonderie, textile, agricole
#### Cancers
- mésothéliome : 2/100 000habi/an, amiante++, DO
- K bronchique primitif
#### Pneumopathie interstitielle diffuse (PID)
- Pneumopathie d\'hypersensibilité : agricole
- Silicose (+cancer bronchique primitif)
- Bérylliose : adénopathies médiastinales, sd infiltrant
parenchymateux
- Sidérose : fumées d\'oxyde de fer, micronodule `\textpm{}`{=latex}
emphysème
- Asbestose : fibrose
#### Liées à l\'amiante
- Cancer : mésothéliome, cancer bronchique primitif
- Pleural (plaques, épaississements, pleurésies), parenchyme (fibrose)
### Reconnaissance
3 conditions : médicale, administrative, professionnelle.
Déclaration à la CPAM (employeur si AT, sinon victime)
Indemnité[^81]
- 60% salaire si \< 28 jours, 80% sinon
- si séquelles, selon taux incapacité permanente : capital (\< 10%),
rente (\> 10%), rentre et autres (\> 40%)
## 182 † - Hypersensibilités et allergies respiratoires
```{=latex}
\begin{figure}[htpb]
\centering
\resizebox{0.5\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
HS non allergique;
HS allergique -> {
Non IgE;
IgE -> {
atopique -> "insectes\\helminthes\\médicaments";
non atopique -> "rhinite\\asthme\\alimentaire\\professionelles";
};
};
};
}
\caption{Hypersensibilité}
\end{figure}
```
### Définitions
Atopie : prédisposition héréditaires à IgE face à des allergènes.\
Allergie : réaction d\'HS par mécanismes immunologiques\
Sensibilisation : test cutané positif à un allergène\
Allergène : capable d\'induire une réaction d\'HS = pneumallergènes
(aéroportés), trophallergènes (alimentaires), professionnels,
recombinants
Hypersensibilité :
- type 1 (immédiate) : la plus fréquente, IgE. Rhinite, asthme
- type 2 : complément et phagocytose. Réactions médicament.
- type 3 : complexes immuns. Pneumonies d\'HS
- type 4 : LT, cytotoxiques 48-72h. Granulome épithélioïde
gigantocellulaire. Dermato.
#### Asthme et rhinite allergique
Polygénique.\
Environnement : infections virales, sensibilitations pneumallergènes,
tabac dès conception, pollution air intérieur.
#### Anomalies voies aériennes (asthme)
Remodelage bronchique : épaississement (membrane basale et muscle lisse
$\wedge$ oedème bronchique) et obstruction $\diameter$ (mucus)
#### Réaction IgE
- Sensibilisation : synthèse IgE spécifiques (lymphocytes B)
- effectrice : fixation de l\'allergène `\thus`{=latex} activation
(histamine, cytokines) `\thus`{=latex} cascade allergique
### Épidémiologie
Atopie = 30-40% population. HS médicament = 7% pop. Allergie alimentaire
: 2% des 9-11 ans
FR :
- génétique (enfants à risque)
- environnement : fréq $\nearrow$ temps, alimentaires, tabagisme
passif maternel, allergènes, pollution atmosphérique ☡ niveau de
preuve
Morbidité forte, mortalité encore forte pour l\'asthme.
### Diagnostic
Clinique : asthme, rhinite, conjonctivite
#### Diagnostic
Unité de temps, lieu et action (perannuels \[acariens, blattes, phanères
d\'animaux, végétaux d\'intérieur, moisissures\] ou saisonniers
\[pollens\]) $\wedge$ IgE spécifiques
Prick-test = référence.
- \$⌀ ≥ 3\$mm / témoin
- acariens, pollens, phanères d\'animaux, blatte, moisissures chez
l\'adulte
- arachide, blanc d\'oeuf, poisson, lait de vache si \< 3 ans
- CI : antihistaminiques, $\beta$-bloquants, eczéma, grossesse si
allergie médic
Autres tests : dosage IgE spécifique (moins sensible), multiallergénique
(sensible mais pas quantitatif)
#### Professionnelles
Boulangers, santé, coiffeurs, peintres pistolets, bois, nettoyage
#### Autres
- Test de provocation = certitude mais dangereux
- Très sécifique : dosage IgE totale, dosage éosinophiles sanguin,
dosage tryptage sérique
### Traitement
#### Éviction allergènes Toujours.
#### Symptomatiques
- antihistaminiques : rhinite, conjonctivite, prurit
- corticoïdes : systématique si urgence (prednisone, prednisolone),
local si traitement fond
#### Immunthérapie spécifique
Faibles doses croissantes d\'allergènes :
- Sous-cutanées/sub-linguale : acariens, pollens, hyménoptères
- orale : pollen
CI : maladies allergiques, dysimmunités, grosses (induction), asthme
sévère non contrôlé, mastocytoses, $\beta$-bloquants
ES :
- syndromique (asthme, rhinite, urticaire) = alerte
- générale (hypotensions, bronchospasme, choc anaphylactique) =
interruption
## 184 † - Asthme, rhinite
Asthme 6%, mortalité 1000 DC/an, en baisse. Morbidité en hausse
Rhinite allergique 24%.
### Définitions
Asthme :
- inflammation chronique modifiant les VAS avec symptômes respi et
obstruction voies aériennes réversible
- interaction gènes-environement, déclencheurs : exercice, HS
aspirine/AINS, irritants inhalés
TVO :
- [VEMS]{acronym-label="VEMS" acronym-form="singular+short"}/CVF \<
0.7
- réversible si +200mL et +12% après BDCA[^82]
Hyperréactivité bronchique : -20%VEMS après métacholine/air sec (VPP =
100%)
Débit expiratoire de pointe (pour urgence)
### Diagnostic
#### Asymptomatique
Diagnostic :
- symptômes caractéristiques (20 min, réversible, variable)
- plusieurs parmi {gêne respiratoire, dyspnée, sifflements,
oppression thoraciques}
- $\nearrow$ nuit/réveil, variable,réversibles, déclenché par
{rire, exercice virus, allergènes, irritants}
- **et** obstruction bronchique : sibilant, TVO réversible ou apparaît
avec métacholine
Sévérité évaluée à 6 mois
#### Exacerbation
↗ symptômes \> 2 jours, non calmée, sans retour état habituel
Signes de sévérité :
- mots (au lieu de phrases), assis en avant, agité
- FR \> 30/min
- muscles respi annexes
- FC \> 120/min, SpO$_{\text{2}}$ \< 90%
- DEP \< 50%
- silence auscultatoire
- respi paradoxale
- troubles conscience, bradycardie, collapsus
#### DD
Sans TVO : cordes vocales, sd hyperventilation
TVO non réversible : {BPCO, bronchectasies, mucoviscidose, bronchiolites
constrictives}, autres (corps étranger, tumeur, insuf. cardiaque)
#### Bilan
Facteurs favorisants, radio thorax, EFR (+test métacholine)
### Traitement
#### Long cours
Ttt de fond : cf Table\~`\ref{tab:ttt_asthme}`{=latex}
```{=latex}
\begin{table}
\centering
\begin{tabular}{ccccc}
\toprule
Palier 1 & Palier 2 & Palier 3 & Palier 4 & Palier 5 \\
\midrule
CSI faible & ALT & CSI moyen/fort & triotropium & CSO faible\\
& & ou (CSI faible et ALT) & ou (CSI fort et ALT) &\\
\bottomrule
\end{tabular}
\caption{Ttt de fond de l'asthme (\textbf{BDCA à la demande}).\\
CSI = Corticostéroïdes inhalés. ALT =
anti-leucotriènes. CSO = Corticostéroïdes oraux}
\label{tab:ttt_asthme}
\end{table}
```
Autre :
- activité physique (sauf plongée)
- facteurs favorisants : rhinite, allergie, tabac, $\beta$-bloquant
(aspirine/AINS), RGO, comorbidités
- vaccins grippe (pneumocoque si asthme sévère)
Efficace ?
- symptômes contrôlés (diurnes \< 2/sem, pas de réveil nocture, BDCA
\< 2/sem, pas limitation d\'activité)
- exacerbations \< 2 corticostéroïdes systém./an
- VEMS/CV \> 0.7 et VEMS $\ge$ 80 %
Si non contrôlé
- CSI faible + BDLA[^83] \< CSI moyen/fort + BDLA \< centre spécialisé
Suivi : périodique, +3mois si changement ttt, mensuel si grossesse
#### Urgence cf figure\~[fig:asthme_urgence](fig:asthme_urgence)
```{=org}
#+name: fig:asthme_urgence
```
```{=latex}
\begin{figure}[htpb]
\centering
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Évaluation" -> {
"Exacerbation\\
sans signes de gravite" ->
"\(\beta_2\) mimétique forte doses\\
chambre inhalation\\
\textbf{Corticothérapie orale} 7j" [draw]
-> Réévaluation 1H;
"Exacerbation \\
avec signes de gravite" ->
"\(\beta_2\)-mimétique forte dose" [level distance=2cm] -> {
"O\(_2\)\\
\(\beta_2\) mimétique nébulisés (5mg/20min)\\
$\pm$ ipratropium\\
\textbf{Corticothérapie orale} " [>"\faHospital", draw];
};
Perte de contrôle ->
"\(\beta_2\) mimétique" [draw] -> Réévaluation 1H;
};
};
\caption{Asthme : traitement d'urgence}
\end{figure}
```
Pas d\'ATB sauf si suspicion bactérienne. Adrénaline seulement pour choc
anaphylactique ☡ pas de BDLA
### Rhinite allergique
Diagnostic :
- PAREO : prurit, anosmie, rhinorrhée, éternuement, obstruction nasale
- fosses nasales au speculum inflammées
- allergique (argumenter !!)
Sévère si persistant (\> 4 semaines/an) et retentissement qualité de vie
TDM
Ttt : laval nasal, allergie, antihistaminique/corticoïdes nasaux, tabac,
stress
## 188 †, 189 Pathologies auto-immunes
Manifestations respi. viennent de (par priorité décroissante) :
- infectieuse (favorisé par ttt)
- toxicité médicamenteuse
- spécicifique
- indépendant
### Complications infectieuses
Immunodépression :
- corticoïdes forte dose \> 1 mois
- méthotrexate
- cyclophosphamide
- anti-TNF$\alpha$ (infliximab)
Tuberculose :
- clinique semblable à l\'ID = 50% extrapulmonaire, 25% disséminé
- prévention si TNF-$\alpha$ : INH 9 mois ou INH-RMP 3 mois
Pneumocystose : si corticoïdes forte dose ou méthotrexate ou
cyclophosphamide
- clinique : début brutal, insuf. respi, mortalité élevée
- radio thorax : condensation alvéolaire/verre dépoli bilat
- penser co-infections
### Médicaments
Méthotrexate : plus fréquent, pneumopathie d\'HS (opacités diffuses),
[LBA]{acronym-label="LBA" acronym-form="singular+short"} lymphocytaire.
Évolution favorable à l\'arrêt + corticothérapie
Inhibiteurs TNF-$\alpha$ : PID/granulomatoses, anaphylactique
### Connectivites
Polyarthrite rhumatoide
- PID[^84] : radio = réticulations, rayons de miels, bronchectasies.
Surveillance seulement
- pleurésie rhumatoïde : unilatérale, peu abondante, exsudative.
Évolution favorable
- nodules pulmonaires rhumatoïdes.
- bronchiolite oblitérante
Sclérodermie systémique : CREST (Calcinose, Raynaud, dyskinésie
oEsophagienne, Sclérodactyie, Télangiectasie), Ac anti-nucléraires
- PID : semblable à PINS[^85] : opacités en verre dépoli,
bronchectasies par traction. Survie 85% à 5 ans
- HTA pulmonaire : dyspnée. Echo. cardiaque + cathéterisme cardiaque
Lupus érythémateux disséminé
- pleurésie lupique : peu abondant, svt bilatéral, svt + péricardite
- infectieux, sd hémorragie alvéolaire
Dermato-, polymyosite
- PID chronique : 1ere cause DC, opacités verre dépoli,
[LBA]{acronym-label="LBA" acronym-form="singular+short"}
lymphocytaire. Ttt : corticothérapie + IS
- PID (sub)aigüe
Sd de Gougerot-Sjögren
- bronchite lymphocytaire chronique : toux sèche chronique
- PID, lymphome pulmonaire primitif
### Vascularites
Granulomatose avec polyangéite : 40-50ans, début ORL+ poumon (+ rein)
- radio : nodules s\'excavant, opacités verre dépoli
- Ttt urgent = corticothérapie, cyclophosphamide
Granumolatose éosinophilique avec polyangéite : hyperéosinophilie,
pneumopathie éosino.
Polyangéite microscopique : sd hémorragique alvéolaire
## 199 † Dyspnée aigüe et chroniques
Examens : ECG, RX thorax, gaz du sang, D-dimère, BNP, NFS a minima
### Aigüe
= quelques heures/jours
Détresses respi aigüe :
- cyanose
- sueur
- FR \> 30/min ou \< 10/min
- tirage, muscle respi accessoires
- respi abdo paradoxale
Hémodynamique :
- FC \> 110/min
- choc (marbrures, oligurie, angoisse, extr. froides)
- PAS \< 80 mmHg
- insuf. ventriculaire droite (turgescence jug, OMI, signe Harzer)
Urgence !!
Voir table\~`\ref{tab:dyspnee_aigue}`{=latex}. Autres :
- cardiaque : tamponnade[^86], troubles
(supra)-ventriculaire, choc cardiogénique
- pulmonaire : SDRA, décompensation aigüe, atélectasies, trauma
```{=latex}
\begin{table}[htbp]
\caption{Étiologies de dyspnée aigüe}
\label{tab:dyspnee_aigue}
\centering
\begin{adjustbox}{max width=\textwidth}
\begin{tabular}{lll}
\toprule
Inspiratoire & Expiratoire & Sinon\\
\midrule
corps étranger (enfant) & asthme (jeune, allergie, sibilants) & EP
(ascul. normale,
douleur
thoracique, phlébite)\\
épiglottite (enfant) & BPCO (tabac, bronchite aigüe, sibilants) & pneumothorax,
épanchement
pleural (sd
pleural,
douleur thoracique)\\
laryngite (enfant) & OAP (âgée, crépitants, expector mousseuse) & pneumopathie
infectieuse
(sd
infectieux,
douleur thoracique)\\
\oe{}dème de Quincke (terrain)& & OAP (âgé, orthopnée, crépitants, expector mousseuse)\\
& & \\
\bottomrule
\end{tabular}
\end{adjustbox}
\end{table}
```
### Chronique
cf table\~`\ref{tab:dyspnee_chronique}`{=latex}. Autres :
- Cardiaque:constriction péricardique
- Pulmonaire : (restrictif) pneumoconioses, post-tuberculose,
paralysie phrénique, cyphoscoliose, obésité morbide
- HTAP
- HT pulmonaire post-embolique
```{=latex}
\begin{table}[htbp]
\caption{Étiologies de dyspnée chroniques}
\label{tab:dyspnee_chronique}
\centering
\begin{adjustbox}{max width=\textwidth}
\begin{tabular}{lll}
\toprule
Sibilants & Crépitants & Auscult normale\\
\midrule
BPCO& PID (toux sèche, maladie systémique) & EP/maladie vasculaire pulmonaire \\
asthme& Insuf cardiaque gauche & Neuromusc \tablefootnote{signe neuro, orthopnée, respi abbdo paradoxale} \\
Insuf cardiaque gauche (ATCD cardiaque, orthopnée, toux) & & Parétiale
(obésité, scoliose)\\
&& Hyperventilation\tablefootnote{C normal, vertige, $\ne$ effort, paresthésie}\\
\bottomrule
\end{tabular}
\end{adjustbox}
\end{table}
```
Quantification : échelle Borg \[0-10\] (aigüe) ou MRC \[0-4\]
(chronique)
## 200 † Toux chronique
☡ Éliminer toux post-infectieuse (\< 3 semaines)
Signes de gravité :
- AEG, sd infectieux
- dyspnée d\'effort, hémoptysie
- modification toux chez fumeur
- dysphonie, dysphagie, fausses routes
- adénopathies cervicales suspectes
- anomalies cardiopulmonaires
```{=latex}
\begin{figure}[htpb]
\centering
\caption{PEC initiale d'une toux chronique}
\resizebox{0.6\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
level distance=40pt,
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
Signe de gravité -> {
Exploration ["oui"];
"Médicaments ?" ["non"] -> {
Test d'éviction ["oui"];
"Coqueluche ?" ["non"] -> {
Test diagnostique ["oui"];
"Radio thorax anormale ?" -> {
Bilan spécialisé ["oui"];
"cf~\nameref{subsec:toux_orientation}" ["non"];
};
};
};
};
};
}
\end{figure}
```
### Orientation diagnostique
```{=latex}
\begin{tcolorbox}
Rhinorrhée chronique, RGO, asthme, tabac, médicaments\footnote{IEC, inhib angiotensine II, \beta{}-bloquants}, coqueluche
\end{tcolorbox}
```
\*ORL\*
- rhinosinusiens : sd rhinorrée postérieur++, obstruction nasale
chronique
- carrefour aérodigestif : diverticule de Zenker, laryngite chronique
**Respiratoire**
- Asthme : TVO réversible/hyperréactivité bronchique
- BPCO : TVO non réversible
- Cancer bronchique, tumeurs, bronchectasise (cf
`\nameref{sub:bronchectasies}`{=latex})
**RGO** : pyrosis. Endoscopie digestive si FR, pHmétrie des 24h
**Allergique**
**Systémique** : sd Gougerot-Sjögren, polychondrite atrophiante, maladie
de Horton, granulomatose avec polyangéite, rectocolite hémorr., maladie
de Crohn.
**Comportement** : dernière étiologie
#### Traitement d\'épreuve (ordre d\'échec):
1. RGO : bromphéniramine + pseudoéphédrine 3 sem
2. asthme si TVO réversible, corticoïdes inhalés ou bronchodilatateurs
inhalés si hyperréactivité bronchique
3. avis spé
Traitement symptomatique : arrêt tabagisme. Éviter si possible
- si toux sèche : opiacés, antihistaminique anticholinergique, non
antihistaminique non opiacés
- si toux productive : mucomodificateurs, kiné
### Bronchectasies (DDB)
Types : bronchectasies (élargissement $\diameter$), bronchocèle (pus),
\"par traction\" (NB: pas des vraies bronchectasies)
Étiologie :
- infection respi sévères : coqueluche, tuberculose (virales respi
enfant, pneumonie bact, suppuration suite sténose)
- mucoviscidose
- non infectieux (poumon radique, aspergillose allergique, SDRA,
systémique, déficit immunitaire)
Évolution : colonisation bactérienne, hémoptysie, TVO (car dilatation
seulement proximale), insuffisance respi
Clinique :
- toux productive quotidienne depuis l\'enfance
- hémoptysie
- EC : (râles bulleux à l\'auscult), (hippocratisme digital)
- infections à {`\bact{influenzae}`{=latex},
`\bact{pneumocoque}`{=latex}} puis {`\bact{dore}`{=latex},
`\bact{aeruginosa}`{=latex}++}
Diagnostic : TDM (certitude) = $\diameter_\text{bronche}$ \>
$\diameter_\text{artère}$, lumière bronchique \> 1/3 parenchyme, pas de
réduction du $\diameter$, grappes de kystes, opacités tubulées
Traitement : ATB si exacerbation, complications parenchymateuses.
Macrolides pour l\'inflammation. Chir si très local + compliqué.
## 201 † Hémoptysie
Urgence
1. Est-ce une hémoptysie ? Hématémèse ou ORL possibles
2. Gravité ? Suivant abondance, terrain, persistance `\thus`{=latex}
risque = hématose et asphyxie
### Étiologies
- Tumeurs bronchopulmonaires++
- Bronchectasies++
- Tuberculose (évolutive/séquelles)++
- Idiopathique++
- Infections : aspergillaires, pneumopathie infectieuses nécrosante
- Vasc : embolie pulmonaire, HT pulmonaire, anévrysmes/malformations
- Hémorragie alvéolaires : insuf. cardiaque gauches,
médicaments/toxiques, vascularites, collagénose, sd Goodpasture
### Diagnostic
Localisation (important !)
Interrogatoire : ATCD respi, cardiaque, histoire médicale
Examens
- clinique : {$SpO_2$, tension, pouls}, mauvaise tolérance respi, gêne
latéralisée, hippocratisme digital
- radio thorax pour siège (verre dépoli/sd alvéolaire), lésion
- scanner plus précis : nature, localisation, carto. vasc.
- (endoscopie : hématémèse, multiples lésions, tumeur proximale)
- (artériographie bronchique : ttt par embolisation)
- autres : gaz du sang, dosage Hb, bilan coagulation, groupe sanguin,
{BK, ECG} si suspicion OAP hémorragique
☡ BPCO $\centernot\implies$ hémoptysie
### Traitement
$O_2$ + vasconstriction IV, protection voies aériennes (décubitus
latéral, ventilation mécanique)
Embolisation artérielle bronchique
Chir si localisé, fonction respi OK et \"à froid\"
## 202 Épanchement pleural
##### Diagnostic
Suspicion clinique, confirmé par imagerie
- douleur thoracique *dépendant de la respiration*, dyspnée, toux
sèche *au changement de position*, hyperthermie
- examen : sd pleural liquidien (silence auscult, matité, $\emptyset$
transmission corde vocales, souffle pleurétique)
- ☡ Signes de gravité : détresse respi, choc septique, choc
hémorragique
Imagerie
- RX : opacité dense, homogène, non sytématisé, limité par ligne
concave[^87]
- échographie pleurale (différencie pleurésie et collapus, guide
ponction)
- TDM : en urgence si embolie pulmonaire ou hémothorax
##### Causes
*Transsudats (protides \< 25g/L)* : IC G, cirrhose, sd néphrotique,
atélectasie (EP)
*Exsudats (protides \> 35 g/L)*[^88] Cf tab
[tab:pleural_exsudat](tab:pleural_exsudat)
Catégorie Cause CAT
-------------- -------------------------- -------------------------------------------- -------------------------------------------------------------------------------------------------------
Néoplasiques pleurésie métastatique++ poumon, sein, œsophage, colon scanner, biopsie aveugle/vue biopsie aveugle/vue
mésothéliome exposition amiante biopsie++ (thorascopie++)
RX: épaississement pleural circonférentiel
, rétraction hémithorax
Infectieux bactérien ATB ± évacuation si compliqué`\tablefootnote{Épanchement abondant, germes, liquide purulent}`{=latex}
virale
tuberculose progressif, amaigrissement biopsie pleurale++
: Étiologies des exsudats (néoplasique, infectieux)
Autres : EP, bénigne liée à l\'amiante (exclusion++), post trauma
(rupture oesophagienne, sous-diaphragme), systémique (lupus,
polyarthrite rhumatoide)
##### Ponction
En majorité (sauf si peu abondant et insuf cardiaque G[^89] ). En
urgence si fébrile, hémothorax ou mauvaise tolérance. Tout évacuer
seulement si étiologique ou non cloisonné
##### Biologie 1ere intention
Biochimie (trans- ou exsudat), cytologie (cf
[tab:etio_exsudat](tab:etio_exsudat)), recherche germes pygènes,
mycobactéries
Cellules tumorales Neutrophiles Lymphocytes Éosinophiles
------------- ---------------------- -------------------- ------------- ----------------------
Néoplasique Métastasique Cancer Cancer
Mésothéliome Lymphome
Hémopathies malignes
Infectieux Parapneumonique Tuberculose Parasitose
Autres Embolie pulmonaire Sarcoïdose Hémothorax
Pancréatite Chylothorax Pneumothorax
Sous-phrénique PR, lupus Embolie pulmonaire
Oesophage Asbestosique bénigne
Médicament
: Épanchements pleuraux avec exsudats : étiologies
## 203 † Opacités et masses thoraciques
- \< 3mm : micronodules
- \$\[3,30\]\$mm : nodules
- \> 30mm : masses
### Nodules
Origine maligne probable si :
- homme, \> 50 ans, fumeur
- carcinogènes professionnels, \> 1cm (\> 3cm ++)
- contours spiculés, polylobés, irrégulier
- attire structures proches
- augmente de taille
- pas de calcifications
- fixe TED-FDG
Certitude = histologie (ponction transpariétale à l\'aiguille)
**Tumeurs malignes**
- cancers bronchopulmonaires primitifs : \> 50 ans, fumeur, souvent
nodule solitaire
- secondaires (métastases) : opacités rondes régulières
**Tumeurs bénignes**
- Hamartochondrome (freq++) : \"pop-corn\", pathognomonique
- Tumeurs carcinoïdes
**Non tumorales**
- infectieux
- abcès à pyogène (contexte aigü fébrile)
- bactérie filamenteuse crossance lente
- tuberculome (`\thus`{=latex} prélèvements)
- kytes hydatiques (\"membrane flottante\")
- aspergillome (opacité ronde + croissant gazeux)
- granumolatose avec polyangéite
- nodules rhumatoïdes
- atélectasies
- masses pseudo-tumorale silicotiques (micronodules, confluents ?)
- malformations artérioveineuses
#### Examens
- TDM et TEP
- Fibroscopie pronchique systématique
- Ponction transpariétale sous TDM (sauf insuffisance respi)
- Autres : thoracotomie, médiastinoscopie si ADP médiastinales fixant
en TEP-FDG
Prélevement si solide, \> 8mm, hypermétabolique. Sinon surveillance TDM
(sauf non solide et image résolutive à 6 semaines)
### Masses/tumeurs du médiastin
Diagnostic : opacité avec limite externe nette, raccord pente douce,
limite interne non visible, tonalité hydrique
DD: intraparenchymateux, pariétal `\thus`{=latex} TMD
#### Médiastin antérieur
- Supérieur : goître plongeant `\thus`{=latex} TMD : continuité glande
thyroïde
- Moyen :
- tumeurs thymiques : épithéliales (thymomes, carcinomes
thymiques), lymphomes thymiques, kystes, tumeurs bénignes
- Tumeurs germinales : bénignes, séminomateuses, non
séminomateuses (carcinomes embryonnaires, vitellines,
choriocarcinomes)
- Inférieur : kystes pleuropéricardiques
#### Médiastin moyen
- Tumoral : cancer bronchopulmonaires, lymphomes, LLC, cancers
extra-thoraciques
- Non tumoral : sarcoïdose, tuberculose, silicose, infections
parenchymateuses chroniques, histoplasmose (Amérique du Nord)
- Autres : insuf. cardiaque gauche
#### Médiastin postérieur \"neurogènes\"
Diagnostic :
- médiastin antérieur :
- $\alpha$-foetoprotéine (tumeurs vitellines), HCG[^90]
(choriocarcinomes)
- ponction transpariétale
- médiastinotomie
- chir si complète et peu mutilante
- médiastin moyen : médiastinoscopie ou ponction transbronchique
- médiastin postérieur :
- ponction transpariétale, transoesophagienne
- chir si complète et peu mutilante
NB : urgence si jeune et suspicion de tumeur germinale non
séminomateuses
## 204 † Insuffisance respiratoire chronique
### Mécanismes
Hypoxémie
- Inadéquation ventilation/perfusion :
- effet shunt (mauvaise ventilation) =\> $O_2$ corrige
- shunt vrai (communication anat. ou non ventilé) =\> $O_2$ ne
corrige
pas
- Hypoventilation alvéolaire : pure (commande, neuromusc) ou effet
\"espace mort\"
(mauvaise perfusion)
- Atteinte de la surface d\'échange
Hypercapnie : hypoventilation alvéolaire (pompe ventilatoire/commande
centrale ou effet espace mort)
### Conséquences
Hypoxémie : Polyglobulie, rétention hydrosodée (fréquente), hypertension
pulmonaire
Hypercapnie : compensée par le rein
### Étiologies
Hypoxémie si PaO$_{\text{2}}$ \< 70mmHg (arbitraire). Voir
table\~`\ref{tab:etio_irc}`{=latex}.
```{=latex}
\begin{table}
\begin{center}
\begin{tabular}{llllll}
\toprule
TV ? & Obstructif & Restrictif & Restrictif & Mixte & Non\\
& & $\frac{T_{LCO}}{V_a}$ bas & $\frac{T_{LCO}}{V_a}$ normal & & \\
\midrule
Patho. & BPCO & Interstitielles & Sd obésité-hypoventil & DDB & HTP\\
& asthme & & Atteinte cage thoracique & Muscoviscidose & \\
& bronchiolite & & & & \\
Mécanisme & $\frac{V_a}{Q}$ & Surf d'échange & Hypoventilation & $\frac{V_a}{Q}$ & Surf d'échange\\
Atteinte & échangeur & échangeur & pompe/central & échangeur & vasculaire\\
\bottomrule
\end{tabular}
\end{center}
\caption{Insuffisance respiratoire chronique : diagnostic simplifié (selon
EFR). $V_a$ ventilation alvéolaire, $Q$ débit sanguin, $T_{LCO}$ capacité de
transfert du CO}
\label{tab:etio_irc}
\end{table}
```
### Diagnostic
#### Symptômes
IRC = dyspnée (sous-évaluée), neuropsy + patho initiale
Physique :
- IRC : cyanose, insuf. cardiaque D (turgescence jugulaire, oedeme MI,
reflux hépato-jugulaire)
- patho :
- obstructive : distension thoracique, dimin. bilat murmure
vésicul
- restrictive : râle crépitant des bases, hippocratisme digital
#### Diagnostic
PaO$_{\text{2}}$ \< 70 mmHg (gaz du sang : hypercapnie)
Étiologie :
- EFR donne TVO (VEMS/CVF \< 70% =\> BPCO), TVR (échangeur/pompe) ou
mixte (DDB, mucov)
- Radio thorax
- Autres : NFS (polyglobulie), ECG (dextrorotation, BDB droite,
repolarisation),
écho cardiaque systématique (éval. ventricule D, dépistage du G)
### Traitement
Cause, arrêt tabac, vaccins (grippe, pneumocoque), réhabilitation respi.
Oxygénothérapie de longue durée : indiquée si 2 mesures à 2 semaines
avec
- obstructive = PaO$_{\text{2}}$ \< 55mmHG ou ( $\in$ \[55, 60\] mmHG
et hypoxie tissulaire\\footnote{Ht \> 55%, HTP, insuf. ventricule D,
SpO$_{\text{2}}$ nocturne $\le$ 88%})
- restrictive = PaO$_{\text{2}}$ \< 60 mmHg
Efficace si IRC après BPCO, 15h/jour, $O_2$ gazeux ou liquide
Ventilation long cours : IRC restrictive, la nuit.
Chir rare (200/an)
### Pronostic
Irréversible, risque = insuf. respi aigüe (surtout causée par insuf.
respi. basse, dysfonction cardiaque G, EP)
## 205 BPCO
##### Épidémio
`\inc`{=latex} dans le monde.
FR : {tabac++, aérocontaminants professionnels}, génétique: *α* − 1
antitrypsine
##### Diagnostic [^91]
Évoqué sur la clinique, confirmé par EFR
- dyspnée/, toux, expectorations.
- Signes physiques : ↗ temps expiratoire, ↘ murmure vésiculaire,
$\searrow$ bruits coeur, distension thoracique
- EFR: [TVO (VEMS/CVF \< 0.7) persistante]{.underline} après
bronchodilateur
Voir tab [tab:bpco_asthme](tab:bpco_asthme)
Asthme BPCO
---------------------------- ------------------------
Obstructive non réversible Obstructive réversible
Jeune, atopique Fumeur, \> 40 ans
Survient \~40 ans Enfance
: Différences asthme-BPCO
Sévérité : échelle GOLD[^92], MRC[^93], fréquences exacerbations ( ≥ 2
/an = grave)
##### Complémentaire
ECG si VEMS \< 50%, NFS, *α* − 1 antitrypsine si besoin
##### Évolution
Perte fonction respi, exacerbations, handicap respi, risque
d\'insuffisance respi, comorbidité CV = 1ere cause de mortalité
Score BODE[^94] pour la prédiction.
##### Traitement
Cf fig\~`\ref{fig:ttt_bpco}`{=latex}. *Arrêt tabac*, vaccins grippe et
pneumocoques, réhabilitation respiratoire, O~2~, chirurgie possibles
```{=latex}
\begin{figure}[htpb]
\centering
\resizebox{0.5\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=4cm,
level distance=2cm,
edges={nodes={fill=white}},
layered layout]
{
"Dyspnée/exacerbations" -> {
BD longue durée[>"oui", draw]->
{
cBD/"Cortico. inhalé\\ + BD longue durée"[draw, >"exacerbation"]
-> ["insuffisant"] c2BD/"Cortico. inhalé\\+ 2 BD longue durée"[draw]
-> reeval/"Réévaluation"[>"dyspnée"];
2BD/"2 BD longue durée" [draw, >"dyspnée"] -> {
c2BD[draw, >"exacerb"];
reeval[>"dyspnée"];
};
};
BD courte durée [>"non", draw];
}
};
}
\caption{Traitement BPCO}
\label{fig:ttt_bpco}
\end{figure}
```
### Exacerbations BPCO
Exacerbation aigüe = aggravation $\ge 2$ jours
##### Diagnostic
Soit BPCO connu avec `\inc`{=latex} dyspnée, toux/expect, soit voir
section [item 354](#detresse_respiratoire)
Déclenchants : *infectieux*[^95] (`\bact{influenzae}`{=latex},
`\bact{pneumocoque}`{=latex}, `\bact{catarrhalis}`{=latex})
DD : PAC, dysfonction cardiaque gauche, EP, pneumothorax, médicaments
CI, trauma/chir thoracique, insuffisance cardiaque gauche aigüe.
##### Explorations (si sévère)
Imagerie thorax, ECG, NFS, CRP, iono, créat, gazométrie
##### Traitement
*Bronchodilatateurs *β* − 2 agonistes courte-durée*
- ± ATB 5-7 jours (si expectoration purulente ou gravité ou BPCO
sévère)
- amox + acide clav/CG3/fluoroquinolones si FR
- amox ± acide clav/pristinamycine/macrolides sans FR
- `\faHospital`{=latex} : oxygénothérapie, kiné, HBPM, (assistance
ventilatoire)
## 206 † Pneumopathies infiltrantes diffuses
### Présentation
Clinique : dyspnée d\'effort prgorsessive.\
EFR : [TVR]{acronym-label="TVR" acronym-form="singular+short"} ( CPT \<
80% et VEMS/CVL \> 70% ) et TLCO \< 70%, hypoxémie, désaturation\
Radio : opacités parenchymateuse non systématisées bilatérales
### PID aigüe
#### Étiologies
Causes connues : lymphangite carcinomateuse, insuf. cardiaque gauche,
médicamenteuse\
Causes inconnues : sarcoïdose, fibrose plumonaire idiopathique
#### Démarche
- Contexte (ATCD, ID, exposition)
- ECG, BNP, echo cardiaque
- LBA si possible
- PEC thérapeutique (réa si détresse respi, $O_2$, ATB probabiliste si
fièvre, arrêt de médic. pneumotoxiques)
### PID subaigüe/chronique
#### Démarches
Interrogatoire++ : terrain (sarcoïdose=25-45 ans,
[FPI]{acronym-label="FPI" acronym-form="singular+short"} si \> 60 ans),
tabac (histiocytose langerhansienne, [DIP]{acronym-label="DIP"
acronym-form="singular+short"}), toxico, médic, ATCD radio, exposition
Clinique : état général, signes de connectivite
```{=latex}
\begin{table}[htbp]
\caption{Biologie PID subaigüe}
\centering
\begin{tabular}{ll}
\toprule
Examen & Maladie\\
\midrule
NFS, CRP & Sd inflammatoire\\
& Hyperéosinophilie, lymphopénie\\
BNP & Insuf. cardiaque\\
Créat & Insuf. rénale\\
Précipitines sériques & Hypersensib. (si contexte)\\
CEA, calcémie, calciurie & Sarcoïdose\\
Facteur rhumatoïdes etc & Connectivites\\
ANCA & Vascularite\\
Séro VIH & Opportuniste\\
\bottomrule
\end{tabular}
\end{table}
```
```{=latex}
\begin{table}[htbp]
\caption{LBA PID subaigüe}
\centering
\begin{tabular}{ll}
\toprule
Normal & 80\% macrophages\\
& < 15\% lymphocytes\\
& < 5\% PNN\\
& < 2\% PNE\\
\midrule
Alvéolite & Hypercellularité totale\\
Histiocytose langerhansienne & Macrophage\\
Sarcoïdose, PHS & Lymphocytaire\\
P. à éosinophiles & Éosinophilique\\
\gls{POC} & Panachées\\
Hémorragie alvéolaire & Rosé\\
Protéinose alvéolaire primitive & Laiteux\\
\bottomrule
\end{tabular}
\end{table}
```
Examens complémentaires :
1. fibro et LBA (+ biopsie bronchique)
2. soit biopsie pulmonaire chir (pas de diagnostic), soit biopsie
transbronchique et ADP médiastinales
#### Oedème pulmonaire
Mécanisme : Surcharge hémodynamique\
Clinique : HTA, coronaropathie, valvulopathie mitrale\
Diagnostic : ECG, BNP, écho coeur\
Imagerie : Péri-hilaire
#### Tuberculose
Mécanisme : BK\
Clinique : Contage, AEG, hémoptysie\
Diagnostic : Expectorations (ED, culture, biopsie transbronchique)\
Imagerie :
- pulmonaire = nodules, infiltrats, excavations
- miliaire = micronodules diffus
#### Médicaments
Imagerie : condensations, verre dépoli, épanchement pleural
#### Pneumopathies d\'hypersensibilité
Mécanisme : Ag organiques\
Clinique :
- aigüe : sd peudo-grippal quelques heurs
- subaigüe : semaines/mois avec toux, fébricule, râles crépitants,
squeaks
- chronique : dyspnée, toux sèche
Diagnostic : Sérologie, LBA\
Imagerie : Micronodules centrolobulaires flous, verre dépoli (lobes
supérieurs)\
Traitement : éviction Ag
#### Pneumoconioses
Mécanisme : Amiante, silice\
Clinique : Exposition\
Imagerie :
- silicose : opacités micronodulaires diffuses $\implies$ masses
pseudotumorales. Peut donner un cancer bronchique
- asbestose : opacités linéaires non septales des bases $\parallel$ ou
$\bot$ plèvre, réticulations et rayons de miels comme FPI. Évolue
vers insuf respi chronique.
#### Sarcoïdose
Mécanisme : Signes extra-respiratoires\
Diagnostic : anapath : extra-pulmonaire, biopsie éperons bronchiques et
transbronchique. ADP médiastinales\
Imagerie : Nodules, micronodules (ditribution lymphatique), adénopathie,
hyperdensités, distorsions bronchiques
#### Fibrose pulmonaire idiopathique
Clinique : Dyspnée d\'effort progressive, toux sèche, hippocratisme
digital, crépitants sec base\
EFR : TVR, diminution TLCO\
Imagerie : Réticulations, bronchectasies, rayons de miel. Domine
sous-pleural et bases
#### Connectivites
Mécanisme : Dysimmunitaire\
Clinique : Extra-respi (polyarthrite rhumatoide, sclérodermie, lupus,
vascularite)\
Diagnostic : Ac spécifiques\
Imagerie : Réticulations, hyperdensités, bronchectasies
#### Pneumopathie interstitielle non spécifique
Origine : connectivite, médicaments (idiopathique)\
Imagerie : verre dépoli, réticulations, bronchectasies (sauf extrême
périphérie du poumon)
#### Proliférations tumorales
Lymphangite carcinomateuse : toux sèche, rebelle.\
Radio : épaississements nodulaires des septas intralobulaires.\
Diagnostic : biopsies des éperons\
Carcinome lépidique : verre dépoli.
## 207 † Sarcoidose
Maladie : systémique, cause inconnue, hétérogène, ubiquitaire. Début
25-45ans dans 2/3\
Atteinte médiastino-pulmonaire 90
### Expression
#### Pulmonaire
Toux (dyspnée) Radio : 4 stades
- I : adénopathies hilaires bilatérales symétriques
- II : + atteinte parenchyme (micronodulaire diffus, parties moyennes
supérieures)
- III : atteinte parenchyme isolée
- IV : fibrose = opacités parenchymateuses rétractiles + ascension
hiles, distorsion bronchovasc (sup et post)
TDM : atteinte parenchyme = micronodule selon lymphatiques. Utile pour :
formes atypiques ou détection précoce (fibrose, complications \[greffe
aspergillaire\])\
EFR : sd restrictif, DLCO \$↘\$\
(Endoscopie bronchique : normal/muqueuse en \"fond d\'oeil\".)\
Biopsie : {éperons, LBA} \> {ponction ganglions médiastinaux,
transbronchique} \> médistanoscopie\
Formes atypiques : TVO, cavitaires, pseudonodulaires/alvéolaires
#### Extra-pulmonaire
- Oeil : uvéite antérieure aigue (toujours cherche uvéite postérieure)
- Peau : nodules cutanés, lupus pernio, érythème noueux
- ADP
- Foie
- Moins fréquentes : nerveux (sd méningé, paires craniennes), ORL
(obstruction nasale,
sd Mikulicz, sd Heerfordt), ostéo-articulaire (bi-arthrite cheville =
spécfique++), coeur (BAV, bloc branche droit), rein ($\nearrow$
créatininémie)
- Généraux : asthénie (pas de fièvre sauf sd de Löfgren)
Sd de Löfgren = érythème noueux + ADP hilaires médiastinales (+ fièvre)
#### Biologie
- Hypercalciurie
- Lymphopénie CD4
- Hypergammaglobulinémie
- Enzyme de conversion de l\'angiotensine sérique (ECA)
### Diagnostic
Clinique + radio + lésions granulomateuses tuberculoides sans nécrose
caséeuse + élimination DD
### Évolution
\< 2 ans : évolution favorable sans traitement.\
Chronique \> 2 ans : attention au vital/fonctionnel\
Suivi : 3-6 mois\
Pronostic : 80% favorable sans traitement, 10% séquelles, 5% DC
```{=latex}
\begin{table}[htbp]
\caption{Pronostic de la sarcoidose}
\centering
\begin{tabular}{ll}
\toprule
Négatif & Positif\\
\midrule
> 40 ans & Érythème noueux\\
Chronicité & Forme aigüe\\
Stade III, IV & Stade 1 asymptomatique\\
Extra-respi grave & \\
\bottomrule
\end{tabular}
\end{table}
```
Atteintes :
- pulmonaire : insuf. respir chronique, principace cause DC
- extra-thoracique : attention fonctionnel/vital
### Traitement
Atteinte respi : pas de ttt si sd de Löfgren ou stade I asymptomatique\
- 1ère intention : Corticoïdes \> 12 mois à 0.5mg/kg (décroissance par
6-12 semaines)
- 2eme intention : hydroxychloroquine, méthotrexate, azathioprine
- 3eme intention : cyclophsamide, anti-TNF-$\alpha$
## 222 † Hypertension artérielle pulmonaire
##### Physiopatho
Circulation : (basse pression, faible résistante) `\thus`{=latex} forte
résistance
##### Définition
acrshort:PAPm $\ge 25$ mmHG et
```{=latex}
$\begin{cases}
\text{\gls{PAPO}} \le 15 & \text{mmHG si précapillaire} \\
\text{PAPO} > 15 & \text{mmHG si postcapillaire}
\end{cases}$
```
5 groupes :
1. HT [A]{.underline} P[^96] : pré-capillaire
2. **cardiopathie gauche** : post-capillaire (fréq+++)
3. HTP maladie **respiratoire chronique** : pré-capillaire (freq++)
4. HTP post-embolique chronique : pré-capillaire
5. HTP multi-factorielles : pré-capillaire
##### Pronostic
6 cas/million (idiopathique), femme. Survie avec ttt : 58% à 3 ans
##### Diagnostic
Cathétérisme cardiaque D/ avec **PAPm $\ge 25$ mmHg**. Découvert sur
dyspnée, dépistage
- Interrogatoire : ATCD, anorexigènes, toxiques, maladie (sclérodermie
: sd de Raynaud, dysphagie, dyspepsie)
- dyspnée d\'effort+++ progressive (lipothymie à l\'effort, syncope,
asthénie, douleurs angineuses, palpitations, hémoptysies)
- HTP (signe de Carvallo[^97], éclat B2, souffle diastolytique
d\'insuf pulmonaire), insuf cardiaque D[^98]
- RX thorax normale ou dilatation artères pulmonaires, élargissement
coeur D
- ECG : hypertrophie D, trouble rythme
- *Écho cardiaque transthoracique* = non invasif de référence.
##### Démarche
Si écho cardiaque compatible avec HTP :
- Cardiopathies G, maladies respi + exams pour groupe 2 et 3. Si
confirmé : `\faStop`{=latex}
- Sinon regarder signes thrombo-embolie chronique (scinti, angioscan)
: Si groupe 4, `\faStop`{=latex}
- Sinon confirmer HTP précapillaire
- Si confirmée, tester pour groupe 1 (connectivites, médicaments, VIH,
cardiopathie congénitale, HT portale, schistosomiase) ou groupe 5
### Enfant
##### Physiopatho
Augmentation du débit ou des résistances
##### Clinique
- Nouveau-né : cyanose réfractaire à l\'$O_2$, détresse respi/circ
`\thus`{=latex} échocardio en
urgence ☡
- Enfant : dépistage si cardiopathie congénitale, patho. respi.
chronique, maladie de
systèmes, ATCD familiaux (signes tardifs ![^99] )
##### Diagnostic
Échocardio, confirmé par cathétérisme
Scanner (parenchyme), écho hépatiques (shunt porto-cave)
## 224 † Embolie pulmonaire et thrombose veineuse profonde
[MTEV]{acronym-label="MTEV" acronym-form="singular+short"} =
{[EP]{acronym-label="EP" acronym-form="singular+short"},
[TVP]{acronym-label="TVP" acronym-form="singular+short"}}
Maladie fréquente (1 cas /10 000 si \< 40 ans, 1/100 si \> 75 ans) et
grave. 3eme cause de DC en france.
TVP : obstruction thrombotique d\'un tronc veineux profond. EP : idem
mais artères pulmonaires ou leurs branches (secondaires TVP à 70%)
#### Physiopatho stase veineuse, lésions pariétales, anomalies de l\'hémostase `\thus`{=latex}
obstruction/lyse. Si migre dans les artères pulmonaires : symptômes si
obstruction à 30-50% `\thus`{=latex} anomalie hémodynamique
`\thus`{=latex} insuf respi
#### Évolution
TVP distales asymptomatique (postop) : 20% deviennent proximales\
TVP distales symptomatique : récidive (9% si ttt anticoagulant)\
TVP proximal symptomatique : risque important !\
EP : TVP + 3/7 jours, mortelle dans l\'heure à 10%
Facteurs de risque :
- acquis : majeurs = chir \< 3mois, trauma MI[^100],
`\faHospital{}`{=latex} aigü, cancer en cours ttt, sd
antiphospholipide, sd néphrotique
- constit : rare = déficit (antithrombine, prot. C, S), fréq =
(mutation {Leiden, prothrombine}, facteur VIII \> 150%)
Complications : DC, récidive (mortelle ou non), séquelle (HTP
thrombo-embolique chronique si EP, sd post-phlébite si TVP)
Risque de récidive dépend de la clinique : élevé si (non provoqué par
facteur majeur ou modéré) ou (`\og`{=latex} facteur persistant)
Conséquence :
- hémodynamique : $\nearrow$ pression artérielle pulmonaire,
dilatation VD[^101], compression VG
- respiratoire : hypoxémie (effet espace mort (non perfusé)
`\thus`{=latex} effet shunt (ventil/perfusion diminué))
### Diagnostic de l\'embolie pulmonaire
#### Clinique pas spécifique : dyspnée, douleur thoracique, syncope,
crachats hémoptoïques, asymptomatique
Radio thoracique, ECG : élimine les DD
Gaz du sang : hypoxie-hypocapnie
`\thus`{=latex} score probablitié (Genève, Wells)
```{=latex}
\begin{figure}[htpb]
\centering
\resizebox{0.3\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
level distance=2cm,
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Proba. clinique" -> {
"D-dimères" [>"faible", draw] -> {
"Pas de ttt" [>"négatif"];
"\texttt{\$examen}" [>"positif", draw];
};
"\texttt{\$examen}" [>"forte", draw] -> {
Ttt [>"positif"];
};
};
};
}
\caption{Diagnostic général pour l'EP, TVP}
\label{fig:ep-diag}
\end{figure}
```
#### Examens
Voir la figure\~`\ref{fig:ep-diag}`{=latex} avec `examen` =
angioscanner.
D-dimère positifs = \$max (âge, 50) × 10 μ\$g/L
CI à l\'angioscan : insuf. rénale sévère (\< 30ml/min) `\thus`{=latex}
scintigraphie
Si angioscan ou scintigraphie négatif : pas d\'EP !
```{=latex}
\begin{tcolorbox}
\danger{} si EP grave (état de choc) : angioscan immédiatement ou ETT en
attendant.
{} Thrombolyse/embolectomie après écho si pas d'accès à l'angioscan
\end{tcolorbox}
```
Sur l\'écho, chercher dilatation cavité D, HTP, septum paradoxal
*Si grossesse* : D-dimères `\thus`{=latex} écho. veineuse
`\thus`{=latex} angioscanner (prévenir le pédiatre )
#### Évolution favorable. Complications : choc cardiogénique réfractaire
(DC), rédicive, HTAP chronique post-embolique (rare mais grave)
### Diagnostic de TVP
#### Clinique = orientation
Douleur du MI, oedème unilatéral, signes inflammatoires, dilatation
veines superficielles ou asymptomatique
*DD* : traumatisme, claquage musc/, kyste synovial, {SPT, insuf veineuse
primaire}, {sciatique, compression extrinsèque}, {érysipèle,
lymphangite, cellulite}, lymphoedeme, insuf cardiaque
droite/rénale/hépatique
Score de probablitié clinique : Wells (faible/interm/forte)
#### Diagnostic
Voir la figure\~`\ref{fig:ep-diag}`{=latex} avec `examen` = échographie
veineuse des MI
#### Étiologies
- FR transitoire (chir, fracture \< 3 mois, immobilisation \> 3 j) ?
Sinon, \"non
provoquée\"
- Recherche de thrombophilie si
- 1er épisode : (non provoqué \< 60 ans) ou (femme âge procrééer)
- ou récidive : (MTEV proximale) ou (TVP distale non provoquée)
`\thus`{=latex} 1ere intention : [AT]{acronym-label="AT"
acronym-form="singular+short"}, prot. C et S, mutation G20210A,
homocysténiméie, Ac antiphospholipides
- Recherche cancer : \> 40 ans ou bilan thrombophilie négatif
Formes particulières :
- thromboses veineuse superficielles : (sur trajet saphène,
douloureux, rouge, inflammatoire, cordon induré `\thus`{=latex}
écho-doppler
- TVP pelvienne
- thrombose veine cave inférieure
- phlébite bleue : très rare mais grave
Si grossesse : bilan thrombophilie si ATCD familaux/personnels MTEV
Si cancer : HBPM long cours
#### Évolution : favorable si bien conduit mais récidive toujours
possible. Complications :
- SPT : lourdeur de jambes, oedeme de cheville, dilat veineuses
superficielles, troubles trophiques sans ulcère, ulcères
sus-malléolaires
- EP
### Traitement (TVP + EP)
#### Principes
Urgence `\thus`{=latex} anticoagulant
CI : coagulopathie sévère, hémorragie intracrânienne spontanée,
hémorragie active difficilement contrôlable, chir récente, (thrombopénie
à l\'héparine)
#### Types de traitement
Option 1 : Héparines + relais AVK dès injection IV
- HBPM, fondaparinux \> HNF, sauf si IR sévère (\< 30ml/min)
- arrêt si 5 jours d\'AVK et IV (ensemble) $\wedge$ INR $\in [2,3]$ à
24h
Option 2 : Anticoagulants oraux directs : rivaroxaban, apixaban (France)
- rapide, demi-vie courte
- facteur X
- CI : IR sévère, grossesse, interaction médic (cytochrome 3A4 ou
P-glycoprroténie)
Éucation thérapeutique\
Autres :
- filtre cave (si CI absolu aux anti-coagulant ou EP récidivant)
- fibrinolyse (si EP + choc, sauf si hémorragie active, AIC[^102]\< 2
mois, hémorragie intracrânienne)
- embolectomie (très rare)
- contention veineuse (sauf si EP sans TVP)
- lever +1h
#### Stratégie
Score sPESI = `90 100 110 C C` [^103]:
Risque faible (sPESI = 0) : `\faHospital{}`{=latex} courte \< 48h,
anticoagulation\
Risque intermédiaire (sPESI \> 0)
- dysfonction VD ou élévation biomarqueurs[^104] :
`\faHospital{}`{=latex} médecine, anticoagulation
- dysfonction VD $\wedge$ élévation biomarqueurs : urgence ☡
`\thus`{=latex} USI
- $O_2$, scope
- anticoag : HNF/HBPM puis AVK/AOP à 48-72h\
(trombolyse si choc)
Haut risque (choc : PAS \< 90mmHG ou -40mmHg) : urgence `\thus`{=latex}
réa
- $O_2$ (ventilation méca.), scope
- anticoag HNF (!)
- thrombolyse avec arrêt HNF tant que TCA \> 2x témoin
- (embolectomie)
#### Durée
3 mois si 1ere EP/TVP provoqué par facteur majeur transitoire ou risque
hémorragique élevée. 6 mois ou plus sinon
#### Étiologie
Chercher cancer occulte dans tous les cas (clinique, radio poumon, NFS
VS, dépistage globux)
Bilan coag : {antithrombine, prot C, S}, mutation {Leiden,
prothrombine}, sd antiphospholipides
#### Prophylaxie
- Post-op : (chir et \> 40 ans) ou (chir hanche/genou/caricinologique,
anomalie coag, (\> 40 ans et ATCD MTEV))
- polytrauma ou ({rhumato, inflammatoire intestin, infectin} + 1 FR)
#### Cas particuliers
-
TVP distale : symptomatique : anticoagulement 6 semaines seulement si
premier épisode. Dans tous les cas, compression $\ge 2$ ans
- [TVS]{acronym-label="TVS" acronym-form="singular+short"} : **pas**
d\'AINS, antiocoagulants en curatif, chirurgie
- cancer : HBPM, arrêt si plaquettes \< 50g/L
Prévention :
- risque modéré : HBPM/HNF/fondaparinux, compression
- risque élevé : idem sans HNF
Nouveau anticoagulant oraux (rivaroxaban) :
- prévention chir hanche-genou
- curatif TVP, EP
- pas si insuf rénale sévère ou insuf hépatique
- pas de surveillance bio
## 228 † Douleur thoracique aigüe et chronique
### Signes de gravité
- Respi : cyanose, tachypnée, lutte avec tirage, balancement
thoraco-abdominal
- CV : pâleur, tachycardie, hypotension, choc (marbrures, extrémités
froides)
- neuro : lipothymie/syncope, agitation/trble vigilance, général
(sudation)
☡ arrêt cardio-respi ! Y penser si bradypnée, (bradycardie et choc et
troubles vigilance)
### Examens
Fréquence respi, $SpO_2$, radio thorax, ECG. Si {brady, tachy}pnée ou
$SpO_2 < 95\%$, gaz du sang
### Urgences vitales
Cf table\~`\ref{tab:urgences_douleur_thoraciques}`{=latex}
```{=latex}
\begin{table}
\centering
\begin{tabular}{ll}
\toprule
Urgence & Orientation\\
\midrule
Syndrome coronaire aigü (fréquent++ 1/3) & ECG + troponines\\
Embolie pulmonaire (fréquent) & Suspicion si douleur thorax, pas d'anomalie ascult\\
& RX thorax "normale" \textit{surtout} si hypoxémie + FR\\
& Dyspnée ou douleur thoracique aigüe chez TVP = EP\\
dissection aortique (exceptionnelle) & Échocardio + angioscanner\\
Tamponnade (peu fréq) & suspicion (hypotension réfractaire, insuf. cardiaque D
aigüe,\\
& microvoltage + alternance ECG) \thus echo cardiaque\\
Pneumothorax & ATCD (!), radio thorax \\
pneumomédiastin (rare) & scanner\\
\bottomrule
\end{tabular}
\caption{Urgences vitales pour douleur thoraciques}
\label{tab:urgences_douleur_thoraciques}
\end{table}
```
- Embolie pulmonaire (fréquent) : suspicion si douleur thorax, pas
d\'anomalie ascult, RX thorax \"normale\" *surtout* si hypoxémie +
facteurs de risque\
Dyspnée ou douleur thoracique aigüe chez TVP = EP
- dissection aortique (exceptionnelle) : échocardio + angioscanner
- Tamponnade (peu fréq) : suspicion (hypotension réfractaire, insuf.
cardiaque D aigüe, microvoltage + alternance ECG) `\thus`{=latex}
echo cardiaque
- Pneumothorax : ATCD (!), radio thorax\
pneumomédiastin (rare) : scanner
### Non urgent
Rythmées par respiration :
- post-traumatique
- pneumonie infectieuses : radio thorax
- épanchement pleural (douleur latéral-base, majorée inspiration,
toux)
- infarctus pulmonaire (douleur basithoracique, faible hémoptysie)
- trachéobronchite aigüe
- musculosquelettique, nerfs : tumeurs costales, lésions vertèbres,
névralgies cervicobrachiales
Non rythmées :
- angor d\'effort stable (calmée 2-5min post-effort)
- péricardite (viral si aigü, tuberculose/néoplasie sinon)
- cocaïne (fréquente) : SCA, myopéricardite,pneumothorax
- zona thoracique (brûlures, hyperesthésie 24h avant)
- digestives : reflux gastro-oesophagen, spasmes oesophagiens. Exclure
SCA
- psychogènes
## 306 † Tumeurs du poumon
### Épidémiologie, étiologies
1ere cause de mortalité par cancer en France (♂ : constante, ♀
$\nearrow$)
Tabac : 90% (âge de début et durée) pour actif, 25% passif
Professionel : 15%
#### Histologie
- \"Non à petites cellules\" (CBNPC) (80%) : adénocarcinomes
(périphérie), carcinomes épidermoïdes (proximal), indifférenciés à
grandes cellules
- neuro-endocrine \"à petites cellules\" (CBPC) (proximal, médiastin)
### Manifestations
```{=latex}
\begin{tcolorbox}
Y penser si (AEG et tabagique) ou (symptôme fonctionnel respiratoire
chez tabagique > 40A)
\end{tcolorbox}
```
*Respiratoires* : toux (souvent révélatrice, sèche, quinteuse),
hémoptysie (\< 10%), bronchorrée (propre), dyspnée, pneumonie/bronchite
(☡ si récidive dans même territoire), douleur thoracique
*Locorégionales* : pleurésies, dysphonies, sd cave supérieur, douleurs
thoraciques (fixes, tenaces), sd de Pancoast-Tobias[^105], paralysie
phrénique
*Extrathoracique* : thromboses inexpliquées (y penser !), métastase
(SNC, foie, os, surrénales)
*Sd paranéoplasiques* (à distance, réapparition `\thus`{=latex} rechute)
: hippocratisme digital, hypercalcémie, hyponatrémie, sd de Cushing,
neurologique (pseudomyasthénie de Lamert Eaton, neuropathies périph,
encéphalopathies)
### Imagerie
Initial = radio thorax chez fumeur \> 40 ans
#### Radiothorax
- projection (juxta-)hilaires
- atélectasies
- opacités arrondies intraparenchymateuses
- cavitaires néoplasiques
#### TDM injection
Stade N0 sans adénopathie, N1 si hilaire, N2 si médiastin homolatéral,
N3 si médiastin controlatéral
#### TEP au 18-FDG
Pas dans le cerveau !
Faux positifs : ganglions inflammatoires, infectieux
Faux négatifs : \< 1 cm, non solide (verre dépoli)
### Diagnostic histologique
- lésion centrale : fibroscopie bronchique
- périphérique : ponction transpariétale
- entre les 2 : fibro ou ponction ou thoracotomie
Chercher mutations EGFR, réarrangements ALK, ROS1
### Bilan préthérapeutique
*Extension* : T(tumeur) = locale, N (node) = ganglionnaire, M
(métastase) = à distance.\
si M : TDM abdo, IRM cérébrale, TEP-TDM
État général (Performance Status de 0 à 4), nutritionnel (-5% en 1 mois
ou -10% en 6 mois = ☹)
*Cardiorespiratoire* : ECG, écho cardio, épreuve d\'effort, doppler
artériel des MI/cou, coronarographie.\
Règle : 1 lobe = -25% de VEMS. Opération ssi VEMS post-op \> 30%
### Traitement
#### CBPNC
- localisé (stade I, II) : local (lobectomie ou radiothérapie)
- localement avancé (stade III) : systémique (chimio) + local (radio
ou chir)
- disséminé (stade IV) : systémique =
```{=latex}
$\left \{
\begin{array}{lr}
\text{\gls{ITK} si altération moléculaire ciblable} & \text{Médiane > 2 ans}\\
\text{chimio IV et 3e génération sinon} & \text{Médiane 12 mois}\\
\end{array}
\right.$
```
#### CBPC[^106]
Pas de chir !
```{=latex}
$
\left \{
\begin{array}{l}
\text{radio + chimio (+ irradiation encéphale) si limitée}\\
\text{chimio sinon}
\end{array}
\right.
$
```
#### Symptomatique
*Douleur* : Antalgiques, radiothérapie, chir, AINS, vertébroplastie
*Dyspnée* : lymphangite carcinomateuses (difficile), obstruction
bronchique (bronchoscopie), pleurésie exsudative (pleuroscopie), sd cave
supérieur (anticoag, corticoïdes)
#### Plan cancer
Réunion de concertation pluridisciplinaire, consultation d\'annonce,
plan personnalisé de soin
#### Suivi
CBNPC : arrêt tabac, TDM 2-3 mois, clinique, bio (rein, NFS,
hypercalcémie, hyopnatrémie)
CBPC : médiane de survie = 16-20 mois si limitée, 8-12 mois si
métastatique
### Cancers secondaires
Clinique : pauvre (dyspnée, toux, douleur thoracique, généraux),
chercher extension ganglionnaire
Imagerie :
- lâcher de ballons ou miliaire
- épanchement pleural
- interstitiel (lymphangite carcinomateuses)
Diagnostic : clinique,
- inconnu : chercher accessibles à ttt spécifique, TEP. Sinon :
- épidermoïde, adénocarcinome
- sinon : ♀ = {gynéco, mammo}, ♂ = {PSA, TR, écho prostate}
- connu : radio peut suffir
- ancien : métastases 10 ans plus tard possibles
## 333 † Oedème de Quincke et anaphylaxie
### Définition, épidémiologie
HS systémique immédiate sévère. 2 types :
- allergique : production IgE spécifiques. Libération de médiateurs
par mastocytes et basophiles `\thus`{=latex} vasodilatation,
bronchoconstriction
- non-allergique : pas d\'exposition préalable, moins sévère
Déf : symptômes CV, respi, cutané/digestif mettant en jeu le pronostic
vital immédiatement après contact
#### Épidémiologie
35 DC (alimentaire), 40 DC (piqûre) / an\
Agents :
- aliments (90% enfant) : arachide++, protéine oeuf/lait, fruits
exotiques
- médicaments (15-20%)
- venin hyménoptères (15-20%)
- autres : latex, effort
### Clinique
Délai \< 1h (5min si médic. IV, 15 si piqûre, 30 si alimentaire).
Manifestations :
- CV : PAS \< 100mmFg (ou -30%), tachycardie, pâleur, hypotonie,
malaise, perte connaissance, trouble rythme/conduction, ischémie
myocardique
- respi : de la toux à l\'asthme (mortalité $\nearrow$ si asthme mal
contrôlé)
- cutanées, muqueuses : prurit, rash cutané érythémateux, urticaire et
surtout
- angioedeme : gonflement mal limité ferme, non érythémateux, sans
prurit
- oedème de Quincke : angioedeme larynx et cou : gêne respi haute
(dysphonie++, dysphagie++).\
Clinique : gonflement langue, luette, paupière lèvre ou face\
Possiblement létal
- digestives
**Hautement probable** si
- gêne respi haute ou asthme ou choc mettent en jeu le pronostic vital
- cutanéomuqueux
- début brutal, progression rapide
Sévérité I. cutanéomuqeux généralisé II. multiviscérale modérée III.
multiviscérale sévère IV. arrêt respiratoire V. DC
#### Diagnostic
Clinique + contexte.
Doser systématiquement tryptase sérique (confirmation) : H+0, H+1, H+24
Étiologie : interrogatoire, {prick-tests, IDR}, dosage IgE
DD :
- choc anaphylactique : choc {vagal, septique, cardiogénique},
hypoglycémie, mastocytose
- Oedeme de Quincke : sd cave sup, érysipèle du visage, angi-eodeme à
bradykinine, inhalation de corps étranger (toujours y penser !!)
### Traitement
#### Urgence
Adrénaline : 0.01mg/kg (\< 0.5mg) adulte à `\faHospital{}`{=latex} ou
0.3mg auto-injection $\rightarrow$ répéter /5 min jusque stabilisation\
Voie IM (pas de SC ou d\'IV ☡)
Remplissage vasc : 50-100mL adulte
$O_2$, libérer voie aériennes, bronchodilatateurs (courte durée)
Glucagon si adrénaline ne fonctionne pas.
#### Hors urgence
Anithistaminique, corticoïdes, arrêt agent.
NB : alerter, allongé jambes relevées (pas vertical ☡ ), PLS si
inconscient
#### Préventif
Trousse avec adrénaline si (absolument) :
- anaphylaxie antérieure (aliment, insecte ou latex), induite par
l\'effort ou idiopathique
- allergie alimentaire et asthme persistant modéré non contrôlé
- allergie hyménoptères avec réaction systémique antérieure (adulte)
ou plus sévère que cutanéomuqueux (enfant)
## 354 † Corps étranger des voies aériennes
Pics =
- \< 3 ans : graines d\'oléagineux avec symétrie G-D
- âgé si troubles déglutition, mauvaise dentition. 2 tableaux :
asphyxie aigüe (viande) ou pneumonie à répétition/suppuration
bronchique
- rarement chez l\'adulte/ado : trauma facial (dents), bricolage,
trouble de conscience. Plutôt à droite
### Diagnostic
#### Clinique et radio
Dans les heures post-inhalation :
- CE mobile (sd de pénétration) : toux quinteuse, suffocation avec
tirage, cornage, cyanose. Résolutif en qq secondes
- soit CE expulsé (pétéchies visage/tronc ou bouche/conjonctive)
- plus rarement enclavement
- proximal (enfant) : diminution murmure vésiculaire, wheezing
- distal (adulte) : asymptomatique
- exceptionnellement : oropharynx, larynx, lumière trachéale
Radio : le plus souvent normale. Sinon : atélectasie, hyperclarté
$\nearrow$ expiration
Mois/années post-inhalation : à évoquer si respi chronique/récidivante
ne répondant pas au tt ou anomalies radio persistantes dans même
territoire
#### DD
(sub)aigü :
- détresse respi aigüe à début brutal, tirage, cornage : épiglottite
aigüe (fièvre, modif voix, hypersaliv)
- infection respi basse : PAC, bronchite sifflante (\< 3 ans)
Chronique/récidive :
- trouble ventilation persistant : tumeur bronchique obstructive,
sténose bronchique
- infection respi même territoire : tumeur bronchique obstructive,
foyer bronchectasies
### CAT
#### Asphyxie aigüe
Toux ou Heimlich (si conscient) ou réanimation. Si \< 2 ans, tapes dos
puis pressions sternum.
#### Sd pénétration non régressif
Supposer que CE toujours présent !! (sauf confirmation entourage).
Clinique : dimination unilat murmure, wheezing, persistance {toux,
dyspnée, cornage, tirage}
RX : piégage (expiration) $\wedge$ diminution unilatérale murmure
`\thus`{=latex} CE endobronchique (90%)
#### Extraction
Bronchoscopie rigide (ou souple). Chez l\'enfant, centre spécialisé !
## 354 † Détresse respiratoire aigüe
[]{#detresse_respiratoire}
Définition : Inadéquation charge - capacité de l\'appareil respiratoire
### Dianostic
Signes de luttes
- polypnée superficielle
- recrutemente muscles (scalènes $\wedge$ intercostaux), abdominaux,
dilatateurs des voies aériennes supérieures (très petit enfant)
Signes de faillite
- respi abdo paradoxale {} défaillance court terme
- cyanose (hypoxémie profonde) `\thus`{=latex} $O_2$ ASAP
- neuro : astérixis, altérations comportement/vigilance. Glasgow \< 9
`\thus`{=latex} assitance ventilatoire
Appareil circulatoire
- coeur pulmonaire aigu[^107]
- pouls paradoxal
- hypercapnie : {céphalées, hypervasc des conjonctives}, {tremblements
sueurs, tachy, hypotension}
État de choc
- peau froide, marbrures, $\nearrow$ temps recoloration cutanée
- PAs \< 90 mmHg ou -50mmHg
- tachy \> 120min, FR \> 25-30/min
- oligurie
- confusion, altération vigilance
### PEC
Surveillance, $O_2$, voie veineuse gros calibre, assistance
ventilatoire, ventilation (non)invasive
Pour l\'étiologie : radiothorax, ECG, prélèvement (gaz du sang, NFS,
iono, urée, créat, acide lactique)
### Diagnostic
```{=latex}
\begin{figure}[htpb]
\centering
\resizebox{0.8\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Obstruction VAS ?" ->["non"] Radiothorax -> {
Anormale -> {
Atélectasies [draw];
"Anomalies\\pleurales" ->
"Épanchement\\
pleural compressif\\
Pneumothorax" [draw];
"Opacités\\parenchyme" ->
"Pneumonie infect\\
OAP\\
Patho. infiltrative" [draw];
};
Normale -> {
"Asthme\\
aigu grave\\
EP" [draw];
"BPCO\\
Anomalie paroi\\
Neuromusc" [draw];
}
};
};
}
\caption{Diagnostic détresse respiratoire aigǜe}
\label{fig:diag_detresse_respi}
\end{figure}
```
Précision de la figure\~`\ref{fig:diag_detresse_respi}`{=latex}
1. *Obstruction* : corps étranger, laryngite, oedème de Quincke,
sténose trachée, tumeur laryngées
2. *Anomalie radio* Priorité = pneumonie inf, OAP, PTX[^108] sous
tension\
Indication =
- OAP : {ATCD = insuf. cardiaque}, {expectoration mousseuse,
orthopnée}, {opacités bilat diffuses, périhilaire}
- Pneumonie infectieuse : {début brutal}, {expector. purulente},
{sd inflammatoire}
3. *Radio normale* de novo = EP, PTX compressif, asthme. Si chronique,
dans l\'ordre BPCO, paroi thoracique (obésité, déformation),
neuromusc\
Orientation :
- EP : fébricule, turgescence jugul, radio normale
- Pneumothorax : {longiligne}, {pas de vibration vocale}, murmure
vésicul, {hyperclarté}
- asthme : ATDS, toux purulente, râles ou silence
### SDRA
Détresse respi \< 7 jours sans défaillance cardiaque, sans surcharge
volémique avec opacités radio bilat diffuses
Mécanisme = oedème lésionnel.
Étiologies :
- exogène = infectieuse, toxique
- endogènes : réponse inflammatoire systémique
## 356 † Pneumothorax
### Définitions
Air dans l\'espace pleural `\thus`{=latex} collapsus
#### Spontané
Primaire = poumon sain, sujet jeune, non grave
Secondaire = patho, \> 40 ans, peut décompenser
- Blebs (\< 1 cm, plutôt primaires)
- bulles d\'emphysème : à la corticalité, tabagismes
- lésions kystiques
- cataménial
#### Traumatique
Femé (côte fracturée) ou ouverts
#### Épidémiologie
Spontané primaire : \< 35 ans, masculin, longiligne et de grande taille,
fumeur !
Spontané secondaire : BPCO (plus rarement asthme, mucoviscidose)
facteurs favorisants : $\Delta P_{atm}$, vols aérien, plongée
subaquatique, tabagisme actif (PAS efforts physiques)
### Diagnostic
Clinique :
- fonctionnel : douleur thoracique (brutale, homolatérale, latérale,
augmente toux), toux sèche irrit
- physique : diminution murmure vésicul, pas de vibration vocales,
tympanisme percusion
Radio : pas en expiration ! 3 catégorise : apical, axillaire, complet
Grave si dyspnée sévère ou collapsus tensionnel (! pas déviation
médiastin)
`\thus`{=latex} le plus souvent (pneumothorax compressif secondaire à
fistule à soupape) ou (PTX avec réserve ventilatoire réduite)
#### Atypique
Récidive : 30% (premier épisode), 50% (second épisode)
Rarement avec pneumomédiastin
Sous ventilation mécanique : y penser si $\nearrow$ brutal pression
d\'insufflation, collapsus brutal, plaie plèvre
#### DD
Facile : douleur thoracique \"respiro-dépendante\".
Difficile : Dyspnée aigüe sans sd pleural
### Traitement
- Rien si décollement \< 2cm
- PTX compressif = urgence `\thus`{=latex} aiguille simple + immédiat
- Pneumotthorax spontané primaire (bien ou mal toléré ) :
exsufflation(petit cathéter sur voie thoracique antérieur) puis
drain si échec
- Pour tous les autres : drain
Prévention récidive par pleurodèse (accolement des feuillets) : si
récidive homolat, PTX persistant 5 jours, compliqué ou bilat
Sevrage tabac !!
Attention altitude si PNO existant (seulement existant)
VIH: traitement aussi pneumocystose
## Gaz du sang
Le pH est déterminé par l\'équilibre entre les bicarbonates
(`\ch{HCO_3-}`{=latex}) et $PCO_2$ :
```{=latex}
\begin{equation}
pH = K_1 + log\frac{[\ch{HCO_3-]}}{K_2 p_{CO_2}}
\end{equation}
```
avec $K_1$, $K_2$ constante.
Un déséquilibre sur un terme induit une compensation sur l\'autre. Si le
déséquilibre n\'est pas compensé, on aboutit à une acidose ou une
alcose.
```{=latex}
\begin{table}[htpb]
\centering
\caption{Gaz du sang artériel}
\label{tab:gds}
\begin{tabular}{ll}
\toprule
\(PO_2\) & [80, 100] mmHg\\
\(SaO_2\) & [95, 98] \%\\
\(PCO_2\) & [35, 45] mmHg\\
\ch{HCO_3^-} & [22, 29] mmol/L\\
pH & [7.38, 7.42]\\
\bottomrule
\end{tabular}
\end{table}
```
Interprétation :
1. Déterminer si acidose ou alcolose selon le pH
2. Respiratoire ou métabolique ? Si $PCO_2$ essaie de compenser (en
sens inverse du pH), c\'est respiratoire. Sinon métabolique.
NB : la compensation ne normalise pas le pH! NB :
- acidose pulmonaire : hypoventilation alvéolaire
- alcalose pulmonaire : hyperventilation alvéolaire
- alcalose métabolique : pertes digestives \[vomissements\]
## Physiologie
$P_{alv}$ = pression alvéolaire, $P_{ip}$ = pression interpleurale (dans
la plèvre), pression transpulmonaire = $P_{ip} - P_{alv}$.
```{=latex}
\begin{figure}[htpb]
\centering
\caption{Inspiration (gauche), expiration (droite)}
\tikz \graph [ nodes={align=center}, layered layout]
{
Contraction diaphragme -> Expansion thorax -> "$P_{ip} < P_{atm}$"
-> Hausse pression transpulmonaire -> Expansion poumons
-> "$P_{alv} < P_{atm}$"
-> Arrivée d'air dans les alvéoles;
};
\tikz \graph [ nodes={align=center}, layered layout]
{
"Arrêt contraction\\ diaphragme et intercostaux" -> Rétraction thorax
-> "Valeur initiale de $P_{ip}$"
-> Valeur initiale pression transpulmonaire
-> Rétraction poumons
-> "$P_{alv} > P_{atm}$"
-> Expulsion d'air depuis les alvéoles;
};
\end{figure}
```
# Ophtalmologie
## 21 † Rétinopathie diabétique
[]{#retinopathie_diabetique} Diabète = défini par risque d\'une
rétinopathie. Complications dont on peut éviter la cécité !
30% diabétique en ont une. Diabète 1 : 90% après 20 ans. Diabète 2 : 60%
à 15 ans
FR = durée et intensité de l\'hyperglycémie
Physiopatho : hyperglycémie
`\thus {accumulation sorbitol, glycation, stress
oxydatif}`{=latex}
`\thus {inflammation, activation rénine-angiotensine, modif flux
sanguin rétinien, production VEGF}`{=latex} puis
- occlusion capillaire et néovascularisation
- œdème maculaire
Cécité possible du jour au lendemain
### Diagnostic
Photographie du FO = référence et dépistage
- microanévrisme rétitiens : dilatations punctiformes rouges
(postérieure)
- hémorragie rétiniennes punctiformes
- nodules cotonneux
- signes d\'ischémie : hémorragies intrarétiniennes \"en taches\" ou
en flammèche, anomalies microvasculaire intrarétinienne, dilatations
veineuses \"en chapelet\", néovaisseaux prérétiniens et
précapillaires, hémorragie prérétiniennes/intravitréennes
- [complications]{.underline} : hémorragie intravitréenne, décollement
de la rétine *par traction*, néovascularisation irienne
(`\thus`{=latex} glaucome néovasculaire !)
- signes maculaires : œdème maculaire (cystoïde), exsudats lipidiques
(souvent en couronne)
Complémentaire : OCT pour diagnostic et suivi œdème maculaire, echo en
mode B pour décollement de rétine par traction
### Dépistage RD
Diabète 1 : photo FO à la découverte puis surveillance annuelle
- enfant: pas avant 10 ans
- grossesse : avant puis tous les 3 mois (tous les mois si RD !)
Diabète 2 : dès découverte
Surveillance :
- ∅ RD on non proliférante minime : annuelle
- sinon tous 4 à 6 mois
- renforcé si puberté, adolescence, si équilibrage trop rapide de la
glycémie, chir bariatrique, diabète ancien mal équilibré, chir de la
cataracte, œdème maculaire
Classification :
- ∅ RD
- RD non proliférante : minime, modérée, sévère (si hémorragie
rétiniennes dans 4 quadrants ou dilatations veineuses 2 quadrants ou
AMIR 1 quadrant)
- RD proliférante (néovaisseaux): minime, sévère, compliquée
(décollement de rétine par traction, gls:GNV)
Progression lente, aggravations rapides possibles. ☡ prolifération
néovasc peut donner cécité
### Traitement
Médical :
- équilibre glycémique et hypertension pour 2 diabètes !
- pas de ttt médicamenteux
RD proliférante
- photocoagulation panrétinienne : régression dans 90%. Indication :
RD proliférante ou (RD non proliférante sévère si grossesse, sujet
jeune diabétique 1 avec normalisation rapide glycémie, chir
cataracte)
- injection intravitréenne anti-VEGF (pour néovasc. iridienne,
glaucome néovasculaire)
- chir si RD proliférante avec hémorragie intravitréenne
persistante/décollement de rétine tractionnel
Œdème maculaire
- photocoagulation au laser si exsudats lipidiques ou liquides
- injection anti-VEGF mensuelle. Dexaméthasone retard possible mais
cataracte, risque d\'hypertonie oculaire (30%)
### Autres complications
cataracte (+ freq), glaucome néovasculaire (redoutable), paralysie
oculomotrice (régresse spontanément qq mois)
# Glossaire
`\printglossaries`{=latex}
[^1]: ES : myalgies, `\inc`{=latex} CPK, `\inc`{=latex} transaminases,
`\inc`{=latex} risque diabète 2 CI : HS, *grossesse*, allaitement
[^2]: $\frac{N}{N_e/10}\times 100$ avec N = nb grossesses accidentelles,
$N_e$ nombres de mois d\'exposition
[^3]: Dilatation variqueuse des veines du cordon spermatique
[^4]: Hypothalamus n\'arrive pas à libérer la GnRH au bon rythme.
[^5]: Séborrhéee, acné, hirsutisme, `\inc`{=latex} testostérone
[^6]: V \> 10mL, ≥ 19 follicule par ovaires
[^7]: Transmission mère-fils. Expansion instable des triplets CGG
jusqu\'à l\'absence de transcript de FMR1 (Fragile X Mental
Retardation 1).\
☡ Risque d\'IOP pour la pré-mutation seulement `\thus`{=latex}
dépister chez ♀ + IOP \< 40 ans par PCR et Southern Blot
[^8]: ☡ Testostérone, FSH, LH interprétables \[6mois, puberté\]
[^9]: Percutané, transdermique : limite `\inc`{=latex} facteur de
coagulation.
[^10]: Se fixe à la testostérone, estradiol
[^11]: Baisse libido, testostérone totale \< 3 ng/mL
[^12]: Efficace si stimulation sexuelle (même chez diabétique)
[^13]: Secondaires autres : digestives, générale, génétique,
médicaments, autres. Il existe aussi des ostéoporoses primaires
[^14]: Faire bilan hormonal : natrémie, testostérone totale et
libre/ostradiol, FSH, LH, T4L, TSH, prolactine
[^15]: adénome hypophysaire 90%, méningiome, craniopharyngiome, patho
inflammatoires infiltratives
[^16]: Atteinte poumon évocatrice, `\inc{}`{=latex} ACE, pas de
tuberculose, granulome non caséeux (histologie)
[^17]: Coefficient de saturation de la transferrine
[^18]: Si la surrénale produit plus d\'aldostérone : régulation négative
par la rénine (en théorie)
[^19]: Physiologique = minimal à minuit, donc mesure à minuit. Mesure
salivaire possible.
[^20]: 1mg de dexaméthasone à minuit Action de rétrocontrôle négative du
cortisol donc on vérifie que le cortisol plasmatique le lendemain à
8h a bien diminué
[^21]: 8mg au lieu de 2mg pour DXM et pendant 2 jours au lieu d\'un
[^22]: Thyroglobuline
[^23]: \[T4\] n\'est à l\'équilibre que +5 semaines après modification
de T4
[^24]: Asthénie, somnolence, hypothermie, frilosité, constipation,
bradycardie, prise poids modeste
[^25]: Clinique discrète : ictère prolongé, constipation, hypotonie,
pleurs rauques, difficulté succin, fontanelles larges, hypothermie
[^26]: Par compression des voies optiques. Fond d\'oeil, acuité visuelle
OK.
[^27]: Céphalées violentes, sd méningé sd confusionnel, troubles visuel.
[^28]: Stimulé par ACTH, rétrocontrole nég. sur ACTH
[^29]: Analogue de l\'ACTH
[^30]: Surrénalectomie bilatére, anticortisolique de synthèse, nécrose
hémorragique
[^31]: ☡ éliminer phéochromocytomes avant biopsie surrénale
[^32]: S\'associe souvent à d\'autres insuffisances de l\'axe
hypothalamo-hypophysaire
[^33]: Pli cutané, hypotension
[^34]: Dyspnée de Kussmaul, haleine acétonique
[^35]: Atrophie optique, surdité, diabète insipide \< 20 ans
[^36]: Surdité, dystrophie maculaire, cardiomyopathie transmission par
la mère
[^37]: Latent Autoimmune Diabetes in the Adult
[^38]: ES = diarrhées. CI = insuf rénale (?), hépatique, respiratoire
[^39]: 1ere intention = metformine. Si besoin, +sulfamide. Si besoin :
DPP4 si écart \< 1% sinon insuline (ou GLP-1 si IMC \> 30)
[^40]: \< 6.5% si découverte
[^41]: Microalbuminurie, macro quand détectable à la BU
[^42]: 30-300mg/24h ou 20-200mg/L
[^43]: Thrombus bloquant l\'aorte abdominale avant bifurcation
[^44]: Grosses fibres
[^45]: Grosses fibres
[^46]: Sensible mais pas interprétable \> 60 ans ou patho
bronchorespiratoire
[^47]: Calcul par les études UKPDS ou SCORE (mais ×2-4 pour ce dernier)
[^48]: \< 55 ans ♂, \< 65 ans ♀
[^49]: \< 45 ans
[^50]: \> 102cm ♂, \> 88cm ♀
[^51]: Sclérose réractile de l\'aponévrose palmaire moyenne
[^52]: (Pré-)Albumine, IGF-1, ferritine sérique
[^53]: Insuffisance antéhypophysaire complète
[^54]: Obésité abdominale : \> 88cm ♀, \> 102cm ♂
[^55]: CI : troubles cognitifs sévères, troubles sévères non stabilisés
du comportement alimentaire, dépendances à l\'alcool / substances
psychoactives, pas de PEC médicale, pronostic vital mis en jeu, CI à
l\'anesthésie générale, incapacité à faire un suivi médical prolongé
[^56]: Médecin qualifé pour : alpinisme, armes à feu, mécaniques,
aériens, sous-marins, de combat avec HS
[^57]: Pour 1er certificat puis tous les 3 ans puis tous les 5 ans
jusque 35 ans
[^58]: Thiamine, riboflavine, niacine, B6
[^59]: Vit C, E, \\beta{xcarotène
[^60]: Une partie du calcium est lié à l\'albumine
[^61]: Cataracte sous-capsulaire, calcification des noyaux gris centraux
[^62]: Hypoplasie des parathyroïdes et du thymus, dysmorphie faciale,
anomalies cardiaques
[^63]: Sauf si acidose, hyperprotidémie, `\inc`{=latex}
phosphore/sulfate sériques
[^64]: La PTH est produite par la parathyroïde...
[^65]: Ostéite fibrokystique de von Recklinhausen, exceptionnelle.
[^66]: Néoplasie endocirinienne multiple de type 1
[^67]: Tumeurs souvent \> 10cm, kystique, multiloculaire, unlatérale
[^68]: Peut appartenir à : complexe Carney, sd Petuz-Jeghers
[^69]: Retard croissance intra-utérin
[^70]: Index d\'Apnées et Hypopnées (nb par heure)
[^71]: Sévère si IAH $\ge$ 30.
[^72]: Obésité abdo et (2 parmi : HTA, glycémie $\ge$ 5.6 mmol/L, HDL
bas, hypertriglycéridémie)
[^73]: Rétrognathisme, macroglossie, hypertrophie du palais mou ou des
amygdales, obstruction nasale
[^74]: Flux naso-buccal, mouvement thoraco-abdominaux, capteur de son,
SpO~2~, ECG
[^75]: Enregistre en plus EEG, électro-oculogramme, EMG muscles houppe
du menton
[^76]: prise en charge
[^77]: Remboursement si IAH \> 30/h (ou IAH \> 10/h sur
polysomnographie)
[^78]: (PaCO~2~ \> 45 mmHg) et PaO~2~ \< 70 mmFg) et (IMC \> 30 kg/m^2^
sans d\'autre cause.
[^79]: Confusion, fréquence Respiratoire ≥ 30min, (Blood) PAs \< 90mmHg
ou PAd ≥ 60mmg, Age ≥ 65 ans
[^80]: (8-14 si légionellose, 21j si légionelles graves/ID)
[^81]: Pour l'amiante : caisse d'assurance malaide ou FIVA
[^82]: Broncho-dilatateurs à courte durée d'action
[^83]: Broncho-dilatateur à longue durée d'action
[^84]: Pneumopathie interstitielle diffuse
[^85]: Pneumopathie interstitielle non spécifique
[^86]: orthopnée, tachy, assourdissement bruits, ascult pulmonaire
normale, turgescence jugulaire, pouls paradoxal
[^87]: DD atélectasie : médiastin dévié vers l\'opacité
[^88]: Ou critère de Light : (LDH \> 200 UI/L) ou (protides
pleuraux/sérique \> 0.5) ou (LDH pleuraux/sérique \> 0.6)
[^89]: Sauf si unilat/asymétrique ou douleur pleurale/fièvre ou
traitement insuffisant)
[^90]: Hormone gonadotrophine chorionique
[^91]: On peut inclure dans BPCO **si TVO** : bronchite chronique (toux
productive quotidienne ≥ 3 mois/an et ≥ 2 ans), emphysème
(élargissement espaces aériens distaux + destructions parois
alvéolaires) inclus dans BPCO
[^92]: Pour l\'obstruction : stade 1 (VEMS $\ge 80\%$) à 4 (VEMS \< 30%)
[^93]: Pour dyspnée : 0 = efforimportant, 1 = à plat, 2 = doit
s\'arrêter pour marche à plat, 3 = qq minutes à plat, 4= pour
s\'habiller
[^94]: Body mass index, Obstruction, Dispnea, Exercice
[^95]: Mais souvent pas de facteur précis
[^96]: Idiopathique, héritable, médicaments, maladie veino-occlusive,
hémangiomatose capillaire pulmonaire, HTP persistante du nouveu-né
[^97]: Souffle holosystolique d\'insuf. tricuspid majoré à
l\'inspiration
[^98]: Tachy, galop, turgescence jugulaire, reflux hépato-jugulaire,
HMG, OMI, anasarque
[^99]: Dyspnée d\'effort, syncope, fatigue
[^100]: Membres inférieurs
[^101]: Ventricule droit
[^102]: Accident ischémique cérébral
[^103]: Sat \< 90%, PAS \< 100 mmHg, FC \> 110/min, Cancer, insuf
Cardiaque chronique
[^104]: eBNP, NT-pro-BNP, troponine
[^105]: Névralgie cervicobrachiale avec douleurs radiculaire C8-D1, sd
Claude-Bernard-horner
[^106]: Chimiosensible rechutes fréquentes et rapides
[^107]: Turgescence jugulaire, reflux hépato-jugulaire, hépatomégalie
douleureuse, signe de Harzer
[^108]: Pneumothorax
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\newacronym{ADP}{ADP}{Adénopathie}
\newacronym{ARA II}{ARA II}{Antagonistes des récepteurs de l'angiotensine}
\newacronym{ATS}{ATS}{Antithyroïdiens de synthèse}
\newacronym{AT}{AT}{Antithrombine}
\newacronym{BAV}{BAV}{Bloc auriculoventriculaire}
\newacronym{BBG}{BBG}{Bloc de branche gauche}
\newacronym{BD}{BD}{Bronchodilatateur}
\newacronym{BGT}{BGT}{bilirubine glucoronide-transférase}
\newacronym{BSA}{BSA}{Bloc sinuso-atrial}
\newacronym{CAIS}{CAIS}{Complete Androgen Insensitivity Syndrome}
\newacronym{CHC}{CHC}{Carcinome hépato-cellulaire}
\newacronym{CLU}{CLU}{Cortisol libre urinaire}
\newacronym{CPRE}{CPRE}{Cholangio-pancréatographie rétrograde endoscopique}
\newacronym{CST}{CST}{Coefficient de saturation de la transferrine}
\newacronym{DAI}{DAI}{Défibrillateur automatique implantable}
\newacronym{DIP}{DIP}{Pneumopathie Interstitielle Desquamante}
\newacronym{DMLA}{DMLA}{Dégénérescence maculaire liée à l'âge}
\newacronym{DO}{DO}{Déclaration obligatoire}
\newacronym{DT}{DT}{Delirium tremens}
\newacronym{ECPA}{ECPA}{Echelle comportementale d'évaluation de la douleur chez la personne âgée}
\newacronym{EI}{EI}{Endocardite infectieuse}
\newacronym{EN}{EN}{Echelle numérique}
\newacronym{EP}{EP}{Embolie pulmonaire}
\newacronym{EVA}{EVA}{Echelle visuelle analogiqu}
\newacronym{EVS}{EVS}{Echelle verbale simple}
\newacronym{FA}{FA}{Fibrillation atriale}
\newacronym{FE}{FE}{Fraction d'ejection}
\newacronym{FIVA}{FIVA}{Fonds d'indemnisation des victimes de l'amiante}
\newacronym{FIV}{FIV}{Fibrinolyse intra-veineuse}
\newacronym{FO}{FO}{Fond d'oeil}
\newacronym{FPI}{FPI}{Fibrose Pulmonaire Idiopathique}
\newacronym{GH}{GH}{Hormone de croissance (Growth hormone)}
\newacronym{GNV}{GNV}{Glaucome néovasculaire}
\newacronym{GPAO}{GPAO}{Glaucome primitif à angle ouvert}
\newacronym{HAD}{HAD}{Hospital Anxiety and Depression Scale}
\newacronym{HMG}{HMG}{Hépatomégalie}
\newacronym{HSH}{HSH}{Hommes ayant des relations sexuelles avec des hommes}
\newacronym{HVG}{HVG}{Hypertrophie ventriculaire gauche}
\newacronym{IC}{IC}{Insuffisance cardiaque}
\newacronym{ID}{ID}{Immunodéprimé}
\newacronym{IEC}{IEC}{Inhibiteurs de l'enzyme de conversion}
\newacronym{IOP}{IOP}{Insuffisance ovarienne primitive}
\newacronym{IPC}{IPC}{Intervention coronaire percutanée}
\newacronym{IS}{IS}{Insuffisance surrénale}
\newacronym{ITK}{ITK}{Inhibiteur de tyrosine kinase}
\newacronym{IVA}{IVA}{Artère intraventriculaire antérieure}
\newacronym{JPDC}{JPDC}{Jusqu'à preuve du contraire}
\newacronym{LBA}{LBA}{Lavage Broncho-Alvéolaire}
\newacronym{MTEV}{MTEV}{Maladie Thrombo-Embolique Veineuse}
\newacronym{NOIA}{NOIA}{Neuropathie optique ischémique antérieure}
\newacronym{OCA}{OCA}{Occlusion coronaire aigüe}
\newacronym{OGD}{OGD}{Oestro-gastro-duodénale}
\newacronym{OGE}{OGE}{Organes génitaux externes}
\newacronym{OG}{OG}{Oreillette gauche}
\newacronym{OMI}{OMI}{Oedème des membres inférieurs}
\newacronym{PAD}{PAD}{Pression artérielle diastolique}
\newacronym{PAPm}{PAPm}{Pression de l'artère pulmonaire moyenne}
\newacronym{PAS}{PAS}{Pression artérielle systolique}
\newacronym{PA}{PA}{Pression artérielle}
\newacronym{PEV}{PEV}{Potentiels évoqués visuels}
\newacronym{PGG}{PGG}{Paragangliomes}
\newacronym{PINS}{PINS}{Pneumonpathie Interstitielle Non Spécifique}
\newacronym{POC}{POC}{Pneuompathie organisée cryptogénique}
\newacronym{QCD}{QCD}{Questionnaire Concis de la Douleur}
\newacronym{QDSA}{QDSA}{Questionnaire Douleur Saint-Antonne}
\newacronym{RCT}{RCT}{Rapport cardiothoracique}
\newacronym{RGO}{RGO}{Reflux gastro-oesophagien}
\newacronym{RPM}{RPM}{Réflexe photomoteur}
\newacronym{SAS}{SAS}{Syndrome d'apnée du sommeil}
\newacronym{SMG}{SMG}{Splénomégalie}
\newacronym{SOPK}{SOPK}{Syndrome des ovaires polymicrokystiques}
\newacronym{SPT}{SPT}{Syndrome post-thrombotique}
\newacronym{TAVI}{TAVI}{Transcatheter Aortic Valve Implantation.}
\newacronym{TG}{TG}{Tryglycérides}
\newacronym{TIH}{TIH}{Thrombopénie induite par l'héparine}
\newacronym{TVO}{TVO}{Troubles Ventilatoires Obstructifs}
\newacronym{TVP}{TVP}{Thrombose veineuse profonde}
\newacronym{TVR}{TVR}{Troubles Ventilatoires Restrictif}
\newacronym{TVS}{TVS}{Thrombose veineuse superficielle}
\newacronym{VAS}{VAS}{Voies Aériennes Supérieures}
\newacronym{VBP}{VBP}{Voie biliaire principale}
\newacronym{VG}{VG}{Ventricule gauche}
\newglossaryentry{NEM1}{name={NEM1},
description={Néoplasie endocrinienne multiple 1. 3 "P" : hyperParathyroïdie primaire, adénome hyPophysaire, tumeur neuro-endocrine du Pancreas. Voir aussi NEM2}}
\newglossaryentry{NEM2}{name={NEM2},
description={Néoplasie endocrinienne multiple 2. Cancer médullaire de la thyroïde et phéochromocytome. Voir aussi \gls{NEM1}}}
\newglossaryentry{Leydigcell}{name={cellule de Leydig},description={Produit de la testostérone. Localisé près des tubules séminifères (testicules)}. Activé par LH}
\newglossaryentry{NF1}{name=NF1, description={Neurofibromatose 1. Tâches café au lait, neurofibromes (cutanées, nodulaires [le long d'un trajet d'un nerf] ou plexiformes [K possible]), nodules de Lisch sur l'iris.}}
\newglossaryentry{PCC}{name={Phéochromocytomes}, description={Tumeur de la médullo-surrénale}}
\newglossaryentry{PTH}{name={Parathyroide Hormone (PTH)},description={Stimule la résorbtion osseuse (ostéoclastes) pour libérer plus de calcium}}
\newglossaryentry{SHBG}{name=SHBG,description={Sex Hormone-Binding Globulin. Diminue avec des androgènes, augmente avec les oestrogènes}}
\newglossaryentry{Sertolicell}{name={cellule de Sertoli},description={Participe à la production du sperme. Localisé dans un tubule séminifère. Activé par FSH}}
\newglossaryentry{TPO}{name={Thyroid peroxydase (TPO)},description={Enzyme de la thyroïde servant à générer la thyroxine (T4) et triiodothyroine (T3)}}
\newglossaryentry{VHL}{name={von Hippel-Lindau}, description={Hémangioblastome du cervelet/moelle épinière, de la rétine, phéochromocytome}}
\newglossaryentry{trophozoïtes}{name={Trophozoïtes},description={Formes végétatives mobiles}}
\newglossaryentry{sdMetabolique}{name={Syndrome métabolique},
description={IMC > 28 kg/$m^2$, HTA,
(HDL < 0.35g/L ou TG > 2g/L ou dyslipidémie traitée),
ATCD diabète familial/gestionnel, temporairement induit.
Autre définition (NCEP III) : (\diameter abdo > 100cm \male ou 88cm \female),
hyperglycémie (glycémie à jeun > 1g/L),
dyslipidémie (TG > 1.5g/L et (HDL < 0.4g/L \male ou 0.5g/L \female)),
HTA (> 130mmHg systole ou > 85mmHg diastole)}}
\newglossaryentry{sdmetabolique}{name={Syndrome métabolique},
description={$\diameter \ge 94$ cm $\male{}$, 80 cm $\female{}$,
TG $\ge$ 1.7mmol/L, HDL < 1 mmol/L $\male{}$ ou 1.3mmol/L $\female{}$,
PAs $\ge 130$ mmHg ou PAd $\ge 85$ mmHg, glycémie jeun $\ge$ 1 g/L
}}
\newglossaryentry{VEMS}
{
name={VEMS},
description={volume expiratoire maximal en 1s (après inspiration maximale)}
}
\newglossaryentry{CV}
{ name = Capacité Vitale,
description = volume total mobilisable maximal = VC + VRI + VRE
}
\newglossaryentry{VC}
{ name=Volume courant,
description={volume mobilisé pendant une respiration normale}
}
\newglossaryentry{VRI}
{ name = Volume de réserve inspiratoire,
description = volume supplémentaire (par rapport au VC) avec
une inspiration forcé
}
\newglossaryentry{VRE}
{ name = Volume de réserve expiratoire,
description = idem VRI mais en expiration forcée
}
\newglossaryentry{VR}
{ name = Volume résiduel,
description = volume restant (impossible à expirer)
}
\newglossaryentry{CVF}
{ name = Capacité Vitale Forcée,
description = volume expulsé avec force (CPT - VR)
}
\newglossaryentry{CVL}
{ name = Capacité Vitale Lente,
description = idem CVF mais lentement
}
\newglossaryentry{CPT}
{ name = {Capacité Pulmonaire Totale},
description = {Capacité Vitale + volume résiduel}
}
\newglossaryentry{PAPO}{
name = PAPO,
description = Pression artérielle pulmonaire occluse $\approx$ pression
capillaire pulmonaire
}
\newacronym{MDPH}{MDPH}{Maison département des personnes handicapées}
\newacronym{CNSA}{CNSA}{Caisse nationale de solidarité pour l'autonomie}
\newacronym{AAH}{AAH}{Allocation aux Adultes Handicapés}
\newacronym{CDAPH}{CDAPH}{Commission des droits et de l'autonomie des personnes handicapées (départemental)}
\newacronym{PAF}{PAF}{Polypose adénomateuse familiale}
\newacronym{BPCO}{BPCO}{Bronchopneumopathie chronique obstructive}
\newacronym{VNI}{VNI}{Ventilation non invasive}
\newacronym{TIPMP}{TIPMP}{Tumeurs intracanalaires papillaire mucineuses pancréatiques}
\newacronym{FID}{FID}{Fossie Iliaque droite}
\newacronym{FIG}{FIG}{Fossie illiaque gauche}
\newacronym{TFI}{TFI}{Troubles fonctionnels intestinaux}
\newglossaryentry{PET1}{name={Polyendocrinopathie auto-immune de type 1},description={Hypoparathyroïdie, candidose, insuf. surrénale}}
\newglossaryentry{PET2}{name={Polyendocrinopathie auto-immune de type 2},description={insuf. surrénale + 1 maladie autoimmune parmi thyroïdite d'Hashimoto, maladie de Basedow, diabète type 1}}
\newacronym{SPUPD}{SPUPD}{Syndrome polyuro-polydipsique}
\newglossaryentry{IPS}{name={Index de pression systolique},description={Pression systolique cheville/bras}}
\author{Alexis Praga}
\date{\today}
\title{}
\hypersetup{
pdfauthor={Alexis Praga},
pdftitle={},
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\begin{document}
\tableofcontents
\section{Cardiologie}
\label{sec:orgd428186}
\def\arrow{$\rightarrow$}
\subsection{220 Dyslipidémies}
\label{sec:orgd36ca82}
\subparagraph{Diagnostic}
\label{sec:org5922280}
Clinique :
\begin{itemize}
\item hypercholestérolémie : arc cornéen (< 50A), xanthélasmas, xanthomes
tendineux/fesses ou mains/coudes
\item hyperTG : HMG stéatosique, SMG, xanthomes cutanés éruptifs
\end{itemize}
Bio
\begin{itemize}
\item lipides = hypercholestérolémie : CT/TG > 2.5, hyperTG : TG/CT > 2.5, mixte sinon
\item sérum clair/limpide si hypercholestérolémie, lactescent sinon
\end{itemize}
Bilan normal : LDL < 1.6g/L, HDL > 0.4g/L, TG < 1.5g/L
\subparagraph{Classification}
\label{sec:org95771c2}
Tab \ref{tab:org8d824a0}, \ref{tab:org4855194}
\begin{table}[htbp]
\caption{\label{tab:org8d824a0}Hyperlipidémies primaires}
\centering
\begin{tabular}{llllll}
Impact & Classif & Type & Fréquence & Dépôts & Risque\\
\hline
Cholestérol & IIa & familale monogénique & & oui & CV\\
& & - hétérozygote & freq & parfois & \\
& & - homozygote & très rare & fréquents & \\
& & - mutation apoB & freq & & \\
& & polygénique & freq++ & rare & \\
TG & IV & familiale & rare & rare & \\
& I, V & hypercholymicronémie primitive & très rare & inconstant & \danger TG > 10g/L !\\
& & & & & pancréatite aigüe\\
Mixte & IIb & familiale combinée & freq & rares & \\
& III & dys\(\beta\)lipoprotéinémie & rare & inconstant & \\
\end{tabular}
\end{table}
\begin{table}[htbp]
\caption{\label{tab:org4855194}Hyperlipidémies secondaire}
\centering
\begin{tabular}{lll}
Cause & Diagnostic & Impact\\
\hline
Hypothyroïdie & TSH & cholestérol, mixte\\
Sd néphrotique, grossesse & protéinurie, \oe{}dème & cholestérol\\
Cholestase & Bilirubine, phosphatase alcaline & cholestérol\\
IR chronique, & créatinine & TG, mixte\\
Alcoolisme & interrogatoire & TG\\
Diabète & glycémie & TG\\
\hline
Iatrogène : ciclosporine, corticoïdes & oestrogènes oraux, rétinoïdes, & IFN-\(\alpha\), antétroviraux, neuroleptiques\\
diurétiques thiazidiques, \(\beta\)bloquant & & \\
\end{tabular}
\end{table}
\paragraph{Risque faible (0 FR), intermédiaire (\(\ge\) 1 FR), haut (ATCD)}
\label{sec:org74f9106}
FR semblables au\textasciitilde{}\hyperref[subsec:fr]{score précédent} : tabac \(\le\) 3 ans, HTA, diabète, HDL < 0.40g/L, âge > 50
(\male) ou 60 (\female), ATCD familiaux IDM ou mort subite
\subparagraph{Traitement}
\label{sec:org15a8837}
Hypercholestérolémies : primaire si LDL élèvé à ttt+6 mois, secondaire si complication ischémique
\begin{itemize}
\item Objectifs LDL < 0.7g/L si risque très élevé, < 1g/L si élevé, < 1.15g/L sinon
\item hypercholestérolémies : \uline{statines}\footnote{ES : myalgies, \inc CPK, \inc transaminases, \inc risque diabète 2
CI : HS, \emph{grossesse}, allaitement} (sinon ézétimibe)
\item hypertriglycéridémies : \uline{diététique} \textpm{} statines si TG > 2g/L (fibrates si échec)
\end{itemize}
Diététique
\begin{itemize}
\item lipides < 40\%, graisses : mono- et polyinsaturées, cholestérol alimentaire < 300mg/j
\item 5 fruits ou légumes/j, sodium < 6g/j, \dec poids
\item HyperTG :
\begin{itemize}
\item modérées : -20\% calories ++, \inc activité physique
\item majeur : arrêt alcool, régime hypocalorique avec < 30g lipides (obèse)
\end{itemize}
\end{itemize}
\section{Endocrinologie}
\label{sec:orge3831a8}
\subsection{32 \textdagger{} Allaitement maternel}
\label{sec:org65c64a0}
\subsection{35 \textdagger{} Contraception}
\label{sec:orge7bb55a}
\subsubsection{Contraception hormonale}
\label{sec:org91f8a92}
Oestroprogestatifs
\begin{itemize}
\item Contient \{oestrogène, progestatif (gen 1,2 ou 3), autres progestatif\}
\item Administration orale, transdermique ou vaginale
\item Action : \{pas d'ovulation, endomètre peu à apte à la nidation, glaire
cervicale imperméable aux spermatozoïdes\}
\end{itemize}
Progestatifs seuls
\begin{itemize}
\item Microprogestatifs : action sur glaire cervicale, endomètre
\item Macroprogestatifs : si CI oestroprogestatifs
\item Administration : orale, injection, implant, intra-utérin (stérilet)
\end{itemize}
\subsubsection{Pratique}
\label{sec:org30d2f10}
Oestroprogestatifs : le premier jour des règles pendant 21j puis 7 j
d'arrêt. \emph{Tjrs au même moment}. Si oubli < 12h, ASAP sinon contraception mécanique \(\ge 7\) jours
Microprogestatifs : toujours à la même heure. Si oubli < 3h, ASAP, sinon
contraception mécanique \(\ge 7\) jours
Macroprogestatifs : commencer le 5eme jour du cycle
\subsubsection{Contre-indications}
\label{sec:orgf3c36c7}
Oestroprogestatifs : absolues =
\begin{itemize}
\item thromboemboliques veineux/artériels, prédisposition thromboses
\item lupus évolutif, connectivites, porphyries
\item vasc, cardiaque, cérébrales, oculaires
\item valvulopathie, troubles rythmes thrombogènes
\item HTA non contrôlée
\item diabète et micro/macroangiopathie
\item tumeur hormono-dépendantes (sein, utérus\ldots{})
\item hépatiques sévères
\item hémorragies génitales non diagnostiquées
\item (tumeurs hypophysaires)
\end{itemize}
Macro/microprogestatifs : cancers \{sein, endomètre\}, insuf hépatique, accident
TEV récents
\subsubsection{Recommandation}
\label{sec:orgea9844a}
Sans CI, oestroprogestatif minidosé et progestatif 2eme génération monophasique
(Minidril)
\subsubsection{Efficacité}
\label{sec:org1f9afa6}
Indice de Pearl\footnote{\(\frac{N}{N_e/10}\times 100\) avec N = nb grossesses
accidentelles, \(N_e\) nombres de mois d'exposition} < 0.07\% pour oestroprogestatif
(< 2\% pour les microprogestatifs)
Attention : certains inducteurs enzymatiques réduisens l'efficacité (ou
millepertuis).
Ado : sous- ou mal utilisée
\subsubsection{Tolérance}
\label{sec:org570eec7}
Oestroprogestatifs :
\begin{itemize}
\item bien tolérée, pas de perte de poids
\item surveiller métabolisme
\item active coagulation mais \inc fibrinolyse. Légère augmentation du risque
d'accident TEV
\item vasc : faible \inc PA
\item cancer : ovaire = risque -50\%, idem pour l'endomètre, faible \inc pour sein
\end{itemize}
Microprogestatifs : troubles des règles (spotting, aménorrhées), grossesse
extra-utérine
Macroprogestatifs : hypoestrogénie, aménorrhées, spotting
\subsubsection{Surveillance}
\label{sec:org9a0e24e}
Consulter si céphalée, déficit sensitivomoteur, (douleur ou oedème) MI, dyspnée,
douleur thoracique
Examen clinique :
\begin{itemize}
\item préthérapeutique : gynéco, frottis cervico-vaginal dès 25 ans si
asymptomatique.
\item PA à +3mois puis tous 6 mois
\item hyperoestrogénie (tension mammaire), hypoestrogénie (sécheresse vaginale)
\end{itemize}
Biologie : cholestérol total, triglycérides, glycémie à jeun à +3mois. Si FR, le
faire avant (!) prescription
Gynéco : métrorragies, spottings.
Frottis cervico-utérin dès 25 ans (+1 an puis tous 3 ans) indépendamment contraception
\subsubsection{Femmes à risques}
\label{sec:orga6d3929}
Diabétique :
\begin{itemize}
\item non hormonale : si diabète 1 > 15 ans ou micro/macroangiopathie \thus locale
(nullipare, peu de rapports) ou intra-utérin (multipare, diabète équilibré)
\item hormonale :pas d'oestropregestatifs si \{tabac, non équilibré, HTA, surpoids,
diabète compliqué\} \thus progestatif
\end{itemize}
Dyslipidémie : oestroprogestatif si < 3g/L cholestérol total, triglycérides <
2g/L
Thrombose veineuse
\begin{itemize}
\item prédisposant : anomalies de l'hémostase (génétique, acquises), ATCD familiaux
\item dépistage : thrombose, multiples fausses couches, ATCD thrombose < 45 ans
\item CI oestrogène, acétate de chlormadinone à la place
\end{itemize}
Autres :
\begin{itemize}
\item HTA : oestroprogestatifs si 0 FR
\item tabac = CI
\item si migraine et vascularite, voir spécialiste
\end{itemize}
\subsubsection{Contraception d'urgence}
\label{sec:org3ff8664}
\begin{itemize}
\item lévonorgestrel ASAP < 72h
\item ulipristal acétate ASAP < 120h mais 3x plus cher
\end{itemize}
\subsection{37 \textdagger{} Stérilité du couple}
\label{sec:org2de2ca5}
Infertile : 0 grossesse après 1 an de rapports non protégés. Stérilité si
définitif.
Stérilité = partagée !!
\subsubsection{Interrogatoire}
\label{sec:org4c43b0a}
\begin{itemize}
\item Couple
\item Femme : âge++ (détérioration après 35 ans), \{grossesses antérieure,
avortements\}, infections/curetages++, ATCD chir/infectieux, douleurs
pelviennes (rapports, règles), conditions de vie, radio/chimio
\item Homme : trouble libido/érection, ATCD cryptorchidie/trauma testiculaire, ATCD
chir pelvienne/scrotale, ATCD médicaux (orchite ourlienne++), tabac/anabolisants\ldots{}
\end{itemize}
\subsubsection{Examen clinique}
\label{sec:org347b41d}
\begin{itemize}
\item \female : âge++, obésité/maigreur, tour taille et hanche, pilosité, PA,
galactorrhé provoqué, gynéco.
\begin{itemize}
\item Si anovulation (a/oligo-ménorrhée) : hyperprolactinémie, hyperandrogénie,
troubles comportement alimentaire, bouffées chaleur
\end{itemize}
\item \male : IMC, pilosité, hypoandrisme, cicatrice chir, varicocèle\footnote{Dilatation variqueuse des veines du cordon spermatique},
gynécomastie, gynoïde/enuchoïde
\begin{itemize}
\item volume testiculaire++, palpation cordospermatiques
\end{itemize}
\end{itemize}
\subsubsection{Examens complémentaires}
\label{sec:orgd2f44e1}
Premiere intention, femme
\begin{itemize}
\item Hormonale++ : oestradiol, LH, FSH, prolactine plasmatique. Puis progestérone plasmatique (si cycle réguliers)
\item Écho ovarienne++
\item Hystérographie++
\end{itemize}
Première intention, homme :
\begin{itemize}
\item spermogramme++ (concentration, mobilité, morphologie). Attention aux variabilités !
\item hormonale++ si oligo-/azoo-spermie : testostérone, LH, FSH puis gls:SHBG
\end{itemize}
Test poist-coïtal (discuté)
\subsubsection{Étiologie}
\label{sec:org0b0e201}
Femme :
\begin{itemize}
\item \emph{anovulation} : très fréquent ! Souvent aménorrhées ou irrégularités. Causes :
gls:SOPK, hyperprolactinémie, insuf ovarienne primitive, déficit gonadotrope, psycho-nutritionnel
\item \emph{obstacle mécanique} :
\begin{itemize}
\item anomalie du col utérin et insuf glaire cervicale : post-conisation/curetage
\item obstacle, anomalie utérine : manoeuvres post-partum, polypes muqueux\ldots{} \thus
echographie
\item obstacle tubaire : cause majeure++. Souvent salpingite (Chlamydia++)
\end{itemize}
\item \emph{endométriose} : rarement en cause si modérée. hystérosalpingographie puis coelioscopie
\end{itemize}
Homme :
\begin{itemize}
\item \emph{azoospermie}
\begin{itemize}
\item \emph{sécrétoire} : diagnostic = volume testiculaire < 10ml, concentration FSH
faible
\end{itemize}
\thus caryotype, analyse bras long Y, écho testiculaire (élimine K), déficit gonadotrope (rare)
\begin{itemize}
\item \emph{obstructive} : volume et concentration ormale, volume séminal \dec \thus
examen clinique
\begin{itemize}
\item cause congénitale : agénésie bilat des canaux déférent++ (soit anomalie
biallélique gène CFTR, soit isolée)
\item acquis : infectieux (gonocoque, tuberculose, Chlamydia) \thus échographie
\end{itemize}
\item exploration chir testiculaire et des voies excrétrices : si azoospermie
confirmée par plusieurs spermogrammes, bilan génétique
\end{itemize}
\item \emph{oligo-asthéno-térato-spermie} : \dec nombre et mobilité, \inc formes anormales
\thus caryotype, brang long Y. Traitement = assistance médicale procréation
\end{itemize}
\subsection{40 \textdagger{} Aménorrhée}
\label{sec:org528f07c}
Déf: absence de cycle menstruel après 16 ans (primaire) ou interruption chez
femme réglée (secondaire). Physiologique : grossesse, lactation, ménopause
Tout arrêt > 1 mois \thus enquête étiologique \danger
Atteinte de l'axe hypothalamo-hypophysio-ovarien ou anomalie tractus utérin
\begin{tcolorbox}
Pas de traitement oestrogénique sans enquête étiologique
\end{tcolorbox}
\subsubsection{Conduite}
\label{sec:orgcfc0f91}
\paragraph{Primaire}
\label{sec:orgec73915}
Forte proba de cause génétique/chromosomique. Chercher carences nutritionnelle
\begin{itemize}
\item Si absence de dév. pubertaire : doser FSH, LH
\begin{itemize}
\item Si basses, tumeur hypothalamo-hypophysaire, dénutrition ou génétique : \{sd
de Kalmann (anosmie), mutation récepteur GnRH (rare), atteinte
gonadotrophines (exceptionnels), mutation LH\}
\item Si hautes : sd de Turner (caryotype 45, X0),
\end{itemize}
\item Examen gynéco, écho pelvienne
\begin{itemize}
\item Pas d'utérus : sd de Rokitanski, tissu testiculaire dans les canaux
inguinaux (ex: acrshort:CAIS)
\item ambiguité acrshort:OGE : dysgénésie gonadique, hyperplasie congénitale surrénales,
anomalies sensibilité/biosynthèse androgènes
\end{itemize}
\end{itemize}
\paragraph{Secondaire}
\label{sec:org7e3bd87}
Souvent acquises.
Interrogatoire : médic, maladie endoc/chronique,
gynoc/obstétriques, insuf ovarienne (bouffées de chaleur). Douleurs pelviennes
cycliques : cause utérine
Examen clinique :
\begin{itemize}
\item poids et taille (carence nutritionnelle)
\item hyperandrogénie : gls:SOPK, déficit 21-hydroxylase, (sd Cushing)
\item carence oestrogénique : pas de glaire +2 semaines après saignement \thus
anovulation
\item pas de signe d'appel : enquête nutritionnelle
\end{itemize}
Dosages hormonaux : cf Table \ref{tab:amenorrhe_second}
\begin{table}
\begin{tabular}{llllll}
\toprule
hCG & prolactine \inc & FSH \inc & estradiol& testostérone > 1.5ng/mL & sinon\\
& & & LH, FSH \dec & & \\
\midrule
grossesse & médicaments & \acrshort{IOP} & tumeur H-H & tumeur surrénales & \gls{SOPK}\\
& adénome à prolactine & & nutrition & tumeur ovarienne sécrét. & \\
& tumeur H-H & & & & \\
\bottomrule
\end{tabular}
\caption{Évaluation hormonale d'une aménorrhée secondaire. H-H = hypothalamo-hypophysaire}
\label{tab:amenorrhe_second}
\end{table}
\subsubsection{Causes}
\label{sec:org8a0f8db}
\paragraph{1. Déficit gonadotrope organique/fonctionnel}
\label{sec:orgaffcea9}
\subparagraph{Prolactine normale \footnote{Hypothalamus n'arrive pas à libérer la GnRH au bon rythme.}}
\label{sec:org0309a56}
\begin{itemize}
\item Atteintes organiques : tumeur/infiltration \thus IRM
\begin{itemize}
\item macroadénomes hypophysaires, craniopharyngiomes
\item chercher hyperprolactinémie, insuf antéhypophysaire associé
\end{itemize}
\item Atteintes fonctionnelles : apports nutritionnels insufisants par rapport à l'activité physique intense+++
\end{itemize}
\subparagraph{Hyperprolactinémie}
\label{sec:org7402127}
Atteinte hypothalamo-hypophysaire (majeure++)
Médicaments ou tumeurs \thus pas de traitement dopaminergique sans imagerie \danger
\subparagraph{Autres}
\label{sec:org2f3ce71}
\begin{itemize}
\item Endocrinopathies : sd de Cushing, dysthyroïdes déficits 21-hydroxylase
\item Hypophysaire (rare) : auto-immune (majorité), sd de Sheehan (très rare, nécrose hypophysaire post-partum)
\end{itemize}
\paragraph{2. Anovulation non hypothalamique}
\label{sec:org9691d2e}
\subparagraph{SOPK (majorité)}
\label{sec:orgd508f6a}
Pas de pic de LH, ni de progestérone. Oestradiol mais non cycliques
Irrégularité menstruelles, puis aménorrhées avec acné, hirsutisme
Diagnostic :
\begin{itemize}
\item 2 parmi : \{hyperandrogénie clinique\footnote{Séborrhéee, acné, hirsutisme, \inc testostérone}, oligo-/a-novulation, hypertrophie
ovarienne/folliculaire\footnote{V > 10mL, \(\ge\) 19 follicule par ovaires} (écho)\}
\item exclure bloc 21-hydroxylase, tumeur de l'ovaire, sd Cushing
\item exclure hyperprolactinémie
\end{itemize}
Diagnostic parfois difficile :
\begin{itemize}
\item sans hyperandrogénie \thus écho
\item \{atteinte partielle axe gonadotrope, macroprolactinémie\} peuvent y ressembler
\end{itemize}
Acné : cherche hyperandrogénie, régularité cycle menstruel \thus éliminer
hyperplasie congénitale des surrénales
2 causes :
\begin{itemize}
\item tumeur ovarienne ou résistance insuline
\begin{itemize}
\item virilisation si tumeur
\item imagerie si testostérone > 1.5ng/mL. Si normale, cherche hypothécose
(obésité morbide androïde, acanthosis nigricans, insulino-résistance)
\end{itemize}
\item pathologie surrénale :
\begin{itemize}
\item sd de Cushing si signes hypercortisolisme \thus cortisol libre urinaire et
freinage minute
\item tumeur surrénale \thus scanner des surrénales
\item déficit enzymatique en 21-hydroxylase (\danger formes tardives qui peuvent
mimer SOPK)
\end{itemize}
\end{itemize}
\paragraph{3. Insuf ovarienne primitive}
\label{sec:orgaaabeb6}
\inc FSH
Causes :
\begin{itemize}
\item chir, chimio, radiothérapie
\item anomalie caryotype (sd Turner)
\item anomalie gènes \emph{FMR1} (sd X fragile)\footnote{Transmission mère-fils. Expansion instable des triplets CGG jusqu'à
l'absence de transcript de FMR1 (Fragile X Mental Retardation 1). \\
\danger Risque d'IOP pour la pré-mutation seulement \thus dépister chez
\female + IOP < 40 ans par PCR et Southern Blot}
\item auto-immune
\end{itemize}
\paragraph{4. Anomalie utérine}
\label{sec:orgc6d03d2}
\subparagraph{Congénitales}
\label{sec:orgbf75a60}
Si dév pubertaire normal :
\begin{itemize}
\item et douleurs pelviennes cycliques : imperforation hyménéale/malformation vaginale \thus examen gynéco.
\item ou sans douleurs \thus agénésie utérus ?
\end{itemize}
Difficulté : différence agénésie mullérienne isolée (46,XX)- anomalies androgènes
(46,XY) \thus testostérone
\subparagraph{Secondaires}
\label{sec:org22c9a8f}
Synéchies utérines (trauma de l'utérus), tuberculose utérine
\subsection{47 \textdagger{} Puberté}
\label{sec:org601d2cc}
\subsubsection{Normale}
\label{sec:orge70a372}
\textasciitilde{}4 ans, acquisition de la taille définitive, fonction de
reproduction. Classification de Tanner (5 stades)
\begin{table}[htbp]
\caption{Puberté normale}
\centering
\begin{tabular}{llll}
\female & & \male & \\
\hline
seins & 11 ans [8,13] & volume testiculaire & 11.5 ans [9.5,14]\\
règles & 13 ans [10,15] & \inc taille verge & 12.5 ans\\
croissance & 5 \(\rightarrow\) 8cm/an & croissance & 5 \(\rightarrow\) 10cm/an\\
taille & 163cm & taille & 175cm\\
\end{tabular}
\end{table}
\subsubsection{Retards}
\label{sec:org9028eba}
\begin{tcolorbox}
\male : volume testiculaire < 4mL après 14 ans \footnotemark\\
\female : pas de seins à 13 ans, pas de règles à 15 ans
\end{tcolorbox}
\footnotetext{ou longueur < 25mm}
\begin{tcolorbox}
Hypogonadisme\footnotemark central ou périphérique ?
\begin{itemize}
\item FSH, LH \inc : pour compenser le manque des gonades (hypergonadotrope = primaire)
\item FSH, LH N ou \dec : problème hypothalamo-hypophysaire\footnotemark (hypogonadotrope = secondaire)
\end{itemize}
\end{tcolorbox}
\footnotetext{Chez \male, manque de testostérone}
\footnotetext{Rappel : LH entraîne la production de testostérone}
\begin{itemize}
\item centrale : congénital (pas de cassure de croissance, ni micropénis, ni
cryptorchidie), acquis (tumeur ?), "fonctionnel" (maladie générale, trouble
comportement alimentaire), isolé
\item périphérique : sd de Turner chez \female, sd Klinefelter \male
\item retard simple (élimination)
\end{itemize}
Clinique :
\begin{itemize}
\item parents, grossesse, courbe de croissance. Chercher trbles digestifs, polyuro-polydispsie, céphalée, anomalies champ visuel
\item pathologie acquise, OGE, testicules, anosmie (Kallmann)
\end{itemize}
Âge osseux : 13 ans \male, 11 ans \female
Biologie : stéroïdes sexuels
\begin{itemize}
\item FSH, LH basses \thus hypothalamo-hypophysaire
\item testostérone chez \male, oestradial/écho chez \female
\end{itemize}
IRM indispensable si déficit gonadotrope (tumeur) \danger
Caryotype si :
\begin{itemize}
\item FSH élevé
\item toujours chez \female{} de taille < -2DS avec retard pubertaire/gonadotrophine \inc
\end{itemize}
\paragraph{Étiologies}
\label{sec:org5432bae}
Hypogonadotropes
\begin{itemize}
\item congénitaux : isolés, sd de Kallman, autres déficits hypophysaires, sd
polymalformatifs
\item acquis : tumeurs hypophysaires, post-radiothérapie
\end{itemize}
Hypogonadotropes fonctionnels
\begin{itemize}
\item maladies chroniques digestives/cardiaques/respi
\item sport intense
\item maladies endocriniennes
\end{itemize}
Hypergonadotropes
\begin{itemize}
\item congénitaux : sd Turner, sd Klinefelter, autres atteintes primitives
\item acquis : castration, trauma, oreillons, chimio/radio
\end{itemize}
\paragraph{Traitement}
\label{sec:orgdb3ab8e}
Cause si possible. Sinon doses \inc de testostérone (\male) ou oestrogènes puis
oestroprogestatif (\female)
\subsubsection{Précoces}
\label{sec:org253b15e}
Avant 8ans \female ou 9.5 ans \male
\paragraph{Centrales}
\label{sec:orgc9e6e1e}
8x plus fréquent chez \female{} que \male{}. Chez \female{}, causes
idiopathiques. Chez \male{}, causes tumorales à 50\%
Clinique :
\begin{itemize}
\item dév prématuré harmonieux (pas de règles chez \female)
\item crises de rires (harmatome hypothalamique), tâches cutanées (neurofibromatose
I ou sd McCune-Albright)
\end{itemize}
Biologie :
\begin{itemize}
\item testostérone élevée chez \male{} mais variabilité d'oestradiol chez \female{}
\end{itemize}
IRM hypothalamo-hypophysaire indispensable \danger (petite taille
définitive). Écho pelvienne pour \female{}
Traitement si risque de petite taille adulte : analogues GnRH jusque âge normal
de puberté
\paragraph{Périphériques}
\label{sec:org44f1084}
Clinique : \inc vitesse de croissance, avance maturation osseusse
Stéroïdes élevées, LH et FSH bas. Écho pelvienne chez fille
Étiologie :
\begin{itemize}
\item tumeurs ovarienne (rares) : écho puis histologies
\item kystes folliculaires : bénins, régression spontanée possible
\item sd McCune-Albright :
\begin{itemize}
\item \{puberté précoce ovarienne, taches cutanées "café-au-lait", dysplasie fibreuses os\}. \danger tableau pas toujours complet !
\item oestradiol élevé, gonadotrophines basses, écho = utérus stimulé, kystes ovariens. Dominance \female
\end{itemize}
\item médicaments
\item testotoxicose (rare, cellule de Leydig activé et LH basses), adénome leydigien
(très rare)
\item tumeurs à hCG (\male)
\end{itemize}
\paragraph{Avances dissociées}
\label{sec:org7b3ba32}
\begin{itemize}
\item Isolé des seins : beaucoup de filles ( de 3 mois à 3 ans)
\item Métrorragies isolées : chercher vulvite, vulvovaginite, prolapsus urétrale,
corps étranger. Éliminter kyste ovarien, sd McCune-Albright par l'absence des
sein
\end{itemize}
\thus écho pelvienne
\begin{itemize}
\item Pilosité pubienne isolée : chercher forme d'hyperplasie congénitale des
surrénales (\inc 17-hydroxyprogestérone, stimulation ACTH), prémature pubarche
(élimination !)
\end{itemize}
\subsection{48 \textdagger{} Cryptorchidie}
\label{sec:orge109198}
\subsubsection{Enfant}
\label{sec:org6586e5e}
Localisation anormale et inaboutie du testicule. Très fréquente : 3\%
nouveaux-nés, 20\% préma. 2/3 descendent spontanément à 1 an de vie
Clinique : chercher micropénis (< 2cm, hypospadias, autres)
Explorations : endocrinienne pour toute cryptorchidie \danger
\begin{itemize}
\item bilatérale : doser 17-hydroxyprogestérone chez \female{} virilisée pour éliminer hyperplasie
congénitale des surrénales
\item testostérone, gls:Leydigcell (INSL3), gls:Sertolicell (AMH, inhibine B sérique), FSH, LH mesurée jusque 4-6mois\footnote{\danger Testostérone, FSH, LH interprétables [6mois, puberté]}
\item si bilatéral, écho (vérifier l'absence de dérivés mülleriens)
\end{itemize}
Étiologie
\begin{itemize}
\item hypogonadisme hypogonadotrope congénital
\item anorchidie rare
\item si hypospade en plus, chercher dysgénésie testiculaire
\item sd polymalformatif
\end{itemize}
Suivre l'âge de l'apparition de la puberté !
Traitement : chir dès 2 ans, indispensable ! (risque de cancer)
\subsubsection{Adulte}
\label{sec:orgefdc659}
\begin{itemize}
\item Risque : hypogonadisme, infertilité, cancer testicule
\item Examen clinique : scrotum, gynécomastie, signes d'hypogonadisme
\item Complémentaire : \{FSH, LH, testostérone\}, hCG si tumeur à la palpation, écho
scrotale, spermogramme
\end{itemize}
\subsection{51 \textdagger{} Retard de croissance}
\label{sec:org67e6f06}
\danger Ne pas passer à côté de pathologies sévères
Phases :
\begin{itemize}
\item foetale (rapide, \{nutrition, insuline, IGF-2\})
\item précoce 0-3ans (rapide, \{insuline, IGF, hormones thyroïdiennes\})
\item prépubertaire (plus lente, décroît, \{génétique, GH/IGF, hormones thyroïdiennes\})
\item pubertaire (\{stéroïdes sexuels, GH, nutrition\})
\end{itemize}
Retard statural = \{taille < -2DS, ralentissements croissance, croissance \(\le\) parents\}
Prise de poids, obésité, ralentissement croissance \thus chercher
hypercorticisme, tumeux craniopharyngiome sur l'hypothalamus, hypopituitarisme
Examen :
\begin{itemize}
\item ATCD : taille, parents, néonatale, médicaux/chir, contexte social
\item morphotype, dév. pubertaire, tous les système, psychoaffectif
\end{itemize}
\subsubsection{Principales causes}
\label{sec:org6ee9e07}
\begin{itemize}
\item Si poids < poids idéal : cf table \ref{tab:orgcd962b1}
\item Si poids \(\ge\) poids idéal : cf table \ref{tab:orgb58b7a0}. Précisions :
\begin{itemize}
\item Test de stimulation de l'hormone de croissance (\danger si doute, IRM)
\item Ralentissement sévère \thus bilan en urgence (craniopharyngiome, thyroïdite de
Hashimoto)
\item\relax [0, 3] ans : digestives pédiatrique (coeliaque, mucoviscidose), [3,puberté] :
endoc constitutionnelle, à la puberté : déficit hormone, patho osseuse
\item Savoir différencier retard pubertaire simple d'un vrai retard
\end{itemize}
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:orgcd962b1}Causes de retard pondéral}
\centering
\begin{tabular}{ll}
Maladie coeliaque & IgA totales, IgA anti-transglutamase, fibro\\
Crohn & VS, écho anse grêle\\
Mucoviscidose & Test sueur\\
Anorexie mentale & Courbe de poids\\
Insuf rénale chroniques & Créat, iono, explo fonctionnelles\\
Anémie chroniques & NFS\\
Rachitisme hypophosphatémique & Bilan phosphocalcique\\
Patho mitochondriales & lactate/pyruvate, génétique, biopsie musc, fond d'oeil\\
Nanisme psychosocial & \\
\end{tabular}
\end{table}
\begin{table}[htbp]
\caption{\label{tab:orgb58b7a0}Causes de retard statural}
\centering
\begin{tabular}{lll}
Endocrino & Déficit GH (congénital, acquis [tumeur]) & IRM\\
& Hypothyroïdie & T4L, TSH, Ac anti-TPO\\
& Hypercorticisme (iatrogène) & Cortisol libre urinaire/à 23h, ACTH\\
& Déficit hormones sex. & Testostérone, GnRH, IRM\\
\hline
Constitutionelles & Sd Turner & Caryotype\\
& Sd Noonan & Gène PTPN11\\
\hline
Autres & Osseuses (a-/hypo-chondroplasie) & Radio\\
& RCIU & Taille naissance\\
& Petite taille idiopathique & Élimination\\
\end{tabular}
\end{table}
\subsubsection{Exploration :}
\label{sec:orgc783281}
\begin{itemize}
\item Caryotype : fille taille < -2DS ou < -1.5DS sous taille parentale moyenne
\item NFS, VS, foie, rein
\item IgA totales, anti-transglutaminase
\item GF-1, T4L, TSH
\item Radio
\end{itemize}
\subsection{69 \textdagger{} Troubles des conduites alimentaires (à compléter)}
\label{sec:orgbb3c4a0}
\subsection{78 \textdagger{} Dopage}
\label{sec:orgd33e482}
\subsubsection{Substances augmentant la testostérone}
\label{sec:org6cad35c}
\begin{itemize}
\item Stéroïdes anabolisant, testostérone : \inc masse musc, puissance
\item Risque : thrombotique, rupture musculo-tendineuse, trouble personnalité, foie, trouble libido, adénome/cancer de la prostate
\item Femmes : masculinisation, hirsutisme, acné, aménorrhée, anovulation, hypertrophie clitoridienne, libido exacerbée
\end{itemize}
\vspace*{0.5cm}
\begin{itemize}
\item \emph{Testostérone} : test chromatographique + spectrométrie de masse (très sensible
et spécifique)
\item \emph{Dihydrotestostérone} (DHT) : traitement gynécomastie
\item \emph{Anabolisants} : \inc tissu cellulaire (muscle).
\end{itemize}
ES : rétention hydrosodée, HTA, IDM, hépatite
\begin{itemize}
\item \emph{hCG} : diminuer épitestostérone/testostérone après dopage (IM, SC). Testée dans
le sang ou urine.
\item \emph{Anti-oestrogène} : stimule production testiculaire de stéroïdes
\end{itemize}
\subsubsection{Hormone de croissance (GH), IGF-1}
\label{sec:org0581239}
\begin{itemize}
\item GH \inc masse musculaire, modifie architecture sequelette, acromégalie \emph{mais}
pas d'effet sur volume d'activité physique. Détection difficile : approche
indirecte (cascade biologique) et mesure des forme circulante et comparaison à r-hGH
\item IGF-1 mime certains effet GH
\end{itemize}
\subsubsection{Glucocorticoïdes, ACTH}
\label{sec:orgd9172f8}
\begin{itemize}
\item Glucocorticoïdes : antalgiques, psychostimulants, combativité. ES : HTA,
oedème, rupture ligament/tendon
\end{itemize}
\danger arrêt brutal = dangereux
\subsection{120 \textdagger{} Ménopause et andropause}
\label{sec:org19ac9c3}
\label{sec:120}
\subsubsection{Ménopause}
\label{sec:org60252ed}
Déf: plus de règle > 1 an \textpm{} sd climatérique, lié à une carence
oestrogénique. Vers 51 ans.
Pré-ménopause : irrégularités cycles puis dysovulation puis anovulation \textasciitilde{}5 ans
avants.
\paragraph{Diagnostic}
\label{sec:orge36f298}
Clinique seulement !! : plus de règles \(\ge\) 1 an, sd climatérique (bouffées de chaleur, troubles du
sommeil et humeur, sueurs nocturnes, sécheresse vaginal), \female > 50 ans.
Bio seulement si hystérectomie \thus \dec oestradiol et \inc FSH
En pratique : progestatif seul 10j/mois x3 \thus pas de saignement à l'arrêt =
diagnostic
Aménorrhée < 40 ans = pathologique !
\paragraph{Conséquences}
\label{sec:org48e86f2}
Court terme : sd climatérique
Moyen terme : douleurs ostéoarticulaires, \inc perte osseuse (selon ATCD d'insuf
ovarienne prématurée, fractures non traumatiques, médicaments, calcium/vit D)
Long terme : \inc risque CV. Incertitude sur SNC
\paragraph{Traitement}
\label{sec:orgcd3e2ca}
Bénéfices
\begin{itemize}
\item court terme : qualité de vie à +5-10 ans
\item long terme :
\begin{itemize}
\item prévention ostéoporose
\item cardiovasculaire et neuro = incertain
\item cancer du côlon
\end{itemize}
\end{itemize}
Risques :
\begin{itemize}
\item \inc cancer du sein, accident veineux thromboemboliques (mais chiffres absolus
faibles)
\item \inc AVC ischémique, lithiase bilaires
\end{itemize}
\subparagraph{Thérapeutique}
\label{sec:org66a30dd}
\begin{itemize}
\item oestrogène (17\(\beta\)-oestradiol) oral/percutané/transdermique\footnote{Percutané, transdermique : limite \inc facteur de coagulation.} 25 jours/mois
\item \textbf{et} progestatif (au moins les 12 derniers jours) per os/transdermique
\end{itemize}
\danger hémorragie de privation possible. Si pendant le traitement, faire écho
pelvienne, hystéroscopie
\subparagraph{CI}
\label{sec:org0c9f44d}
Cancer du sein, endomètre, ATCD thromboembolique artériel (ischémique,
cardiopathie embolinogène) ou veineux, hémorragie génitale sans diagnostic, hépatique
\subparagraph{Mise en route}
\label{sec:org3e290d9}
\begin{itemize}
\item Interrogatoire : ATCD \{cancer, métabolique, vasculaire\}, carence oestrogénique
\item Examen physique : poids, PA, palpation seins, gynéco, frottis cervico-vaginal
\item Mammographie !
\item Cholestérol, triglycérides, glycémie
\end{itemize}
\subparagraph{En pratique}
\label{sec:orgc8a72ca}
1ere intention si trouble fonctionnels importants. 2eme si risque
d'ostéoporose. Sinon au cas par cas.
\subparagraph{Surveillance}
\label{sec:org80512ac}
3-6mois (surdosage = douleur, tension mammaire). Puis tous les 6-12 mois,
mammographie tous les 2 ans, frottis CV tous les 3 ans.
Traitement \(\ge\) 5 ans !!
\subparagraph{Alternatives}
\label{sec:orgef144d3}
\begin{itemize}
\item Modulateurs spécifiques du récepteur des oestrogènes : raloxifène
\item tibolone
\item traitement local préserve tractus urogénital
\end{itemize}
NB : Dépister FR CV. Promouvoir exercice, calcium, vit D
\subsubsection{Andropause}
\label{sec:orge615047}
Chez majorité des hommes mûrs/âgés en bonne santé non obèse, baisse de
testostérone inconstante (2\%).
\paragraph{Démarche}
\label{sec:org88c94cd}
\begin{itemize}
\item Interrogatoire : libido, érection, énergie vitale, mobilité/activité physique
\item Examen clinique : IMC, virilisation, gynécomastie, palper testicules
\item Mesure de testostérone totale :
\begin{itemize}
\item > 3.2ng/mL = normale \thus étiologies non endocrino
\item \(\in\) [2.3, 3.2] : doser SHBG\footnote{Se fixe à la testostérone, estradiol}, calculer index de T libre, si bas, chercher cause
\item < 2.3 ng/mL : chercher cause
\end{itemize}
\end{itemize}
\paragraph{Étiologie}
\label{sec:orgdfa6748}
Si FSH, LH élevée, \emph{insuf testiculaire primitive}
\begin{itemize}
\item lésionnelle : chimio, radiation, alcoolisme surtout. Autres : castration,
torsion, orchite ourlienne
\item cryptorchidie bilatérale
\item chromosomique : sd Klinefelter++
\item lié à sénescene, cause génétique (rare !)
\end{itemize}
Sinon \emph{hypogonadisme hypogonadotrope}
\begin{itemize}
\item tumeur région hypothalamo-hypophysaire : craniopharyngiome, adénome
hypophysaire++, autres
\item infiltratif : sarcoïdose, hémochromatose
\item chir, radiothérapie, trauma
\item hyperprolactinémie, carence nutritionnelle, Cushing, tumeur testiculaire
\end{itemize}
\subsection{122 \textdagger{} Troubles de l'érection}
\label{sec:org33260db}
Nécessite : réseau vasculaire, appareil musculaire lisse, retour veineux, signal nerveux,
appareil hormonal et psychisme fonctionnels
Déf : incapacité persistante à obtenir/maintenir érection pour rapport sexuel satisfaisant
Âge = FR (car déficit neurosensoriel, \inc testostérone, comorbidités)
\subsubsection{Conduite diagnostique}
\label{sec:org621ff08}
\paragraph{Interrogatoire}
\label{sec:org8b9e8ad}
\begin{itemize}
\item DD avec perte désir, trouble éjaculation, douleurs pendant, anomalies morphologiques
\item Caractérisation : primaire/secondaire, brutal/progressif,
permanent/situationnel, sévérité (délai trouble-consult, capacité résiduelle,
masturbation)
\item Pathologies, facteur :
\begin{itemize}
\item primaire : trouble psychogène perso, complexe identitaire, trouble
relationnel, conflit socioprof, anomalie génitale
\item secondaire : ATCD abdo-pelvien, diabète, FR CV, patho CV, neuro, trouble
miction, endocrinopathie, troubles sommeil, traitement, déficit
androgénique, sd dépressif, troubles addictifs
\end{itemize}
\end{itemize}
\paragraph{Clinique}
\label{sec:org2d7456e}
\begin{itemize}
\item Gynécomastie, hypoandrisme, petits testicules, anomalies du pénis (La Peyronie)
\item CV : HTA, pouls, souffle
\item neuro : sensibilités périnée, MI
\item endoc : anomalie CV
\end{itemize}
\paragraph{Bio}
\label{sec:orgcd751f4}
Glycémie, lipidique (si > 1 an), \{NFS, iono, créat\}, foie (si > 5 ans), déficit
androgénique
Doser prolactine, hormones thyroïdiennes
\subsubsection{Bilan secondaire et approfondi}
\label{sec:org012a58c}
Secondaire : sexo/psychologique, épreuve pharmacologique (prostaglandine,
inhibiteur de la phospohdiestérase 5)
\subsubsection{Étiologies}
\label{sec:orgefbf669}
Plus fréquentes :
\begin{itemize}
\item vasculaire : FR = HTA
\item endocrino++ : diabète
\item génito-pelvien : chir pelvienne
\item trauma médullaire
\item neuro dégénératif
\item iatrogène : antihypertenseur
\end{itemize}
\subsubsection{Aspects endocriniens}
\label{sec:org28260d6}
\paragraph{Androgènes circulants}
\label{sec:org3a6f32e}
Influe libido, intérêt sexuel, érection (seulement spontanée!)
Hypogonadisme (diag difficile) :
\begin{itemize}
\item asthénie, gynécomastie, dépilation, perte force musculaire, adiposité androïde
\item doser testostérone totale \textpm{} SHBG, prolactine. FSH, LH pour l'origin
\end{itemize}
\paragraph{Hyperprolactinémie}
\label{sec:orga8966a5}
Tumeur hypophysaire (IRM), champ visuel si tumeur
supra-sellaire, \{T4L, cortisol, IGF-1, testostérone\}
\thus correction par agoniste dopaminergique
\paragraph{Diabète}
\label{sec:orgcb26834}
sucré = 1ere cause de trouble érectile (TE). TE fréquents chez diabètique.
Facteurs : mal équilibré, complications, âge, ancienneté diabète
Physiopatho : neuropathie autonomie, microangiopathie \thus défaut relaxation
musculaire. Macroangiopathie \thus ischémie organes érectiles
\danger facteurs psychogènes prédominent !
Diabète et TE \thus mesure testostérone systématique (hypogonadisme ?)
Clinique :
\begin{itemize}
\item TE peut révéler diabète.
\item diabète et TE : cherche trouble endoc, vasc, neuro, médicament, dépression
\item TE = FR d'ischémie myocardite silencieuse \danger
\end{itemize}
\subsubsection{PEC}
\label{sec:org254c9fc}
Ttt étiologie seulement pour : trouble psychogène pur, chir possible, endocrino
\paragraph{Trouble endocrinien}
\label{sec:org0d15d84}
\begin{itemize}
\item Si hypogonadisme confirmé par bio\footnote{Baisse libido, testostérone totale < 3 ng/mL} : androgène oraux/intramusc/transderm
\item CI : nodule prostatique palpable, PSA > 3ng/mL
\item Surveiller prostate, foie, hématocrite
\end{itemize}
\paragraph{Pharmacologique}
\label{sec:org999ccc7}
\begin{itemize}
\item FR, Hb glyquée < 7\%, psycho/sexologique
\item 1ere intention
\begin{itemize}
\item inhibiteurs des phosphodiésterases type 5\footnote{Efficace si stimulation sexuelle (même chez diabétique)}
\item Sinon apomorphine, yohimbine = peu efficace
\item "Pompe" = efficace mais résistance psycho
\end{itemize}
\item 2eme intention : drogue vasoactive = efficace mais douleurs peniennes, priapisme
\item Prothèses péniennes = dernier recours, par chirurgien spécialisé
\end{itemize}
\subsection{124 Ostéopathies secondaires endocrines \footnote{Secondaires autres : digestives, générale, génétique, médicaments,
autres. Il existe aussi des ostéoporoses primaires}}
\label{sec:org146c240}
Ostéoporose : -score < -2.5 DS de la valeur moyenne par DXA
Marqueurs : résorption (Tx, NTx), formation osseuse : ostéocalcine, phosphatases alcalines osseuses
\subparagraph{Hypogonadisme}
\label{sec:org9e4cd73}
Carence oestrogénique \inc ostéoclastogénèse. Tab \ref{tab:org3fcf9b9}
\begin{table}[htbp]
\caption{\label{tab:org3fcf9b9}Types d'ostéoporose dûes à un hypogonadisme}
\centering
\begin{tabular}{llll}
Type & & Conséquences & Ttt\\
\hline
Anorexie mentale & Formation os \dec, résorption N & Risque de fractures \(\times 7\) & Multidisciplinaire\\
& & & + oestroprégestatif\\
AP intensive & Origine hypothalamique & \inc résorption os, & \dec activité ou oestroprogestatifs\\
& & \inc fractures de fatigue & \\
Lésion hypophysaire & Doit impacter l'axe gonadotrope & Perte osseuse rapide & \oe{}strogènes\\
Iatrogène & Agonistes GnRH\tablefootnote{patho utérines}, & & Arrêt\\
& inhibiteurs aromatase\tablefootnote{cancer sein} & & \textpm{} isphosphonates, denosumab\\
& & & \\
Sd Turner & \dec ontinue à l'adolescence & \inc fracture (adulte) & Estrogénisation + GH\\
& & & Oestroprogestatif\\
\end{tabular}
\end{table}
\subparagraph{Non hypogonadique}
\label{sec:org739c9c6}
Tab \ref{tab:orgd52fe76}
\begin{table}[htbp]
\caption{\label{tab:orgd52fe76}Autres ostéoporoses secondaires endocrino}
\centering
\begin{tabular}{lllll}
Type & Systématiquement & Physio & Atteinte & PEC\\
\hline
Hyperthyroïdie & \emph{doser TSH} & \inc remodelage & Cortical & densitométrie \textpm{} bisphosphonates (âgé)\\
hormones thyroïdiennes & & & & surveillance (ttt suppressif)\\
Hypercortisolisme & \emph{Prévention} & \dec formation osseuse, & Vertébres & vitamine + calcium\\
corticothérapie & & \inc résorbtion. & & \textpm{} bisphosphonates \tablefootnote{si prednison > 7.5mg/j et T-score \le -1.5)}\\
Hyperparathyroïdie & \emph{Dépistage} DXA & PTH \inc résorption & Cortical & chir si T-score < -2.5.\\
primitive & (ménopausée++) & & & Sinon anti-ostéoclastiques\tablefootnote{oestrogènes,aloxifène, bisphosphonates},\\
& & & & calcimimétique\tablefootnote{cinacalcet}\\
\end{tabular}
\end{table}
\subparagraph{Chez l'homme}
\label{sec:orgf784900}
Pas de T-score reconnu.
Surtout : hypercorticisme, hypogonadisme congénital/acquis/iatrogène, alcoolisme, hypercalciurie
idiopathiques, génétique
\begin{tcolorbox}
\begin{itemize}
\item bisphosphonates (prévention ostéoporose cortisonique++) sinon dénosumbab
\item raloxifène (si faible risque fractures périphériques)
\item tériparatide (si \ge 2 fractures vertébrales)
\end{itemize}
\end{tcolorbox}
\subsection{207 \textdagger{} Sarcoidose}
\label{sec:orgea7d671}
Atteinte hypothalamo-hypophysaire exceptionnelle. Conséquences : diabète
inspide central, insufisance gonadotrope
Radio : IRM centrée sur hypothalamo-hypophyse = référence (T1,T2 injecté) \thus
infiltration plancher 3eme venticule, infundibulum, tige hypophysaire épaissie
\textpm{} hypophyse augmente de volume
DD : tuberculose, histiocytose, lymphome, autres tumeurs de la région
Si patient avec sarcoïdose connue : diagnostic = déficit endocrinien et imagerie\footnote{Faire bilan hormonal : natrémie, testostérone totale et libre/ostradiol,
FSH, LH, T4L, TSH, prolactine}
Sinon : atteinte rare\footnote{adénome hypophysaire 90\%, méningiome, craniopharyngiome, patho
inflammatoires infiltratives}, diag = radio et arguments sarcoïdose\footnote{Atteinte poumon évocatrice, \inc{} ACE, pas de tuberculose, granulome
non caséeux (histologie)}.
Traitement : sarcoïdose et déficits hormonaux
\subsection{215 \textdagger{} Hémochromatose}
\label{sec:org52d10da}
Hémochromatose primitive : génétique, surcharge en fer. 5 pour 1 000 !
Physiopatho :
\begin{itemize}
\item Absorption intestinale régule stockage de fer
\item Fer entre dans l'entérocyte (DMT1), puis stocké via ferritine ou relargé par ferroportine
\item Hepcidine \dec quand besoins fer \inc (!)
\item Hémochromatose : hepcidine effondrée, DMT1 et ferroportine \inc
\end{itemize}
Génétique : gène HFE à 95\% et mutation C282Y/C282Y ou C282Y/H63D
\subsubsection{Clinique}
\label{sec:orga6b87bb}
En pratique, suspicion aux "3 A" : asthénie, arthralgies, \inc ALAT
\paragraph{Atteintes :}
\label{sec:org8dfa2c0}
\begin{itemize}
\item foie : \inc ALAT ou hépatomégalie. Cirrhose \(\approx\) 90\% décès
\item coeur : cardiopathie dilatée, troubles rythme
\item endocrino :
\begin{itemize}
\item diabète++ (accumulation pancréatique de fer) insulino-pénie/-résistance
\item hypogonadisme+ : impuissance \male, aménorrhée \female, \dec libdio,
ostéoporose
\item insuf thyriodienne exceptionnelle
\end{itemize}
\item articulaire : arthrite chronique ("poignée de main douloureuse"), chrondocalcinose
\item cutané : mélanodermie (tardive)
\end{itemize}
\subsubsection{Diagnostic}
\label{sec:org37b6e3e}
\begin{itemize}
\item Si CS-Tf\footnote{Coefficient de saturation de la transferrine} < 45\% : si ferritine \inc, cherche hépatosidérose dysmétabolique,
acéruléoplasminémie, mutation gène de la ferroportine 1
\item Sinon, CS-Tf > 45\% :
\begin{itemize}
\item si C282Y/C282Y ou C282Y/H63D : diagnostic
\item sinon, si ferritine \inc, test génétique de 2eme intention, biopsie
hépatique
\end{itemize}
\end{itemize}
Examen complémentaires : pancréas (glycémie), foie (transaminases, écho abdo), ECG \textpm{} écho
cardiaque, radio articulation, bilan testostérone
Dépistage chez parents (1er degré) : bilan martial \textpm{} dépistage génétique. \danger mutation \(\neq\) maladie
\subsubsection{Stades}
\label{sec:org94be75c}
\begin{enumerate}
\item Asymptomatique, CS-Tf, ferritinémie normaux
\item CS-Tf \inc
\item CS-Tf \inc et ferritine \inc
\item Idem et expression clinique affectant qualité de vie
\item Idem et expression clinique affectant pronostic vital
\end{enumerate}
\subsubsection{Traitement}
\label{sec:org6667087}
À partir du stade 2
\paragraph{Saignées = référence}
\label{sec:orga065ad9}
Objectif : ferritine < 50 g/L (hebdomadaire) puis entretien tous les
2-4 mois. Ne pas dépasser 550mL !
CI : anémie sidéroblastique, thalassémie majeure, cardiopathies sévères
\paragraph{Autres}
\label{sec:org665d31f}
\begin{itemize}
\item Érythraphérèse : coûteuse, plus difficile
\item Chelation du fer : 2eme intention (coût, effets indésirable)
\item diététique : pas d'alcool, éviter vitamine C mais \textbf{conserver} apports en fer !
\item Symptomatique
\end{itemize}
\subsubsection{Suivi}
\label{sec:org35ed9be}
Résultats en 3-6 mois sur état générale.
Bilan ferrique (stade 0,1) ferritinémie, hémoglobine (stade 2 à 4)
\subsection{221 HTA, causes endocriniennes}
\label{sec:orgbced6ba}
Déf: \(\ge\) 140/90 mmHg.
Enquête :
\begin{itemize}
\item initiale : ATCD familiaux HTA, souffle para-ombilical, rein/masse abdo à la
palpation, signe d'hypercortisolisme/acromégalie, bio \thus
protéinurie/hématurie, imagerie, hormonale (selon signes)
\item si résistance malgré 3 antihypertenseurs (dont 1 diurétique), chercher toutes
les cause d'HTA
\end{itemize}
\subparagraph{Épidémiologie}
\label{sec:org196fe2a}
10\% des HTA sont secondaires et 5\% sont guéries \thus hyperaldostéronisme
primaire, phéochromocytomes, sd Cushing
\subsubsection{Hyperminéralocorticisme primaire (HAP)}
\label{sec:orgf1a68dd}
Physiopatho : aldostérone, cortisol, désoxycorticostérone \thus rétention sodée
\thus HTA et inhibe sécrétion de rénine\footnote{Si la surrénale produit plus d'aldostérone : régulation négative par la rénine (en théorie)}.
\subparagraph{Diagnostic}
\label{sec:orgb9eb178}
Aldostérone \inc (plasma/urine) et urine basse
\begin{itemize}
\item suspicion : hypokaliémie (< 3.5mmol/L) ou HTA résistante
\item confirmation : \ref{algo:HAP}
\begin{algorithm}
\caption{Explorations des HAP}
\label{algo:HAP}
Arrêt diurétiques\;
Vérifier natriurèse+, kaliurèse > 20mmol/j\;
\If{aldostérine/rénine \times 2}{
aldo \inc et rénine \dec : HAP\;
aldo \inc et rénine \inc : hyperaldo. secondaire\;
aldo \dec et rénine \dec : autre minéralocorticisme\;
}
\end{algorithm}
\end{itemize}
\subparagraph{Ttt selon étiologie}
\label{sec:org5efcec6}
Adénome de Conn : ndule unilatéral hypodense \(\in\) [10, 20] mm au scanner
\begin{itemize}
\item prouver sécrétion aldostérone par cathétérisme si scanner douteux/patient jeune/HTA résistante
\item chir possible (mais tumeur bénigne, risque récidive)
\end{itemize}
Hyperplasies idiopathique: spironolactone à vie (hypoK) + contrôle PA
\subparagraph{Hyperminéralocorticismes familiaux}
\label{sec:orga65a623}
Lié à l'aldostérone, désoxycorticostérone, cortisol
\subsubsection{HTA endocrines iatrogènes}
\label{sec:org73c7c4f}
Contraception oestroprogestative, corticostéroides, réglisse
\subsubsection{Phéochromocytomes, paragangliomes fonctionnels}
\label{sec:org1606065}
\subparagraph{Physiopatho}
\label{sec:orgb63880f}
gls:PCC : médullosurrénale. gls:PGG fonctionnels : autres ganglions sympathiques
\{\} PCC : spontanément mortel.
\subparagraph{Dépistage :}
\label{sec:org5f0c42c}
\begin{itemize}
\item HTA avec céphalées, sueurs, palpitations (triade de Ménard), HTA paroxystiques/diabète sans
surpoids
\item sd familial : gls:NF1, gls:VHL, gls:NEM2, sd phéochromocytomes-paragangliomes familiaux
\end{itemize}
\subparagraph{Diagnostic}
\label{sec:org9129ab4}
\inc métanéphrines
\subparagraph{PEC}
\label{sec:orgd07afbd}
\begin{itemize}
\item Scanner/IRM/écho : PCC = uniques, \textasciitilde{}5cm, PCC siègent dans l'organe de Zuckerkandl, vessie\ldots{}
\item Médicine nucléaire
\item Traitement chir mais surveillance long terme
\end{itemize}
\subsubsection{Sd de Cushing (hypersécrétion de cortisol)}
\label{sec:orgcd71543}
\subparagraph{Diagnostic}
\label{sec:org7511450}
Suspicion clinique + cortisol plasmatique \footnote{Physiologique = minimal à minuit, donc mesure à minuit. Mesure salivaire possible.}, cortisolurie 24h, test de freinage rapide\footnote{1mg de dexaméthasone à minuit Action de rétrocontrôle négative du
cortisol donc on vérifie que le cortisol plasmatique le lendemain à 8h a bien diminué}
\begin{itemize}
\item clinique: acné, ecchymoses, faiblesse musc, hirsutisme, oedèmes, ostéoporose, PAd
> 105mmHg, vergetures pourpres
\end{itemize}
\subparagraph{Étiologie}
\label{sec:orgeac6acf}
\begin{itemize}
\item ATCH diminuée \thus adénome, corticosurrénalome, hyperplasie bilatérale
\item ATCH normale ou \inc \thus test CRH, test freinage fort\footnote{8mg au lieu de 2mg pour DXM et pendant 2 jours au lieu d'un}. si positif : tumeur ectopique ou
maladie de Cushing (adénome hypophysaire)
\end{itemize}
\subsubsection{Causes rare}
\label{sec:org3e2cd85}
Tumeurs à rénine, acromégalie
\subsection{238 \textdagger{} Hypoglycémie}
\label{sec:org3f0b84d}
Diagnostic : neuroglucopénie et glycémie < 0.50g/L (0.60 chez diabétique) et correction symptômes
à normalisation (triade de Whipple)
Causes :
\begin{itemize}
\item sécrétion inappropriée d'insuline (hypoglycémiante)
\item (rare) : défaut de sécrétion d'hormones hyperglycémiantes (GH, glucagon,
catécholamine, cortisol), déficit néoglucogénèse, défaut substrat
\end{itemize}
\subsubsection{Symptômes}
\label{sec:org58466c6}
Neuroglucopénie : faim brutale, troubles concentration, troubles moteurs,
troubles sensitifs, troubles visuels, convulsions focales/généralisése,
confusion
Coma hypoglycémique : début brutal, agité (sueurs), irritation pyramidale, hypothermie
\begin{itemize}
\item souvent signes adrénergiques : anxiété, tremblements, nausées, sueurs,
pâleur, tachycardie
\end{itemize}
\subsubsection{Causes}
\label{sec:org1774761}
\paragraph{Diabétique}
\label{sec:org4ebc963}
Si traité par insulines, hypoglycémiants oraux
Ttt : sucre (3 morceaux) si CS, sinon glucagon 1mg par IM/SC (CI si
sulfonylurée : glucose en perfusion)
\paragraph{Insulinome}
\label{sec:org18e1a55}
1ere cause tumorale (mais rare). Maligne dans 10\%, < 2cm (90\%)
Clinique : manif. adrénergiques surtout
Diagnostic : épreuve de jeûne, cf table \ref{tab:org36a6bfc}
\begin{table}[htbp]
\caption{\label{tab:org36a6bfc}Diagnostic d'hypoglycémie (jeûne) avec DD}
\centering
\begin{tabular}{llll}
& Insulinome & Insuline cachée & Sulfonylurée cachée\\
\hline
Glycémie & basse & basse & basse\\
Signes & neuroglucopénie & & \\
Insulinémie & normale mais inadaptée & dosable & dosable\\
Peptide C & augmenté & \emph{basse} & augmenté\\
Sulfamides & 0 & 0 & \emph{oui}\\
pro-insuline & augmenté & basse & \\
\end{tabular}
\end{table}
Scanner en coupe fine du pancréas et écho-endoscopie si médecin habitué
Traitement : chir
\begin{tcolorbox}
Hypoglycémie par sécrétion inaproppriée d'insuline : triade de Whipple, glycémie \le 0.45g/L\footnotemark avec
insulinémie \ge 3 mUL/L, peptide C \ge 0.6ng/mL
\end{tcolorbox}
\footnotetext{Spontanément/jeûne}
\subsection{239 \textdagger{} Goitre, nodules thyroïdiens, cancers thyroïdiens}
\label{sec:org01c05c5}
Besoins en iode quotidiens (synthèse hormones thyroïdiennes) : \(\approx\) 150 \(\mu\)g/jour (ado,
adulte, \texttimes{} 2 chez enceinte)
Goitre = hypertrophie de la thyroïde :
\begin{itemize}
\item palpation > dernière phalange du pouce
\item écho : volume > 20 \(cm^3\) (18 femme adulte, 16 ado)
\end{itemize}
\subsubsection{Évaluation}
\label{sec:orgd843321}
Clinique : mobile déglutition/visible cou en extension/visible à
distance. Chercher : gene fonctionelle, signes de compression, signes de
dysfonction thyroïdienne, acrshort:ADP
Bio :
\begin{itemize}
\item TSH++ : \inc, déficit production, si \dec, imprégnation excessive en hormones thyroïdiennes.
\item compléter par T4, et si TSH \inc : Ac anti-TPO, anti-Tg
\end{itemize}
Échographie
\subsubsection{Goitre simple}
\label{sec:orgb1484af}
Hypertrophies normo-fonctionnelles non inflammatoires non cancéreuses
Facteurs : \female, tabac, déficience iodée
\paragraph{Évolution}
\label{sec:orgb135ff8}
Constitution à l'adolescence (cliniquement latente) puis plurinodulaire : gêne
cervicale \thus TSH, écho, ponction, scintigraphie
\danger cherche caractère plongeant sur radio !
À ce stade, complications : hématocèle, strumite, hyperthyroïdie, compression
organes de voisinages, cancerisation (5\%)
\paragraph{PEC}
\label{sec:orgb68c6e9}
\begin{itemize}
\item Ado : levothyroxine (1 à 1.5 \(\mu\)g/kg/j) jusque V normal. Vérifier TSH
\item Adulte/agé : si multinodulaire non malin, surveillance. Si symptomatique,
thyroïdectomie totale
\item Goitre ancien, négligé : iode 131
\end{itemize}
Dans tous les cas, \inc iode (grossesse)
\paragraph{Autres pathologies responsables}
\label{sec:org0ea4ece}
\begin{itemize}
\item Maladie de Basedow
\item Thyroïdites :
\begin{itemize}
\item Hashimoto = hypertrophique. Goitre très ferme, expose à l'hypothyroïdie. Ac Ant-TPO\inc\inc{}, écho : goitre diffus, hypoéchogène
\item autres thyroïdites
\end{itemize}
\item Troubles de l'hormonosynthèse
\end{itemize}
\subsubsection{Nodules thyroïdes}
\label{sec:org9111882}
Déf : toute hypertrophie localisée de la gande thyroïde. Majorité = bénin (5\%
cancers, de très bon pronostic)
Prévalence \(\approx\) décennie du sujet. \texttimes{} 2 chez \female. \inc si grossesse,
déficience iode, irradiation cervicale
\paragraph{Évaluation :}
\label{sec:org69dd6d1}
Si signe d'accompagnement :
\begin{itemize}
\item nodule douloureux brutal : hématocèle
\item nodule douloureux + fièvre : thyroïdite subaigüe
\item nodule compressif + ADP : cancer
\item nodule + hyperthyroïdie : nodule toxique
\item nodule + hypothyroïdie : thyroïdite lymphocytaire
\end{itemize}
Si isolé :
\begin{itemize}
\item TSH \dec : nodule hyperfonctionnel ? \thus scintigraphie
\item TSH N : tumeur \thus écho, cytologie
\item TSH \inc : thyroïdite lymphocytaire ? \thus Ac anti-TPO
\end{itemize}
Pronostic plutôt suspect :
\begin{itemize}
\item homme, enfant/âgé, ATCD irradiation cervicale, > 3cm, ovalaire, dur, irrégulier, > 20\% en un an
\item écho : hypoéchogène, contour irrégulier, microcalcifications, ADP
\end{itemize}
Bio : TSH surtout.
\begin{itemize}
\item si nodule, calcitonine > 100pg/mL = argument solide pour cancer médullaire thyroïde.
\item calcitonine \(\in\) [20,50]pg/mL : idem ou hyperplasise des cellules C ou insuffisant rénal
\end{itemize}
Examens :
\begin{itemize}
\item Échographie (classification TI-RAD de 1 à 6)
\item Cytologie si nodule suspect (classification Bethesda de 1 à 6)
\item Scinti si cytologie ininterprétable 2 fois ou indéterminée
\end{itemize}
\paragraph{Thérapeutique}
\label{sec:org9ead6fa}
\begin{itemize}
\item Chir si suspect clinique/écho/cyto/calcitonine \inc\inc{} : thyroïdectomie si dystrophie controlatérale
\item Surveillance sinon
\item Hormonal si bénin dans familles avec goitres plurinodulaire, < 50 ans.
\end{itemize}
Kystes, hématocèles : anéchogène \thus ponction \textpm{} hormonothérapie , alcoolisation.
Grossesse : chir possible 2e trimestre ou après accouchement
Nodule oculte : < 1cm. Risque de cancer 5\%, faible pouvoir agressif
\begin{itemize}
\item \danger si ADP, hérédité cancer médullaire thyroïde, fixation au TEP
\item ponction seulement si hypoéchogène et > 8mm
\end{itemize}
\subsubsection{Cancers thyroïdiens}
\label{sec:orgfa7c68c}
1.5\% cancers, 4eme chez la femme
Découverte : fortuite++, ADP cervicale, signes de compression, flushes/diarrhée,
localisation métastatique
Anatomie :
\begin{itemize}
\item carcinomes différenciés d'origine vésiculaire : papillaire (85\%, excellent
pronostic), vésiculaires (5\%), peu différenciés (2\%)
\item carcinomes anaplasiques (1\%)
\item carcinomes médullaires au dépens des cellules C
\item autres
\end{itemize}
Risque de rechute/décès :
\begin{itemize}
\item taille tumeur, effraction capsule thyroïdienne, métastase (clasif TNM de I à IV)
\item mortalité \(\propto\) âge, dépend de l'histologie, exérèse
\end{itemize}
\paragraph{Thérapeutique}
\label{sec:org618e165}
\begin{itemize}
\item Plan cancer
\item Chir en 1ere intention (anatomopatho pendant = certitude) : thyroïdectomie
totale. Curage ganglionnaire si besoin (systémique si carcinome médullaire,
si enfant/ado). \\
Complications : hémorragie postopératoire , hypoparathyroïdie (calcium + vit D), paralysie transitoire/définitive nerfs récurrents
\end{itemize}
\vspace*{10pt}
\emph{Cancers différenciés d'origine vésiculaire}
\begin{itemize}
\item iode 131 : seulement post-thyroïdectomie totale (haut risque). Nécéssite
stimulation par L-T4 ou injection TSH. Puis hospit après en chambre 2-5 j
et contraception 6-12 mois. \\
ES : \{nausées, oedèmes\}, \{agueusie, sialadénite\}. \\
Scinti obligatoire à +2-8j : fixation extracervicale à distance = métastases
\item hormonal : L-T4 si haut risque ou échec traitement initial. Puis mesurer TSH à
+6sem-2mois (pas avant !)
\item surveillance : 80\% des récidives à 5 ans \thus écho cervicale, rhTSH,
Tg\footnote{Thyroglobuline} à 6-12mois : cytoponction puis imagerie si Tg > seuil. Sinon \dec LT4
\item traitement récidives : chir si cervicale. Plus compliqué si métastases
(iode131 si fixant sinon ttt local ou molécules ciblées). Maintenir LT4
\end{itemize}
\emph{Cancers anaplasiques}\\
Tuméfaction cervicale rapidement progressive, dure, adhérente, sujet âgé \thus radio-chimio. Pronostic très péjoratif
\emph{Cancers médullaires}
\begin{itemize}
\item TTT : chir \textpm{} curage ganglionnaire
\item Surveillance : calcitonine > 150\(\mu\)g/L \thus bilan de localisation.
\item Temps doublement : 6 mois = pronostic très mauvais.
\item Traitement métastases = local.
\end{itemize}
Étude génétique dans tous les cas : positif \thus chercher phéochromocytome,
hyperparathyroïdie + enquêtes apparentés
\subsection{240 \textdagger{} Hyperthyroïdie}
\label{sec:org168b72c}
\begin{tcolorbox}
Examen en 1ere intention : TSHus (puis T4L !)
\end{tcolorbox}
Déf : hyperfonctionnement de la glande thyroïdienne. Sd de thyrotoxicose =
conséquence sur les tissus.
Prévalence élevée, 7\texttimes{} femme
Physiopatho :
\begin{itemize}
\item TSH, gls:TPO et Tg peuvent être des auto-antigènes
\item thyroïde produit surtout thyroxine (T4\footnote{[T4] n'est à l'équilibre que +5 semaines après modification de T4}), convertie en T3 par foie, muscle
squelette.
\item effet :
\begin{itemize}
\item \inc production chaleur, \inc production énergie, \inc consommation \(O_2\)
\item \inc débit cardiaque, système nerveux, \inc ostéclasie, \inc lipolyse, \inc
glycémie, rétrocontrole négatif hypophysaire
\end{itemize}
\end{itemize}
\subsubsection{Sd de thyrotoxicose}
\label{sec:orgda5217e}
Clinique (par fréquence \dec) :
\begin{itemize}
\item CV : tachycardie (régulière, repos, \inc effort), \inc intensité bruits
coeurs, \inc PAs
\item neuropsy : nervosité, tremblement fin régulier des extrémités, fatigue
générale, troubles sommeil
\item thermophobie, hypersudation,
\item amaigrissement rapide, important, avec appétit conservé
\item autre : polydipsie, amyotrophie, \inc frequence selles, rétraction paupière
supérieure (gynécomastie, troubles règle)
\end{itemize}
Examen complémentaire : TSH effondrée. T4 ou T3 libre pour l'importance
Complications :
\begin{itemize}
\item cardiaque (surtout personnes fragiles) : troubles rythme supraV (FA), insuf
cardiaque (droite, avec débit N ou \inc), aggravation insuf coronaire
\item crise aigüe thyrotoxique (exceptionnelle)
\item musculaire (âgé)
\item ostéoporose (\female ménopausée) : rachis
\end{itemize}
\subsubsection{Étiologies (fréquence \dec)}
\label{sec:orgbb48a0a}
\paragraph{Auto-immunes}
\label{sec:org0b1b329}
\emph{Maladie de Basedow}\\
1\% population. Auto-immune, sur terrain génétique. Poussées puis rémissions
Clinique :
\begin{itemize}
\item goitre diffus homogène, élastique, souffle
\item oculaire (spécifique, inconstant) : rétraction et asynérgie palpébrale,
inflammation, exophtalmie, oedème paupières, inflammation conjonctive,
limitation mouvement regard
\thus examen ophtalmo ! (acuité visuel, cornée, papille, oculomotricité, tonus
intraoculaire)\\
Mauvais pronostic : exophtalmie importante, paralysie complète, neuropathie
optique, hypertonie oculaire avec souffrance papillaire
\item dermopathie (exceptionnelle) placard rouge, surélevé, induré, face ant jambes
\end{itemize}
Diagnostic : manif oculaire suffit. sinon : écho (hypoéchogène, vascularisé),
(scinti), Ac anti-récepteur TSH\\
\emph{Autres auto-immune}
\begin{itemize}
\item Thyroïdite post-partum (5\%) : hyperthyroïdie transitoire puis hypothyroïdie. Ac
anti-TPO mais pas Ac anti-récepteur TSH
\item Thyroïdite d'Hashimoto : goitre irrégulier, très ferme. Écho :
hypoéchogène. Ac anti-TPO mais pas anti-récepteur TSH
\end{itemize}
\paragraph{Nodules thyroïdiens hypersécrétans}
\label{sec:org2618a98}
Âge plus avancé, sd de thyrotoxicose pur (pas de manif oculaire)
\begin{itemize}
\item Goitre multinodulaire toxique : à la clinique, puis écho. Scinti : "en damier"
\item Adénome toxique : palpation nodule unique, écho : tissulaire/partiellement
kystique. Scinti nécessaire : reste du parenchyme "froid"
\end{itemize}
\paragraph{Iatrogènes}
\label{sec:org54ce878}
\begin{itemize}
\item Iode : produits contraste, amiodarone. 2 formes : fonctionnelle ou lésionnelle
(lyse des cellules)
\end{itemize}
\danger sous amiodarone : T4L \inc mais T3L, TSH N
\begin{itemize}
\item Hormones thyroïdiennes : pour maigrir. Diag : scinti (pas de fixation), Tg
effondrée
\item Interféron (fréq++)
\end{itemize}
\paragraph{Thyroïdite subaigüe de De Quervain}
\label{sec:orgfccbae2}
Affection banale virale. Diagnostic clinique (goitre dur et douleureux). Hyper-
puis hypo-thyroïdie. Echo = hypoéchogène
\paragraph{Thyrotoxicose gestionnelle transitoire}
\label{sec:orge709def}
Fréquent (2\% grossesse). 1er trimestre : nervosité, tachycardie, pas de prise de
poids
DD : Basedow (pas Ac anti-récepteur TSH)
\paragraph{Rares}
\label{sec:org92220f2}
Mutations activatrices du récepteur TSH, métastase massives sécrétantes (K
thyroïdiens vésiculaire différencié), tumeurs placentaires/testiculaires, \{sd
résistance hormones thyroïdiennes, adénome hypophysaire\}
\subsubsection{Forme clinique}
\label{sec:org0217aaf}
\begin{itemize}
\item Enfant : généralement Basedow (néonatale/acquise) : avance staturale et
osseuses, hyperactivité \textpm{} signes oculaires
\item Femme enceinte : passage d'Ac \thus hyper- ou hypo-thyroïde. Passage
d'antithyroïdiens de synthèse \thus goitre, hypothyroïdie possible. Contraception !
\item Âgé : évolution discrète (AEG, fonte musculaire, cachexie, insuf
cardiaque). Penser thyrotoxicose si troubles rythme/insuf cardiaque
\end{itemize}
\subsubsection{Traitement}
\label{sec:org08ba339}
\{\} Urgence : crise aigüe thyrotoxicose, cardiothyréose chez âgé/cardiqaue,
orbitopathie maligne, cachexie vieillard, Basedow chez \female{} enceinte
Repos, sédatifs, bêtabloquant, contraception
gls:ATS :
\begin{itemize}
\item -mazole (30-60mg/j), -thiouracile (300-600mg/j) : bloque TPO
\item ES : allergies cut, \inc enzymes hépatiques, neutropénie, agranulocytose++
( !!)
\item surveillance : T4 libre jusque N puis T4L et TSH. NFS 10jours pendant 2 mois (agranulocytose)
\end{itemize}
Chir : thyroidectomie totale sauf si adénome toxique (lobectomie)
Radio-iode : simple, sans risque génétique/cancérisation secondaire (\danger{} orbitopathie\ldots{}). CI : femme enceinte.
\paragraph{Résultats}
\label{sec:orge5fd7ac}
\begin{itemize}
\item Basedow : thyroïdectomie \thus hypothyroïdie définitive. Radio-iode \thus
hypothyroïdie 50\%, risque aggravation orbitopathie. Donc ttt médical (1-2
ans) puis chir/iode si récidive
\item Adénome/goitre multinodulaire toxique : chir, iode
\item Induite par l'iode : arrêt si possible
\item Thyroïdite subaigüe : anti-inflammatoire (AINS/corticoïde)
\end{itemize}
\paragraph{Formes particulières}
\label{sec:orga2fe8e4}
\begin{itemize}
\item Cardiothyréose : propanolol et anticoag. Si insuf cardiaque : tonicardiaque,
diurétiques, vasodilatateurs, betabloquant, anticoag. Pour thyrotoxicose : ATS
puis chir/iode 131
\item Crise aigüe thyrotoxique : soins intensifs, réa, ATS, propanolol, corticoïdes,
iode131 après 24h ATS
\item Orbitopathie : pas d'effet ATS, iode peut aggraver !! Si simple, collyre. Si maligne : cf spécialiste
\item Femme enceinte : si transitoire, repos. Si Basedow : repos si mineur. Si forme
importante : ATS faible dose. Si formes grave, chir (2eme trimestre) possible)
\end{itemize}
\thus surveillance avant et après accouchement
\subsection{241 \textdagger{} Hypothyroïdie}
\label{sec:org0e3f94a}
\begin{tcolorbox}
Rappel : TRH (hypothalamus) stimule la production de TSH (hypophyse) qui stimule la thyroïde
\end{tcolorbox}
\begin{itemize}
\item Atteinte de la glande thyroïde : \inc TSH et
\begin{itemize}
\item soit T4L N : hypothyroïdie frustre
\item soit T4L \dec : hypothyroïdie patente
\end{itemize}
\item Ou hypothalamo-hypophysaire : T4L \dec et
\begin{itemize}
\item soit TSH légèrement \inc : hypothalamus
\item soit TSH \dec ou N : hypophysaire
\end{itemize}
\end{itemize}
\subsubsection{Sémiologie}
\label{sec:org14b3c10}
Général :
\begin{itemize}
\item sd d'hypométabolisme\footnote{Asthénie, somnolence, hypothermie, frilosité, constipation, bradycardie,
prise poids modeste}
\item peau pâle/jaune, sèche, squameuse, dépilée; cheveux secs cassants
\item myxoedeme cutanéomuqueux : faciès "lunaire", voix rauque, hypoacousie,
macroglossie
\item neuromusc : crampes, myalgies
\item endocrinien : (galactorrhée), troubles règles, troubles libido
\end{itemize}
Cliniques (rare, diag fait avant) :
\begin{itemize}
\item CV : bradycardie sinusale, \dec contractilité, (insuf cardiaques, troubles
rythme V), épanchement péricardique, favorise athérome coronarien
\item neuromusc, neuropsy : dépressif, sd confusionnel, démence, myopathie prox,
apnée sommeil
\item coma myxoedemateux : si hypothyroïdie primaire profonde et
aggression. Convulsion, EEG non spécifique. Hyponatrémie. Pronostic sévère
\end{itemize}
Palpation : glande ferme hétérogène, pseudonodulaire
Grossesse :
\begin{itemize}
\item complication mère : HTA, prééclampsie, fausse couche, hémorragie post-partum
\item complications foetus : troubles developpement neuro-intellectuel, hypotrophie
\item 1er trimestre : TSH \dec, T4L limite sup. Puis TSH normale, T4L basses
(physiologique !)
\end{itemize}
Anomalies bio :
\begin{itemize}
\item hémato : anémie normocytaire normochrome (si macrocytose, penser anémie de
Biermer) troubles de coagulation,hémostase
\item hypercholestérolémie, \inc CPK, hyponatrémie dilution
\end{itemize}
\subsubsection{Étiologies}
\label{sec:org4cf693b}
\paragraph{Hypothyroïdie primaire}
\label{sec:orge0d0196}
Auto-immunes :
\begin{itemize}
\item Thyroïdite d'Hashimoto :
\begin{itemize}
\item goitre ferme, irégulier, Ac anti-TPO.
\item infiltration lymphocytaire du parenchyme thyroïdien. Facteurs environnementaux,
terrain génétique.
\item penser à lymphome si \inc rapide du goitre
\item écho thyroïdiennes : hypoéchogène, hétérogène, vasc hétérogène (scint
inutile)
\end{itemize}
\item Thyroïdite atrophique : pas de goitre, Ac anti-thyroidiens moins
élevés. Souvent une évolution d'Hashimoto, > 50 ans.
\item Thyroïdite du post-partum : idem, petit goitre. Normalement résolutif dans
l'année. 5\% des grossesses
\end{itemize}
Non auto-immune :
\begin{itemize}
\item thyroïdite subaigüe de De Quervain : inflammation du parenchyme. Phase de
thyrotoxicose puis hypothyroïdie
\item thyroïdite sans Ac
\item thyroïdite iatrogène : interferon++, amiodarone, ATS, iode131, radiothérapie
cervicale, lithium, ttt anti-tyrosine kinase (cancéro)
\end{itemize}
Autres : carences iodées (endémie++), hypothyroïdie congénitale (dépistage à
naissance + 72h\footnote{Clinique discrète : ictère prolongé, constipation, hypotonie, pleurs
rauques, difficulté succin, fontanelles larges, hypothermie})
\paragraph{Démarche diagnostique}
\label{sec:org9c2a7c9}
TSH puis (T4L (profondeur) et Ac anti-TPO, échographie pour étiologie)
\paragraph{Insuffisance thyréotrope}
\label{sec:orgfbf334c}
\begin{itemize}
\item compression région hypothalamo-hypophysaire (HH) par tumeur (adénome hypophysaire
souvent)
\item séquelle post-chir, post-radio des tumeurs de la région HH
\item séquelles méningite, trauma crânien, hémorragie méningée
\item génétiques (rare)
\end{itemize}
IRM systématique !
\subsubsection{Traitement}
\label{sec:orgaf1874a}
Lévothyroxine (T4)
\begin{itemize}
\item hypothyroïdie patente : L-T4 50 à 150 \(\mu\)g/j. Si coronarien : \inc progressivement
de 12.5 à 25\(\mu\)g/j. \danger Surveillance ! (ECG hebdo si grave, hospit si coronarien
récent, sinon patient doit consulter si douleurs thoraciques)
\item hypothyroïdie frustre : 3 cas
\begin{itemize}
\item TSH > 10mUI/L ou Ac anti-TPO : ttt
\item TSH < 10mUI/L et pas d'Ac anti-TPO : surveillance
\item si grossesse : dès TSH \(\ge\) 3mUI/L
\item à discuter sinon
\end{itemize}
\end{itemize}
Suivi
\begin{itemize}
\item hypothyroïdie primaire : objectif : TSH \(\in [0.5, 2.5]\) mUI/L (\(\approx\) 10mUI/L pour âgé, et < 2.5mUI/L pour femme eceinte)
\item insuf thyréotrope : suivi sur T4L seulement
\end{itemize}
Situations particulières:
\begin{itemize}
\item grossesse : \inc posologie dès diagnostic grossesse
\item \inc si interférence avec l'absorption intestinale\{sulfate de fer, carbonate de calcium, hydroxyde
d'alimunie, cholestyramine\}, la clairance \{phénobabrital, carbamazépinex, rifampicine,
phénytoïne, sertraline, chlooriqune\}, oestrogenes
\item néonatale : L-T4 à vie
\end{itemize}
\subsubsection{Dépistage ?}
\label{sec:org1499e9a}
\begin{itemize}
\item Adulte : si risque : signes clinique, goitre, hypercholestérolémie, ATCD
thyroïdiens, auto-immunité thyroïdienne, irradiation cervicale, \{amiodarone,
lithium, interféron, cytokines\}
\item Femme enceinte : si signes, contexte thyroïdien (perso/familial), auto-immunité
\end{itemize}
\subsection{242 Adénome hypophysaire}
\label{sec:orgf02ab66}
\subparagraph{Révélé par sd tumoral}
\label{sec:org84a4d7b}
Suspicion sur clinique, confirmé par IRM
\begin{itemize}
\item Clinique : céphalées, "voile" visuel \footnote{Par compression des voies optiques. Fond d'oeil,
acuité visuelle OK.}, quadra-/hémi-anopsie temporale
\item \danger apoplexie hypophysaire \footnote{Céphalées violentes, sd méningé sd confusionnel, troubles visuel.}(rare) thus imagerie en urgence \danger
\item IRM : microadénome (reste hypointense après injection) ou macro adénome (>
10mm, hyperintense après injection).
\item DD : craniopharyngiome intra-sellaire , méningiome intra-sellaire
\end{itemize}
\subparagraph{Révélé par sd d'hypersécrétion (Tab \ref{tab:org6feca11})}
\label{sec:org78d1aaa}
\begin{table}[htbp]
\caption{\label{tab:org6feca11}Syndromes d'hypersécrétion}
\centering
\begin{tabular}{lll}
Hypersécrétion & Signes & Diagnostic\\
\hline
Hyperprolactinémie & galactorrhée et & 1. Confirmer\\
(prolactine) & \female: trouble cycle menstruel & 2. Éliminer grossesse, médicaments, hypothyroïdie\\
& \male: gynécomastie, troubles sexuels. & périphérique, IR\\
& & 3. IRM : microadénome\\
& & ou \{macroadénome, tumeur non prolactinique\}\\
\hline
Acromégalie & Sd dysmorphique \tablefootnote{Extrémités élargies, visage (nez élargi, front bombé, lèvres épaisses, tendance prognathisme} & Pas de freinage à HGPO\\
(acrshort:GH) & Signes fonctionnels \tablefootnote{sueurs, céphalées, paresthésies mains, douleurs articulaires, asthénie fréquente, HTA} & IGF-1 \inc\\
& Hypertrophie myocarde (IC \thus DC ) & \\
& Diabète, SAOS & \\
& Goitres, polypes côlon & \\
\hline
Sd Cushing & amyotrophie ceinture et abdomen, & 1. CLU \inc, freinage minute\tablefootnote{Cortisolémie matin après 1mg dexaméthasone à 23h (rétrocontrole négatif des glucocorticoïdes sur cortisol)} négatif\\
(glucocorticoïdes) & peu amincie (mains), ecchymoses, vergétures & 2. Si ACTH \dec: adénome surrénalien ou\\
& & corticosurrénalome malin\\
& graisse facio-tronculaire, bosse de bison, & 3. Sinon freinage fort\tablefootnote{Dexmathéasone toutes les 6h})\\
& ostéoporose , hyperandrogénie & + test stimulation ACTH (CRH, métopirone\\
& spanioménorrhée \female, impuissance \male, \dec libido, & - positif : Cushing (adénome hypophysaire)\\
& HTA, troubles psy & - sinon sécrétion ectopique\\
& & DD : stress, dépression, psychose, alcoolisme\\
\end{tabular}
\end{table}
\subparagraph{Révélé par insuffisance antéhypophysaire (Tab \ref{tab:org823ff5b})}
\label{sec:org6e7a908}
Clinique : face pâle, "veillot", dépigmentation aréole mammaire et OGE,
dépilation complète aisselles pubis
IRM si déficit hypophysaire
\begin{table}[htbp]
\caption{\label{tab:org823ff5b}Insuffisance antéhypophysaire}
\centering
\begin{tabular}{lll}
Type & Signes & Diagnostic\\
\hline
Gonadotrope & \male = \{\dec libido, pilosité visage \dec, & \male{} : troubles sexuels \dec testostérone\\
& petits testicules mou, infertile\} & \\
& \female = \{aménorrhée, dyspareunie\} & \female{} préménopause : aménorrhée, oestradiol \dec,\\
& & gonadotrophines N\\
& ostéoporose, (retard pubertaire) & \female{} postménopause : gonadotrophines \dec \footnotemark\\
Corticotrope & asthénie, hypotension, amaigrissement & test Métopirone,\\
& pas de déficit en aldostérone ! & cortisol < 200ng/mL si hypoglycémie\\
& Risque de collapsus CV & (cortisolémie, synacthène, CRH)\\
Thyréotrope & hypothyroïdie modérée & \dec{} T4L sans augmentation de TSH\\
Somatotrope & adulte = \{\dec masse et force musc, adiposité abdo\} & stimulation GH \(\times 2\)\\
& enfant = retard croissance, hypoglycémies & stimulation GH\\
\end{tabular}
\end{table}\footnotetext[28]{\label{orgb93c69f}Ou dans les valeurs des femmes jeunes}
\subsection{243 Insuffisance surrénale}
\label{sec:orgfdf61bc}
\subsubsection{Insuffisance surrénale lente}
\label{sec:org56032a3}
Rare mais grave
Surrénales sécrètent :
\begin{itemize}
\item glucocorticoïdes \(\approx\) cortisol \footnote{Stimulé par ACTH, rétrocontrole nég. sur ACTH} : hyperglycémiant, \inc catabolisme protidique et tonus vasculaire, \dec
ADH, anti-inflammatoire et antipyrétique,
Minimum 0-2h, maximum 7-9h
\item minéralocorticoïde \(\approx\) aldostérone : réabsportion Na+ et Cl-, excrète K+
\item androgènes surrénalien (stimulé par ACTH)
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:org9962f89}Insuffisance surrénale primaire (maladie d'Addison)/secondaire : clinique}
\centering
\begin{tabular}{ll}
Primaire (surrénale) & Secondaire (hypophysaire)\\
\hline
Fatigue, dépression, anorexie, nausées & \\
\dec poids, hypotension, hypotension orthostatique & \\
Hyperpigmentation & Pâleur\\
HyperK, hypoNa (manque sel) & HypoNa (dilution)\\
\end{tabular}
\end{table}
\subparagraph{Diagnostic}
\label{sec:org7902d06}
Cortisol + ACTH \danger ne pas attendre résultats pour commencer traitment
\begin{itemize}
\item clinique : \ref{tab:org9962f89}
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:org47c075c}Insuffisance surrénale : diagnostic}
\centering
\begin{tabular}{lll}
& Primaire & Secondaire\\
\hline
cortisolémie à 8h & basse & basse\\
ACTH & haute & basse\\
aldostérone & basse & N\\
rénine & haute & N\\
Synacthène & réponse insuffisante du cortisol & réponse insuffisante\\
\end{tabular}
\end{table}
\begin{itemize}
\item cortisolémie (max = 8h) puis : ACTH \inc{} si primaire, rénine \inc si primaire
\item test Synacthène\footnote{Analogue de l'ACTH} (+ Métopirone ou hypoglycémie insulinique si doute)
NB : femme enceinte = \{\inc seuil, faisceau d'args\}, enfant : répéter dosages
voire ttt probabiliste
\end{itemize}
\subparagraph{Étiologies de l' acrshort:IS primaire}
\label{sec:org111c8c1}
\begin{itemize}
\item Auto-immune (80\% adulte, 20\% enfant) : gls:PET1, gls:PET2 \thus autoAc anti-21-hydroxylase, scanner (surrénales atrophiques)
\item \emph{tuberculose bilatérale surrénale} (10\%) : transplanté ou ID avec TCD tuberculose
\thus scanner surrénales
\item \emph{VIH} (stade avancé) : iatrogène, infection opportuniste (CMV++), atteinte de
l'hypophyse (lymphome, CMV), corticoïde anti-inflammatoire et ritonavir
\end{itemize}
\danger dénutrition \thus spécialiste
\begin{itemize}
\item autres : \emph{iatrogènes}\footnote{Surrénalectomie bilatére, anticortisolique de synthèse, nécrose hémorragique}, \emph{métastases bilatérales}\footnote{\danger éliminer phéochromocytomes avant biopsie surrénale}, lymphomes, maladies
infiltratives, causes vasculaires
\item enfant : génétiques surtout = \emph{bloc enzymatique} (dépistage obligatoire), adrénoleucodystrophie
\end{itemize}
\subparagraph{Étiologies de l'IS secondaire}
\label{sec:org1584b47}
\begin{itemize}
\item \emph{interruption corticothérapie prolongée} surtout (> 7mg prednisone)
\item autres\footnote{S'associe souvent à d'autres insuffisances de l'axe hypothalamo-hypophysaire} : tumeur région hypothalamo-hypophysaire, hypophysite (auto-immune),
granulomatose, trauma, chir hypophysaire, radiothérapie, sd de Sheehan
\end{itemize}
\subparagraph{Prise en charge}
\label{sec:org4830c2e}
Ttt cause et ttt substitutif :
\begin{itemize}
\item glucocorticoïdes (hydrocortisone) 15-25mg/j
\item minéralocorticoïde (fludrocortisone) 50-150\(\mu\)g/j si IS primaire
\end{itemize}
Éducation du patient : régime normosodé, pas de laxatif, ttt à vie, hydrocortisone en SC si > 2 vomissement/diarrhées en < 1/2 journée
Surveillance clinique : surdosage en hydrocortisone/fludocortisone, cortisolémie et ACTH inutile !!
\subsubsection{Insuffisance surrénale aigüe}
\label{sec:orga7a5ac2}
\subparagraph{Diagnostic}
\label{sec:orgc5a4af1}
Si diagnostic \textbf{non} posé : cortisol + ATCH. Ne pas attendre les résultats
\begin{itemize}
\item clinique : déshydratation extracellullaire\footnote{Pli cutané, hypotension} , confusion, trouble dig, douleurs musc, fièvre
\item biologie : IR, fonctionnelle++, hypoNa, hyperK++
\end{itemize}
\subparagraph{Causes}
\label{sec:orgc06ac03}
\begin{itemize}
\item Insuf surrénale chronique décompensée++
\item D'emblée si bloc enzymatique surrénalien (21-hydroxylase) complet (néonatale)
ou hémorragie bilat surrénale ou apoplexie hypophysaire
\item Décompensation par n'importe quelle patho intercurrente
\end{itemize}
\subparagraph{PEC}
\label{sec:orgc0564c4}
\danger Urgence extrème
\begin{itemize}
\item 100mg hydrocortisone (IV, IM, SC) \thus \faHospital (réa)
\begin{itemize}
\item perfusion NaCL (et G30\% si hypoglycémie)
\item ttt facteur déclenchant
\item surveiller : PA, FC, FR, oxymétrie de pouls, diurèse, T, glycémie, CS, ECG
si hyperK
\end{itemize}
\end{itemize}
Ttt préventif : patient doit \inc ses doses, médecin traitant au courant
\subsubsection{Arrêt d'une corticothérapie}
\label{sec:org879418f}
Risque = ebond de la maladie causale, insuf surrénale secondaire (corticotrope), sd de sevrage
À risque : (ttt \(\ge\) 3 semaines par \(\ge\) 20mg prednisone) ou (corticoïdes et inhib enzymatique du
cytochromie P450 (ritonavir)) ou sd Cushing iatrogène
\subsection{244 \textdagger{} Gynécomastie}
\label{sec:orgf9fa618}
Hyperplasie tissue glandulaire mammaire, fréquente. Dû à oestrogène \inc{} et testostérone \dec{}. Regarder aussi TeBG,
SHBG
\subsubsection{Démarche}
\label{sec:org4c24cfc}
\begin{itemize}
\item Clinique : palpation = ferme/rugueux, mobile arrondi, centré par le mamelon (rien si adipomastie)
\item Mammographie si doute : opacité nodulaire/triangulaire (rien si adipomastie). Élimine cancer du sein (rare)
\item Physiologique ?
\begin{itemize}
\item 2/3 des nouveaux-nés
\item pubertaire : de 13 jusque 20 ans, rétrocède . Palper testicule pour atrophie testiculaire/tumeur
\item fréquente > 65 ans. Palpation testiculaire
\end{itemize}
\end{itemize}
\subsubsection{Étiologie}
\label{sec:org9b1b94a}
\begin{tcolorbox}
Causes fréquentes : médic, idiopathique, cirrhose, insuf testiculaire/gonadotrope, (tumoral)
\end{tcolorbox}
Évidente :
\begin{itemize}
\item insuf rénale chronique, cirrhose, médicaments (surtout spironolactone,
antiandrogène, kétoconazole, neuroleptiques, ATB antirétroviraux, antiulcéreux)
\end{itemize}
Sinon exploration hormonale : T4L, TSH, hCG, testostérone totale, LH, FSH,
prolactine, oestradiol
Causes endocriniennes :
\begin{itemize}
\item hyperthyroïdie
\item insuffisance testiculaire/hypogonadisme périphérique (8\%) : sd de Klinefelter
le plus fréquent
\item hypogonadisme d'origine hypothalamique/hypophysaire: testostérone basse, LH,
FSH normales/abaissées \thus imagerie hypophysaire, dosage
prolactine. Hyperprolactinémie ou tumorale
\item tumeur sécrétant oestrogène : oestradiol \inc, testostérone \dec \thus tumeur
testiculaire (ou surrénalienne rarement) \thus echo testiculaire ou scanner
abdo
\item tumeur sécrétant hCG : \inc hCG \thus écho testiculaire, scanner
cérébrales. Dans les bronches ou le foie parfois. Chimio.
\item Résistance androgènes (exceptionnelle) : testostérone \inc, LH \inc
\item idiopathique (25\%)
\end{itemize}
\subsubsection{Traitement}
\label{sec:org8b7a389}
Traiter la cause. Sinon
\begin{itemize}
\item Pubertaire : ne rien faire
\item Idiopathique : androgènes non aromatisables 3 mois. Si inefficace, chir
plastique possible
\end{itemize}
\subsection{245 Diabète}
\label{sec:orgeb0cfc7}
\begin{tcolorbox}
Définition : glycémie à jeun \ge 1.26g/L (2 reprises) ou (aléatoire \ge 2g/L et signes hyperglycémie)\footnotemark
\end{tcolorbox}
\footnotetext{Normale à jeûn < 1.10g/L}
Caractéristiques diabète 1 (le diabète 2 s'y oppose) :
\begin{itemize}
\item ATCD familiaux rares, < 25 ans, début rapide explosif avec symptomatologie bruyante
\item poids normal ou \dec, hyperglycémie majeure > 23g/L
\item souvent cétose
\item pas de complications dégénératives
\item mortalité par insuf rénale (CV pour diabète 2)
\end{itemize}
\subsubsection{Diabète 1}
\label{sec:org0c6bf60}
Prévalence : 1/200 000 (10\% des diabétiques). Peut survenir à tout âge. \inc
incidence. Sex-ratio = 1
\subparagraph{Physiopathologie}
\label{sec:orgead90bf}
Carence en insuline par destruction cellules beta du pancréas. Auto-immun++ ou idiopathique.
Prédisposition génétique, facteurs environnementaux.
\danger 10\% d'autres maladies auto-immunes \thus doser Ac anti-TPO (Basedow,
thyroïdite), anti-surrénale (Addison), anti-transglutaminase \textpm{} anti-endomysium
(coeliaque), anti-paroi gastrique, anti-facteur intrinsèque (Biermer)
\subparagraph{Diagnostic}
\label{sec:orgf864338}
Clinique = glycémie \(> 2g/L\), maigrissement, cétonurie \textpm{} acrshort:SPUPD
\begin{itemize}
\item NB : signes d'acidose\footnote{Dyspnée de Kussmaul, haleine acétonique} possibles
\item \emph{si doute} : Ac anti-GAD (\textpm{} anti-ilôtsq anti-IA2, anti-insuline, anti-ZnT8)
\item \emph{si négatif} :
\begin{itemize}
\item hérédité dominante : MODY, mutation SUR1/KIR6-2 (si diabète néonatal)
\item sd de Wolfram \footnote{Atrophie optique, surdité, diabète insipide < 20 ans}, mitochondropathie\footnote{Surdité, dystrophie maculaire, cardiomyopathie transmission par la mère}
\item secondaire : cancer pancréas, pancréatite chronique, mucoviscidose, hémochromatose, médicaments
\end{itemize}
\end{itemize}
Formes : diabète 1 lent (LADA\footnote{Latent Autoimmune Diabetes in the Adult}), (révélé par acidocétose), non insulinodépendantes, cétosique du sujet noir d'origine africaine : mécanisme
auto-immun
\subparagraph{Évolution}
\label{sec:orgf7f4f5b}
Schéma théorique : estruction cellules \(\beta\), clinique (85\% détruites), séquellaire
Diabète instable :
\begin{itemize}
\item itérations de cétoacidoses ou hypoglycémies sévères, psycho.
\item DD : gastroparésie, déficit systèmes contra-insuliniques, Ac anti-insuline
\end{itemize}
\subparagraph{PEC}
\label{sec:org7a0c698}
Insuline à vie (Table \ref{tab:org8963bff} ) + alimentation variée sans interdits, exercice physique
\begin{itemize}
\item Stylo à insuline (pompe si échec) :analogue lent (1-2/j) et analogue rapide (3-4) \thus
éducation nutritionnelle
\item ES : hypoglycémie, lipoatrophie (immuno), lipohypertrophie (piqûres au même endroit)
\end{itemize}
Objectifs : HbA1c < 7\% (enfants : entre 7.5 et 8.5, complication/sujet âgé : 8\%)
\begin{itemize}
\item 4 glycémies/jour, injection d'insuline, adapter ttt, contrôle de l'alimentation \thus
éducation thérapeutiques
\item Surveillance :
\begin{itemize}
\item HbA1c
\item diabétologue/pédiatre endocrinologue 3/an
\item \{lipides, créat, microalbuminurie\}
\item ophtalmo, cardiologie 1/an (sympto/âgé,compliqué), dentiste 1/an
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:org8963bff}Traitement insulinique du diabète 1}
\centering
\begin{tabular}{llll}
Type & Injection & Durée & Utilisation\\
\hline
insuline humaine recombinante (Actrapid) & IV, IM, SC & 7-8 & Prandiale, hyperglycémie\\
analogue rapide (Humalog, Novorapid, Apidra) & IV, IM, SC & 4-6h & Pompe\\
forme lente (NPH) & SC & 9-16h & \\
analogue lents (Lantus) & & 16-40h & \\
\end{tabular}
\end{table}
\end{itemize}
\subparagraph{Cas particuliers}
\label{sec:org6751fed}
\begin{itemize}
\item Enfant/ado : \danger cétoacidoses
\item Femme (cf Sec. \ref{orgf0d741f}
\begin{itemize}
\item oestrogestatif à discuter
\item grossesse : équilibre dès conception !! par analogue de l'insuline.
\item CI absolue : insuf coronaire instable
\end{itemize}
\item Pas d'arrêt de l'insuline (lent si examen à jeun)
\end{itemize}
\subsubsection{Diabète 2}
\label{sec:orgaa41ab8}
90\% de diabète. Prévalence 4\%.
FR = obèse, anomalie métabolisme glucidique, ATCD familiaux diabète 2, ethnie noire/hispanique.
\subparagraph{Physiopatho}
\label{sec:org3443202}
Insulinorésistance : causée par la génétique, sédentarité, excès pondéral. Au niveau du muscle, foie, lipolyse
\emph{Et} déficit insulinosécrétion.
\subparagraph{Dépistage}
\label{sec:org8883028}
Signes cliniques de diabètes, > 45 ans (tous les 3 ans), \(\ge\) 1 FR.
Non caucasien/migrant, \glslink{sdMetabolique}{sd métabolique}
DD : diabète 1 lent, génétique (MODY2, mitochondrial), secondaire (pancréatopathie, hémochromatose,
mucoviscidose, médicaments)
\subparagraph{Évolution}
\label{sec:orgdf1f597}
Insulinopénie \thus insulinoréquerant. Pronostic selon complications.
\paragraph{Traitement}
\label{sec:org74514eb}
\begin{itemize}
\item Activité physique 3-5/semaine: intensité modérée \(\ge\) 30min/j et intense (> 60\% \(VO_{2max}\)) de 20min
\begin{itemize}
\item CI : insuf coronarienne, rétinopathie proliférante non stabilisée
\item surveiller risque hypoglycémie, pieds !
\end{itemize}
\item Alimentation : équilibrée, objectif = poids -5 à 10\%
\item Metformine++\footnote{ES = diarrhées. CI = insuf rénale (?), hépatique, respiratoire} en oral \textpm{} sulfamide/glinides/inhibiteurs
DPP-4/inhibiteurs \(\alpha\)-glucosidase/analogues GLP-1\footnote{1ere intention = metformine. Si besoin, +sulfamide. Si besoin : DPP4 si
écart < 1\% sinon insuline (ou GLP-1 si IMC > 30)}
\item \textpm{} insulinothérapie quand insulinorequérance, mal équilibré(cf diabète 1)
\end{itemize}
Objectifs : HbA1c < 7\%\footnote{< 6.5\% si découverte} (8\% si grave, 9\% si agé dépendante)
\begin{itemize}
\item autosurveillance glycémique : pas systématique si ttt oral (1-3 cycles/j),
nécessaire si insuline
\end{itemize}
\subsubsection{Complications}
\label{sec:org3dc2e27}
Souffrance vasculaire : micro- (rein, oeil, nef) et macro-angiopathie (\inc
athérosclérose). AOMI x6-10
\subparagraph{Physiopatho}
\label{sec:orgb33d2eb}
Excès de glucose \thus aggression des vaisseaux (endothélial++), inhibition des
mécanismes de défense cellulaires
Conséquences : épaississement des membranes basales, troubles perméabilité
vasculaire, prolif vasculaire (rétine), fibrose (rein)
\subparagraph{Rétinopathie diabétique}
\label{sec:org6cad983}
Cf \hyperref[orgd703da6]{chap 21 d'ophtalmo}
\paragraph{Néphropathie}
\label{sec:orga3ea97d}
\begin{itemize}
\item Diabète = 1ere cause d'IR terminale. Risque CV x10 chez DT1, 30\% DC IR terminale
chez DT1 (5\% chez DT2)
\end{itemize}
\subparagraph{Physiopatho}
\label{sec:orgc74abb0}
\inc pression intra-glomérulaire \thus dilatation des glomérules. Puis sclérose) avec \inc albumine\footnote{Microalbuminurie, macro quand détectable à la BU}.
\subparagraph{Dépistage}
\label{sec:orgb7afc77}
1 BU/an protéinurie, hématurie, infection urinaire), albuminurie/créatinurie
\subparagraph{Diagnostic}
\label{sec:org98698af}
Rétinopathie , plusieurs excrétions urinaire d'albumine \inc
\begin{itemize}
\item si doute : ponction-biopsie rénale :
\begin{itemize}
\item diabète 1 : hypertrophie mésangiale/glomérulaire < épaississement membrane basale, dépôts
mésangiaux < hyalinose artériolaire < glomérulosclérose nodulaire
\item diabète 2 : 1/3 typique\ldots{}
\end{itemize}
\item 5 stades :
\begin{enumerate}
\setcounter{enumi}{3}
\item Néphropathie incipiens : microalbuminurie\footnote{30-300mg/24h ou 20-200mg/L}
\item Néphropathie : PA élevée, DFG \dec de 10mL/min/an, nodule de sclérose,
hyalinose artériolaire
\item Insuffisance rénale
\end{enumerate}
\end{itemize}
\subparagraph{Traitement}
\label{sec:org8add430}
Prévention
\begin{itemize}
\item primaire (diabète, FR HTA)
\end{itemize}
\begin{itemize}
\item secondaire : Tab \ref{tab:org7463954}. Surveiller glycémie !! Éviter AINS,
produits contrastes iodés
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:org7463954}tab:nephro\textsubscript{diabete}}
\centering
\begin{tabular}{lll}
Stade & Objectifs & Moyens\\
\hline
microalbuminurie & : HbA1c < 7\%, PA < 140/85 & \uline{IEC/sartans}\tablefootnote{\danger sténose artère rénales : doser K+, créat}, FR\\
& & \emph{et} PEC tabac, régime hypoprotidique, sel < 6g/j\\
macroalbuminurie & PA < 140/85mmHg & IEC/sartan + diurétique thiazidique.\\
& Protéinurie < 0.5g & \\
IR & PAs < 130mmHg & \\
- DFG \(\in\) [30, 60] & & adapter poso\\
- DFG < 30mL/min & HbA1c < 8\% & autorisé : insuline, répaglinide, inhib \(\alpha\)-glucosidase,\\
- DFG < 25 & & autorisé : inhib DPP4\\
\end{tabular}
\end{table}
NB : infections urinaires : \(\times 3\) dont 90\% asymptomatique (basses) \thus
ttt si symptomatique. Risque = contamination du haut appareil urinaire aggravation néphropathie glomérulaire.
\paragraph{Neuropathie}
\label{sec:orgd87f4a5}
\begin{itemize}
\item Autonome : tardive
\item Périphérique : 50\% des diabètes à 20 ans. FR : grande taille, tabac, âge,
AOMI, carences nutritionnelles/vitaminiques, alcool, insuf rénale
\end{itemize}
Atteinte métabolique et vasculaire.
\subparagraph{Diagnostic}
\label{sec:org7f7f730}
Examen clinique et interrogatoire (+ complémentaires si autonome)
\subparagraph{Sensorimotrice}
\label{sec:org0d9db9b}
En "chaussettes" puis en "gants")
\begin{itemize}
\item Polynévrite symétrique distale++ :
\begin{itemize}
\item hypoesthésie pression/tact/thermique/proprioceptique ignorée
\item \textpm{} paresthésies distales, douleurs "arc électrique"
\item ROT achilléen aboli (puis rotulien)
\item voûte plantaire se creuse (tardivement)
\item complication : pied "cubique" de Charcot
\end{itemize}
\item Plus rare : polynévrite asymétrique proximale, polyradiculopathie
thoracique, mononévrite, multinévrite
\end{itemize}
\subparagraph{Autonome}
\label{sec:org8b5d3fb}
\begin{itemize}
\item CV : tachycardie sinusale, bradycardie, allongement QT
\item Vasomotrice : hypotension orthostatique \emph{sans} accélération du pouls
\item Troubles sudation : sécheresse cutanée MI
\item Digestive : parésie, dysphagie, gastroparésie (fréq), diarrhée, constipation
\item Vésicale : résidu post-miction \thus IU \thus clinique, écho (prostate, vessie)
\item Dysfonction érectile : psychogène, (sd de Leriche\footnote{Thrombus bloquant l'aorte abdominale avant bifurcation}). DD : examen génital, testostérone, prolactinémie.
\end{itemize}
Examen
\begin{itemize}
\item interrogatoire , inspection pieds, ROT abolis (niveau troubles sensitifs), monofilament, sensibilité épicritique, thermoalgique, vibratoire\footnote{Grosses fibres\label{org3b44ad5}}, proprioceptiques\textsuperscript{\ref{org3b44ad5}}
\item ECG annuel, EMG si atypique
\item \(\Delta\) FC inspiration - expiration\footnote{Sensible mais pas interprétable > 60 ans ou patho bronchorespiratoire}, rapport RR long/court pendant épreuve de
Valsalva, \(\Delta\) FC couché - debout
\end{itemize}
DD : neuropathies métaboliques (insuf rénale, amylose, hypothyroïdie), toxiques
(alcool, tabac, iatrogène), paranéoplasiques, carentielles, inflammatoire,
infectieuse (Lyme, lèpre), autre (Charcot-Marie-Tooth, péri-artérite noueuse)
Traitement :
\begin{itemize}
\item préventif = glycémie. FR : alcool, tabac, insuf rénale, carence vitamines B, médicaments.
\item Si installées, stabiliser et éviter les complications (mal perforant plantaire++)
\item Antalgiques, hydratation peau
\end{itemize}
\paragraph{Macroangiopathie}
\label{sec:orgeaa975f}
\diameter > 200 \(\mu\)m. Plus fréquente et sévère. Artères visibles sur radio.
Prévention CV = \textbf{problème majeur} des diabétiques 2 : \(\frac{3}{4}\) DC d'une cause
CV. Risque CV \texttimes{}2-3 (\texttimes{}3-4 chez \female).
\subparagraph{Dépistage}
\label{sec:org63de8a2}
Risque > 1\% = élevé\footnote{Calcul par les études UKPDS ou SCORE (mais \texttimes{}2-4 pour ce dernier)}
\begin{enumerate}
\item \emph{FR} :
\begin{itemize}
\item CV : âge > 50 ans \male \footnote{> 60 \female}, diabète > 10 ans, ATCD IDM/mort
subite\footnote{< 55 ans \male, < 65 ans \female}, ATCD AVC \footnote{< 45 ans}, tabac, HTA permanente, HDLc < 0.4g/L, microalbuminurie > 30mg/24h
\item autres : obésité abdominale \footnote{> 102cm \male, > 88cm \female}, IMC > 30k/m\textsuperscript{2}, sédentarité, > 3 verres vin/j, pyschosociaux
\end{itemize}
\item Montrer atteinte artérielle :
\begin{itemize}
\item coronaropathie : ECG repos annuel, scinti avec épreuve d'effort ou coronarographie
\item carotides ? auscultation \thus écho si AIT possible
\item AOMI ? pieds, pouls, claudication, IPS cheville/bras < 0.7 ? Écho-doppler
\end{itemize}
\end{enumerate}
\subparagraph{Diagnostic}
\label{sec:org94d40ac}
\begin{itemize}
\item \emph{Ischémie myocardique} silencieuse fréquente ! \thus dépistage systématique si
trouble dig, asthénie effort\ldots{}
\item AOMI : 1/3 proximale (HTA), 1/3 distale sous genou (glycémie, tabac), 1/3 proximale et distale
\item : diabète + microangiopathie sévère, diabète + atteinte vasculaire
\end{itemize}
\subparagraph{Traitement}
\label{sec:org397e18d}
Objectif HbA1c < 6.5\% (7\% si âgé ou à risque.
\begin{itemize}
\item Activité physique
\item LDL < 1.3g/L (1.0 si risque CV élevée ou néphropatie) : statines \uline{ou} fibrates
\item PAs \(\in\) [130, 139] et PAd < 90mmHg.
\item Poids : IMC < 25kg/m\textsuperscript{2}
\item Arrêt tabac,
\item Prévention thrombose si \(\ge\) 1 FR : aspirine 75-150mg
\end{itemize}
Si revascularisation : stents par défaut et chir si atteinte 3 coronaires.
\paragraph{Pied diabétique}
\label{sec:org5817b73}
1 patient sur 10 à risque d'1 amputation d'orteils. Éviter les plaies pour prévenir l'amputation
\subparagraph{Mal perforant plantaire (MPP)}
\label{sec:org4b30b5d}
Neuropathies \thus hypoesthésie, déformations ostéoarticulaires \thus durillons
puis fissure et infection \thus dermo-hypodermite.
Autres
\begin{itemize}
\item Ischémie/nécrose : peau froide, fine, dépilée, livedo. \thus revasculariser en urgence
\item Nécrose + MPP
\item Dermo-hypodermite nécrosante : très rare, \thus débrider en urgence, ATB.
Cas particulier : gangrène gazeuse à \bact{perfringens} \thus urgence vitale \danger
\end{itemize}
CAT
\begin{itemize}
\item Radio pieds bilatérale (ostéite ?), si infection : NFS, iono, CRP
\item décharge, excision kératose à domicile si suffit
\item réhydratation \textpm{} équilibre glycémie, anticoag, accin anti-tétanos !
\item si infection : parage et drainage, ATB (cocci G+ si récent, sinon bacille G-)
\item si artério : revascularisation
\item si ostéite : résection chirurgicale ou ATB 6-12semaine et sans l'appui
\end{itemize}
\paragraph{Autres}
\label{sec:orgac09c50}
\begin{itemize}
\item Peau : nécrobiose lipoïdique (rare), dermopathie diabétique (fréquente),
lipodystrophie, acanthosis nigricans, vitiligo, xanthomatose éruptives
\item Infections : otite nécrosante (urgence !), mucormycose (urgence !)
\item Foie : hépatologue dès anomalie transaminases ou \(\gamma\)-GT
\item Articulations : capsulite rétractile, maladie de Dupuytren\footnote{Sclérose réractile de l'aponévrose palmaire moyenne}, Chéiroarthropathie, arthrose
\item Dents : maladie parodontale \thus dentiste tous 6 mois
\end{itemize}
\begin{tcolorbox}
\begin{itemize}
\item annuel : FO, ECG repos
\item tous les 5 ans : écho-doppler MI (si > 40 ans, diabète > 20 ans) tous 5 ans
\item bio : HbA1c 4/an, glycémie veineuse, lipides 1/an, microalbuminurie 1/an,
créatininémie jeun, clairance créat 1/an, TSH
\end{itemize}
\end{tcolorbox}
\paragraph{Complications métaboliques}
\label{sec:org4d877eb}
\subparagraph{Coma cétoacidosique}
\label{sec:org28bfa52}
\begin{itemize}
\item acétonurie, glycosurie, glycémie 2.5g/L, pH veineux < 7.25, bicarbonate <
15mEg/L
\item cause : déficit insuline absolu/relatif, inconnue
\item évolution : cétose puis cétoacidose (Kussmaul, stupeur, déshydratation mixte)
\item gravité : âgé, ph < 7, kaliémie 4-6 mmol/L, coma profond, TA instable, pas de
diurèse après 3h, vomissements incoercibles
\item DD : urgence abdo, coma hyperosmolaire
\item Régression sous ttt en 24-48h :
\begin{itemize}
\item éducation : si cétose, maintenir injections, supplément insuline rapide,
acétonurie si glycémie > 2.5g/L
\item curatif : insuline rapide IV, recharge volumique, K+, glucose
si besoin, facteur déclenchant
\end{itemize}
\end{itemize}
\subparagraph{Coma hyperosmolaire :}
\label{sec:orgc2a43b6}
\begin{itemize}
\item glycémie > 6g/L, osmolalité > 350mmol/kg, natrémie corrigée > 155mmol/L, pas
de cétose ni d'acidose
\item FR : > 80 ans, infection aigüe, diurétique, \uline{pas d'accès aux boissons}, corticothérapie
\item ttt : réhydratation prudente, lente, insuline IV, surveillance, héparine
préventive, ttt causal
\end{itemize}
\subparagraph{Hypoglycémie}
\label{sec:org35012ea}
Inévitable mais pas mortelle
\subsection{246 \textdagger{} Prévention par la nutrition}
\label{sec:orged1700f}
\subsection{247 \textdagger{} Modifications thérapeutiques du mode de vie}
\label{sec:org004c1da}
\subsection{248 \textdagger{} Dénutrition (à compléter)}
\label{sec:org612622b}
\subsection{249 \textdagger{} Amaigrissement}
\label{sec:orgc7e1fa0}
Fréquent
\subsubsection{Interrogatoire}
\label{sec:org0107177}
\begin{itemize}
\item Histoire pondérale, conditions, de vie, psychologique, activité physique excessive et apports alimentaires insuffisants
\item Anorexie, \{troubles digestifs, palpitations, sd polyuro-polydipsie\}, troubles
libido/érection, amnénorrhée (anorexie mentale ou hypothalamique
fonctionnelle), médicaments (nausée, anorexie), dépression masquée++
\end{itemize}
\subsubsection{Examens :}
\label{sec:org30cc3e0}
Clinique : poids, taille, IMC, pli cutané, fonte musculaire, carences vitamines,
pâleur cutanéomuqueuse
Complémentaires :
\begin{itemize}
\item bio : NFS (anémie), VS/CRP (inflammatoire), iono (hyponatrémie \thus insuf
surrénale), BU (glycosurie), calcémie, \{transaminase, \(\gamma\)-GT\}(foie), TSH
(hyperthyroïdie), \{B12, folates, TP, albuminémie\}, graisses fécales ?
(pancréatite chronique calcifiante), dénutrition\footnote{(Pré-)Albumine, IGF-1, ferritine sérique}
\item Radio thoracique (tuberculose), écho abdo (abcès/tumeur), fibro (obstacle),
DEXA (composition corporelles)
\end{itemize}
\subsubsection{Étiologie}
\label{sec:org9a8780c}
\begin{itemize}
\item Poids stables, apports nutritionnels normaux, examens normaux : maigreur
constitutionnelle
\item Si perte de poids confirmée, éliminer anorexie mentale, maladies digestives,
iatrogène, cancer extradigestif, maladies infectieuses, neuro, grande
défaillance cardiaque/rénale/respi/hépatique, alcool
\item Sinon, causes endocrines :
\begin{itemize}
\item diabète 1 ou 2 : glycémie, HbA1C
\item hyperthyroïdie : TSH \dec\dec, hormones thyroïdiennes \inc
\item hypercalcémie : si gls:PTH inadaptée, hyperparathyroïdie primaire
\item insuf surrénalienne : cortisol, ACTH plasmatique
\item panhypopituitarisme\footnote{Insuffisance antéhypophysaire complète} : cortisol \dec
\item phéochromocytomes : (nor)métanéphrines dans urines 24h, imagerie surrénales
\end{itemize}
\end{itemize}
\subsection{250 \textdagger{} Troubles nutritionnels chez sujet âgé (à compléter)}
\label{sec:orga34c683}
\subsection{251 \textdagger{} Obésité(à compléter)}
\label{sec:orga8c0e37}
\subsubsection{Adulte}
\label{sec:org729c469}
Surpoids = IMC \(\in\) [25, 29.9]kg/m\textsuperscript{2}. Obésité :
\begin{itemize}
\item grade 1 : IMC \(\in\) [30, 34.9]kg/m\textsuperscript{2}.
\item grade 2 : IMC \(\in\) [35, 39.9]kg/m\textsuperscript{2}.
\item grade 3 : IMC \(\ge\) 40kg/m\textsuperscript{2}.
\end{itemize}
Limites : sous-estimé chez asiatiques. Seulement pour [18,65] ans
Phases : prise de poids, constituée, perte, rechutes
Localisation : viscéral (scanner, IRM), sous-cutanée, ectopique (muscle, foie)
Épidémio : +27.5\% 1980-2013 (monde). France : de plus en plus jeune, \inc chez >
65 ans
Étiologie :
\begin{itemize}
\item génétique: envisager si précoce (naissance +24 mois), troubles du
comportement alimentaire
\item obésités communes liées à des facteurs environementaux (majorité) : surtout
déséquilibre apport caloriques- dépense
\begin{itemize}
\item antipsychotiques, glucocorticoïdes, antidépresseurs,
antiépileptiques, antidiabétiques
\item arrêt du tabac, privation de sommeil (?), hypothalamique (rare)
\end{itemize}
\end{itemize}
Complications : \inc RR mortalité, métabolique, CV, respi, ostéoarticulaire,
digestive, rénale, gynéco, cutanée, néoplasiques, psychosociale
\paragraph{Clinique}
\label{sec:orgd5c0f81}
\begin{itemize}
\item Interrogatoire :
\begin{itemize}
\item ATCD familiaux d'obésité, poids naissance, âge surpoids,
poids max et min, circonstances déclenchantes, tentatives antérieures, phases
\item Comportement alimentaire (carnet), évaluation dépense énergétique, pyscho-comportementale
\item Complications (SAS)
\end{itemize}
\item Examen : poids, taille, PA, tour de taille\footnote{Obésité abdominale : > 88cm \female, > 102cm \male}, obésité secondaire
\item Complémentaires : glycémie à jeune, lipides, hépatique, uricémie, ECG repos
\end{itemize}
\paragraph{Traitement}
\label{sec:orgee6fc98}
\begin{itemize}
\item Diététique, activité physique (\(\forall\) IMC)
\item Psychologique
\item Médicaments (IMC \(\ge\) 30 ou (\(\ge\) 27 et comorbidités)) : orlistat
\item Chir bariatrique : \{anneau gastrique ajustable, sleeve gastrectomie\},
\{court-circuit gastrique, dérivation biliopancréatique\} : < 65 ans. Prise en
charge 6 mois avant et post-op à vie (carences vitaminiques)\footnote{CI : troubles cognitifs sévères, troubles sévères non stabilisés du
comportement alimentaire, dépendances à l'alcool / substances psychoactives, pas
de PEC médicale, pronostic vital mis en jeu, CI à l'anesthésie générale,
incapacité à faire un suivi médical prolongé}
\end{itemize}
\subsubsection{Enfant/ado}
\label{sec:org16431ff}
\danger{} évolutivité. Surpoids : IMC > 25. Obésité
\begin{itemize}
\item grade 1 : > 30kg/m\textsuperscript{2}
\item grade 2 : > 35kg/m\textsuperscript{2}
\item grade 3: > 40kg/m\textsuperscript{2}
\end{itemize}
Épidémio : stabilisation mais obésités sévères \texttimes{}4
\paragraph{Étiologies}
\label{sec:orgf723b15}
\begin{itemize}
\item génétiques : mutation sur récepteur de la mélanocortine type 4 = 2.5-5\%
\item communes (majorité) : facteurs environnementaux et prédisposition génétique
\begin{itemize}
\item repond d'adiposité à 6 ans. Risque d'obésité \(\propto\) précocité du rebond
\item tour de taille/taille > 0.62 = forte valeur prédictive
\item FR : surpoids parent, poids excessif/tabac pendant grossesse, anomalie de
croissance foetale, \inc\inc poids à naissance + 2ans, difficulté
socio-éoc, manque d'activité physique, troubles sommeil, psychopatho
\end{itemize}
\item secondaires (rare) : ralentissement de la vitesse de croissance naturelle
\end{itemize}
\paragraph{Complications}
\label{sec:org198271a}
\begin{itemize}
\item HTA : > 97e percentile + 10mmHg
\item Insulinorésistance avec glycémie normale fréquente
\item \inc TG et \dec HDL
\item Stéatose hépatique non alcoolique
\item Rachialgies, gonalgies, troubles statique vertébrales. Penser à l'épiphysiolyse
de la tête fémorale : garçons [10,15] ans avec douleur mécanique de hanche
\thus radio de profil
\item Psychologique
\end{itemize}
\paragraph{Clinique}
\label{sec:org596c5d4}
Interrogatoire :
\begin{itemize}
\item ATCD familaux,
\item personnels : poids, taille naissance, âge d'appartition, changements environnementaux, tentatives antérieures, troubles des règles
\item comportement alimentaire (difficile)
\end{itemize}
Examen clinique :
\begin{itemize}
\item poids, taille, PA, tour de taille, pli-cutané (masse grasse < 20\% après 5 ans), courbes de
croissance (ralentissement = pathologique !), dermato (acanthosis nigricans =
insulinorésistance, vergétures= hypercorticisme, intertrigo, mycose)
\end{itemize}
Pas d'examens complémentaires !
\paragraph{Traitement}
\label{sec:org19ad848}
Prévention surtout. Modifier style de vie (efficacité faible). Chir possible
avec équipes spécialisées
\subsection{252 \textdagger{} Diabète gestationnel + nutrition et grossesse (à compléter)}
\label{sec:orgd07b208}
\label{orgf0d741f}
Physio chez femme enceinte selon moitié:
\begin{itemize}
\item non diabétique : (\inc insulinéme, insulinosensibilité) puis (insulinorésistance
\thus hyperinsulinisme ou diabète gestationnel)
\item à risque de diabète : (hypoglycémie, cétose) puis (insulinosécrétion
postprandiale insuffisante)
\end{itemize}
\subsubsection{PEC du diabète pré-gestationnel}
\label{sec:orga7730cb}
Grossesse à risque mais fécondité normale (sauf si sd ovaires polykystiques).
\danger{} Normalisation glycémie préconception \(\rightarrow\) accouchement
\begin{itemize}
\item HbA1c \(\le\) 6.5\%
\item glycémie à jeun \(\in\) [0.6, 0.9]g/L
\item glycémie repas + 1h < 1.40g/L et +2h 1.20g/L
\end{itemize}
\paragraph{Risque foetus}
\label{sec:org1bfe4da}
\begin{itemize}
\item Fausses couches spontanées \texttimes{}2, \(\propto\) hémoglobine glycquée
\item Malformation congénitales \texttimes{}2, constituée pendant 8 premières semaines :
cardiaque, neuro, rénale \thus \inc fausses couches spontanées, mortalité
foeatale/néonatale, malfomations
\item 2e trimestre : macrosomie, hypoxie tissulaire, retard maturation pulmonaire,
hypertrophie cardiaque septale
\item 3e trimestre : mort foetale
\item Accouchement : \inc prématurés, césariennes. Danger : trauma foetal,
hypoglycémie sévère, hypocalcémie, hyperbilirubinémie/polyglobulie, détresse
respi transitoire, maladie des membranes hyalines
\item Long terme : surpoids/obésité et diabète 2
\end{itemize}
\paragraph{Risque mère}
\label{sec:org2f22a54}
\begin{itemize}
\item HTA (30\%) : si > 20 SAc, risque de toxémie gradivique. \texttimes{}5 si
diabète 1. Risque vital
\item Rétinopathie : ttt préalable si rétinopathie proliférative. CI : rétinopathie
proliférative floride non traitée
\item Néphropathie :
\begin{itemize}
\item FR = \{HTA, déséquilibre glycémique, rétinopathie évoluée dès
départ, diabète ancien, insuf rénale, hydramnios, correction trop rapide d'une
hyperglycémie chronique\}.
\item Insuf rénale \thus hypotrophie foetale, prééclampsie. Si IR préexistante : 50\%
mortalité foeatale \textbf{in utero}
\item dépistage : créat plasmatique, microalbuminurie, protéinurie
\item IEC contre-indiqués
\end{itemize}
\item Coronaropathie : exceptionnelle mais gravissime. Dépister si diabète ancien et
complications microvasculaire (ECG, effort)
\item Infection urinaire \inc, risque pyélonéphrite, décompensation diabétique
\item Diabète 1 : \inc risque dysfonction thyroïdiennes
\end{itemize}
\paragraph{PEC}
\label{sec:org5669fef}
\begin{itemize}
\item Avant grossesse : glycémie \(\in\) [0.7, 1.20] préprandial, \(\in\) [1, 1.4]
postprandial et HbA1c < 7\%
\begin{itemize}
\item diabète 1 : \inc insuline
\item diabète 2 : insuline si régime ne suffit pas/arrêt ttt oral
\end{itemize}
\item Pendant
\begin{itemize}
\item équilibre glycémique++ (6 glycémies capillaires/jour)
\begin{itemize}
\item \danger variations physiologiques : insuline \dec puis \inc puis \dec\dec
\item cétonémie/cétonurie si glycémie > 2g/L
\end{itemize}
\item \(\ge\) 1600kcal/j 2eme et 3eme tri
\item surveiller poids, PA, créat plasmatique, microalbuminurie, protéinurie, FO,
BU, protéinurie
\item surveillance obstétricale : dater++ (12-14SA), malformations (22-24), placenta et liquide
amniotique (32-34SA), cardiomyopathie hypertrophique (32-34SA), bien-être
foetal
\item pas de bêtamimétique si prématuré
\end{itemize}
\end{itemize}
\paragraph{(Post)partum}
\label{sec:orge08e7b8}
Accouchement programmé souvent, facilité si rétinopathie sévère, insuline
SC/IV et glucosé avec surveillance horaire
Puis : insuline selon besoin pré-grossesse (D1) ou arrêt (D2)
\subsubsection{Diabète gestationnel}
\label{sec:org4030fa7}
Si lié à la grossesse, apparait en 2eme partie. Risque : pré-éclampsie,
césarienne (\(\propto\) hyperglycémie matenrelle). FR : surpoids
Même complications liées à l'hyperinsulinisme que pré-gestationnel
\paragraph{Dépistage}
\label{sec:org504134b}
Si FR seulement :
\begin{itemize}
\item \(\ge\) 35ans
\item IMC \(\ge\) 25kg/m\textsuperscript{2}
\item ATCD : diabète gestationnel, macrosomie, diabète chez parents 1er degré
\end{itemize}
Diagnostic :
\begin{itemize}
\item début de grossesse si glycémie jeun \(\ge\) 0.92g/L \thus PEC immédiate
\item sinon à 24-28SA et (glycémie jeun < 0.92g/L ou non faite) : hyperglycémie
provoquée oralement
\end{itemize}
\paragraph{Traitement}
\label{sec:orgab55548}
\begin{itemize}
\item Diététique (30-35kcal/kg [25 si surpoids]), activité physique, antidiabétique
CI , insuline si régime ne suffit pas après 8 jours
\item Surveillance : glycémie (6/jour puis 4/jour), cétonurie (si glycémie > 2g/L),
HTA
\item Objectif : glycémie jeun < 0.95g/L et postprandiale +2h < 1.20g/L
\end{itemize}
Post-partum : arrêt insuline et surveillance glycémie (diabète antérieur
?). Vérifier glycorégulation à 3 mois. Risque de récidive si grossesse
\subsection{253 \textdagger{} Nutrition chez le sportif}
\label{sec:org644dd65}
\subsubsection{Examen d'aptitude}
\label{sec:org5f2eafd}
Dépister les pathologies induisant un risque vital/fonctionnel grave : mort
subite (1-4/100 000 après 35 ans)
Obligation légale si compétition (licencié ou non)\footnote{Médecin qualifé pour : alpinisme, armes à feu, mécaniques, aériens, sous-marins, de combat
avec HS}
Examen :
\begin{itemize}
\item ATCD sportif, médicaux familiaux (CV, hypercholestérolémie familiale),
conduites à risque, alimentaire, ttt, toxiques
\item Clinique :
\begin{itemize}
\item poids, taille, IMC, (courbe de croissance)
\item maturation pubertaire
\item ostéoarticulaire, cardiorespiratoire, test dynamique sous-maximal
(Ruffier-Dickson)
\end{itemize}
\item Complémentaire : ECG repos\footnote{Pour 1er certificat puis tous les 3 ans puis tous les 5
ans jusque 35 ans}, CV
\end{itemize}
\subsubsection{Bénéfices/inconvénients}
\label{sec:orgd018590}
Adulte :
\begin{itemize}
\item Bénéfices :
\begin{itemize}
\item maintien santé : \dec mortalité prématurée, \inc qualité de vie, \inc
autonomie (âgé), régule poids
\item prévention : cancers (colon, sein), CV, métabolique, ostéoporose \female
\item ttt : anxiété, cardiomyopathie ischémique, BPCO, obésité, diabète 2, neuro,
rhumatismales, dégénératives
\end{itemize}
\item Surveillance : dépistage d'insuf coronarienne > 40 ans, \danger nutrition et
hydratation si > 3h/semaine
\item Recommandation : 150min/semaine (modéré) ou 75min/semaine (soutenu). Idéal : x2
\end{itemize}
Enfant :
\begin{itemize}
\item Bénéfices :
\begin{itemize}
\item dev psychosocial : \dec stress, anxiété, \inc intégration sociale, \inc
confiance en soi
\item dev psychomoteur : concentration, coordination, équilibre
\item \inc masse maigre, \inc densité osseuse
\item prévention : sd métabolique, surpoids, CV
\end{itemize}
\item Surveillance : nutrition (éviter retards de croissance/pubertaire), attitude
alimentaires restrictives
\item Recommandation : 60min/jour (modéré-soutenu) et renforcement musculaire,
osseux 3x/semaine
\end{itemize}
\subsubsection{Besoins nutritionnels}
\label{sec:orgd9eb3fb}
\begin{center}
\begin{tabular}{llll}
Intensité & durée & Energie & Limitation\\
\hline
Très intense & secondes & ATP, P-Cr & \\
Intense & minutes & Glycogène musculaire & Lactate\\
Faible-élevée & prolongée & glycogène musculaire/lipides & VO\textsubscript{2} max\\
\end{tabular}
\end{center}
Macronutriments :
\begin{itemize}
\item Glucides : détermine l'épuisement si endurance \thus index glycémique faible à
distance, IG élevé juste avant. Pendant : maintenir glycémie. Après :
reconstituer les stocks de glycogène
\item Lipides à limiter si intensité élevé/compétition
\item Protides : endurance 1.2-1.4g/kg/j, force : 1.3-1.5g/kg/j si maintien masse, sinon jusque 2.5g-kg/j
\end{itemize}
Hydrosodé : avant = 500ml en 2h (prévention). Pendant : NaCl si \(\ge\) 1h selon
intensité (jusque 1.5L/h). Après : 150\% perte pondérale.
Minéraux, vitamines:
\begin{itemize}
\item attention situation à risque : déficit en fer, contrainte de poids,
alimentation glucidiques mais faible densité nutritionnelle, exclusion de
groupes d'aliments
\item endurance : vit B énergétiques\footnote{Thiamine, riboflavine, niacine, B6} , vit. "antioxydantes"\footnote{Vit C, E, \(\beta\)\{xcarotène}
\item force : \inc vit B6, \inc "antioxydantes"
\end{itemize}
\paragraph{Enfant}
\label{sec:org5753d0a}
Apport insuffisants \thus retard croissance staturo-pondéral ou pubertaire,
\dec masse musculaire, déminéralisation osseuse, déficit immunitaire.
Surveiller calcium, vit D, fer.
\subsection{265 \textdagger{} Hypocalcémie, dyskaliémie, hyponatrémie}
\label{sec:org47ebbaf}
\subsubsection{Hypocalcémie (hypoCa)}
\label{sec:orgbfe1d21}
Éliminer fausses hypoCa dues à l'hypoalbuminémie\footnote{Une partie du calcium est lié à l'albumine}.
Calcémie = équilibre absorption intenstinale, résorption osseuse, excrétion
rénale. Régulé par PTH, calcitriol
Clinique :
\begin{itemize}
\item hyperexcitabilité neuromusc : paresthésie main, pieds, péribuccales
(spontanées/effort), signe de Trousseau ("main d'accoucheur"), signe de
Chvosteck (peu spécifique), crises de tétanie (paresthésie, fasciculation
pouvant entraîner arrêt respi)
\item chronique : sd de Fahr\footnote{Cataracte sous-capsulaire, calcification des noyaux gris centraux} \thus signes extrapyramidaux, crises comitiales
\item \inc QTc \thus troubles du rythmes
\item dans l'enfance : musc, neuro, cardiaques
\end{itemize}
\paragraph{Principales causes}
\label{sec:orgf110e8d}
\begin{itemize}
\item Hypoparathyroïdes : anamnèse et \{hypoCa, PTH \dec, phosphatémie
normale/haute\}.
\begin{itemize}
\item post-chir++ : parathyroïdectomie totale
\item congénitale : sd Di George++\footnote{Hypoplasie des parathyroïdes et du thymus, dysmorphie faciale, anomalies cardiaques}
\end{itemize}
\item Pseudoparathyroïdies : génétiques : résistance à la PTH \thus PTH
\inc. Chondrodysplasie possible
\item Anomalie vitamine D
\begin{itemize}
\item carence vit D = 1ere cause hypoCa chez nourrisson \thus rachitisme
carentiel. Chez l'adulte, seulement si déficit prolongé et profond
\item malabsorption digestive, insuf rénale chronique, cirrhose
\end{itemize}
\end{itemize}
\paragraph{TTt}
\label{sec:org54d9526}
\begin{itemize}
\item Aigüe = urgence \thus calcium IV lente (2-3x10ml). Suspension des ttt qui \inc
QTc, réduction digoxine
\item Chronique : vit D (ou dérivés actifs) et calcium per os
\end{itemize}
\subsubsection{Hyper-/hypo-kaliémie,}
\label{sec:orga27c026}
Retentissement cardiaque \thus vital
\paragraph{HyperK}
\label{sec:orga7c663c}
Principales causes
\begin{itemize}
\item Acidose (sort K+ de la cellule) et insulinopénie (réduit entrée K+) : ttt par
insuline à risque d'hypoK \danger \thus apport K+ dès normokaliémie
\item Hypoaldostéronisme
\begin{itemize}
\item insuf surrénale périphérique
\item secondaire : chez > 65 ans, diabétiques. Risque = aggravation si IEC ou ARA II
\end{itemize}
\item Pseudo-hypoaldostéronisme : résistance à l'aldostérone (génétique)
\end{itemize}
\paragraph{HypoK}
\label{sec:orgf25196e}
\begin{itemize}
\item Dénutrition sévère : anorexique, post-chir bariatrique sans suivi
\item Insulinothérapie : si cétoacidose et troubles digestifs majeurs \thus
insulinothérapie seulement après normokaliémie, sinon arrêt cardiocirculatoire
\item \inc activité \(\beta\)adrénergique
\item Paralysie périodique famililiale : exceptionnelle, paralysie brutale
transitoire des 4 membres
\item Hyperaldostéronisme ou hypercorticisme : y penser si HTA (non constante) et hypoK avec
kaliurèse \inc
\item Polyurie : hyperglycémie \inc
\item Hypomagnésémie : si Mg \dec, malabsorption, pertes digestives causées par
IPP. Sinon : pertes urinaires acquises/génétique
\item Bloc 11-\(\beta\)hydroxystéroïde déshydrogénase : tableau similaire à
hyperaldostéronisme primaire mais avec aldostérone \dec. Si HTA et hypoK,
vérifier réglisse et pastis (glycyrrhizine)
\end{itemize}
\subsubsection{Hyponatrémie endocrinienne}
\label{sec:orgd3b9c58}
HypoNa = anomalie électrolytique la plus commune chez hospitalisés
Osmolarité (mosm/L) : 2\texttimes{}([Na+] + [K+]) + glycémie + urée
\begin{figure}[htpb]
\centering
\resizebox{0.9\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
level distance=1.5cm,
edges={nodes={fill=white}},
layered layout]
{
Osmolalité -> {
Augmentée -> "Hyperglycémie";
Normale -> "HyperTG\\Hyperprotidémie";
Diminuée -> Volémie -> {
"Augmentée\\(hyperhydrat. extracell)" -> "Insuf cardiaque\\Cirrhose\\Sd néphrotique"
-> "Sérum salé\\isotonique";
"Normal\\(hyperhydrat intracell)" -> "Hypothyroïdie\\Insuf corticotrope\\SIADH"
-> "Sérum salé\\hypertonique";
"Diminué\\(déshydrat extracell)" -> "Perte digestives\\rénales, cérébrales\\Insuf corticosurrénales aigüe"
-> "Restriction hydrosodée";
};
};
};
}
\caption{Démarche diagnostique et ttt devant une hyponatrémie}
\end{figure}
Physiopatho : hormone anti-diurétique (ADH) : répond au stimulus osmotique,
volémique et stress etc. Action vasoconstrictive, corticotrope (stress),
antidiurétique
\paragraph{SIADH}
\label{sec:orgfdae7c5}
PA et FC normale, pas de pli cutané, (déshydratation extra-cellulaire) ni
d'oedème (hyperhydratation extra-cellulaire)
DD : cf figure. Si hyponatrémie hypoosmolaire normovolémique :
\begin{itemize}
\item insuf corticotrope : cortisolémie et ACTH
\item insuf surrénale aigüe
\item hyporthyroïdie proto-thyroïdienne : TSH \inc
\item hypopituitarisme antérieure : cortisolémie, TSH, T4L
\end{itemize}
Étioliogies :
\begin{itemize}
\item iatrogènes : neuroleptiques, antidépresseurs, chimio, carbamazépine,
desmopressine
\item quasi toutes affections neuro, notament intervention trans-sphénoïdale
(adénome corticotrope)
\item pulmonaires
\item tumeurs malignes : cancer bronchique à petites cellules++
\item rares : mutation récepteur V2 ADH, marathonien, VIH
\item Intoxication aigüe à l'eau
\end{itemize}
\paragraph{Traitement}
\label{sec:orgb23461c}
Urgence si < 115mmol/L ou \{délire, coma, convulsion\} \thus sérum salé
hypertonique jusque Natrémie = 120mmol/L (puis restriction hydrique).
\danger{} < 12mmol/24h sinon tableau d'AVC (myélinolysie centropontine) !!
Thérapeutique :
\begin{itemize}
\item restriction hydrique : mal tolérée
\item déméclocycline : induit diabète inspidie néphrogénique
\item aquarétique (tolvaptan)
\end{itemize}
Indications :
\begin{itemize}
\item symptômes cliniques sévères/récent : sérum salé hypertonique
\item symptômes plus modérés : sérum et tolvaptan
\item sinon restriction hydrique et tolvaptan (ou déméclocycline)
\end{itemize}
\subsection{266 \textdagger{} Hypercalcémie}
\label{sec:org140c532}
Diagnostic = double dosage calcémie. Étiologie selon parathormone (PTH)
Physio : calcémie régulée par PTH et calcitriol
\begin{itemize}
\item PTH: \inc absorption intestinale du calcium et phosphore, \inc résorption
osseuse, \dec réabsorption phoshpore et \inc absorption calcium (rein)
\item PTH régulée par récepteur sensible au calcium (CaSR)
\end{itemize}
Bio : calcémie totale = \{calcium ionisé, calcium lié = \{lié à l'albumine,
complexé aux anions\}\}. Calcium ionisé \(\approx\) 50\% calcium total\footnote{Sauf si acidose, hyperprotidémie, \inc phosphore/sulfate sériques}
Clinique : asthénie, \{polyuro-polydipsie, lithiases rénales\}, \{anorexie,
constipation, nausées\}, \{apathie, somnolence, confusion, psychose, coma\}, \{HTA,
\dec QT\}
\danger hyperglycémie maligne = urgence \{\} avec déshydratation, \{confusion,
coma, insuf rénale\} et risques de troubles du rythme cardiaque, bradycardie avec asystolie
\subsubsection{Étiologies}
\label{sec:orgea34c39}
\paragraph{Hypercalcémie PTH dépendante (PTH N ou \inc)}
\label{sec:org40cf09f}
\begin{itemize}
\item \textbf{Hyperparathyroïdie\footnote{La PTH est produite par la parathyroïde\ldots{}} primaire} (55\%) : lésion parathyroïde.
\begin{itemize}
\item Signes cliniques précédents avec rénaux, osseux (clinique et radio\footnote{Ostéite fibrokystique de von Recklinhausen, exceptionnelle.}) \thus créatinine
plasmatique, scénal rénal non injecté
\item Surtout densité osseuse (tier distal du radius)
\item Bio : hypercalcémie et PTH non adaptée (N ou \inc).
\begin{itemize}
\item \danger corriger déficit vitamine D avant doser calcémie.
\item \danger DD : sd hypercalcémie-hypocalciurie familiale,
hyperparathormonémie avec ttt au lithium
\item calcémie et phosphorémie n'ont de sens qu'avec une fonction rénale normale
\item calciurie : si augmentée, enlève les DD précédents
\end{itemize}
\item imagerie : bio primaire mais sert si indication opératoire seulement (écho, scinti)
\item étiologie :
\begin{itemize}
\item majorité : sporadique, isolé
\item NEM1\footnote{Néoplasie endocirinienne multiple de type 1} (1\%) : hyperparathyroïdie primaire = 95\%. Recherche tumeurs
endocrines pancréas et duodenum, adénomes hypophysaires
\item NEM2 : cancer médullaire de thyroïde puis phéochromocytome bilat et
hyperparathyroïdie primaire avec atteinte multiglandulaire
\item \danger hyperparathyroïdie primaire chez jeune = suspicion transimission
génétiques
\item hyperparathyroïdie \emph{secondaire} : adaptation à hypocalcémie (chercher chez
insuf rénaux chronqiue)
\item hyperparathyroïdie \emph{tertaire} : insuf rénaux chronique
\end{itemize}
\end{itemize}
\item \textbf{hypercalcémie-hypocalciurie familiale bénigne} : hypercalcémie,
hypophosphorémie, (hypermagnésémie), calciurie \dec\dec{}, PTH inadaptées
(N ou \inc)
\item Lithium
\end{itemize}
\paragraph{hypercalcémie PTH-indépendante}
\label{sec:org86ed114}
\begin{itemize}
\item \textbf{Hypercalcémie des affections malignes} (30\%) : PTH \dec\dec{}.
\begin{itemize}
\item Tumeurs : poumon, sein, rein, tractus digestif
\item Production tumorale de PTHrp (mime PTH)
\end{itemize}
\item Autres :
\begin{itemize}
\item granulomatose : hyperphosphorémie, PTH \dec
\item iatrogènes : vitamine D (hypercalcémie, hyperphosphorémie, PTH passe),
vitamine A (asthénie sévère, douleurs musc et osseuse, alopécie des
sourcils, chéilite fissuraire), diurétiques thiazidique, buveurs de laits
(plutôt fortes doses d'antiacide ou carbonate de calcium)
\end{itemize}
\end{itemize}
\subsubsection{Traitement}
\label{sec:org287d216}
Hyperparathyroïdie primitive : guérison par ablation des adénome(s) par chir
conventionnelle ou mini-invasive (faire imagerie avant !)
Sinon, traitement palliatif : bisphosphonates (inhibe résorption osseuse),
calcimimétiques (\dec PTH),
\danger Hypercalcémie maligne = urgence \{\} :
\begin{itemize}
\item sérum phy
\item bisphosphonate en perf lente ou corticothérapide IV (myélome/hémopathie) ou dialyse (maligne)
\end{itemize}
\subsection{303 \textdagger{} Tumeurs de l'ovaire (hormono-sécrétante)}
\label{sec:org28b5773}
\subsubsection{Sécrétant des oestrogènes}
\label{sec:orgb7fb0bb}
Tumeurs de la granulosa :
\begin{itemize}
\item malignes, les plus fréquentes des tumeurs des cordons sexuels et du stroma.
\item plutôt femmes [30,50] ans
\item jeune fille : pseudo-puberté précoce. Femme :
aménorrhées/ménométrorragie. Ménopausée : saignement vaginal dû à hyperplasie
endométriale\footnote{Tumeurs souvent > 10cm, kystique, multiloculaire, unlatérale}
\item ttt : ovariectomie unilatérale mais récidives 10-33\%
\end{itemize}
Thécomes :
\begin{itemize}
\item très rare, surtout péri-/post-ménopause
\item Tumeurs solides, bénignes \thus exérèse = guérison
\end{itemize}
Sd Peutz-Jeghers (très très rare)
\subsubsection{Sécrétant des androgènes}
\label{sec:org4832623}
Tumeurs à cellules de Sertoli-Leydig
\begin{itemize}
\item sécrète testostérone
\item rare. Y penser si hirsutisme récent avec signes de virilisation
\item DD : corticosurrénalome (faire scanner surrénales), sd Cushing (faire freinage
minute), block 21-hydroxylase (doser 17-hydroxyprogestérone)
\item femme 30-40ans
\item détecté à l'écho ovarienne vaginale ou IRM pelvienne
\item si < 5 cm, bon pronostic \thus ttt conservateur chez femme jeune
\end{itemize}
Tumeurs à cellules de Leydig
\begin{itemize}
\item cristaux de Reinke (caractéristique)
\item typiquement : virilisantes chez ménopausée
\item petite taille, bénigne \thus ovariectomie bilatérale
\end{itemize}
Tumeurs germinales sécrétantes
\begin{itemize}
\item tumeur ovarienne sécrétant de l'hCG : chez femme jeune, aménorrhée, douleurs
abdo/métrorragie. Tttt : conservateur si jeune, chimio si étendu
\item gonadoblastome : chez sd de Turner avec mosaïque et chromosome Y (risque
7-20\%) \thus gonadectomie préventive
\item autres : sécrétant hCG, T4, sérotonine
\end{itemize}
\subsection{305 \textdagger{} Tumeurs du pancréas (endocrine)}
\label{sec:orge95d03f}
Rare, concerne pancréas et duodénome. Diagnostic histologique, compléteté par
immunohistochimie
Pronostic péjoratif : > 2 cm, invasion vasculaire, dissémination métastase
\begin{table}[htbp]
\caption{Caractéristiques des tumeurs endocrines duodéno-pancréatiques}
\centering
\begin{tabular}{ll}
Sécrétion & Clinique\\
\hline
Insuline & Hypoglycémie organiques\\
Gastrine & Ulcère oestro-gastro-duodénaux, diarrhées\\
ACTH & Cushing\\
Glucagon & Diabète, érythème migrateur, diarrhée, amaigrissement, thromboses\\
VIP & Diarrhée hydroélectrolytique profuse, hypokaliémie\\
GHRH & Acromégalie\\
\end{tabular}
\end{table}
Imagerie : scanner spiralé TAP \textpm{} IRM abdo
Formes familiales : NEM1, neurofibromatose 1, von Hippel-Lindau
\subsection{310 \textdagger{} Tumeurs du testicule (aspects endocriniens)}
\label{sec:orga6c5484}
Prévalence : 9/100 000, ado/adulte jeune
\subsubsection{Tumeurs stromales}
\label{sec:org19f5d80}
Cellules de Leydig. Unilatérales, bénignes
\begin{itemize}
\item Garçon < 9 ans : pseudo-puberté précoce \thus testostérone plasmatique, écho
testiculaire
\item Adulte : féminisation, infertilité \thus oestradiol \inc, testostérone N ou \dec
\end{itemize}
Cellules de Sertoli : rares (enfant) ou exceptionnelles
(adulte). Féminisation/pseudo-puberté précoce à 50\%. Testostérone/oestradial
\inc, LH et FSH \dec, inhibine B \inc.\footnote{Peut appartenir à : complexe Carney, sd Petuz-Jeghers}
\subsubsection{Autres}
\label{sec:org41b2e35}
\begin{itemize}
\item Tumeurs germinales : fréquentes, écho testiculaire
\begin{itemize}
\item séminomateuses : fréquentes, pronostic bon
\item non séminomateuses : pronostic réservé
\end{itemize}
\item Inclusion surrénaliennes : par excès ACTSH. Marqueur : 17-hydroxyprogestérone
\end{itemize}
\subsubsection{PEC}
\label{sec:org2d75297}
Glucocorticoïdes si inclusion surrénaliennes. Sinon chir 1ere intention. Chimio si métastases pulmonaires/ganglionnaires.
\subsection{Annexes}
\label{sec:org86b575d}
\subsubsection{Hormones}
\label{sec:orgeb64c0a}
\begin{figure}[htpb]
\centering
\resizebox{!}{5cm}{
\tikz \graph [decision]
{
ht/hypothalamus[organ] -> ["CRH"] hh/hypophyse[organ] -> ["ACTH"] cs/corticosurrénale[organ];
cs -> cort/cortisol;
cort ->[bend left=60, "-"] ht;
cs -- ["+"] hh;
hh --["+"] ht;
};
}
\resizebox{!}{5cm}{
\tikz \graph [decision, layer distance=1.5cm]
{
ht/hypothalamus[organ] -> ["GnRH"] hh/hypophyse[organ] -> "FSH, LH" -> {
testicules[organ] -> test/testosterone;
ovaires[organ] -> est/estrogène;
};
test -> [bend left=70, "-"] ht;
test -> [bend left=60, "-"] hh;
est -> [bend right=70, "-"] ht;
};
}
\resizebox{!}{5cm}{
\tikz \graph [decision, layer distance=1.5cm]
{
ht/hypothalamus[organ] -> ["TRH"] hh/antéhypophyse[organ]
->["TSH"] th/thyroide[organ] -> ["T4"] "foie,muscles" -> "T3";
th -> [bend left=60, "-"] hh;
th -> [bend left=70, "-"] ht;
};
}
\resizebox{!}{5cm}{
\tikz \graph [decision, layer distance=1.5cm]
{
ht/hypothalamus[organ] -> ["GHRH"] hh/hypophyse[organ] -> ["GH"] Foie[organ] -> "IGF-1" -> {
os;
muscle;
graisse..;
}
};
}
\end{figure}
\begin{table}[htbp]
\caption{Hormones produite par les surrénales (du moins au plus profond)}
\centering
\begin{tabular}{ll}
Zone de la surrénale & Hormones\\
\hline
corticale (glomerusa) & minéralocorticoïdes (aldostérone)\\
corticale (fasciculata) & glucocorticoïdes (cortisol)\\
corticale (reticularis) & androgènes\\
médullaire & épinephrine, norepinéphrine\\
\end{tabular}
\end{table}
\subsubsection{Syndromes génétiques}
\label{sec:orgd12d40e}
\begin{center}
\begin{tabular}{llll}
& Klinefelter & Turner & Kallmann\\
\hline
Sexe & \male & \female & \male{}, \female\\
Frequence & 1/500 & 1/2000 \female & 1/30 000 \male{}, 1/250 000 \female{}\\
Caryotype & 46 XX,Y & genes manquants & \\
& & sur bras court d'un chr. X & \\
Caractéristiques & Hypogonadisme, infertilité & Petite taille & Anosmie\\
& gynécomastie & Aménorrhée & \male : Micropénis, cryptorchidie\\
& trouble apprentissage, comm. & Pas de seins ? & Pas de dev. sexuel secondaire\\
& & & \\
\end{tabular}
\end{center}
\section{Pneumologie}
\label{sec:org62f7388}
\subsection{73 Addiction au tabac}
\label{sec:org57839e1}
Tabagisme : primaire (inspiré), secondaire (passif++), tertiaire (exhalé)
Produits : nicotine (dépendance), fumée de tabac (0.3 \(\mu\)m), goudrons
(cancérigène), CO (hypoxie, risque ischémie)
16 millions de fumeurs en 2013 (France). Éducation et cat. sociale faible = plus
tabagiques
\subparagraph{Pathologies liées au tabac}
\label{sec:org80f10aa}
\begin{itemize}
\item K : \emph{broncho-pulmonaires} (90\% dû à actif, 25\% au passif). Voies aérodigestives sup, vessie, pancréas, rein, col de l'utérus
\item Respiratoires : BPCO, asthme
\item CV: cardiopathies ischémiques, artérite, HTA, cérébro-vasculaires, athérome,
\end{itemize}
maladie coronaire
\begin{itemize}
\item Autres : digestives, kératites, retard consolidation os, agueusie, anosmie
\end{itemize}
Passif :
\begin{itemize}
\item +25\% risque cancer bronchique, +25\% maladies CV, aggrave asthme, BPCO
\item nourrisson : RCIU\footnote{Retard croissance intra-utérin}, \(\nearrow\) risque
infections respi, mort-subite (1ere cause identifiée)
\end{itemize}
\subparagraph{Prise en charge}
\label{sec:org432b82d}
Évaluer : consommation (paquets/années), dépendance, autres (alcool = déclencheur,
cannabis), motivation, comorbidités (psy, CV, respi)
\subparagraph{Traitement}
\label{sec:org9184a24}
Conseil, motivationnel.
Substitut nicotinique, varénicline [\danger suivi], bupropion), TCC, cigarette électronique
Sevrage : réussi si \(\ge 1\) an
\subsection{108 - Troubles du sommeil}
\label{sec:orgca9fc5d}
\subparagraph{Définitions}
\label{sec:org7a10c07}
SAOS =
\begin{itemize}
\item somnolence diurne non expliquée
\item \emph{ou} 2 parmi \{ronflements, étouffement, éveils répétés, sommeil non réparateur, fatigue diurne, trble concentration, nycturie)\}
\item \emph{et} IAH\footnote{Index d'Apnées et Hypopnées (nb par heure)} \(\ge\) 5 \footnote{Sévère si IAH \(\ge\) 30.}
\end{itemize}
NB: Apnée obstructive (arrêt débit), centrale (idem, \uline{sans} efforts ventilatoires) ou mixte
\subparagraph{Épidémiologie}
\label{sec:org0d456d7}
2\% des \female, 4\% des \male.
FR : obésité, homme, âge, anomalie voie aériennes supérieures.
Comorbidités : \emph{somnolence diurne excessive}, HTA, AVC, maladie coronaire, sd
métabolique \footnote{Obésité abdo et (2 parmi : HTA, glycémie \(\ge\) 5.6 mmol/L, HDL bas, hypertriglycéridémie)}, diabète, dylipidémie
\subparagraph{Diagnostic}
\label{sec:orgf8c814a}
Suspicion clinique, confirmation par polygraphie
\begin{itemize}
\item clinique : nuit = \{ronflements, pause respi, étouffement, nycturie\}, journée =
somnolence excessive (questionnaire d'Epworth)
\item examen : IMC, obésité abdo (\(\ge\) 94 cm \male, 80cm \female), ORL\footnote{Rétrognathisme, macroglossie, hypertrophie du palais mou ou des
amygdales, obstruction nasale}, CV, respi
\item polygraphie \footnote{Flux naso-buccal, mouvement thoraco-abdominaux, capteur de son, SpO\textsubscript{2}, ECG} ou polysomnographie\footnote{Enregistre en plus EEG, électro-oculogramme, EMG muscles houppe du menton} (cher++)
\item faire aussi EFR (dépistage BPCO) et gaz du sang (complications BPCO + SAOS)
\end{itemize}
DD : hypersomnie diurne (insomnie, sd dépressif, sédatif, hygiène de sommeil, neuro)
\subparagraph{Traitement}
\label{sec:org83b7850}
\begin{itemize}
\item Général : PEC\footnote{prise en charge} surpoids, éviction \{benzodiazépines, myorelaxants, morphiniques\}, PEC CV
\item \emph{Pression positive continue}\footnote{Remboursement si IAH > 30/h (ou IAH > 10/h sur polysomnographie)}. Sinon : orthèse d'avancée mandibulaire, voire chir
\end{itemize}
\subparagraph{Autres}
\label{sec:org87ad9b3}
\begin{itemize}
\item Sd d'apnée de type central : IC sévère, atteinte tronc cérébral, séjour altitude, morphiniques
\item Hypoventilation alvéolaire : Traitement = VNI
\item Sd obésité hypoventilation\footnote{(PaCO\textsubscript{2} > 45 mmHg) et PaO\textsubscript{2} < 70 mmFg) et (IMC > 30 kg/m\textsuperscript{2} sans d'autre cause.} : Traitement = VNI
\end{itemize}
\subsection{151 \textdagger{} - Infections broncho-pulmonaires communautaires}
\label{sec:orge1d98f3}
\subsubsection{Bronchite aigue}
\label{sec:orga8ebb9d}
Très fréquente, virale 90\%.
Diagnostic clinique : épidémie, toux sèche \(\to\) productive, expectorations,
\uline{pas} de crépitants.\\
Ttt symptomatique seulement ! (pas d'ATB, ni corticoïdes\ldots{})
\subsubsection{EBPCO (cf chap BPCO)}
\label{sec:orgbf680d8}
\subsubsection{Pneumonie aigue communautaire}
\label{sec:org7ad1eb0}
\subparagraph{Diagnostic}
\label{sec:orgc48490c}
Radio
\begin{itemize}
\item Clinique : \{toux, expect purulentes, dyspnée\} + \{fièvre, asthénie\} + crépitants
\end{itemize}
\subparagraph{PEC}
\label{sec:org8a0a7c8}
Si \faHospital : hémocultures, ECBC, antigenurie pneumocoque (\textpm{} PCR,
antigenurie légionelle)\\
\faHospital : signes de gravité (score CRB65\footnote{Confusion, fréquence Respiratoire \(\ge\) 30min, (Blood) PAs < 90mmHg ou PAd \(\ge\) 60mmg, Age \(\ge\) 65 ans} ge ) / incertitude / échec domicile / comorbidité / inobservance
\subparagraph{Étiologies (Tab \ref{tab:org0bf695a}}
\label{sec:orgce5d6bd}
\begin{table}[htbp]
\caption{\label{tab:org0bf695a}Orientation clinique (non discriminant !)}
\centering
\begin{tabular}{llll}
& Pneumocoque & Atypique & Légionellose\\
\hline
Début & Brutal & Progressif & Rapidement progressif\\
Signes & Thoraciques & Extra-thoraciques & Myalgie, digestif\\
Biologie & & Anémie hémolytique & Hyponatrémie, rhabdomyolyse\\
Microbio & CG+ chainettes/Ag pneumocoque + & & Ag légionelle +\\
RX thorax & condensation systématisée & Opacités multifocales & CS ou OM\\
\end{tabular}
\end{table}
\begin{itemize}
\item Pneumocoque : fréquent+++. Pas de transmission interhumaine
\item Atypique : \bact{mpneumoniae}, \bact{cpneumoniae}, \bact{psitacci}
\item Legionnella : pas d'isolement. DO
\item Pneumonie virale : signes respi + sd grippal. Grippale = diagnostic PCR, traitement = inihbiteur neuramidase \danger \bact{dore}
\end{itemize}
\subparagraph{Traitement}
\label{sec:org67e5a1e}
Urgent, probabiliste. Oral, 7j\footnote{(8-14 si légionellose, 21j si légionelles graves/ID)} Réévalué 48-72h
\begin{itemize}
\item Ambulatoire : \emph{Amoxicilline} ou \emph{macrolide} \(\to\) switch
\item \faHospital \emph{Amoxicilline} \(\to\) réévaluation
\item Réa : \emph{C3G IV + macrolide IV} / \emph{FQ} pour pneumocoque
\end{itemize}
Échecs :
\begin{itemize}
\item épanchement pleural, abcès, obstacle
\item observance, pharmacocinétique, hors spectre
\item diagnostic (EP, PID aigǜes, K, tuberculose pulmonaires, infarctus pulmonaire, vascularite\ldots{})
\end{itemize}
\subparagraph{Prévention}
\label{sec:org135ea13}
Vaccin : 2 doses + rappel enfant, 2 doses adulte (ID, comorbidité)
\subparagraph{Immunodéprimé}
\label{sec:orgdc0a268}
Pneumocystose pulmonaire :
\begin{itemize}
\item RX : sd interstitiel diffus bilatéral symétrique.
\item ATB cotrimoxazole 21j
\end{itemize}
\subsection{180 \textdagger{} - Accidents du travail}
\label{sec:org935883d}
Maladie professionnelle = lente, prolongée (\(\neq\) accident du travail)
\subsubsection{Maladies}
\label{sec:org0943699}
\paragraph{Asthmes}
\label{sec:orgf0c9158}
10-15\% des asthmes. On a
\begin{itemize}
\item asthme professionnel : (avec latence [immunologique]) ou (sans latence
[exposition unique])
\item asthme aggravé par le travail
\end{itemize}
Métiers : boulangers, santé, coiffeurs, peintres pistolets, bois, nettoyage\\
Diagnostic : de novo, profession, rythme
\paragraph{BPCO}
\label{sec:org09b2658}
\gls{TVO} lente progressive + inflammation
poumons. Facteurs professionnels = 10-20\% BPCO\\
Métiers : mines, BTP, fonderie, textile, agricole
\paragraph{Cancers}
\label{sec:org09be2a2}
\begin{itemize}
\item mésothéliome : 2/100 000habi/an, amiante++, DO
\item K bronchique primitif
\end{itemize}
\paragraph{Pneumopathie interstitielle diffuse (PID)}
\label{sec:org10543b4}
\begin{itemize}
\item Pneumopathie d'hypersensibilité : agricole
\item Silicose (+cancer bronchique primitif)
\item Bérylliose : adénopathies médiastinales, sd infiltrant parenchymateux
\item Sidérose : fumées d'oxyde de fer, micronodule \textpm{} emphysème
\item Asbestose : fibrose
\end{itemize}
\paragraph{Liées à l'amiante}
\label{sec:org11547d3}
\begin{itemize}
\item Cancer : mésothéliome, cancer bronchique primitif
\item Pleural (plaques, épaississements, pleurésies), parenchyme (fibrose)
\end{itemize}
\subsubsection{Reconnaissance}
\label{sec:org7efcee4}
3 conditions : médicale, administrative, professionnelle.
Déclaration à la CPAM (employeur si AT, sinon victime)
Indemnité\footnote{Pour l'amiante : caisse d'assurance malaide ou FIVA}
\begin{itemize}
\item 60\% salaire si < 28 jours, 80\% sinon
\item si séquelles, selon taux incapacité permanente : capital (< 10\%), rente
(> 10\%), rentre et autres (> 40\%)
\end{itemize}
\subsection{182 \textdagger{} - Hypersensibilités et allergies respiratoires}
\label{sec:org47f0cfe}
\label{sec:182_hypersensibilites_et_allergies_respiratoires}
\begin{figure}[htpb]
\centering
\resizebox{0.5\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
HS non allergique;
HS allergique -> {
Non IgE;
IgE -> {
atopique -> "insectes\\helminthes\\médicaments";
non atopique -> "rhinite\\asthme\\alimentaire\\professionelles";
};
};
};
}
\caption{Hypersensibilité}
\end{figure}
\subsubsection{Définitions}
\label{sec:orgb9ab656}
Atopie : prédisposition héréditaires à IgE face à des allergènes.\\
Allergie : réaction d'HS par mécanismes immunologiques\\
Sensibilisation : test cutané positif à un allergène\\
Allergène : capable d'induire une réaction d'HS = pneumallergènes (aéroportés),
trophallergènes (alimentaires), professionnels, recombinants
Hypersensibilité :
\begin{itemize}
\item type 1 (immédiate) : la plus fréquente, IgE. Rhinite, asthme
\item type 2 : complément et phagocytose. Réactions médicament.
\item type 3 : complexes immuns. Pneumonies d'HS
\item type 4 : LT, cytotoxiques 48-72h. Granulome épithélioïde gigantocellulaire.
Dermato.
\end{itemize}
\paragraph{Asthme et rhinite allergique}
\label{sec:org063bd56}
Polygénique.\\
Environnement : infections virales, sensibilitations pneumallergènes, tabac dès
conception, pollution air intérieur.
\paragraph{Anomalies voies aériennes (asthme)}
\label{sec:org79418bb}
Remodelage bronchique : épaississement (membrane basale et muscle lisse \(\wedge\) oedème
bronchique) et obstruction \(\diameter\) (mucus)
\paragraph{Réaction IgE}
\label{sec:org2b3f938}
\begin{itemize}
\item Sensibilisation : synthèse IgE spécifiques (lymphocytes B)
\item effectrice : fixation de l'allergène \thus activation (histamine,
cytokines) \thus cascade allergique
\end{itemize}
\subsubsection{Épidémiologie}
\label{sec:org2101787}
Atopie = 30-40\% population. HS médicament = 7\% pop. Allergie alimentaire : 2\%
des 9-11 ans
FR :
\begin{itemize}
\item génétique (enfants à risque)
\item environnement : fréq \(\nearrow\) temps, alimentaires, tabagisme passif
maternel, allergènes, pollution atmosphérique \danger niveau de preuve
\end{itemize}
Morbidité forte, mortalité encore forte pour l'asthme.
\subsubsection{Diagnostic}
\label{sec:orge27bed1}
Clinique : asthme, rhinite, conjonctivite
\paragraph{Diagnostic}
\label{sec:orged7db49}
Unité de temps, lieu et action (perannuels [acariens,
blattes, phanères d'animaux, végétaux d'intérieur, moisissures] ou saisonniers
[pollens]) \(\wedge\) IgE spécifiques
Prick-test = référence.
\begin{itemize}
\item \$\diameter \(\ge\) 3\$mm / témoin
\item acariens, pollens, phanères d'animaux, blatte, moisissures chez l'adulte
\item arachide, blanc d'oeuf, poisson, lait de vache si < 3 ans
\item CI : antihistaminiques, \$\(\beta\)\$-bloquants, eczéma, grossesse si
allergie médic
\end{itemize}
Autres tests : dosage IgE spécifique (moins sensible), multiallergénique (sensible mais
pas quantitatif)
\paragraph{Professionnelles}
\label{sec:org7fa3181}
Boulangers, santé, coiffeurs, peintres pistolets, bois, nettoyage
\paragraph{Autres}
\label{sec:orgdfe315b}
\begin{itemize}
\item Test de provocation = certitude mais dangereux
\item Très sécifique : dosage IgE totale, dosage éosinophiles sanguin, dosage tryptage sérique
\end{itemize}
\subsubsection{Traitement}
\label{sec:org432cb97}
\paragraph{Éviction allergènes Toujours.}
\label{sec:org09ef763}
\paragraph{Symptomatiques}
\label{sec:org4491574}
\begin{itemize}
\item antihistaminiques : rhinite, conjonctivite, prurit
\item corticoïdes : systématique si urgence (prednisone, prednisolone), local
si traitement fond
\end{itemize}
\paragraph{Immunthérapie spécifique}
\label{sec:org8d92318}
Faibles doses croissantes d'allergènes :
\begin{itemize}
\item Sous-cutanées/sub-linguale : acariens, pollens, hyménoptères
\item orale : pollen
\end{itemize}
CI : maladies allergiques, dysimmunités, grosses (induction), asthme sévère non
contrôlé, mastocytoses, \$\(\beta\)\$-bloquants
ES :
\begin{itemize}
\item syndromique (asthme, rhinite, urticaire) = alerte
\item générale (hypotensions, bronchospasme, choc anaphylactique) =
interruption
\end{itemize}
\subsection{184 \textdagger{} - Asthme, rhinite}
\label{sec:orgdd8389b}
Asthme 6\%, mortalité 1000 DC/an, en baisse. Morbidité en hausse
Rhinite allergique 24\%.
\subsubsection{Définitions}
\label{sec:orgdb90174}
Asthme :
\begin{itemize}
\item inflammation chronique modifiant les VAS avec symptômes respi et obstruction voies aériennes réversible
\item interaction gènes-environement, déclencheurs : exercice, HS aspirine/AINS,
irritants inhalés
\end{itemize}
TVO :
\begin{itemize}
\item \gls{VEMS}/CVF < 0.7
\item réversible si +200mL et +12\% après BDCA\footnote\{Broncho-dilatateurs à courte durée
d'action\}
\end{itemize}
Hyperréactivité bronchique : -20\%VEMS après métacholine/air sec (VPP = 100\%)
Débit expiratoire de pointe (pour urgence)
\subsubsection{Diagnostic}
\label{sec:org1e9587c}
\paragraph{Asymptomatique}
\label{sec:org9f86903}
Diagnostic :
\begin{itemize}
\item symptômes caractéristiques (20 min, réversible, variable)
\begin{itemize}
\item plusieurs parmi \{gêne respiratoire, dyspnée,
sifflements, oppression thoraciques\}
\item \(\nearrow\) nuit/réveil, variable,réversibles, déclenché par \{rire, exercice
virus, allergènes, irritants\}
\end{itemize}
\item \textbf{et} obstruction bronchique : sibilant, TVO réversible ou apparaît avec métacholine
\end{itemize}
Sévérité évaluée à 6 mois
\paragraph{Exacerbation}
\label{sec:org2d34cd3}
\nearrow{} symptômes > 2 jours, non calmée, sans retour état habituel
Signes de sévérité :
\begin{itemize}
\item mots (au lieu de phrases), assis en avant, agité
\item FR > 30/min
\item muscles respi annexes
\item FC > 120/min, SpO\(_{\text{2}}\) < 90\%
\item DEP < 50\%
\item silence auscultatoire
\item respi paradoxale
\item troubles conscience, bradycardie, collapsus
\end{itemize}
\paragraph{DD}
\label{sec:orgb735564}
Sans TVO : cordes vocales, sd hyperventilation
TVO non réversible : \{BPCO, bronchectasies, mucoviscidose, bronchiolites
constrictives\}, autres (corps étranger, tumeur, insuf. cardiaque)
\paragraph{Bilan}
\label{sec:org7066002}
Facteurs favorisants, radio thorax, EFR (+test métacholine)
\subsubsection{Traitement}
\label{sec:orgcdc18b6}
\paragraph{Long cours}
\label{sec:org2841791}
Ttt de fond : cf Table\textasciitilde{}\ref{tab:ttt_asthme}
\begin{table}
\centering
\begin{tabular}{ccccc}
\toprule
Palier 1 & Palier 2 & Palier 3 & Palier 4 & Palier 5 \\
\midrule
CSI faible & ALT & CSI moyen/fort & triotropium & CSO faible\\
& & ou (CSI faible et ALT) & ou (CSI fort et ALT) &\\
\bottomrule
\end{tabular}
\caption{Ttt de fond de l'asthme (\textbf{BDCA à la demande}).\\
CSI = Corticostéroïdes inhalés. ALT =
anti-leucotriènes. CSO = Corticostéroïdes oraux}
\label{tab:ttt_asthme}
\end{table}
Autre :
\begin{itemize}
\item activité physique (sauf plongée)
\item facteurs favorisants : rhinite, allergie, tabac, \(\beta\)-bloquant
(aspirine/AINS), RGO, comorbidités
\item vaccins grippe (pneumocoque si asthme sévère)
\end{itemize}
Efficace ?
\begin{itemize}
\item symptômes contrôlés (diurnes < 2/sem, pas de réveil nocture, BDCA < 2/sem, pas
limitation d'activité)
\item exacerbations < 2 corticostéroïdes systém./an
\item VEMS/CV > 0.7 et VEMS \(\ge\) 80 \%
\end{itemize}
Si non contrôlé
\begin{itemize}
\item CSI faible + BDLA\footnote{Broncho-dilatateur à longue durée d'action} < CSI
moyen/fort + BDLA < centre spécialisé
\end{itemize}
Suivi : périodique, +3mois si changement ttt, mensuel si grossesse
\paragraph{Urgence cf figure\textasciitilde{}\ref{org1b938d5}}
\label{sec:org0db479d}
\begin{figure}[htpb]
\centering
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Évaluation" -> {
"Exacerbation\\
sans signes de gravite" ->
"\(\beta_2\) mimétique forte doses\\
chambre inhalation\\
\textbf{Corticothérapie orale} 7j" [draw]
-> Réévaluation 1H;
"Exacerbation \\
avec signes de gravite" ->
"\(\beta_2\)-mimétique forte dose" [level distance=2cm] -> {
"O\(_2\)\\
\(\beta_2\) mimétique nébulisés (5mg/20min)\\
$\pm$ ipratropium\\
\textbf{Corticothérapie orale} " [>"\faHospital", draw];
};
Perte de contrôle ->
"\(\beta_2\) mimétique" [draw] -> Réévaluation 1H;
};
};
\caption{Asthme : traitement d'urgence}
\label{org1b938d5}
\end{figure}
Pas d'ATB sauf si suspicion bactérienne. Adrénaline seulement pour choc anaphylactique
\danger pas de BDLA
\subsubsection{Rhinite allergique}
\label{sec:orgead8341}
Diagnostic :
\begin{itemize}
\item PAREO : prurit, anosmie, rhinorrhée, éternuement, obstruction nasale
\item fosses nasales au speculum inflammées
\item allergique (argumenter !!)
\end{itemize}
Sévère si persistant (> 4 semaines/an) et retentissement qualité de vie
TDM
Ttt : laval nasal, allergie, antihistaminique/corticoïdes nasaux, tabac, stress
\subsection{188 \textdagger{}, 189 Pathologies auto-immunes}
\label{sec:org3e8a639}
\label{sec:pathologies_auto_immunes}
Manifestations respi. viennent de (par priorité décroissante) :
\begin{itemize}
\item infectieuse (favorisé par ttt)
\item toxicité médicamenteuse
\item spécicifique
\item indépendant
\end{itemize}
\subsubsection{Complications infectieuses}
\label{sec:org334a16a}
Immunodépression :
\begin{itemize}
\item corticoïdes forte dose > 1 mois
\item méthotrexate
\item cyclophosphamide
\item anti-TNF\(\alpha\) (infliximab)
\end{itemize}
Tuberculose :
\begin{itemize}
\item clinique semblable à l'ID = 50\% extrapulmonaire, 25\% disséminé
\item prévention si TNF-\(\alpha\) : INH 9 mois ou INH-RMP 3 mois
\end{itemize}
Pneumocystose : si corticoïdes forte dose ou méthotrexate ou
cyclophosphamide
\begin{itemize}
\item clinique : début brutal, insuf. respi, mortalité élevée
\item radio thorax : condensation alvéolaire/verre dépoli bilat
\item penser co-infections
\end{itemize}
\subsubsection{Médicaments}
\label{sec:org45eefe5}
Méthotrexate : plus fréquent, pneumopathie d'HS (opacités diffuses), \gls{LBA}
lymphocytaire. Évolution favorable à l'arrêt + corticothérapie
Inhibiteurs TNF-\(\alpha\) : PID/granulomatoses, anaphylactique
\subsubsection{Connectivites}
\label{sec:org3b64835}
Polyarthrite rhumatoide
\begin{itemize}
\item PID\footnote{Pneumopathie interstitielle diffuse} : radio =
réticulations, rayons de miels, bronchectasies. Surveillance seulement
\item pleurésie rhumatoïde : unilatérale, peu abondante, exsudative. Évolution
favorable
\item nodules pulmonaires rhumatoïdes.
\item bronchiolite oblitérante
\end{itemize}
Sclérodermie systémique : CREST (Calcinose, Raynaud, dyskinésie oEsophagienne,
Sclérodactyie, Télangiectasie), Ac anti-nucléraires
\begin{itemize}
\item PID : semblable à PINS\footnote\{Pneumopathie interstitielle non
spécifique\} : opacités en verre dépoli, bronchectasies par traction. Survie
85\% à 5 ans
\item HTA pulmonaire : dyspnée. Echo. cardiaque +
cathéterisme cardiaque
\end{itemize}
Lupus érythémateux disséminé
\begin{itemize}
\item pleurésie lupique : peu abondant, svt bilatéral, svt + péricardite
\item infectieux, sd hémorragie alvéolaire
\end{itemize}
Dermato-, polymyosite
\begin{itemize}
\item PID chronique : 1ere cause DC, opacités verre dépoli, \gls{LBA} lymphocytaire.
Ttt : corticothérapie + IS
\item PID (sub)aigüe
\end{itemize}
Sd de Gougerot-Sjögren
\begin{itemize}
\item bronchite lymphocytaire chronique : toux sèche chronique
\item PID, lymphome pulmonaire primitif
\end{itemize}
\subsubsection{Vascularites}
\label{sec:org9d19f2c}
Granulomatose avec polyangéite : 40-50ans, début ORL+ poumon (+ rein)
\begin{itemize}
\item radio : nodules s'excavant, opacités verre dépoli
\item Ttt urgent = corticothérapie, cyclophosphamide
\end{itemize}
Granumolatose éosinophilique avec polyangéite : hyperéosinophilie, pneumopathie
éosino.
Polyangéite microscopique : sd hémorragique alvéolaire
\subsection{199 \textdagger{} Dyspnée aigüe et chroniques}
\label{sec:orgc31b98b}
\label{sec:199_dyspnee_aigue_et_chronique}
Examens : ECG, RX thorax, gaz du sang, D-dimère, BNP, NFS a minima
\subsubsection{Aigüe}
\label{sec:org88e6d1d}
= quelques heures/jours
Détresses respi aigüe :
\begin{itemize}
\item cyanose
\item sueur
\item FR > 30/min ou < 10/min
\item tirage, muscle respi accessoires
\item respi abdo paradoxale
\end{itemize}
Hémodynamique :
\begin{itemize}
\item FC > 110/min
\item choc (marbrures, oligurie, angoisse, extr. froides)
\item PAS < 80 mmHg
\item insuf. ventriculaire droite (turgescence jug, OMI, signe Harzer)
\end{itemize}
Urgence !!
Voir table\textasciitilde{}\ref{tab:dyspnee_aigue}. Autres :
\begin{itemize}
\item cardiaque : tamponnade\footnote\{orthopnée, tachy, assourdissement bruits,
ascult pulmonaire normale, turgescence jugulaire, pouls paradoxal\}, troubles
\end{itemize}
(supra)-ventriculaire, choc cardiogénique
\begin{itemize}
\item pulmonaire : SDRA, décompensation aigüe, atélectasies, trauma
\end{itemize}
\begin{table}[htbp]
\caption{Étiologies de dyspnée aigüe}
\label{tab:dyspnee_aigue}
\centering
\begin{adjustbox}{max width=\textwidth}
\begin{tabular}{lll}
\toprule
Inspiratoire & Expiratoire & Sinon\\
\midrule
corps étranger (enfant) & asthme (jeune, allergie, sibilants) & EP
(ascul. normale,
douleur
thoracique, phlébite)\\
épiglottite (enfant) & BPCO (tabac, bronchite aigüe, sibilants) & pneumothorax,
épanchement
pleural (sd
pleural,
douleur thoracique)\\
laryngite (enfant) & OAP (âgée, crépitants, expector mousseuse) & pneumopathie
infectieuse
(sd
infectieux,
douleur thoracique)\\
\oe{}dème de Quincke (terrain)& & OAP (âgé, orthopnée, crépitants, expector mousseuse)\\
& & \\
\bottomrule
\end{tabular}
\end{adjustbox}
\end{table}
\subsubsection{Chronique}
\label{sec:orge9e3394}
cf table\textasciitilde{}\ref{tab:dyspnee_chronique}.
Autres :
\begin{itemize}
\item Cardiaque:constriction péricardique
\item Pulmonaire : (restrictif) pneumoconioses, post-tuberculose, paralysie phrénique, cyphoscoliose, obésité morbide
\item HTAP
\item HT pulmonaire post-embolique
\end{itemize}
\begin{table}[htbp]
\caption{Étiologies de dyspnée chroniques}
\label{tab:dyspnee_chronique}
\centering
\begin{adjustbox}{max width=\textwidth}
\begin{tabular}{lll}
\toprule
Sibilants & Crépitants & Auscult normale\\
\midrule
BPCO& PID (toux sèche, maladie systémique) & EP/maladie vasculaire pulmonaire \\
asthme& Insuf cardiaque gauche & Neuromusc \tablefootnote{signe neuro, orthopnée, respi abbdo paradoxale} \\
Insuf cardiaque gauche (ATCD cardiaque, orthopnée, toux) & & Parétiale
(obésité, scoliose)\\
&& Hyperventilation\tablefootnote{C normal, vertige, $\ne$ effort, paresthésie}\\
\bottomrule
\end{tabular}
\end{adjustbox}
\end{table}
Quantification : échelle Borg [0-10] (aigüe) ou MRC [0-4] (chronique)
\subsection{200 \textdagger{} Toux chronique}
\label{sec:orgd3cee69}
\label{sec:200_toux_chronique}
\danger Éliminer toux post-infectieuse (< 3 semaines)
Signes de gravité :
\begin{itemize}
\item AEG, sd infectieux
\item dyspnée d'effort, hémoptysie
\item modification toux chez fumeur
\item dysphonie, dysphagie, fausses routes
\item adénopathies cervicales suspectes
\item anomalies cardiopulmonaires
\end{itemize}
\begin{figure}[htpb]
\centering
\caption{PEC initiale d'une toux chronique}
\resizebox{0.6\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
level distance=40pt,
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
Signe de gravité -> {
Exploration ["oui"];
"Médicaments ?" ["non"] -> {
Test d'éviction ["oui"];
"Coqueluche ?" ["non"] -> {
Test diagnostique ["oui"];
"Radio thorax anormale ?" -> {
Bilan spécialisé ["oui"];
"cf~\nameref{subsec:toux_orientation}" ["non"];
};
};
};
};
};
}
\end{figure}
\subsubsection{Orientation diagnostique}
\label{sec:org39e0c38}
\label{subsec:toux_orientation}
\begin{tcolorbox}
Rhinorrhée chronique, RGO, asthme, tabac, médicaments\footnote{IEC, inhib angiotensine II, \beta{}-bloquants}, coqueluche
\end{tcolorbox}
\textbf{ORL}
\begin{itemize}
\item rhinosinusiens : sd rhinorrée postérieur++, obstruction nasale chronique
\item carrefour aérodigestif : diverticule de Zenker, laryngite chronique
\end{itemize}
\textbf{Respiratoire}
\begin{itemize}
\item Asthme : TVO réversible/hyperréactivité bronchique
\item BPCO : TVO non réversible
\item Cancer bronchique, tumeurs, bronchectasise (cf
\nameref{sub:bronchectasies})
\end{itemize}
\textbf{RGO} : pyrosis. Endoscopie digestive si FR, pHmétrie des 24h
\textbf{Allergique}
\textbf{Systémique} : sd Gougerot-Sjögren, polychondrite atrophiante, maladie
de Horton, granulomatose avec polyangéite, rectocolite hémorr., maladie de
Crohn.
\textbf{Comportement} : dernière étiologie
\paragraph{Traitement d'épreuve (ordre d'échec):}
\label{sec:org5afef3d}
\begin{enumerate}
\item RGO : bromphéniramine + pseudoéphédrine 3 sem
\item asthme si TVO réversible, corticoïdes inhalés ou bronchodilatateurs inhalés si
hyperréactivité bronchique
\item avis spé
\end{enumerate}
Traitement symptomatique : arrêt tabagisme. Éviter si possible
\begin{itemize}
\item si toux sèche : opiacés, antihistaminique anticholinergique, non
antihistaminique non opiacés
\item si toux productive : mucomodificateurs, kiné
\end{itemize}
\subsubsection{Bronchectasies (DDB)}
\label{sec:org14cd5bf}
\label{sub:bronchectasies}
Types : bronchectasies (élargissement \(\diameter\)), bronchocèle (pus), "par
traction" (NB: pas des vraies bronchectasies)
Étiologie :
\begin{itemize}
\item infection respi sévères : coqueluche, tuberculose (virales respi enfant,
pneumonie bact, suppuration suite sténose)
\item mucoviscidose
\item non infectieux (poumon radique, aspergillose allergique, SDRA,
systémique, déficit immunitaire)
\end{itemize}
Évolution : colonisation bactérienne, hémoptysie, TVO (car dilatation seulement
proximale), insuffisance respi
Clinique :
\begin{itemize}
\item toux productive quotidienne depuis l'enfance
\item hémoptysie
\item EC : (râles bulleux à l'auscult), (hippocratisme digital)
\item infections à \{\bact{influenzae}, \bact{pneumocoque}\} puis \{\bact{dore},
\bact{aeruginosa}++\}
\end{itemize}
Diagnostic : TDM (certitude) = \(\diameter_\text{bronche}\) > \(\diameter_\text{artère}\), lumière
bronchique > 1/3 parenchyme, pas de réduction du \(\diameter\), grappes de kystes,
opacités tubulées
Traitement : ATB si exacerbation, complications parenchymateuses. Macrolides
pour l'inflammation. Chir si très local + compliqué.
\subsection{201 \textdagger{} Hémoptysie}
\label{sec:orgac7dc31}
\label{sec:201_hemoptysie}
Urgence
\begin{enumerate}
\item Est-ce une hémoptysie ? Hématémèse ou ORL possibles
\item Gravité ? Suivant abondance, terrain, persistance \thus risque = hématose et asphyxie
\end{enumerate}
\subsubsection{Étiologies}
\label{sec:org9424d89}
\begin{itemize}
\item Tumeurs bronchopulmonaires++
\item Bronchectasies++
\item Tuberculose (évolutive/séquelles)++
\item Idiopathique++
\item Infections : aspergillaires, pneumopathie infectieuses nécrosante
\item Vasc : embolie pulmonaire, HT pulmonaire, anévrysmes/malformations
\item Hémorragie alvéolaires : insuf. cardiaque gauches, médicaments/toxiques,
vascularites, collagénose, sd Goodpasture
\end{itemize}
\subsubsection{Diagnostic}
\label{sec:org8c3fa23}
Localisation (important !)
Interrogatoire : ATCD respi, cardiaque, histoire médicale
Examens
\begin{itemize}
\item clinique : \{\(SpO_2\), tension, pouls\}, mauvaise tolérance respi, gêne
latéralisée, hippocratisme digital
\item radio thorax pour siège (verre dépoli/sd alvéolaire), lésion
\item scanner plus précis : nature, localisation, carto. vasc.
\item (endoscopie : hématémèse, multiples lésions, tumeur proximale)
\item (artériographie bronchique : ttt par embolisation)
\item autres : gaz du sang, dosage Hb, bilan coagulation, groupe sanguin, \{BK,
ECG\} si suspicion OAP hémorragique
\end{itemize}
\danger BPCO \(\centernot\implies\) hémoptysie
\subsubsection{Traitement}
\label{sec:orgc113f52}
\(O_2\) + vasconstriction IV, protection voies aériennes (décubitus latéral,
ventilation mécanique)
Embolisation artérielle bronchique
Chir si localisé, fonction respi OK et "à froid"
\subsection{202 Épanchement pleural}
\label{sec:orgf2250f5}
\subparagraph{Diagnostic}
\label{sec:orgbcc5852}
Suspicion clinique, confirmé par imagerie
\begin{itemize}
\item douleur thoracique \emph{dépendant de la respiration}, dyspnée, toux sèche \emph{au
changement de position}, hyperthermie
\item examen : sd pleural liquidien (silence auscult, matité, \(\emptyset\) transmission
corde vocales, souffle pleurétique)
\item \danger Signes de gravité : détresse respi, choc septique, choc hémorragique
\end{itemize}
Imagerie
\begin{itemize}
\item RX : opacité dense, homogène, non sytématisé, limité par ligne concave\footnote{DD atélectasie : médiastin dévié vers l'opacité}
\item échographie pleurale (différencie pleurésie et collapus, guide ponction)
\item TDM : en urgence si embolie pulmonaire ou hémothorax
\end{itemize}
\subparagraph{Causes}
\label{sec:orgd050d8e}
\emph{Transsudats (protides < 25g/L)} : IC G, cirrhose, sd néphrotique, atélectasie (EP)
\emph{Exsudats (protides > 35 g/L)}\footnote{Ou critère de Light : (LDH > 200 UI/L) ou (protides pleuraux/sérique > 0.5) ou (LDH
pleuraux/sérique > 0.6)}
Cf tab \ref{tab:org24ae670}
\begin{table}[htbp]
\caption{\label{tab:org24ae670}Étiologies des exsudats (néoplasique, infectieux)}
\centering
\begin{tabular}{llll}
Catégorie & Cause & & CAT\\
\hline
Néoplasiques & pleurésie métastatique++ & poumon, sein, \oe{}sophage, colon & scanner, biopsie aveugle/vue biopsie aveugle/vue\\
& mésothéliome & exposition amiante & biopsie++ (thorascopie++)\\
& & RX: épaississement pleural circonférentiel & \\
& & , rétraction hémithorax & \\
Infectieux & bactérien & & ATB \textpm{} évacuation si compliqué\tablefootnote{Épanchement abondant, germes, liquide purulent}\\
& virale & & \\
& tuberculose & progressif, amaigrissement & biopsie pleurale++\\
\end{tabular}
\end{table}
Autres : EP, bénigne liée à l'amiante (exclusion++), post trauma (rupture
oesophagienne, sous-diaphragme), systémique (lupus, polyarthrite rhumatoide)
\subparagraph{Ponction}
\label{sec:org9b2cb09}
En majorité (sauf si peu abondant et insuf cardiaque G\footnote{Sauf si unilat/asymétrique ou douleur pleurale/fièvre ou traitement insuffisant)} ). En urgence si
fébrile, hémothorax ou mauvaise tolérance. Tout évacuer seulement si étiologique ou non cloisonné
\subparagraph{Biologie 1ere intention}
\label{sec:org7a39481}
Biochimie (trans- ou exsudat), cytologie (cf \ref{tab:org954af4a}), recherche germes pygènes, mycobactéries
\begin{table}[htbp]
\caption{\label{tab:org954af4a}Épanchements pleuraux avec exsudats : étiologies}
\centering
\begin{tabular}{lllll}
& Cellules tumorales & Neutrophiles & Lymphocytes & Éosinophiles\\
\hline
Néoplasique & Métastasique & & Cancer & Cancer\\
& Mésothéliome & & Lymphome & \\
& Hémopathies malignes & & & \\
\hline
Infectieux & & Parapneumonique & Tuberculose & Parasitose\\
\hline
Autres & & Embolie pulmonaire & Sarcoïdose & Hémothorax\\
& & Pancréatite & Chylothorax & Pneumothorax\\
& & Sous-phrénique & PR, lupus & Embolie pulmonaire\\
& & Oesophage & & Asbestosique bénigne\\
& & & & Médicament\\
\end{tabular}
\end{table}
\subsection{203 \textdagger{} Opacités et masses thoraciques}
\label{sec:org8b44ee6}
\label{sec:203_opacites_et_masses_thoraciques}
\begin{itemize}
\item < 3mm : micronodules
\item \$[3,30]\$mm : nodules
\item > 30mm : masses
\end{itemize}
\subsubsection{Nodules}
\label{sec:org4fd0cc2}
Origine maligne probable si :
\begin{itemize}
\item homme, > 50 ans, fumeur
\item carcinogènes professionnels, > 1cm (> 3cm ++)
\item contours spiculés, polylobés, irrégulier
\item attire structures proches
\item augmente de taille
\item pas de calcifications
\item fixe TED-FDG
\end{itemize}
Certitude = histologie (ponction transpariétale à l'aiguille)
\textbf{Tumeurs malignes}
\begin{itemize}
\item cancers bronchopulmonaires primitifs : > 50 ans, fumeur, souvent nodule
solitaire
\item secondaires (métastases) : opacités rondes régulières
\end{itemize}
\textbf{Tumeurs bénignes}
\begin{itemize}
\item Hamartochondrome (freq++) : "pop-corn", pathognomonique
\item Tumeurs carcinoïdes
\end{itemize}
\textbf{Non tumorales}
\begin{itemize}
\item infectieux
\begin{itemize}
\item abcès à pyogène (contexte aigü fébrile)
\item bactérie filamenteuse crossance lente
\item tuberculome (\thus prélèvements)
\item kytes hydatiques ("membrane flottante")
\item aspergillome (opacité ronde + croissant gazeux)
\end{itemize}
\item granumolatose avec polyangéite
\item nodules rhumatoïdes
\item atélectasies
\item masses pseudo-tumorale silicotiques (micronodules, confluents ?)
\item malformations artérioveineuses
\end{itemize}
\paragraph{Examens}
\label{sec:orgb3239d0}
\begin{itemize}
\item TDM et TEP
\item Fibroscopie pronchique systématique
\item Ponction transpariétale sous TDM (sauf insuffisance respi)
\item Autres : thoracotomie, médiastinoscopie si ADP médiastinales fixant en TEP-FDG
\end{itemize}
Prélevement si solide, > 8mm, hypermétabolique. Sinon surveillance TDM (sauf non solide et image résolutive à 6 semaines)
\subsubsection{Masses/tumeurs du médiastin}
\label{sec:org1805799}
Diagnostic : opacité avec limite externe nette, raccord pente douce, limite interne non
visible, tonalité hydrique
DD: intraparenchymateux, pariétal \thus TMD
\paragraph{Médiastin antérieur}
\label{sec:orgdbb0df6}
\begin{itemize}
\item Supérieur : goître plongeant \thus TMD : continuité glande thyroïde
\item Moyen :
\begin{itemize}
\item tumeurs thymiques : épithéliales (thymomes, carcinomes thymiques),
lymphomes thymiques, kystes, tumeurs bénignes
\item Tumeurs germinales : bénignes, séminomateuses, non séminomateuses
(carcinomes embryonnaires, vitellines, choriocarcinomes)
\end{itemize}
\item Inférieur : kystes pleuropéricardiques
\end{itemize}
\paragraph{Médiastin moyen}
\label{sec:org5bd59d2}
\begin{itemize}
\item Tumoral : cancer bronchopulmonaires, lymphomes, LLC, cancers
extra-thoraciques
\item Non tumoral : sarcoïdose, tuberculose, silicose, infections
parenchymateuses chroniques, histoplasmose (Amérique du Nord)
\item Autres : insuf. cardiaque gauche
\end{itemize}
\paragraph{Médiastin postérieur "neurogènes"}
\label{sec:org6c7ea20}
Diagnostic :
\begin{itemize}
\item médiastin antérieur :
\begin{itemize}
\item \$\(\alpha\)\$-foetoprotéine (tumeurs vitellines), HCG\footnote{Hormone gonadotrophine chorionique} (choriocarcinomes)
\item ponction transpariétale
\item médiastinotomie
\item chir si complète et peu mutilante
\end{itemize}
\item médiastin moyen : médiastinoscopie ou ponction transbronchique
\item médiastin postérieur :
\begin{itemize}
\item ponction transpariétale, transoesophagienne
\item chir si complète et peu mutilante
\end{itemize}
\end{itemize}
NB : urgence si jeune et suspicion de tumeur germinale non séminomateuses
\subsection{204 \textdagger{} Insuffisance respiratoire chronique}
\label{sec:org93330f9}
\label{sec:org6d633b6}
\subsubsection{Mécanismes}
\label{sec:org3965a3c}
\label{sec:org47f478d}
Hypoxémie
\begin{itemize}
\item Inadéquation ventilation/perfusion :
\begin{itemize}
\item effet shunt (mauvaise ventilation) => \(O_2\) corrige
\item shunt vrai (communication anat. ou non ventilé) => \(O_2\) ne corrige
\end{itemize}
pas
\item Hypoventilation alvéolaire : pure (commande, neuromusc) ou effet "espace mort"
\end{itemize}
(mauvaise perfusion)
\begin{itemize}
\item Atteinte de la surface d'échange
\end{itemize}
Hypercapnie : hypoventilation alvéolaire (pompe ventilatoire/commande centrale
ou effet espace mort)
\subsubsection{Conséquences}
\label{sec:org6bf628f}
\label{sec:orgf6b3986}
Hypoxémie : Polyglobulie, rétention hydrosodée (fréquente), hypertension pulmonaire
Hypercapnie : compensée par le rein
\subsubsection{Étiologies}
\label{sec:org1d34163}
\label{sec:org5310651}
Hypoxémie si PaO\(_{\text{2}}\) < 70mmHg (arbitraire). Voir table\textasciitilde{}\ref{tab:etio_irc}.
\begin{table}
\begin{center}
\begin{tabular}{llllll}
\toprule
TV ? & Obstructif & Restrictif & Restrictif & Mixte & Non\\
& & $\frac{T_{LCO}}{V_a}$ bas & $\frac{T_{LCO}}{V_a}$ normal & & \\
\midrule
Patho. & BPCO & Interstitielles & Sd obésité-hypoventil & DDB & HTP\\
& asthme & & Atteinte cage thoracique & Muscoviscidose & \\
& bronchiolite & & & & \\
Mécanisme & $\frac{V_a}{Q}$ & Surf d'échange & Hypoventilation & $\frac{V_a}{Q}$ & Surf d'échange\\
Atteinte & échangeur & échangeur & pompe/central & échangeur & vasculaire\\
\bottomrule
\end{tabular}
\end{center}
\caption{Insuffisance respiratoire chronique : diagnostic simplifié (selon
EFR). $V_a$ ventilation alvéolaire, $Q$ débit sanguin, $T_{LCO}$ capacité de
transfert du CO}
\label{tab:etio_irc}
\end{table}
\subsubsection{Diagnostic}
\label{sec:org407304d}
\label{sec:orgf8776e2}
\paragraph{Symptômes}
\label{sec:org7b8c6de}
\label{sec:org35a8cf3}
IRC = dyspnée (sous-évaluée), neuropsy + patho initiale
Physique :
\begin{itemize}
\item IRC : cyanose, insuf. cardiaque D (turgescence jugulaire, oedeme MI, reflux
hépato-jugulaire)
\item patho :
\begin{itemize}
\item obstructive : distension thoracique, dimin. bilat murmure vésicul
\item restrictive : râle crépitant des bases, hippocratisme digital
\end{itemize}
\end{itemize}
\paragraph{Diagnostic}
\label{sec:org172de7e}
\label{sec:org7599c0f}
PaO\(_{\text{2}}\) < 70 mmHg (gaz du sang : hypercapnie)
Étiologie :
\begin{itemize}
\item EFR donne TVO (VEMS/CVF < 70\% => BPCO), TVR (échangeur/pompe) ou
\end{itemize}
mixte (DDB, mucov)
\begin{itemize}
\item Radio thorax
\item Autres : NFS (polyglobulie), ECG (dextrorotation, BDB droite, repolarisation),
\end{itemize}
écho cardiaque systématique (éval. ventricule D, dépistage du G)
\subsubsection{Traitement}
\label{sec:org3780f55}
\label{sec:org870a2d5}
Cause, arrêt tabac, vaccins (grippe, pneumocoque), réhabilitation respi.
Oxygénothérapie de longue durée : indiquée si 2 mesures à 2 semaines avec
\begin{itemize}
\item obstructive = PaO\(_{\text{2}}\) < 55mmHG ou ( \(\in\) [55, 60] mmHG et hypoxie
tissulaire\footnote\{Ht > 55\%, HTP, insuf. ventricule D, SpO\(_{\text{2}}\) nocturne \(\le\) 88\%\})
\item restrictive = PaO\(_{\text{2}}\) < 60 mmHg
\end{itemize}
Efficace si IRC après BPCO, 15h/jour, \(O_2\) gazeux ou liquide
Ventilation long cours : IRC restrictive, la nuit.
Chir rare (200/an)
\subsubsection{Pronostic}
\label{sec:orga882ed2}
\label{sec:org2ec66b4}
Irréversible, risque = insuf. respi aigüe (surtout causée par insuf. respi. basse, dysfonction
cardiaque G, EP)
\subsection{205 BPCO}
\label{sec:orgcf36f1d}
\subparagraph{Épidémio}
\label{sec:org5ef4651}
\inc dans le monde.
FR : \{tabac++, aérocontaminants professionnels\}, génétique: \(\alpha\)-1 antitrypsine
\subparagraph{Diagnostic \footnote{On peut inclure dans BPCO \textbf{si TVO} : bronchite chronique (toux
productive quotidienne \(\ge\) 3 mois/an et \(\ge\) 2 ans), emphysème (élargissement espaces aériens distaux + destructions parois
alvéolaires) inclus dans BPCO}}
\label{sec:org18a4b1f}
Évoqué sur la clinique, confirmé par EFR
\begin{itemize}
\item dyspnée/, toux, expectorations.
\item Signes physiques : \nearrow temps expiratoire, \searrow murmure vésiculaire, \(\searrow\) bruits coeur, distension thoracique
\item EFR: \uline{TVO (VEMS/CVF < 0.7) persistante} après bronchodilateur
\end{itemize}
Voir tab \ref{tab:org62246bc}
\begin{table}[htbp]
\caption{\label{tab:org62246bc}Différences asthme-BPCO}
\centering
\begin{tabular}{ll}
Asthme & BPCO\\
\hline
Obstructive non réversible & Obstructive réversible\\
Jeune, atopique & Fumeur, > 40 ans\\
Survient \textasciitilde{}40 ans & Enfance\\
\end{tabular}
\end{table}
Sévérité : échelle GOLD\footnote{Pour l'obstruction : stade 1 (VEMS \(\ge 80\%\)) à 4 (VEMS < 30\%)}, MRC\footnote{Pour dyspnée : 0 = efforimportant, 1 = à plat, 2 = doit s'arrêter pour
marche à plat, 3 = qq minutes à plat, 4= pour s'habiller}, fréquences exacerbations (\(\ge\) 2 /an = grave)
\subparagraph{Complémentaire}
\label{sec:org825b382}
ECG si VEMS < 50\%, NFS, \(\alpha\)-1 antitrypsine si besoin
\subparagraph{Évolution}
\label{sec:org43f1352}
Perte fonction respi, exacerbations, handicap respi, risque
d'insuffisance respi, comorbidité CV = 1ere cause de mortalité
Score BODE\footnote{Body mass index, Obstruction, Dispnea, Exercice} pour la prédiction.
\subparagraph{Traitement}
\label{sec:org1dea37c}
Cf fig\textasciitilde{}\ref{fig:ttt_bpco}.
\emph{Arrêt tabac}, vaccins grippe et pneumocoques, réhabilitation respiratoire, O\textsubscript{2}, chirurgie possibles
\begin{figure}[htpb]
\centering
\resizebox{0.5\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=4cm,
level distance=2cm,
edges={nodes={fill=white}},
layered layout]
{
"Dyspnée/exacerbations" -> {
BD longue durée[>"oui", draw]->
{
cBD/"Cortico. inhalé\\ + BD longue durée"[draw, >"exacerbation"]
-> ["insuffisant"] c2BD/"Cortico. inhalé\\+ 2 BD longue durée"[draw]
-> reeval/"Réévaluation"[>"dyspnée"];
2BD/"2 BD longue durée" [draw, >"dyspnée"] -> {
c2BD[draw, >"exacerb"];
reeval[>"dyspnée"];
};
};
BD courte durée [>"non", draw];
}
};
}
\caption{Traitement BPCO}
\label{fig:ttt_bpco}
\end{figure}
\subsubsection{Exacerbations BPCO}
\label{sec:org77c76f8}
Exacerbation aigüe = aggravation \(\ge 2\) jours
\subparagraph{Diagnostic}
\label{sec:org98e4c08}
Soit BPCO connu avec \inc dyspnée, toux/expect, soit voir section \hyperref[org7752461]{item 354}
Déclenchants : \emph{infectieux}\footnote{Mais souvent pas de facteur précis}
(\bact{influenzae}, \bact{pneumocoque}, \bact{catarrhalis})
DD : PAC, dysfonction cardiaque gauche, EP, pneumothorax, médicaments CI, trauma/chir thoracique, insuffisance cardiaque gauche aigüe.
\subparagraph{Explorations (si sévère)}
\label{sec:orgab229aa}
Imagerie thorax, ECG, NFS, CRP, iono, créat, gazométrie
\subparagraph{Traitement}
\label{sec:orgeab49af}
\emph{Bronchodilatateurs \(\beta\)-2 agonistes courte-durée}
\begin{itemize}
\item \textpm{} ATB 5-7 jours (si expectoration
purulente ou gravité ou BPCO sévère)
\begin{itemize}
\item amox + acide clav/CG3/fluoroquinolones si FR
\item amox \textpm{} acide clav/pristinamycine/macrolides sans FR
\end{itemize}
\item \faHospital : oxygénothérapie, kiné, HBPM, (assistance ventilatoire)
\end{itemize}
\subsection{206 \textdagger{} Pneumopathies infiltrantes diffuses}
\label{sec:orga170edf}
\subsubsection{Présentation}
\label{sec:orgb025018}
Clinique : dyspnée d'effort prgorsessive.\\
EFR : \gls{TVR} ( CPT < 80\% et VEMS/CVL >
70\% ) et TLCO < 70\%, hypoxémie, désaturation\\
Radio : opacités parenchymateuse non systématisées bilatérales
\subsubsection{PID aigüe}
\label{sec:orgd24fcc5}
\paragraph{Étiologies}
\label{sec:org24942f7}
Causes connues : lymphangite carcinomateuse, insuf. cardiaque gauche, médicamenteuse\\
Causes inconnues : sarcoïdose, fibrose plumonaire idiopathique
\paragraph{Démarche}
\label{sec:org5e0ab6b}
\begin{itemize}
\item Contexte (ATCD, ID, exposition)
\item ECG, BNP, echo cardiaque
\item LBA si possible
\item PEC thérapeutique (réa si détresse respi, \(O_2\), ATB probabiliste si fièvre, arrêt de médic. pneumotoxiques)
\end{itemize}
\subsubsection{PID subaigüe/chronique}
\label{sec:orgd42ed33}
\paragraph{Démarches}
\label{sec:org192e3ee}
Interrogatoire++ : terrain (sarcoïdose=25-45 ans, \gls{FPI} si > 60 ans), tabac (histiocytose langerhansienne, \gls{DIP}), toxico, médic, ATCD radio, exposition
Clinique : état général, signes de connectivite
\begin{table}[htbp]
\caption{Biologie PID subaigüe}
\centering
\begin{tabular}{ll}
\toprule
Examen & Maladie\\
\midrule
NFS, CRP & Sd inflammatoire\\
& Hyperéosinophilie, lymphopénie\\
BNP & Insuf. cardiaque\\
Créat & Insuf. rénale\\
Précipitines sériques & Hypersensib. (si contexte)\\
CEA, calcémie, calciurie & Sarcoïdose\\
Facteur rhumatoïdes etc & Connectivites\\
ANCA & Vascularite\\
Séro VIH & Opportuniste\\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htbp]
\caption{LBA PID subaigüe}
\centering
\begin{tabular}{ll}
\toprule
Normal & 80\% macrophages\\
& < 15\% lymphocytes\\
& < 5\% PNN\\
& < 2\% PNE\\
\midrule
Alvéolite & Hypercellularité totale\\
Histiocytose langerhansienne & Macrophage\\
Sarcoïdose, PHS & Lymphocytaire\\
P. à éosinophiles & Éosinophilique\\
\gls{POC} & Panachées\\
Hémorragie alvéolaire & Rosé\\
Protéinose alvéolaire primitive & Laiteux\\
\bottomrule
\end{tabular}
\end{table}
Examens complémentaires :
\begin{enumerate}
\item fibro et LBA (+ biopsie bronchique)
\item soit biopsie pulmonaire chir (pas de diagnostic), soit biopsie
transbronchique et ADP médiastinales
\end{enumerate}
\paragraph{Oedème pulmonaire}
\label{sec:org7702a11}
Mécanisme : Surcharge hémodynamique\\
Clinique : HTA, coronaropathie, valvulopathie mitrale\\
Diagnostic : ECG, BNP, écho coeur\\
Imagerie : Péri-hilaire
\paragraph{Tuberculose}
\label{sec:orga64806f}
Mécanisme : BK\\
Clinique : Contage, AEG, hémoptysie\\
Diagnostic : Expectorations (ED, culture, biopsie transbronchique)\\
Imagerie :
\begin{itemize}
\item pulmonaire = nodules, infiltrats, excavations
\item miliaire = micronodules diffus
\end{itemize}
\paragraph{Médicaments}
\label{sec:org2219fe4}
Imagerie : condensations, verre dépoli, épanchement pleural
\paragraph{Pneumopathies d'hypersensibilité}
\label{sec:orge1b1184}
Mécanisme : Ag organiques\\
Clinique :
\begin{itemize}
\item aigüe : sd peudo-grippal quelques heurs
\item subaigüe : semaines/mois avec toux, fébricule, râles crépitants, squeaks
\item chronique : dyspnée, toux sèche
\end{itemize}
Diagnostic : Sérologie, LBA\\
Imagerie : Micronodules centrolobulaires flous, verre dépoli (lobes supérieurs)\\
Traitement : éviction Ag
\paragraph{Pneumoconioses}
\label{sec:orge4eb82e}
Mécanisme : Amiante, silice\\
Clinique : Exposition\\
Imagerie :
\begin{itemize}
\item silicose : opacités micronodulaires diffuses \(\implies\) masses pseudotumorales. Peut donner un cancer bronchique
\item asbestose : opacités linéaires non septales des bases \(\parallel\) ou \(\bot\) plèvre, réticulations et rayons de miels comme FPI. Évolue vers insuf respi chronique.
\end{itemize}
\paragraph{Sarcoïdose}
\label{sec:org20e623a}
Mécanisme : Signes extra-respiratoires\\
Diagnostic : anapath : extra-pulmonaire, biopsie éperons bronchiques et transbronchique. ADP médiastinales \\
Imagerie : Nodules, micronodules (ditribution lymphatique), adénopathie, hyperdensités, distorsions bronchiques
\paragraph{Fibrose pulmonaire idiopathique}
\label{sec:org64999c9}
Clinique : Dyspnée d'effort progressive, toux sèche, hippocratisme digital, crépitants sec base\\
EFR : TVR, diminution TLCO\\
Imagerie : Réticulations, bronchectasies, rayons de miel. Domine sous-pleural et bases
\paragraph{Connectivites}
\label{sec:org3080327}
Mécanisme : Dysimmunitaire\\
Clinique : Extra-respi (polyarthrite rhumatoide, sclérodermie, lupus, vascularite)\\
Diagnostic : Ac spécifiques\\
Imagerie : Réticulations, hyperdensités, bronchectasies
\paragraph{Pneumopathie interstitielle non spécifique}
\label{sec:orga57dfcc}
Origine : connectivite, médicaments (idiopathique)\\
Imagerie : verre dépoli, réticulations, bronchectasies (sauf extrême périphérie du poumon)
\paragraph{Proliférations tumorales}
\label{sec:orgbd964cf}
Lymphangite carcinomateuse : toux sèche, rebelle. \\
Radio : épaississements nodulaires des septas intralobulaires.\\
Diagnostic : biopsies des éperons\\
Carcinome lépidique : verre dépoli.
\subsection{207 \textdagger{} Sarcoidose}
\label{sec:orga3b5d2d}
Maladie : systémique, cause inconnue, hétérogène, ubiquitaire. Début 25-45ans
dans 2/3\\
Atteinte médiastino-pulmonaire 90
\subsubsection{Expression}
\label{sec:orgd63c43b}
\label{sec:org39048da}
\paragraph{Pulmonaire}
\label{sec:orgf577e00}
\label{sec:org4ec1d7e}
Toux (dyspnée)
Radio : 4 stades
\begin{itemize}
\item I : adénopathies hilaires bilatérales symétriques
\item II : + atteinte parenchyme (micronodulaire diffus, parties moyennes supérieures)
\item III : atteinte parenchyme isolée
\item IV : fibrose = opacités parenchymateuses rétractiles + ascension hiles, distorsion bronchovasc (sup et post)
\end{itemize}
TDM : atteinte parenchyme = micronodule selon lymphatiques. Utile pour : formes atypiques ou détection précoce (fibrose, complications [greffe aspergillaire])\\
EFR : sd restrictif, DLCO \$\searrow\$\\
(Endoscopie bronchique : normal/muqueuse en "fond d'oeil".)\\
Biopsie : \{éperons, LBA\} > \{ponction ganglions médiastinaux, transbronchique\} > médistanoscopie\\
Formes atypiques : TVO, cavitaires, pseudonodulaires/alvéolaires
\paragraph{Extra-pulmonaire}
\label{sec:org842c2a5}
\label{sec:org316c190}
\begin{itemize}
\item Oeil : uvéite antérieure aigue (toujours cherche uvéite postérieure)
\item Peau : nodules cutanés, lupus pernio, érythème noueux
\item ADP
\item Foie
\item Moins fréquentes : nerveux (sd méningé, paires craniennes), ORL (obstruction
nasale,
\end{itemize}
sd Mikulicz, sd Heerfordt), ostéo-articulaire (bi-arthrite cheville =
spécfique++),
coeur (BAV, bloc branche droit), rein (\(\nearrow\) créatininémie)
\begin{itemize}
\item Généraux : asthénie (pas de fièvre sauf sd de Löfgren)
\end{itemize}
Sd de Löfgren = érythème noueux + ADP hilaires médiastinales (+ fièvre)
\paragraph{Biologie}
\label{sec:orgfb503e0}
\label{sec:orgbfe5d87}
\begin{itemize}
\item Hypercalciurie
\item Lymphopénie CD4
\item Hypergammaglobulinémie
\item Enzyme de conversion de l'angiotensine sérique (ECA)
\end{itemize}
\subsubsection{Diagnostic}
\label{sec:org62cfdb3}
\label{sec:org6670330}
Clinique + radio + lésions granulomateuses tuberculoides sans nécrose caséeuse +
élimination DD
\subsubsection{Évolution}
\label{sec:org8f09bcc}
\label{sec:org707f9ea}
< 2 ans : évolution favorable sans traitement.\\
Chronique > 2 ans : attention au vital/fonctionnel \\
Suivi : 3-6 mois\\
Pronostic : 80\% favorable sans traitement, 10\% séquelles, 5\% DC
\begin{table}[htbp]
\caption{Pronostic de la sarcoidose}
\centering
\begin{tabular}{ll}
\toprule
Négatif & Positif\\
\midrule
> 40 ans & Érythème noueux\\
Chronicité & Forme aigüe\\
Stade III, IV & Stade 1 asymptomatique\\
Extra-respi grave & \\
\bottomrule
\end{tabular}
\end{table}
Atteintes :
\begin{itemize}
\item pulmonaire : insuf. respir chronique, principace cause DC
\item extra-thoracique : attention fonctionnel/vital
\end{itemize}
\subsubsection{Traitement}
\label{sec:org33db1b0}
\label{sec:orgc05b9f6}
Atteinte respi : pas de ttt si sd de Löfgren ou stade I asymptomatique\\
\begin{itemize}
\item 1ère intention : Corticoïdes > 12 mois à 0.5mg/kg (décroissance par 6-12 semaines)
\item 2eme intention : hydroxychloroquine, méthotrexate, azathioprine
\item 3eme intention : cyclophsamide, anti-TNF-\(\alpha\)
\end{itemize}
\subsection{222 \textdagger{} Hypertension artérielle pulmonaire}
\label{sec:orgf659f4e}
\subparagraph{Physiopatho}
\label{sec:org3b54a24}
Circulation : (basse pression, faible résistante) \thus forte résistance
\subparagraph{Définition}
\label{sec:org650575f}
acrshort:PAPm \(\ge 25\) mmHG et
$\begin{cases}
\text{\gls{PAPO}} \le 15 & \text{mmHG si précapillaire} \\
\text{PAPO} > 15 & \text{mmHG si postcapillaire}
\end{cases}$
5 groupes :
\begin{enumerate}
\item HT \uline{A} P\footnote{Idiopathique, héritable, médicaments, maladie veino-occlusive, hémangiomatose capillaire
pulmonaire, HTP persistante du nouveu-né} : pré-capillaire
\item \textbf{cardiopathie gauche} : post-capillaire (fréq+++)
\item HTP maladie \textbf{respiratoire chronique} : pré-capillaire (freq++)
\item HTP post-embolique chronique : pré-capillaire
\item HTP multi-factorielles : pré-capillaire
\end{enumerate}
\subparagraph{Pronostic}
\label{sec:orgddfab51}
6 cas/million (idiopathique), femme. Survie avec ttt : 58\% à 3 ans
\subparagraph{Diagnostic}
\label{sec:orgaed950c}
Cathétérisme cardiaque D/ avec \textbf{PAPm \(\ge 25\) mmHg}. Découvert sur dyspnée, dépistage
\begin{itemize}
\item Interrogatoire : ATCD, anorexigènes, toxiques, maladie (sclérodermie : sd de
Raynaud, dysphagie, dyspepsie)
\item dyspnée d'effort+++ progressive (lipothymie à l'effort,
syncope, asthénie, douleurs angineuses, palpitations, hémoptysies)
\item HTP (signe de Carvallo\footnote{Souffle holosystolique d'insuf. tricuspid majoré à l'inspiration}, éclat B2, souffle diastolytique d'insuf pulmonaire), insuf cardiaque D\footnote{Tachy, galop, turgescence jugulaire, reflux hépato-jugulaire, HMG, OMI, anasarque}
\item RX thorax normale ou dilatation artères pulmonaires, élargissement coeur D
\item ECG : hypertrophie D, trouble rythme
\item \emph{Écho cardiaque transthoracique} = non invasif de référence.
\end{itemize}
\subparagraph{Démarche}
\label{sec:orgaec6735}
Si écho cardiaque compatible avec HTP :
\begin{itemize}
\item Cardiopathies G, maladies respi + exams pour groupe 2 et 3. Si confirmé : \faStop
\item Sinon regarder signes thrombo-embolie chronique (scinti, angioscan) : Si
groupe 4, \faStop
\item Sinon confirmer HTP précapillaire
\item Si confirmée, tester pour groupe 1 (connectivites, médicaments, VIH,
cardiopathie congénitale, HT portale, schistosomiase) ou groupe 5
\end{itemize}
\subsubsection{Enfant}
\label{sec:orgf884a7e}
\subparagraph{Physiopatho}
\label{sec:org5daf854}
Augmentation du débit ou des résistances
\subparagraph{Clinique}
\label{sec:org0511d89}
\begin{itemize}
\item Nouveau-né : cyanose réfractaire à l'\(O_2\), détresse respi/circ \thus échocardio en
\end{itemize}
urgence \danger
\begin{itemize}
\item Enfant : dépistage si cardiopathie congénitale, patho. respi. chronique, maladie de
\end{itemize}
systèmes, ATCD familiaux (signes tardifs !\footnote{Dyspnée d'effort, syncope, fatigue} )
\subparagraph{Diagnostic}
\label{sec:org7f11921}
Échocardio, confirmé par cathétérisme
Scanner (parenchyme), écho hépatiques (shunt porto-cave)
\subsection{224 \textdagger{} Embolie pulmonaire et thrombose veineuse profonde}
\label{sec:orgf5dc94f}
\label{sec:224_embolie_pulmonaire_et_thrombose_veineuse_profonde}
\gls{MTEV} = \{\gls{EP}, \gls{TVP}\}
Maladie fréquente (1 cas /10 000 si < 40 ans, 1/100 si > 75 ans) et grave.
3eme cause de DC en france.
TVP : obstruction thrombotique d'un tronc veineux profond. EP : idem mais
artères pulmonaires ou leurs branches (secondaires TVP à 70\%)
\paragraph{Physiopatho stase veineuse, lésions pariétales, anomalies de l'hémostase \thus}
\label{sec:org280b544}
obstruction/lyse. Si migre dans les artères pulmonaires : symptômes si
obstruction à 30-50\% \thus anomalie hémodynamique \thus insuf respi
\paragraph{Évolution}
\label{sec:org752ada9}
TVP distales asymptomatique (postop) : 20\% deviennent proximales\\
TVP distales symptomatique : récidive (9\% si ttt anticoagulant)\\
TVP proximal symptomatique : risque important !\\
EP : TVP + 3/7 jours, mortelle dans l'heure à 10\%
Facteurs de risque :
\begin{itemize}
\item acquis : majeurs = chir < 3mois, trauma MI\footnote{Membres inférieurs},
\faHospital{} aigü, cancer en cours ttt, sd antiphospholipide, sd
néphrotique
\item constit : rare = déficit (antithrombine, prot. C, S), fréq = (mutation \{Leiden,
prothrombine\}, facteur VIII > 150\%)
\end{itemize}
Complications : DC, récidive (mortelle ou non), séquelle (HTP thrombo-embolique
chronique si EP, sd post-phlébite si TVP)
Risque de récidive dépend de la clinique : élevé si (non provoqué par facteur
majeur ou modéré) ou (\og facteur persistant)
Conséquence :
\begin{itemize}
\item hémodynamique : \(\nearrow\) pression artérielle pulmonaire, dilatation
VD\footnote{Ventricule droit}, compression VG
\item respiratoire : hypoxémie (effet espace mort (non perfusé) \thus effet shunt
(ventil/perfusion diminué))
\end{itemize}
\subsubsection{Diagnostic de l'embolie pulmonaire}
\label{sec:orgd3ef0b5}
\paragraph{Clinique pas spécifique : dyspnée, douleur thoracique, syncope,}
\label{sec:org1088d08}
crachats hémoptoïques, asymptomatique
Radio thoracique, ECG : élimine les DD
Gaz du sang : hypoxie-hypocapnie
\thus score probablitié (Genève, Wells)
\begin{figure}[htpb]
\centering
\resizebox{0.3\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
level distance=2cm,
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Proba. clinique" -> {
"D-dimères" [>"faible", draw] -> {
"Pas de ttt" [>"négatif"];
"\texttt{\$examen}" [>"positif", draw];
};
"\texttt{\$examen}" [>"forte", draw] -> {
Ttt [>"positif"];
};
};
};
}
\caption{Diagnostic général pour l'EP, TVP}
\label{fig:ep-diag}
\end{figure}
\paragraph{Examens}
\label{sec:org43f5608}
Voir la figure\textasciitilde{}\ref{fig:ep-diag} avec \texttt{examen} = angioscanner.
D-dimère positifs = \$\(\max\)(\text{âge}, 50) \texttimes{} 10 \(\mu\)\$g/L
CI à l'angioscan : insuf. rénale sévère (< 30ml/min) \thus scintigraphie
Si angioscan ou scintigraphie négatif : pas d'EP !
\begin{tcolorbox}
\danger{} si EP grave (état de choc) : angioscan immédiatement ou ETT en
attendant.
{} Thrombolyse/embolectomie après écho si pas d'accès à l'angioscan
\end{tcolorbox}
Sur l'écho, chercher dilatation cavité D, HTP, septum paradoxal
\emph{Si grossesse} : D-dimères \thus écho. veineuse \thus angioscanner
(prévenir le pédiatre )
\paragraph{Évolution favorable. Complications : choc cardiogénique réfractaire}
\label{sec:org26bffa5}
(DC), rédicive, HTAP chronique post-embolique (rare mais grave)
\subsubsection{Diagnostic de TVP}
\label{sec:orga38c8d7}
\paragraph{Clinique = orientation}
\label{sec:org608e7d5}
Douleur du MI, oedème unilatéral, signes inflammatoires, dilatation veines
superficielles ou asymptomatique
\emph{DD} : traumatisme, claquage musc/, kyste synovial, \{SPT, insuf veineuse
primaire\}, \{sciatique, compression extrinsèque\}, \{érysipèle, lymphangite,
cellulite\}, lymphoedeme, insuf cardiaque droite/rénale/hépatique
Score de probablitié clinique : Wells (faible/interm/forte)
\paragraph{Diagnostic}
\label{sec:orgb488bbd}
Voir la figure\textasciitilde{}\ref{fig:ep-diag} avec \texttt{examen} = échographie veineuse
des MI
\paragraph{Étiologies}
\label{sec:orga8eeb1b}
\begin{itemize}
\item FR transitoire (chir, fracture < 3 mois, immobilisation > 3 j) ? Sinon, "non
\end{itemize}
provoquée"
\begin{itemize}
\item Recherche de thrombophilie si
\begin{itemize}
\item 1er épisode : (non provoqué < 60 ans) ou (femme âge procrééer)
\item ou récidive : (MTEV proximale) ou (TVP distale non provoquée)
\end{itemize}
\thus 1ere intention : \gls{AT}, prot. C et S, mutation G20210A,
homocysténiméie, Ac antiphospholipides
\item Recherche cancer : > 40 ans ou bilan thrombophilie négatif
\end{itemize}
Formes particulières :
\begin{itemize}
\item thromboses veineuse superficielles : (sur trajet saphène, douloureux,
rouge, inflammatoire, cordon induré \thus écho-doppler
\item TVP pelvienne
\item thrombose veine cave inférieure
\item phlébite bleue : très rare mais grave
\end{itemize}
Si grossesse : bilan thrombophilie si ATCD familaux/personnels MTEV
Si cancer : HBPM long cours
\paragraph{Évolution : favorable si bien conduit mais récidive toujours}
\label{sec:org7e03938}
possible. Complications :
\begin{itemize}
\item SPT : lourdeur de jambes, oedeme de cheville, dilat veineuses
superficielles, troubles trophiques sans ulcère, ulcères sus-malléolaires
\item EP
\end{itemize}
\subsubsection{Traitement (TVP + EP)}
\label{sec:orgb70c23a}
\paragraph{Principes}
\label{sec:orgdf4cab3}
Urgence \thus anticoagulant
CI : coagulopathie sévère, hémorragie intracrânienne spontanée, hémorragie
active difficilement contrôlable, chir récente, (thrombopénie à l'héparine)
\paragraph{Types de traitement}
\label{sec:orge82a236}
Option 1 : Héparines + relais AVK dès injection IV
\begin{itemize}
\item HBPM, fondaparinux > HNF, sauf si IR sévère (< 30ml/min)
\item arrêt si 5 jours d'AVK et IV (ensemble) \(\wedge\) INR \(\in [2,3]\) à 24h
\end{itemize}
Option 2 : Anticoagulants oraux directs : rivaroxaban, apixaban (France)
\begin{itemize}
\item rapide, demi-vie courte
\item facteur X
\item CI : IR sévère, grossesse, interaction médic (cytochrome 3A4 ou
P-glycoprroténie)
\end{itemize}
Éucation thérapeutique\\
Autres :
\begin{itemize}
\item filtre cave (si CI absolu aux anti-coagulant ou EP récidivant)
\item fibrinolyse (si EP + choc, sauf si hémorragie active,
AIC\footnote{Accident ischémique cérébral}< 2 mois,
hémorragie intracrânienne)
\item embolectomie (très rare)
\item contention veineuse (sauf si EP sans TVP)
\item lever +1h
\end{itemize}
\paragraph{Stratégie}
\label{sec:org707a6a1}
Score sPESI = \texttt{90 100 110 C C} \footnote{Sat < 90\%, PAS < 100 mmHg, FC > 110/min, Cancer, insuf Cardiaque chronique}:
Risque faible (sPESI = 0) : \faHospital{} courte < 48h, anticoagulation\\
Risque intermédiaire (sPESI > 0)
\begin{itemize}
\item dysfonction VD ou élévation biomarqueurs\footnote{eBNP, NT-pro-BNP, troponine} : \faHospital{}
médecine, anticoagulation
\item dysfonction VD \(\wedge\) élévation biomarqueurs : urgence \danger{}
\thus USI
\begin{itemize}
\item \(O_2\), scope
\item anticoag : HNF/HBPM puis AVK/AOP à 48-72h\\
\end{itemize}
(trombolyse si choc)
\end{itemize}
Haut risque (choc : PAS < 90mmHG ou -40mmHg) : urgence \thus réa
\begin{itemize}
\item \(O_2\) (ventilation méca.), scope
\item anticoag HNF (!)
\item thrombolyse avec arrêt HNF tant que TCA > 2x témoin
\item (embolectomie)
\end{itemize}
\paragraph{Durée}
\label{sec:org17c8ff0}
3 mois si 1ere EP/TVP provoqué par facteur majeur transitoire ou risque
hémorragique élevée. 6 mois ou plus sinon
\paragraph{Étiologie}
\label{sec:org142300e}
Chercher cancer occulte dans tous les cas (clinique, radio poumon, NFS VS,
dépistage globux)
Bilan coag : \{antithrombine, prot C, S\}, mutation \{Leiden, prothrombine\}, sd
antiphospholipides
\paragraph{Prophylaxie}
\label{sec:org6769c2c}
\begin{itemize}
\item Post-op : (chir et > 40 ans) ou (chir hanche/genou/caricinologique, anomalie
coag, (> 40 ans et ATCD MTEV))
\item polytrauma ou (\{rhumato, inflammatoire intestin, infectin\} + 1 FR)
\end{itemize}
\paragraph{Cas particuliers}
\label{sec:org5fad299}
\begin{itemize}
\item
\end{itemize}
TVP distale : symptomatique : anticoagulement 6 semaines seulement si premier épisode. Dans tous les cas,
compression \(\ge 2\) ans
\begin{itemize}
\item \gls{TVS} : \textbf{pas} d'AINS, antiocoagulants en curatif, chirurgie
\item cancer : HBPM, arrêt si plaquettes < 50g/L
\end{itemize}
Prévention :
\begin{itemize}
\item risque modéré : HBPM/HNF/fondaparinux, compression
\item risque élevé : idem sans HNF
\end{itemize}
Nouveau anticoagulant oraux (rivaroxaban) :
\begin{itemize}
\item prévention chir hanche-genou
\item curatif TVP, EP
\item pas si insuf rénale sévère ou insuf hépatique
\item pas de surveillance bio
\end{itemize}
\subsection{228 \textdagger{} Douleur thoracique aigüe et chronique}
\label{sec:org1443bbb}
\label{sec:228_douleur_thoracique_aigue_et_chronique}
\subsubsection{Signes de gravité}
\label{sec:org63f8e83}
\begin{itemize}
\item Respi : cyanose, tachypnée, lutte avec tirage, balancement thoraco-abdominal
\item CV : pâleur, tachycardie, hypotension, choc (marbrures, extrémités
froides)
\item neuro : lipothymie/syncope, agitation/trble vigilance, général (sudation)
\end{itemize}
\danger arrêt cardio-respi ! Y penser si bradypnée, (bradycardie et choc et troubles vigilance)
\subsubsection{Examens}
\label{sec:org61bb6cc}
Fréquence respi, \(SpO_2\), radio thorax, ECG.
Si \{brady, tachy\}pnée ou \(SpO_2 < 95\%\), gaz du sang
\subsubsection{Urgences vitales}
\label{sec:org18f549a}
Cf table\textasciitilde{}\ref{tab:urgences_douleur_thoraciques}
\begin{table}
\centering
\begin{tabular}{ll}
\toprule
Urgence & Orientation\\
\midrule
Syndrome coronaire aigü (fréquent++ 1/3) & ECG + troponines\\
Embolie pulmonaire (fréquent) & Suspicion si douleur thorax, pas d'anomalie ascult\\
& RX thorax "normale" \textit{surtout} si hypoxémie + FR\\
& Dyspnée ou douleur thoracique aigüe chez TVP = EP\\
dissection aortique (exceptionnelle) & Échocardio + angioscanner\\
Tamponnade (peu fréq) & suspicion (hypotension réfractaire, insuf. cardiaque D
aigüe,\\
& microvoltage + alternance ECG) \thus echo cardiaque\\
Pneumothorax & ATCD (!), radio thorax \\
pneumomédiastin (rare) & scanner\\
\bottomrule
\end{tabular}
\caption{Urgences vitales pour douleur thoraciques}
\label{tab:urgences_douleur_thoraciques}
\end{table}
\begin{itemize}
\item Embolie pulmonaire (fréquent) : suspicion si douleur thorax, pas
d'anomalie ascult, RX thorax "normale" \emph{surtout} si hypoxémie +
facteurs de risque\\
Dyspnée ou douleur thoracique aigüe chez TVP = EP
\item dissection aortique (exceptionnelle) : échocardio + angioscanner
\item Tamponnade (peu fréq) : suspicion (hypotension réfractaire, insuf.
cardiaque D aigüe, microvoltage + alternance ECG) \thus echo cardiaque
\item Pneumothorax : ATCD (!), radio thorax \\
pneumomédiastin (rare) : scanner
\end{itemize}
\subsubsection{Non urgent}
\label{sec:org2cdea29}
Rythmées par respiration :
\begin{itemize}
\item post-traumatique
\item pneumonie infectieuses : radio thorax
\item épanchement pleural (douleur latéral-base, majorée inspiration, toux)
\item infarctus pulmonaire (douleur basithoracique, faible hémoptysie)
\item trachéobronchite aigüe
\item musculosquelettique, nerfs : tumeurs costales, lésions vertèbres,
névralgies cervicobrachiales
\end{itemize}
Non rythmées :
\begin{itemize}
\item angor d'effort stable (calmée 2-5min post-effort)
\item péricardite (viral si aigü, tuberculose/néoplasie sinon)
\item cocaïne (fréquente) : SCA, myopéricardite,pneumothorax
\item zona thoracique (brûlures, hyperesthésie 24h avant)
\item digestives : reflux gastro-oesophagen, spasmes oesophagiens. Exclure SCA
\item psychogènes
\end{itemize}
\subsection{306 \textdagger{} Tumeurs du poumon}
\label{sec:orgcb5866f}
\label{sec:306_tumeurs_du_poumon}
\subsubsection{Épidémiologie, étiologies}
\label{sec:orgb4d409c}
1ere cause de mortalité par cancer en France (\male : constante, \female
\(\nearrow\))
Tabac : 90\% (âge de début et durée) pour actif, 25\% passif
Professionel : 15\%
\paragraph{Histologie}
\label{sec:org9c2a737}
\begin{itemize}
\item "Non à petites cellules" (CBNPC) (80\%) : adénocarcinomes (périphérie),
carcinomes épidermoïdes (proximal), indifférenciés à grandes cellules
\item neuro-endocrine "à petites cellules" (CBPC) (proximal, médiastin)
\end{itemize}
\subsubsection{Manifestations}
\label{sec:org52fd2fe}
\begin{tcolorbox}
Y penser si (AEG et tabagique) ou (symptôme fonctionnel respiratoire
chez tabagique > 40A)
\end{tcolorbox}
\emph{Respiratoires} : toux (souvent révélatrice, sèche, quinteuse), hémoptysie (<
10\%), bronchorrée (propre), dyspnée, pneumonie/bronchite (\danger{} si récidive
dans même territoire), douleur thoracique
\emph{Locorégionales} : pleurésies, dysphonies, sd cave supérieur, douleurs thoraciques
(fixes, tenaces), sd de Pancoast-Tobias\footnote\{Névralgie cervicobrachiale avec
douleurs radiculaire C8-D1, sd Claude-Bernard-horner\}, paralysie phrénique
\emph{Extrathoracique} : thromboses inexpliquées (y penser !), métastase (SNC,
foie, os, surrénales)
\emph{Sd paranéoplasiques} (à distance, réapparition \thus rechute) :
hippocratisme digital, hypercalcémie, hyponatrémie, sd de Cushing, neurologique
(pseudomyasthénie de Lamert Eaton, neuropathies périph, encéphalopathies)
\subsubsection{Imagerie}
\label{sec:orge40e48f}
Initial = radio thorax chez fumeur > 40 ans
\paragraph{Radiothorax}
\label{sec:orge3f2deb}
\begin{itemize}
\item projection (juxta-)hilaires
\item atélectasies
\item opacités arrondies intraparenchymateuses
\item cavitaires néoplasiques
\end{itemize}
\paragraph{TDM injection}
\label{sec:orgf507a02}
Stade N0 sans adénopathie, N1 si hilaire, N2 si médiastin homolatéral, N3 si médiastin
controlatéral
\paragraph{TEP au 18-FDG}
\label{sec:org8389ada}
Pas dans le cerveau !
Faux positifs : ganglions inflammatoires, infectieux
Faux négatifs : < 1 cm, non solide (verre dépoli)
\subsubsection{Diagnostic histologique}
\label{sec:orga83b2fc}
\begin{itemize}
\item lésion centrale : fibroscopie bronchique
\item périphérique : ponction transpariétale
\item entre les 2 : fibro ou ponction ou thoracotomie
\end{itemize}
Chercher mutations EGFR, réarrangements ALK, ROS1
\subsubsection{Bilan préthérapeutique}
\label{sec:orgb2b2f8a}
\emph{Extension} : T(tumeur) = locale, N (node) = ganglionnaire, M
(métastase) = à distance. \\
si M : TDM abdo, IRM cérébrale, TEP-TDM
État général (Performance Status de 0 à 4), nutritionnel (-5\% en 1 mois ou
-10\% en 6 mois = \frownie{})
\emph{Cardiorespiratoire} : ECG, écho cardio, épreuve d'effort, doppler artériel des MI/cou,
coronarographie.\\
Règle : 1 lobe = -25\% de VEMS. Opération ssi VEMS post-op > 30\%
\subsubsection{Traitement}
\label{sec:org265564f}
\paragraph{CBPNC}
\label{sec:org12c03a0}
\begin{itemize}
\item localisé (stade I, II) : local (lobectomie ou radiothérapie)
\item localement avancé (stade III) : systémique (chimio) + local (radio ou
chir)
\item disséminé (stade IV) : systémique =
\end{itemize}
$\left \{
\begin{array}{lr}
\text{\gls{ITK} si altération moléculaire ciblable} & \text{Médiane > 2 ans}\\
\text{chimio IV et 3e génération sinon} & \text{Médiane 12 mois}\\
\end{array}
\right.$
\paragraph{CBPC\footnote{Chimiosensible rechutes fréquentes et rapides}}
\label{sec:orgdcd89e6}
Pas de chir !
$
\left \{
\begin{array}{l}
\text{radio + chimio (+ irradiation encéphale) si limitée}\\
\text{chimio sinon}
\end{array}
\right.
$
\paragraph{Symptomatique}
\label{sec:orgd80429f}
\emph{Douleur} : Antalgiques, radiothérapie, chir, AINS, vertébroplastie
\emph{Dyspnée} : lymphangite carcinomateuses (difficile), obstruction bronchique
(bronchoscopie), pleurésie exsudative (pleuroscopie), sd cave supérieur
(anticoag, corticoïdes)
\paragraph{Plan cancer}
\label{sec:org1f260dd}
Réunion de concertation pluridisciplinaire, consultation d'annonce, plan
personnalisé de soin
\paragraph{Suivi}
\label{sec:org42ee7c9}
CBNPC : arrêt tabac, TDM 2-3 mois, clinique, bio (rein, NFS, hypercalcémie,
hyopnatrémie)
CBPC : médiane de survie = 16-20 mois si limitée, 8-12 mois si métastatique
\subsubsection{Cancers secondaires}
\label{sec:org03e84bd}
Clinique : pauvre (dyspnée, toux, douleur thoracique, généraux), chercher extension ganglionnaire
Imagerie :
\begin{itemize}
\item lâcher de ballons ou miliaire
\item épanchement pleural
\item interstitiel (lymphangite carcinomateuses)
\end{itemize}
Diagnostic : clinique,
\begin{itemize}
\item inconnu : chercher accessibles à ttt spécifique, TEP. Sinon :
\begin{itemize}
\item épidermoïde, adénocarcinome
\item sinon : \female{} = \{gynéco, mammo\}, \male{} = \{PSA, TR, écho prostate\}
\end{itemize}
\item connu : radio peut suffir
\item ancien : métastases 10 ans plus tard possibles
\end{itemize}
\subsection{333 \textdagger{} Oedème de Quincke et anaphylaxie}
\label{sec:orgadea966}
\label{sec:333_oedeme_de_quincke_et_anaphylaxie}
\subsubsection{Définition, épidémiologie}
\label{sec:org05162b4}
HS systémique immédiate sévère. 2 types :
\begin{itemize}
\item allergique : production IgE spécifiques. Libération de médiateurs par
mastocytes et basophiles \thus vasodilatation, bronchoconstriction
\item non-allergique : pas d'exposition préalable, moins sévère
\end{itemize}
Déf : symptômes CV, respi, cutané/digestif mettant en
jeu le pronostic vital immédiatement après contact
\paragraph{Épidémiologie}
\label{sec:org2fdceca}
35 DC (alimentaire), 40 DC (piqûre) / an\\
Agents :
\begin{itemize}
\item aliments (90\% enfant) : arachide++, protéine oeuf/lait, fruits exotiques
\item médicaments (15-20\%)
\item venin hyménoptères (15-20\%)
\item autres : latex, effort
\end{itemize}
\subsubsection{Clinique}
\label{sec:org6fe3d1b}
Délai < 1h (5min si médic. IV, 15 si piqûre, 30 si alimentaire).
Manifestations :
\begin{itemize}
\item CV : PAS < 100mmFg (ou -30\%), tachycardie, pâleur, hypotonie, malaise,
perte connaissance, trouble rythme/conduction, ischémie myocardique
\item respi : de la toux à l'asthme (mortalité \(\nearrow\) si asthme mal
contrôlé)
\item cutanées, muqueuses : prurit, rash cutané érythémateux, urticaire et
surtout
\begin{itemize}
\item angioedeme : gonflement mal limité ferme, non érythémateux, sans
prurit
\item oedème de Quincke : angioedeme larynx et cou : gêne respi haute
(dysphonie++, dysphagie++). \\
Clinique : gonflement langue, luette, paupière lèvre ou face\\
Possiblement létal
\end{itemize}
\item digestives
\end{itemize}
\textbf{Hautement probable} si
\begin{itemize}
\item gêne respi haute ou asthme ou choc
mettent en jeu le pronostic vital
\item cutanéomuqueux
\item début brutal, progression rapide
\end{itemize}
Sévérité
I. cutanéomuqeux généralisé
II. multiviscérale modérée
III. multiviscérale sévère
IV. arrêt respiratoire
V. DC
\paragraph{Diagnostic}
\label{sec:orgddd81d3}
Clinique + contexte.
Doser systématiquement tryptase sérique (confirmation) : H+0, H+1, H+24
Étiologie : interrogatoire, \{prick-tests, IDR\}, dosage IgE
DD :
\begin{itemize}
\item choc anaphylactique : choc \{vagal, septique, cardiogénique\}, hypoglycémie, mastocytose
\item Oedeme de Quincke : sd cave sup, érysipèle du visage, angi-eodeme à
bradykinine, inhalation de corps étranger (toujours y penser !!)
\end{itemize}
\subsubsection{Traitement}
\label{sec:org52ac785}
\paragraph{Urgence}
\label{sec:org5322e6c}
Adrénaline : 0.01mg/kg (< 0.5mg) adulte à \faHospital{} ou 0.3mg
auto-injection \(\rightarrow\) répéter /5 min jusque stabilisation\\
Voie IM (pas de SC ou d'IV \danger{})
Remplissage vasc : 50-100mL adulte
\(O_2\), libérer voie aériennes, bronchodilatateurs (courte durée)
Glucagon si adrénaline ne fonctionne pas.
\paragraph{Hors urgence}
\label{sec:org3e97b2b}
Anithistaminique, corticoïdes, arrêt agent.
NB : alerter, allongé jambes relevées (pas vertical \danger{} ), PLS si
inconscient
\paragraph{Préventif}
\label{sec:orgfd190d3}
Trousse avec adrénaline si (absolument) :
\begin{itemize}
\item anaphylaxie antérieure (aliment, insecte ou latex), induite par l'effort
ou idiopathique
\item allergie alimentaire et asthme persistant modéré non contrôlé
\item allergie hyménoptères avec réaction systémique antérieure (adulte) ou
plus sévère que cutanéomuqueux (enfant)
\end{itemize}
\subsection{354 \textdagger{} Corps étranger des voies aériennes}
\label{sec:orge260f88}
\label{sec:354_corps_etranger_des_voies_aeriennes}
Pics =
\begin{itemize}
\item < 3 ans : graines d'oléagineux avec symétrie G-D
\item âgé si troubles déglutition, mauvaise dentition. 2 tableaux : asphyxie
aigüe (viande) ou pneumonie à répétition/suppuration bronchique
\item rarement chez l'adulte/ado : trauma facial (dents), bricolage, trouble
de conscience. Plutôt à droite
\end{itemize}
\subsubsection{Diagnostic}
\label{sec:orgc517a6d}
\paragraph{Clinique et radio}
\label{sec:org27214f0}
Dans les heures post-inhalation :
\begin{itemize}
\item CE mobile (sd de pénétration) : toux quinteuse, suffocation avec tirage,
cornage, cyanose. Résolutif en qq secondes
\item soit CE expulsé (pétéchies visage/tronc ou bouche/conjonctive)
\item plus rarement enclavement
\begin{itemize}
\item proximal (enfant) : diminution murmure vésiculaire, wheezing
\item distal (adulte) : asymptomatique
\item exceptionnellement : oropharynx, larynx, lumière trachéale
\end{itemize}
\end{itemize}
Radio : le plus souvent normale. Sinon : atélectasie, hyperclarté \(\nearrow\)
expiration
Mois/années post-inhalation : à évoquer si respi chronique/récidivante ne
répondant pas au tt ou anomalies radio persistantes dans même territoire
\paragraph{DD}
\label{sec:orgf6c9b7f}
(sub)aigü :
\begin{itemize}
\item détresse respi aigüe à début brutal, tirage, cornage : épiglottite aigüe
(fièvre, modif voix, hypersaliv)
\item infection respi basse : PAC, bronchite sifflante (< 3 ans)
\end{itemize}
Chronique/récidive :
\begin{itemize}
\item trouble ventilation persistant : tumeur bronchique obstructive, sténose
bronchique
\item infection respi même territoire : tumeur bronchique obstructive, foyer
bronchectasies
\end{itemize}
\subsubsection{CAT}
\label{sec:org57ee088}
\paragraph{Asphyxie aigüe}
\label{sec:org68eb853}
Toux ou Heimlich (si conscient) ou réanimation. Si < 2 ans, tapes dos puis
pressions sternum.
\paragraph{Sd pénétration non régressif}
\label{sec:org226af06}
Supposer que CE toujours présent !! (sauf confirmation entourage).
Clinique : dimination unilat murmure, wheezing, persistance \{toux, dyspnée,
cornage, tirage\}
RX : piégage (expiration) \(\wedge\) diminution unilatérale murmure \thus CE
endobronchique (90\%)
\paragraph{Extraction}
\label{sec:org8d699c5}
Bronchoscopie rigide (ou souple). Chez l'enfant, centre spécialisé !
\subsection{354 \textdagger{} Détresse respiratoire aigüe}
\label{sec:org77d4a95}
\label{org7752461}
Définition : Inadéquation charge - capacité de l'appareil respiratoire
\subsubsection{Dianostic}
\label{sec:orge94485a}
Signes de luttes
\begin{itemize}
\item polypnée superficielle
\item recrutemente muscles (scalènes \(\wedge\) intercostaux), abdominaux,
dilatateurs des voies aériennes supérieures (très petit enfant)
\end{itemize}
Signes de faillite
\begin{itemize}
\item respi abdo paradoxale \{\} défaillance court terme
\item cyanose (hypoxémie profonde) \thus \(O_2\) ASAP
\item neuro : astérixis, altérations comportement/vigilance. Glasgow < 9
\thus assitance ventilatoire
\end{itemize}
Appareil circulatoire
\begin{itemize}
\item coeur pulmonaire aigu\footnote\{Turgescence jugulaire, reflux
hépato-jugulaire, hépatomégalie douleureuse, signe de Harzer\}
\item pouls paradoxal
\item hypercapnie : \{céphalées, hypervasc des conjonctives\}, \{tremblements
sueurs, tachy, hypotension\}
\end{itemize}
État de choc
\begin{itemize}
\item peau froide, marbrures, \(\nearrow\) temps recoloration cutanée
\item PAs < 90 mmHg ou -50mmHg
\item tachy > 120min, FR > 25-30/min
\item oligurie
\item confusion, altération vigilance
\end{itemize}
\subsubsection{PEC}
\label{sec:org67d2af7}
Surveillance, \(O_2\), voie veineuse gros calibre, assistance ventilatoire,
ventilation (non)invasive
Pour l'étiologie : radiothorax, ECG, prélèvement (gaz du sang, NFS, iono, urée,
créat, acide lactique)
\subsubsection{Diagnostic}
\label{sec:orgf8a9f90}
\begin{figure}[htpb]
\centering
\resizebox{0.8\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Obstruction VAS ?" ->["non"] Radiothorax -> {
Anormale -> {
Atélectasies [draw];
"Anomalies\\pleurales" ->
"Épanchement\\
pleural compressif\\
Pneumothorax" [draw];
"Opacités\\parenchyme" ->
"Pneumonie infect\\
OAP\\
Patho. infiltrative" [draw];
};
Normale -> {
"Asthme\\
aigu grave\\
EP" [draw];
"BPCO\\
Anomalie paroi\\
Neuromusc" [draw];
}
};
};
}
\caption{Diagnostic détresse respiratoire aigǜe}
\label{fig:diag_detresse_respi}
\end{figure}
Précision de la figure\textasciitilde{}\ref{fig:diag_detresse_respi}
\begin{enumerate}
\item \emph{Obstruction} : corps étranger, laryngite, oedème de Quincke, sténose
trachée, tumeur laryngées
\item \emph{Anomalie radio} Priorité = pneumonie inf, OAP,
PTX\footnote{Pneumothorax} sous
tension\\
Indication =
\begin{itemize}
\item OAP : \{ATCD = insuf. cardiaque\}, \{expectoration mousseuse, orthopnée\},
\{opacités bilat diffuses, périhilaire\}
\item Pneumonie infectieuse : \{début brutal\}, \{expector. purulente\}, \{sd
inflammatoire\}
\end{itemize}
\item \emph{Radio normale} de novo = EP, PTX compressif, asthme. Si
chronique, dans l'ordre BPCO, paroi thoracique (obésité, déformation),
neuromusc\\
Orientation :
\begin{itemize}
\item EP : fébricule, turgescence jugul, radio normale
\item Pneumothorax : \{longiligne\}, \{pas de vibration vocale\}, murmure vésicul,
\{hyperclarté\}
\item asthme : ATDS, toux purulente, râles ou silence
\end{itemize}
\end{enumerate}
\subsubsection{SDRA}
\label{sec:orge803ab9}
Détresse respi < 7 jours sans défaillance cardiaque, sans surcharge volémique
avec opacités radio bilat diffuses
Mécanisme = oedème lésionnel.
Étiologies :
\begin{itemize}
\item exogène = infectieuse, toxique
\item endogènes : réponse inflammatoire systémique
\end{itemize}
\subsection{356 \textdagger{} Pneumothorax}
\label{sec:orga05665b}
\subsubsection{Définitions}
\label{sec:org8d9d7d8}
Air dans l'espace pleural \thus collapsus
\paragraph{Spontané}
\label{sec:org0b52668}
Primaire = poumon sain, sujet jeune, non grave
Secondaire = patho, > 40 ans, peut décompenser
\begin{itemize}
\item Blebs (< 1 cm, plutôt primaires)
\item bulles d'emphysème : à la corticalité, tabagismes
\item lésions kystiques
\item cataménial
\end{itemize}
\paragraph{Traumatique}
\label{sec:orge171399}
Femé (côte fracturée) ou ouverts
\paragraph{Épidémiologie}
\label{sec:orgc254ea2}
Spontané primaire : < 35 ans, masculin, longiligne et de grande taille, fumeur !
Spontané secondaire : BPCO (plus rarement asthme, mucoviscidose)
facteurs favorisants : \(\Delta P_{atm}\), vols aérien, plongée subaquatique,
tabagisme actif (PAS
efforts physiques)
\subsubsection{Diagnostic}
\label{sec:org295d13a}
Clinique :
\begin{itemize}
\item fonctionnel : douleur thoracique (brutale, homolatérale, latérale,
augmente toux), toux sèche irrit
\item physique : diminution murmure vésicul, pas de vibration vocales,
tympanisme percusion
\end{itemize}
Radio : pas en expiration ! 3 catégorise : apical, axillaire, complet
Grave si dyspnée sévère ou collapsus tensionnel (! pas déviation médiastin)
\thus le plus souvent (pneumothorax compressif secondaire à fistule à
soupape) ou (PTX avec réserve ventilatoire réduite)
\paragraph{Atypique}
\label{sec:org468dcde}
Récidive : 30\% (premier épisode), 50\% (second épisode)
Rarement avec pneumomédiastin
Sous ventilation mécanique : y penser si \(\nearrow\) brutal pression
d'insufflation, collapsus brutal, plaie plèvre
\paragraph{DD}
\label{sec:org6d37e7d}
Facile : douleur thoracique "respiro-dépendante".
Difficile : Dyspnée aigüe sans sd pleural
\subsubsection{Traitement}
\label{sec:org8e79895}
\begin{itemize}
\item Rien si décollement < 2cm
\item PTX compressif = urgence \thus aiguille simple + immédiat
\item Pneumotthorax spontané primaire (bien ou mal toléré ) :
exsufflation(petit cathéter sur voie thoracique antérieur) puis drain
si échec
\item Pour tous les autres : drain
\end{itemize}
Prévention récidive par pleurodèse (accolement des feuillets) : si récidive
homolat, PTX persistant 5 jours, compliqué ou bilat
Sevrage tabac !!
Attention altitude si PNO existant (seulement existant)
VIH: traitement aussi pneumocystose
\subsection{Gaz du sang}
\label{sec:org0453bba}
\label{appendix:gds}
Le pH est déterminé par l'équilibre entre les bicarbonates (\ch{HCO_3-}) et
\(PCO_2\) :
\begin{equation}
pH = K_1 + log\frac{[\ch{HCO_3-]}}{K_2 p_{CO_2}}
\end{equation}
avec \(K_1\), \(K_2\) constante.
Un déséquilibre sur un terme induit une compensation sur l'autre. Si le
déséquilibre n'est pas compensé, on aboutit à une acidose ou une alcose.
\begin{table}[htpb]
\centering
\caption{Gaz du sang artériel}
\label{tab:gds}
\begin{tabular}{ll}
\toprule
\(PO_2\) & [80, 100] mmHg\\
\(SaO_2\) & [95, 98] \%\\
\(PCO_2\) & [35, 45] mmHg\\
\ch{HCO_3^-} & [22, 29] mmol/L\\
pH & [7.38, 7.42]\\
\bottomrule
\end{tabular}
\end{table}
Interprétation :
\begin{enumerate}
\item Déterminer si acidose ou alcolose selon le pH
\item Respiratoire ou métabolique ? Si \(PCO_2\) essaie de compenser (en sens
inverse du pH), c'est respiratoire. Sinon métabolique.
\end{enumerate}
NB : la compensation ne normalise pas le pH!
NB :
\begin{itemize}
\item acidose pulmonaire : hypoventilation alvéolaire
\item alcalose pulmonaire : hyperventilation alvéolaire
\item alcalose métabolique : pertes digestives [vomissements]
\end{itemize}
\subsection{Physiologie}
\label{sec:orge5ff730}
\(P_{alv}\) = pression alvéolaire, \(P_{ip}\) = pression interpleurale (dans la
plèvre), pression transpulmonaire = \(P_{ip} - P_{alv}\).
\begin{figure}[htpb]
\centering
\caption{Inspiration (gauche), expiration (droite)}
\tikz \graph [ nodes={align=center}, layered layout]
{
Contraction diaphragme -> Expansion thorax -> "$P_{ip} < P_{atm}$"
-> Hausse pression transpulmonaire -> Expansion poumons
-> "$P_{alv} < P_{atm}$"
-> Arrivée d'air dans les alvéoles;
};
\tikz \graph [ nodes={align=center}, layered layout]
{
"Arrêt contraction\\ diaphragme et intercostaux" -> Rétraction thorax
-> "Valeur initiale de $P_{ip}$"
-> Valeur initiale pression transpulmonaire
-> Rétraction poumons
-> "$P_{alv} > P_{atm}$"
-> Expulsion d'air depuis les alvéoles;
};
\end{figure}
\section{Ophtalmologie}
\label{sec:org42f80e3}
\subsection{21 \textdagger{} Rétinopathie diabétique}
\label{sec:org872083d}
\label{orgd703da6}
Diabète = défini par risque d'une rétinopathie. Complications dont on peut éviter la
cécité !
30\% diabétique en ont une. Diabète 1 : 90\% après 20 ans. Diabète 2 : 60\% à 15
ans
FR = durée et intensité de l'hyperglycémie
Physiopatho : hyperglycémie \thus \{accumulation sorbitol, glycation, stress
oxydatif\} \thus \{inflammation, activation rénine-angiotensine, modif flux
sanguin rétinien, production VEGF\} puis
\begin{itemize}
\item occlusion capillaire et néovascularisation
\item \oe{}dème maculaire
\end{itemize}
Cécité possible du jour au lendemain
\subsubsection{Diagnostic}
\label{sec:org0319dd6}
Photographie du FO = référence et dépistage
\begin{itemize}
\item microanévrisme rétitiens : dilatations punctiformes rouges (postérieure)
\item hémorragie rétiniennes punctiformes
\item nodules cotonneux
\item signes d'ischémie : hémorragies intrarétiniennes "en taches" ou en flammèche, anomalies
microvasculaire intrarétinienne, dilatations veineuses "en chapelet",
néovaisseaux prérétiniens et précapillaires, hémorragie prérétiniennes/intravitréennes
\item \uline{complications} : hémorragie intravitréenne, décollement de la rétine \emph{par
traction}, néovascularisation irienne (\thus glaucome néovasculaire !)
\item signes maculaires : \oe{}dème maculaire (cystoïde), exsudats lipidiques
(souvent en couronne)
\end{itemize}
Complémentaire : OCT pour diagnostic et suivi \oe{}dème maculaire, echo en mode B
pour décollement de rétine par traction
\subsubsection{Dépistage RD}
\label{sec:org39b4ca6}
Diabète 1 : photo FO à la découverte puis surveillance annuelle
\begin{itemize}
\item enfant: pas avant 10 ans
\item grossesse : avant puis tous les 3 mois (tous les mois si RD !)
\end{itemize}
Diabète 2 : dès découverte
Surveillance :
\begin{itemize}
\item \(\emptyset\) RD on non proliférante minime : annuelle
\item sinon tous 4 à 6 mois
\item renforcé si puberté, adolescence, si équilibrage trop rapide de la glycémie,
chir bariatrique, diabète ancien mal équilibré, chir de la cataracte,
\oe{}dème maculaire
\end{itemize}
Classification :
\begin{itemize}
\item \(\emptyset\) RD
\item RD non proliférante : minime, modérée, sévère (si hémorragie rétiniennes dans 4
quadrants ou dilatations veineuses 2 quadrants ou AMIR 1 quadrant)
\item RD proliférante (néovaisseaux): minime, sévère, compliquée (décollement de
rétine par traction, gls:GNV)
\end{itemize}
Progression lente, aggravations rapides possibles. \danger prolifération néovasc
peut donner cécité
\subsubsection{Traitement}
\label{sec:orga833791}
Médical :
\begin{itemize}
\item équilibre glycémique et hypertension pour 2 diabètes !
\item pas de ttt médicamenteux
\end{itemize}
RD proliférante
\begin{itemize}
\item photocoagulation panrétinienne : régression dans 90\%. Indication : RD
proliférante ou (RD non proliférante sévère si grossesse, sujet jeune
diabétique 1 avec normalisation rapide glycémie, chir cataracte)
\item injection intravitréenne anti-VEGF (pour néovasc. iridienne, glaucome
néovasculaire)
\item chir si RD proliférante avec hémorragie intravitréenne persistante/décollement
de rétine tractionnel
\end{itemize}
\OE{}dème maculaire
\begin{itemize}
\item photocoagulation au laser si exsudats lipidiques ou liquides
\item injection anti-VEGF mensuelle. Dexaméthasone retard possible mais cataracte,
risque d'hypertonie oculaire (30\%)
\end{itemize}
\subsubsection{Autres complications}
\label{sec:orgd60793d}
cataracte (+ freq), glaucome néovasculaire (redoutable),
paralysie oculomotrice (régresse spontanément qq mois)
\section{Glossaire}
\label{sec:orgeccb889}
\printglossaries
\end{document}
```{=org}
#+ATTR_LATEX: :environment tabularx :width \textwidth :align XX
```
Forme héréditaire de cancer Gène Name
------------------------------------------------------------- -------------- --------------------------------------------
I. Activation constitutive de la cascade de transduction
Cancer médullaire de la thyroïde (CMT) RET REarranged during Transfection
Cancer papillaire du rein MET Mesenchymal Epithelial Transition
Maladie de Cowden PTEN Phosphatase and TENsin homolog,
Maladie de Von Hippel Lindau VHL idem
Médulloblastome SUFU Suppressor Of Fused Homolog (hedgehog !)
Neurofibromatose de type I NF1 idem
Polypose adénomateuse familiale APC Adenomatous Polyposis coli
Syndrome de Gorlin PTCH PaTCH
Tumeur de Wilms WT1 Wil\'s Tumor
II\. Altération des points de contrôles du cycle cellulaire
Rétinoblastome RB1 idem
Mélanome malin CDKN2A Cyclin Dependent Kinase Inhibitor
Syndrome de Li-Fraumeni TP53 Tumor Protein
III\. Altération des systèmes de réparation de l\'ADN
Cancer du sein et de l\'ovaire BRCA1, BRCA2 BReast CAncer
Polypose adénomateuse autosomique récessive MUTYH Mut Y DNA glycosylase
MLH1 MuLt Homolog
Syndrome de Lynch MSH DNA repair MiSmatcH
Xeroderma pigmentosum XP idem
Autres
Cancers bronchiques ALK Activin receptor-Like Kinase 1
Carcinomes colique, bronchiques KRAS Kirsten RAt Sarcoma viral oncogene homolog
Carcinomes sein, ovaire HER2 Human Epidermal growth factor Receptor 2
Carcinomes+++, gliomes EGFR Epidermal Growth Factor Receptor
GastroIntestinal STromal Tumor KIT
Leucémies aigües myéloïdes FLT3 Fms-Like Tyrosine kinase 3
Leucémies, mélanomes NRAS Neuroblastoma-RAS
Lymphome de Burkitt C-MYC Cellular MYeloCytomatosis
Lymphomes du manteau Cycline D
Mélanome CD4 Cluster of differentiation 4
Mélanomes BRAF
Neuroblastomes N-MYC
Sarcomes, gliomes PDGFR Platelet-derived growth factor receptors
# Consultation
## Première
### Dossier
Général :
- Adresse
- Niveau d'étude
- ATCD
- Désir de grossesse, contraception
Arbre :
- en partant du cas index
- jusqu'aux grand-parents (préciser la ville d'origine pour une éventuelle consanguinité)
- FCS, IMG (bilan si > 4 FCS)
- nuémroter les frères et soeurs avec détails en dessous (nom, date de naissance, ATCD)
### Interrogatoire
ATCD: handicap (ULIS, CLIS ?), décès avant 65A
HDLM:
- grossesse : spontanée, écho, médicamements, toxiques (not. professionnel), fièvre, voyage
- naissance: terme, méthode, APGAR, poids, taille, PC,
(utiliser audiprog pour courbes: noter percentils [notmale = P3-P97, soit -2DS, +2DS)
- développement:
- âge des différentes aquisitions (cf echelle de Denver) : assis [sans appui à 9 mois], marche 4 pattes, debout, marche seul [12-18mois], 1er mots [12-18mois], fait ses nuits, propreté [à 2 ans, propre le jour. nocturne = variable])
- stéréotypie, réveils nocturnes avec cauchemars, sociabilité, trie nourriture, ambiance avec les frères et les soeurs
- compléter les courbes de croissance (poids, taille, PC)
### Examen
Photos++ : visage F+P des 2 côtés, en slip position anatomique (F+P x2), pieds, mains +/- tâches, anomalies, ongles
### Explication et consentement
Consentement à faire signer
- Si mineur : 3 consentement = 1 pour chaque parent (DNAthèque), 1 pour l'enfant (CGH, DNAthèque)
- révocable à tout moment (oral)
- Expliquer les limites de l'analyse (bilan de débrouillage, probablement négatif, pour ne pas passer à côté d'un grand syndrome, variants, compliqué)
Permission pour photo à faire signer
### Examens à prescrire
CGH = en première intention (=ACPA) pour les CNV
Puis exome (voit "tout")
NB : panels : Lyon pour neuro, Paris pour tout (not. épilepsie, corps calleux), Lille pour la surdité (demander GJB2)
Lyon = exome
Centogène = exome
Essayer de récupérer les fiches cliniques à jour
Pour surdité, récupérer bilan ORL
## Rendu
Si positif, par PH
Faire réexpliquer
## Suivi
- Comment se passe l'école, grandit bien (comparer à la littérature)
- Vérifier que la prise en charge est conforme à la littérature/PNDS
- Refaire photo, poids, taille
# Outils
Nomenclature variant :
NM_GEN.TRANSCRIT:c00X A>B
- NM_GEN = transcrit codone avec GEN le numéro (NP si protéine)
- TRANSCRIT = numéro du transcrit (attention à la numérotation avec centogène)
- c : codant
- 00X : position *dans le transcrit* !
- A>B : mutation. Exemple
- Leu1567Val : Leucine -> Valine = missense (aka tronquan
- Leu1567= : synonyme
- Leu1567* : stop
- Leu1567- : intron
Site :
- UCSC : "contient tout" mais nécessite un temps d'apprentissage
- VARsome : score pathologique pour les variants. Utile pour les VOUS (variants of unknown significance)
- OMIM : description des syndromes (notamment les modes de transmission). Valeur sûre
- Genereviews : idem mais plus complet et plus à jour
- AMELIE pour faire une revue rapide de la biblio
- HPO : se faire une idée du syndome, filtrer variant VUS => plutôt utiliser Pubcase finder (liste symptômes)/Monarch/Phenomiser
Score importants :
- CADD : entre 0 et 40 et patho si > 15. Accesible sur UCSC mais pas sur Varsome
- SIFT/SIFT 4G
- PolypheCSC mais pas sur Varsome. Non accessible sur Varsome
Remarques : toujours vérifier si on est en hg19 ou 38 !
Autres site :
- Genematcher : pour trouver des phénotypes nouveaux sur un gène
- SMART pour les domaines de protéines
### Organisation de l'internat
### Avis réa ped
Au téléphone : préciser clinique, quels syndromes sont sopçonnées
Demander à une des PH d'être référente
Exome en urgence (2 semaines)
Examen clinique avec infirmier/interne + photo
# Biologie
## Structure de l\'ADN et ARN
L\'ADN et l\'ARN sont des acides nucléiques, c\'est-à-dire des chaînes
(polymères) de nucléotide. Un nucléotide est composé de
- un groupe phosphate
- une base azotée
- parmi guanine, adenine, cytosine et thymine (ADN)
- ou guanine, adenine, cytosine et *uracil* (ARN)
- un sucre formé de 5 atomes de carbones.
- soit du ribose pour l\'ARN (Acide *Ribo* Nucléique)
- si du désoxyribose pour l\'ADN (Acide *Désoxyribo* Nucléique)
![](../images/genetique/nucleotides.jpg)
### Architecture
1. Séquences répétées
2. Séquences spécifiques
## Rôles de l\'ADN et ARN
![](../images/genetique/adn.png) L\'ADN est dans le noyau mais les
réactions chimiques se passent dans le cytoplasme. Il faut donc un
intermédiaire, l\'ARN, qui va permettre le contrôle de ces réactions par
l\'ADN.
### Types d\'ARN
Les ribosomes produisent des protéines dans le [cytoplasme]{.ul} à
l\'aide de l\'**ARN messager** qui contient la séquence à coder, et de
l\'**ARN de transfert** qui transporte les acides aminés (= blocs
servant à construire les protéines). Les ribosomes servent donc
d\'\"usine\" de production dans le cytoplasme.
```{=org}
#+attr_html: :width 400 px
```
![](./images/ribosomes.png) L\'**ARN ribosomal** construit des blocs de
base des ribosomes dans le nucléole (appartenant au noyau) mais les
ribosomes seront finis d\'être assemblés dans le cytoplysme
Le **micro-ARN** ne code pas mais sert à réguler l\'expression des
gènes. Il va se placer sur une parte de l\'ARN messager avant le
\"traitement\" par le ribosome et va désactiver la traduction de cette
partie. *NB: il existe des versions synthétiques des micro-ARN
(silencing ARN en anglais)*
## Contrôle de l\'activié génétique
### Régulation génétique
Toutes les cellules contiennent le même code génétique mais les gềnes
exprimés ne sont pas les même (myocyte VS cellule rénale).
L\'\"expression\" se juge en fonction de la production des protéines
(qui sont les \"agents\" de l\'ADN)
- \"Promoteur\" basal = le point de départ de la transcription. Or ce
promoteur est influencé par un autre promoteur, en amont, qui va
l\'influencer via des protéines. Et va donc influencer la
traduction.
- enhancer
- insulators : sépare les gènes désactivés des gènes activés
## Mitose et meiose
![](./images/pcr.png){width="400 px"}
## PCR
![](./images/mitose_meiose.png){width="400 px"}
# Syndromes
## Anomalies de nombres de gonosomes
### Turner
- 45, X
- 1/2500
- naissance:
- petite taille, lymphoedème des mains et pieds, excès de peau au
niveau de la nque
- coarctation de l\'aorte, rein en fer à cheval
- enfance : petite taille
- ado : aménorrhée primaire
- Pas de déficience intellectuelle (sauf rares cas)
- Grossesse possible (don d\'ovocyte + surveillance)
### Klinefelter
- 47, XXY
- 1/700 et 1/1000
- diagnostic à la puberté : petit volumes testiculaire +/- signes
hypogonadismes Découvert sur infertilité surtout
- Nombreuses mosaïque
### 47,XXX
- 1/1000
- fertilité, morphologie normale, QI légèrement diminué
- taille supérieure moyenne
### XXX
- 1/1000
- fertilité, morphologie normale, QI légèrement diminué
- taille supérieure moyenne
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\newacronym{CPRE}{CPRE}{Cholangio-pancréatographie rétrograde endoscopique}
\usepackage{adjustbox}
\newacronym{DT}{DT}{Delirium tremens}
\newacronym{ID}{ID}{Immunodéprimé}
\newacronym{HSH}{HSH}{Hommes ayant des relations sexuelles avec des hommes}
\newacronym{DO}{DO}{Déclaration obligatoire}
\newacronym{CHC}{CHC}{Carcinome hépato-cellulaire}
\newacronym{OGD}{OGD}{Oestro-gastro-duodénale}
\newglossaryentry{trophozoïtes}{name={Trophozoïtes},description={Formes végétatives mobiles}}
\newacronym{CST}{CST}{Coefficient de saturation de la transferrine}
\newglossaryentry{sdmetabolique}{name={Syndrome métabolique},
description={$\diameter \ge 94$ cm $\male{}$, 80 cm $\female{}$,
TG $\ge$ 1.7mmol/L, HDL < 1 mmol/L $\male{}$ ou 1.3mmol/L $\female{}$,
PAs $\ge 130$ mmHg ou PAd $\ge 85$ mmHg, glycémie jeun $\ge$ 1 g/L
}}
\newacronym{RGO}{RGO}{Reflux gastro-oesophagien}
\newacronym{IS}{IS}{Immunosuppresseurs}
\newacronym{HMG}{HMG}{Hépatomégalie}
\newacronym{SMG}{SMG}{Splénomégalie}
\newacronym{VBP}{VBP}{Voie biliaire principale}
\newacronym{BGT}{BGT}{bilirubine glucoronide-transférase}
\author{Alexis Praga}
\date{\today}
\title{HGE}
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\begin{document}
\maketitle
\tableofcontents
\section{74 : Addiction à l'alcool}
\label{sec:org9f62e29}
\subsection{Définition}
\label{sec:org4ddba54}
\begin{itemize}
\item Non-usage
\item Usage simple
\item Mésusage :
\begin{itemize}
\item risque
\item nocif
\item dépendance : 3 parmi \{désir puissant, difficulté à contrvôler l'utilisation,
sd de sevrage, tolérance, abandon d'autres plaisirs/intérêt, consommation
malgré conséquences nocives\}
\end{itemize}
\end{itemize}
\subsection{Étiologie}
\label{sec:orgac16204}
Génétique (40-60\%), ATCD paternel, personnalité antisociale, facteurs
socioculturels.
Anatomie : noyau accumbens.
\subsection{Épidémiologie}
\label{sec:org4badc67}
Consommation : \dec{} vin, \inc{} boissons peu/très alcoolisées
Mésusage : 49 000 DC/an. Alcool = 3eme cause de DC. 2 700 DC/an sur route, 20\%
AT.
Souvent + conduite addictive (tabac, benzodiazépine).
50\% DC prématurés = pas de dépendance !
\subsection{Dépistage}
\label{sec:org1f0def7}
20-30\% adultes en CS ont un problème avec l'alcool
1 verre = 10g d'alcool pur\footnote{Contenu d'alcool = \(V_{alcool} \times \rho_{alcool}\) = degré d'alcool
\(\times V_{total} \times 0.8\). Volume en L, degré en pourcentage.}
Questionnaires : AUDIT-C, FACE
\subsection{Biologie \footnote{Biologie normale \(\ne\) pas de mésusage !}}
\label{sec:org7563e8c}
\begin{itemize}
\item alcoolémie
\item \(\gamma\)-GT : peu sensible, peu spécifique. Utile si (transaminases et
phosphatases alcalines normales) ou (transaminases < 5N avec \inc{} ASAT
\item VGM
\item transferrine désialylée
\end{itemize}
\subsection{Clinique}
\label{sec:org6cb05d4}
Intoxications alcoolique aigüe :
\begin{itemize}
\item diagnostic = alcoolémie, régression de qq heures
\item désinhibition et euphorisant puis dépression sur SNC
\item pathologique : excitomotrice, délirante, dépressive/hypomaniaque, amnéie
lacunaire, convulsivante
\item risque = coma alcoolique avec pronostic vital engagé
\end{itemize}
Coma alcoolique : alcoolémie > 3 g/L
\begin{itemize}
\item neuro : coma calme, hypotonique, mydriase bilatérale symétrique
\item dépression repsiration
\item hypotension artérielle, bradycardie, collapsus CV
\item hypothermie
\item \danger cherche : hémorragie cérébroméningée, aVC, hémato sous/extra-durale,
épilepsie, Gayez-Wernicke, encéphalopathie hépatique, \gls{DT}, infection
cérébroméningée si fièvre
\end{itemize}
Dépendance : sevrage
\begin{itemize}
\item \(\frac{1}{3}\) n'ont pas de symptômes de sevrage
\item anxiété, sueurs, tremblemens, vomissement
\item \gls{DT}, épilespise chez 5\%
\end{itemize}
Accidents du sevrage
\begin{itemize}
\item convulsions : dans 48h (mais retard possible). Sans ttt, peut évoluer vers
DT. Éliminer autres causes !
\item DT : début brutal/petits signes de sevrage/crise comitiale. Sans ttt : sd
confusionnel. Sans PEC, DC
\end{itemize}
\subsection{Complications somatiques}
\label{sec:orge5b0ba8}
\begin{tcolorbox}
5 arguments pour rapporter une pathologie à l'alcool : consommation à risque,
complication connue, tableau évocateur, pas d'autre cause, s'améliore avec le sevrage/réduction
\end{tcolorbox}
\begin{table}[htbp]
% \caption{Complications somatiques}
\centering
\begin{tabular}{ll}
\toprule
Cancer & VAS, oesophage, hépatocellulaire, colorectal, sein\\
Digestif & Maladie alcoolique du foie, pancréatite aigüe/(chronique\\
& calcifiante), oesophagite, gastrite, diarrhée montrice\\
SN & Troubles cognitifs, démence, encéphalopathies carentielles, métaboliques,\\
& atrophie cérébelleuse, épilepsie, polyneuropathies SM, neuropathie optique,\\
& traum, hémorragies cérébrales/méningées\\
CV & HTA, troubles rythme, cardiomyopathies non obstructives\\
Rhumato & Nécrose tête fémorale, ostéoporose, ostéomalacie\\
Trauma & Fracture\\
Hémato & Macrocytose, anémie, thrombopénie, leucopénie\\
Métabo & Hypoglyclémie, hyperTG, dénutrition, hyperuircémie\\
Dermato & Aggrav. psoriasis, rhinophyma\\
Psy & Dépression, trouble anxieux\\
Foetus & Dysmorphie, retard mental\\
Dysfonctions sexuelles & \\
\bottomrule
\end{tabular}
\end{table}
\subsection{PEC}
\label{sec:org9dd2327}
Attitude empathique
Intervention brève (5-20min)
Intoxication alcoolique aigüe :
\begin{itemize}
\item éliminer hypoglycémie, autre intoxication,hématome IC, hémorragies méningées \thus EC et complémentaires si trouble
\end{itemize}
conscience.
\begin{itemize}
\item \danger Vitamine B1 avant perfusion glucosée !
\end{itemize}
Usage nocif, dépendance :
\begin{itemize}
\item nocif/dépendance sans comorbidités sévères : réduction conosmmation
\item nocif et complications nombreuses/sévères : addictologie
\item dépendance sévère et comorbidité : arrêt
\item motivation++
\item surveiller ASAT, ALAT, \(\gamma\)-GT, TP, NFS
\end{itemize}
Sevrage :
\begin{itemize}
\item hospit si : ATCD complication sevrage, dépendance sévère ou avec
benzodiazépines, échec de l'ambulatoire, environnement social, terrain
vulnérable
\item arrêt, hydratation orale, vitamine B1 \textpm{} correction troubles
hydroélectriques, \textpm{} benzodiazépnie (diazépam)
\end{itemize}
Complications de sevrage :
\begin{itemize}
\item DT
\begin{itemize}
\item hospit, réhydratation IV, correction trouble hydroélectrique
\item vitamine B1 forte dose avant sérum glucosé
\item diazépam jusque sédation
\end{itemize}
\item Crises convulsive : cf sevrage
\end{itemize}
Médicaments efficaces seulement si suivi psychosocial !
\begin{itemize}
\item \dec{} consommation : nalméfène (CI : opiacés) (ou baclofène)
\item maintien abstinence : acamprosate ou naltrexone (ou disulfirame, baclofène)
\end{itemize}
Autre : PEC comorbidités psy, addictive (tabac, cannabais++), non psy, sociale
\section{163 : Hépatites virales}
\label{sec:org170d341}
Définition : processus inflammatoire du foie. Chronique si > 6 mois.
Causes :
\begin{itemize}
\item \inc{} forte des transaminases :
\begin{itemize}
\item \textbf{médicaments, virale} = \{VHA, VHB, VHC, VHE et Herpes (EBV, HSV, CMV, VZV)\}
\item migration lithiasique, hépatite auto-immune, maladie de Wilson
\end{itemize}
\item \inc{} modérée des transaminases :
\begin{itemize}
\item \textbf{alcool, sd métabolique, VHB, VHC}
\item VHE si \gls{ID}, médicaments, hépatite auto-imune, hémochromatose, maladie de
Wilson, déficit \(\alpha\)-1-antitrypsine
\item DD : maladie coeliaque, myopathie, effort violent, hémolys
\end{itemize}
\end{itemize}
Diagnostic:
\begin{itemize}
\item souvent asymptomatiques, ictère peut manquer (symptômes + 7 à 10j)
\item chercher signes de gravité :
\begin{itemize}
\item TP < 50\% = hépatite sévère \thus centre spécialisé
\item encéphalopathie \thus hospit en urgence
\end{itemize}
\item dans tous les cas : CI médicaments hépatotoxiques, neurosédatifs, éviter
contamination (VHA, VHE)
\end{itemize}
\begin{table}
\caption{Hépatites virales, résumé}
\label{tab:my-table}
\centering
\adjustbox{max width=\linewidth}{
\begin{tabular}{llllll}
\toprule
& VHA & VHB & VHC & VHD & VHE\\
\midrule
& ARN simple brin & ADN double brin & ARN simple brin & ARN simple brin & ARN\\
& Sans enveloppe & Enveloppe & & Enveloppe & monocaténaire\\
Famille & \emph{Hepatovirus} & \emph{Hepadnavirus} & \emph{Flavirus} & & \\
Transmission & Féco-orale, \acs{HSH} & périnatale, sexuelle & parentéral & sang, sexuelle & \\
& & sang, contact & & & \\
Diagnostic & IgM anti-VHA & Ag HBs & Ac antiVHC & IgM/IgG anti-delta & IgM antiVHE\\
& & & \textpm{} ARN & ARN & \\
& \acs{DO} & DO (aigüe) & & & \\
\bottomrule
\end{tabular}
}
\end{table}
\subsection{VHA}
\label{sec:org2d6b308}
Incubation 2-6 semaines
Pas d'infection chronique !
Vaccin efficace.
Fréquent. Asymptotique et bénigne le plus souvent
\subsection{VHB}
\label{sec:org1948ad3}
2 milliards porteurs d'une infection (résolue ou non).
Hépatite aigüe B :
\begin{itemize}
\item incubation 6 sem. - 4 mois
\item Morbidité/mortalité : risque de cirrhose (20\%) ou \gls{CHC}
\item \danger recherche VIH, IST, coinfection VHD.
\item chronique dans 5-10\%
\end{itemize}
Hépatite chronique B : Ag HBs positif > 6mois.
\begin{itemize}
\item asymptomatique jusqu'à cirrhose, CHC
\item 4 phases :
\begin{enumerate}
\item tolérance immunitaire (réplication virale, hépatite peu active) : AgHBe
\item clairance immunitaire (réplication virale, hépatite) : Ag HBe
\item non réplicative (réplication virale faible, pas d'activité hépatite) : Ac
anti-HBe
\item hépatite B résolue : Ac anti-HBs
\end{enumerate}
\item 40\% de mutation
\item \gls{IS} = risque de réactivation
\item CHC possible sans cirrhose \danger
\end{itemize}
\subsubsection{Traitement (chronique)}
\label{sec:orge24f5a4}
ALD, PEC 100\%
Chercher cirrhose : hypertension portable (endoscopie \gls{OGD}), prévention
hémorragies digestives, dépistage CHC (écho abdo tous 6 mois)
2 traitements :
\begin{itemize}
\item à vie : analogues nucléosidiques/nucléotidiques (entécavir, ténofovir) =
antiviral
\item 1 an : antiviral + immunomodulateur (plus rare)
\end{itemize}
Indications :
\begin{itemize}
\item ADN VHB > 2 000 UI/mL et transaminases > N ou fibrose hépatique modérée ou
activité modérée\footnote{Avec le score Metavir : activité \(\ge\) A2 et fibrose \(\ge\) F2 (entre 0 et 3,
entre 0 et 4 respectivement)}
\item ADN > 20 000 UI/mL et transaminases > 2N
\item cirrhose et ADN VHB
\item ACTD familiale de cirrhose/CHC ou atteinte extrahépatique
\item ISN
\end{itemize}
Pas indiqué en phase de "tolérance immunitaire" ou "non réplicative"
Élasticité hépatique (Fibroscan) :
\begin{itemize}
\item < 7kPa : cirrhose peu probable
\item > 17kPa : cirrhose très probable
\end{itemize}
Vaccination :
\begin{itemize}
\item obligatoire nourrison (hexavalent) : sinon rattrapage jusque 15 ans (2 inj. à
6 mois d'écart)
\item dépistage chez femme enceinte avant 10 SA : si positive, sérovaccination à la
naissance
\item professionnels de santé
\item sujet exposé
\item IgG anti-HBs seulement si contage accidentel chez non vacciné
\end{itemize}
\subsection{VHC}
\label{sec:orga8b89ef}
Pas de vaccin !
Chronique dans 75-85\%, cirrhose dans 10-20\% à 20 ans. CHC 1-4\% par an. Manifestations extrahépatiques
Aigüe :
\begin{itemize}
\item incubation très variable (7-8 sem), souvent asymptomatique
\item ARN à +1 semaine
\item Ac anti-VHC à +12semaines
\end{itemize}
Chronique : (sérologie positive, ARN détectable) > 6 mois.
\begin{itemize}
\item \danger ponction biopside non recommandée \footnote{Sans comorbidités}\thus Fibrotest, Fibromètre Fibroscan
\end{itemize}
\subsubsection{Traitement (chronique)}
\label{sec:org440df55}
Cherche cirrhose (cf VHB).
Guérison virologique.
Pas d'interféron, ni ribavirine.
Régression des lésions hépatiques si pas de cirrhose. \danger continuer
dépistage CHC
\subsection{VHD}
\label{sec:orga46f4c0}
Dépend du VHB !
\danger toujours cherche VHD chez VHB
Co/sur-infection. Risque : cirrhose, CHC
Ttt (chronique) : interféron pégylé, peu efficace
\subsection{VHE}
\label{sec:orgcc61a72}
Incubation 3-8semaines, 3-4 jours pré-ictériques.
Guérison sans séquelles en 1 mois souvent. Formes graves : hépatite fulminante, décompensation
Chez l'ID, chercher ARN pour diagnostic
\section{168 : Parasitoses digestives}
\label{sec:org39a7575}
\subsection{Téniasis : cf Tab \ref{tab:org24964bd}}
\label{sec:org8bf9a99}
\begin{table}[htbp]
\caption{\label{tab:org24964bd}
Caractéristiques des \emph{Taenia}}
\centering
\begin{tabular}{lllll}
\toprule
& \emph{saginata} & \emph{solium} & \emph{hymenolepsis} & \emph{Diphyllobothrium}\\
& & & \emph{nana} & \emph{latum}\\
\midrule
Caract & Anneaux, 4-10m, & \danger{} cysticercose\tablefootnote{Larves dans tissus SC, muscle, oeil, cerveau (HTIC, épilepsie !), moelle épinière \danger} & Petit & 10-15m, 10 ans\\
& intestin grêle & & & \\
Contam. & Boeuf mal cuit & Porc mal cuit & & Poisson mal cuit\\
Clinique & Latent & & & \\
Diagnostic & Anneaux selles/vêtement & Sérologie & \OE{}ufs dans selles & \OE{}ufs dans selles\\
& EPS & \textpm{} biopsie-exérèse & & \\
Ttt & Niclosamide & Albendazole & Niclosamidel & Niclosamide\\
& praziquantel & praziquantel & praziquantel & praziquantel\\
& & (+cortico si cérébral) & & \\
Prévention & Cuisson/congélateur\tablefootnote{> qq semaines} & & hygiène des main & Cuisson\\
\bottomrule
\end{tabular}
\end{table}
\subsection{Ascaridiose\footnote{\emph{Ascaris lumbricoides}}}
\label{sec:org287638b}
Pays tropicaux hygène insuffisante
Ingestion \oe{}ufs
Phase de migration : signes allergiques, sd de Löffler\footnote{Fièvre, toux, dyspnée, infiltration radio fugace, hyperéosinophilie}. Phase d'état :
troubles digestifs
Complications : appendicite, angiocholite, pancréatite, occlusion intestinale
Diag: \oe{}ufs dans selles (+2 mois)
Ttt : flubendazole, albendazole
Prév: lavage mains, fruits, crudités, péril fécal
\subsection{Oxyurose \footnote{\emph{Enterobius vermicularis}}}
\label{sec:orgee706ce}
Fréquent (enfants âge scolaire)
Clinique : prurit anal/asymptomatique
Diag : vers blancs mobiles dans selles/Scotch test
Ttt : flubendazole, albendazole, pyrantel. Traiter toute la communaute !
\subsection{Giardiose\footnote{\emph{Giardia intestinalis}}}
\label{sec:orge5fa6ee}
Ingestion eau, aliments contaminés, féco-oral
Clinique :
\begin{itemize}
\item asymptomatique
\item atypique : \{brutal, selles nbs liquide, douleurs épigastriques\}
\item subaigu/chronique (mois/année)
\item malabsorption et dénutrition si déficit immunitaire
\end{itemize}
Diag : kystes/\gls{trophozoïtes} à l'EPS. \texttimes{} 3 si besoin. Biopsie duodénale
si chronique
Ttt : métronidazole (contrôle + 1mois)
Prév : hygiène eau, boisson, aliments
\subsection{Am\oe{}bose\footnote{\emph{Entamoeba histolytica}}}
\label{sec:org8c4004d}
Une des parasitoses les plus fréquentes. Kyste ou trophozoïtes.
Cont: féco-orale\footnote{Ou sexuelles oro-anales}
Dissémination par voie sanguine depuis tube digestif : atteinte intestinale
(tous âges) ou foie (\male{} 20-50 ans), poumons, cerveau
Forme intestinale
\begin{itemize}
\item (sub)Aigue, diarrhée non hémorragiques, douleurs abdo, sans fièvre ni AEG
\item Autres formes : dysentérique aigüe, fébrile, colite aigüe grave amibienne
= urgence
\end{itemize}
Forme hépatique : rare, collection purulente, après am\oe{}bose intestinale
\begin{itemize}
\item qq jours, fièvre élevée, frissons, douleur hypochondre droit/scapula droit
\item foie volumineux, douleureux palpation
\item hyperleucocytose à PNN, légère \inc{} transaminases, phosphatases,
bilirubinémie
\item DD : abcès du foie à pyogènes, tumeur maligne nécrose
\item complications rares, graves
\end{itemize}
\subsubsection{Diagnostic}
\label{sec:org1f0e171}
Intestinale
\begin{itemize}
\item EPS : seulement kyste, et confusion \emph{Entamoeba histolycita} et \emph{dispar} (non
patho)
\item endoscopie : "boutons de chemise", sérologies (sur biopsie)
\end{itemize}
Hépatique
\begin{itemize}
\item sérologie et clinique et écho typique \(\approx\) certittude
\item répéter si séro négative. Si négative et sans argument : ponction avec écho
\end{itemize}
\subsubsection{Traitement}
\label{sec:org88e1b52}
Intestinale : curatif/probabiliste: métronidazole 10 j puis am\oe{}bicide de
contact 10j (tiliquinol)
Hépatique : imidazolé et am\oe{}bicide de contact. Ponction seulement si abcès superficiels au bord
de la rupture
\subsection{Hydatidose}
\label{sec:orgad6a46b}
Parasite adlute (anneaux), hydatide (larve).
Cycle : intestin grêle du chien -> \oe{}ufs -> mammifères herbivores : hydatide
dans foie/poumon -> ingestion de protoscolex par le chien. Homme = accident
Clinique : asymptomatique, lent (années)
\begin{itemize}
\item hépatique :
\begin{itemize}
\item fréquent, 10-15ans. HMG isolée, indolore, bien toléré. pas
de ponction !
\item complications : compression voie biliaires ou veineux porte/cave,
fissuration/ruputre (réaction allergiques, hydatidose secondaire),
infection après fissure
\item IRM hépatique
\end{itemize}
\item autres : radio thorax suspectes, même complications. N'importe quel
endroit. Os = mauvais pronostic
\end{itemize}
Diag: sérologie (90\% hépatique, 70\% pulmonaire). Pas de ponction !!
Ttt : chir (albendazole seul sinon)
Prév : chien, mesures sanitaires
\section{197 : Transplantation d'organes}
\label{sec:org036554a}
Indication num. 1 de greffe hépatique : CHC
Complications :
\begin{itemize}
\item précoces = vasculaire, bilaire et sepsis
\item tardives : récidive maladie initiale, cancers de novo, CV
\end{itemize}
Survie : 62\% à 10 ans
Score "foie" pour défaillance chronique
Consentement présumé, gratuité du don, anonymat donneur-receveur
\section{215 : Pathologies du fer}
\label{sec:org0a499f7}
Absoprtion par les entérocytes du duodénum et jéjunum proximal. Puis stocké par
ferritine ou exporté par ferroportine dans le plasma. Il y est alors transporté
par transferrine.
Régulation : hepcidine influence l'absorption.
Réserve de fer : ferritine (foie, moelle osseuse, rate)
\subsection{Exploration}
\label{sec:org1d493ed}
\begin{itemize}
\item Ferritine = 1ere intention : si \dec, carence en fer, si \inc, pas forcément
un excès\ldots{}\footnote{Lyse cellulaire, sd inflammatoire, alcool, sd métabolique, sd
paranéoplasique, hyperthyroïde}
\item \gls{CST} = transport du fer. Montre surcharge mais sans la quantifié. \dec si
sd inflammatoire, \inc insuf hépatocellulaire, sd néphrotique, sd
inflammatoire
\item récepteur soluble de transferrine = 2eme intention
\end{itemize}
\subsection{Anémie par carence martiale}
\label{sec:org6fac169}
\subsubsection{Mécanisme}
\label{sec:org25cf649}
\begin{itemize}
\item Saignement : occulte. Digestif ou gynéco si femme non ménopausée
\item Malabsorption : hypochlorhydrie franche\footnote{Acide chlorhydrique garde Fe sous forme soluble}, altération muqueuse
duodénojéjunale, court-circuit duodénojéjunal. Maladie c\oe{}liaque ++
\item Carence d'apportA : 1mg/j (\male) ou 2 mg (\female). \inc besoins ou régime
végétarien très strict
\end{itemize}
\subsubsection{Diagnostic}
\label{sec:org8ad765b}
Pâleur, asthénie. Chercher signes de gravité.
Diagnostic biologique : anémie hypochrome microcytaire
\begin{itemize}
\item 1ere intention : ferritine \inc
\item différencier d'un sd inflammatoire et thalassémie (cf encadré)
\end{itemize}
\begin{tcolorbox}
Carence en fer = ferritine \dec, fer sérique \dec, CST \dec et transferrine \inc
\end{tcolorbox}
\subsubsection{Étiologie}
\label{sec:org601cad3}
Clinique : ATCD, médic, gynéco, régles, troubles dig. Chercher masse tumorale,
méléna
Examens :
\begin{itemize}
\item 1ere intention : gynéco, endoscopie \gls{OGD} et coloscopie :
\begin{itemize}
\item NB: > 5 Ans : coloscopie systématique (K colique) \danger
\item pas de lésion à l'endoscopie \thus biopsie duodénale \textpm{} gastrique
\item \textbf{\textbf{pas}} des causes : hernie hiatale sans érosion, polype colique non ulcéré
< 15mm
\end{itemize}
\item 2eme intention : vidéocapsule endoscopie (sauf sis sténose), entéroscopie (biopsie),
scanner spiralé (tumeurs du grêles), scintigraphie au pertechnétate-99m
(diverticule de Meckel)
\item Si exploration négatives : supplémentation Fe
\end{itemize}
\subsubsection{Traitement}
\label{sec:org08b1fe2}
Cause si possible.
Martial : voie orale 150 à 300mg/j hors repas (selles noires, interactions
possibles). IV si intolérance. Contrôle ! Traiter jusque normalisation ferritinémie
\subsection{Surcharge en fer}
\label{sec:orga7f05c3}
Diagnostic =
\begin{itemize}
\item CST < 45\% \thus \textbf{pas} origine génétique. si Ferritine \inc, hépatosidérose
métabolique (\(\in\) sd métabolique)
\item CST > 45\%, répéter test. Si positif et pas d'autres causes, chercher mutation C2V2Y du gène HFE : si
oui, diagnostic positif
\item \textpm{} IRm hépatique
\end{itemize}
DD : surcharge d'apport, malade chronique du foie, porphyrie cutanée, hémopathie
\subsubsection{Hémochromatose}
\label{sec:orgafef2b7}
10 à 20\% des homozygotes ont des symptômes. 4 phases :
\begin{enumerate}
\item asymptomatique
\item surcharge Fe biologique : CST > 45\%, ferritine normale
\item symptômes clinique (30 ans)
\item lésions viscérales (40-60 ans)
\end{enumerate}
Clinique :
\begin{itemize}
\item asthénie
\item mélanodermie, dépilation et cheveux fins et cassants
\item ostéoarticulaire : petite articulations de la main. RX : athropathie sous
chondrale
\item HMG : risque CHC élevé
\item diabète tardif, hypogonadisme hypogonadotrope, cardiqaque
\end{itemize}
Si stade \(\ge\) 2, chercher atteinte pancréas, foie, coeur, gonades, os
Diagnostic des lésions hépatiques : biopsie hépatique \textpm{} IRM hépatique
Diagnostic génétique : individuel (cf supra) ou familal (apparenté 1er degré)
Traitement :
\begin{itemize}
\item soustractions sanguines : 7mL/kg/semaine \(\ge\) 550mL tous les 7-10j puis 1-3
mois. Contrôle : PA, pouls, NFS. \danger arrêt si Hg < 11g/dL
\item chélateurs du fer sinon
\end{itemize}
Suivi des complications cirrhose si besoin
Pronostic \(\approx\) population générale avant cirrhose.
\subsubsection{Hépatosidérose métabolique++}
\label{sec:org449e6d7}
\gls{sdmetabolique} et surcharge en fe
Ferritinémie \inc, CST normal \thus IRM hépatique.
surcharge modérées mais les atteintes peuvent évoluer.
PEC : troubles lipidiques, HTA, diabète, activité physique, équilbre alim. Pas
forcément normalisation Fe !!
\printglossaries
\section{248 : Dénutrition}
\label{sec:org5733b2c}
Référence nutritionnelle pour la population (couvre besoin). Sinon : apport
satisfaisant (apport moyen d'une population)
Besoins
\begin{itemize}
\item Eau : 2L/j \female{}, 2.5L/j \male{} (\(\approx\) 1L dans aliments)
\item Energie : 2400-2500 kcal (ou 35kcal/kg)
\begin{itemize}
\item base = 1500kcal/j \male{} (formule de Harris et Benedict)
\item thermorégulation (< 5\%), alimentation (10\%)
\item musculaire (15-30\%), 150-200 kcal
\item 1g glucide = 1g protide = 4 kcal; 1g lipide = 9 kcal, 1g alcool = 7 kcal
\end{itemize}
\item Nutriments : 10-20\% protides, 35-40\% lipides, 40-55\% glucides avec 0.75 g/kg/j
de protides et acide linoléique et acide alphalinolénique
\item Minéraux, vitamines : calcium, fer, folates, vitamines A, B1, B12, C, E, D
\item Âgé : \inc ea, calcium, vitamine D, folate. 30 kcal/kg/j
\end{itemize}
\subsection{Evaluation}
\label{sec:org3b25a70}
Clinique :
\begin{itemize}
\item interrogatoire (contexte patho, activité physique, fatigabilité, poids
antérieur, anorexie, modification apports
\item EC :
\begin{itemize}
\item épreuve du tabouret, \oe{}dèmes délives, peau, ongles, cheveux, lèvre,
langue, faciès, masse musculaire
\item poids vs poinds antérieur et idéal. IMC \(\in [18.5, 25] kg/m^2\) si < 70 ans
et \([21, 25] kg/m^2\) après\footnote{\danger Obésité sarcopéniques}
\item épaisseur cutanées tricipitale, périmètre bras au milieu
\end{itemize}
\item Biologie :
\begin{itemize}
\item créatinine urinaire sur 24h (\(\approx\) masse musculaire)
\item albuminémie (\(t_{1/2} = 20\) j) : \dec si malnutrition, fuite rénale/digestive\footnote{Ou hémodiluton, insuffisance hépatocellulaire, sd infectieux/inflammatoire}
\item transthyrétine (\(t_{1/2} = 2\) j !)
\end{itemize}
\end{itemize}
Evaluation : protéino-énergétique ou protéique, aigüe ou chronique, grave ?
\subsection{Dénutrition}
\label{sec:org78e4931}
Rechercher chez tout malade en début d'hospitalisation et toutes les semaines :
\begin{itemize}
\item IMC insuffisant ou perte de poids de 2\% (1 semaine) ou 5\% (1 mois) ou 10\% (6
\end{itemize}
mis)
\begin{itemize}
\item doser albuminémie
\end{itemize}
Mécanisme = énergétique (balance énergétique négative), protéique (bilan azoté
négatif) ou mixte
Causes :
\begin{itemize}
\item \dec apport alimentaire = énergétique (marasme).
\begin{itemize}
\item Volontaire, dysphagie, trouble déglutition, troubles digestifs
post-prandiaux
\item Maldigestion, malabsorption intestinale
\end{itemize}
\item Hypermétabolisme : affection septiques, néoplasique, inflammatoire
grave/étendues
\item Perte protéique anormale : cutanées, urinaires\footnote{Perte de plasma et protéines \thus hypoalbuminémie, \oe{}dèmes rapides}
\end{itemize}
Conséquence : sévère et épuisement des réserves lipidiques \thus pronostiv vital
!
\begin{itemize}
\item muscle (sarcopénie) \thus \dec force musculaire, \inc fatigabilité, \dec
ventilation
\item réponse aux aggresion inadaptée
\end{itemize}
PEC :
\begin{itemize}
\item supplémentation alimentaire : débit énergétique basal \texttimes{} facteur
\item nutrition entérale (sonde dans tube digestif supérieur) par voie
nasogastrique, gastrostomie, jéjunostomie.
\begin{itemize}
\item Bien tolérée
\item Broncho-pneumopathie d'inhalaion \thus faible débit et positino demi-assise
(nuit++)
\item 30 kcal/kg/j et 1.25 g/kg/j protéines chez dénutri chroniquue
\end{itemize}
\item nutrition parentérale : cathéter dans veine cave supérieure
\begin{itemize}
\item complication infectieuses (5-20\% patients) cher, difficile à domicile
\end{itemize}
\end{itemize}
À envisager si patho digestive, alimentation orale impossible/insuffisante,
pré-opératoire si dénutri
Privilégier nutrition entérale
\section{268 : Douleurs abdominales/lombaires aigües}
\label{sec:orge84ddc5}
\subsubsection{Clinique}
\label{sec:org319899a}
Irradiation : pointe omoplate droite (hépatobiliaire), épigastrique
(bilio-pancréatique), OGE (urologique)
Installation : brutale (perforation, embolie, rupture), rapide (obstacle,
ischémie, torsion), progressive (inflamation, infection, obstruction)
Exacerbé par marche, inspiration et calmée par décubitus : inflammation
intra-abdominale), soulagement par l'alimentation (ulcère), antéflexion
(pancréas), vomissement (obstruction, occlusion intestinale)
Déclenché par : alcool (pancréatite, hépatique alcoolique), médicaments (AINS,
aspirine), voyage récent
Terrain :
\begin{itemize}
\item signes généraux/organe
\item \female{} penser grossesse extra-utérine, gynéco
\item médicaments : AINS, aspirine (ulcère, gastrite aigüe), anticoagulant
(hématomes des muscle [paroi abdo. antérieure, psoas, paroi tube digestif),
corticoïdes
\end{itemize}
\subsubsection{Examen}
\label{sec:orgedd9e65}
\begin{tcolorbox}
Toujours chercher : cicatrice abdo, hernie, défense/contracture, toucher pelviens
\end{tcolorbox}
\begin{itemize}
\item Fièvre, FC, PA, choc
\item Ictère, pâleur, cyanose, cicatrice abdo++, hernie ballonnement, 0 mouvement
respi
\item palpation++
\item percussion : matité déclive/globe vésical/tympanisme (occlusion ou
pneumopéritoine)
\item auscultation : silence, bruits hydroaériques, souffle abdo (anévrisme de
l'aorte)
\end{itemize}
NB : irritation péritonéale : douleur à la décompression, défense/contracture
abdo, douleur toucher pelvien
\subsubsection{Examens complémentaires}
\label{sec:org3584305}
\begin{tcolorbox}
Aux urgences, penser : BU, \beta-HCG, ECG (IDM, péricardite)
\end{tcolorbox}
\begin{itemize}
\item Biologie : NFS, CRP, iono, hémoc si fièvre, lipasémie, \{transaminases, \(\gamma\)-GT,
phosphatases alcalines, bilirubine totale\} si clinique, BU, \(\beta\)-HCG,
\{hypercalcémie, acidocétose diabétique, insuf. surrénale aigüe\}, TP-TCA et
Rh-RAI si hémorragie digestive
\item ECG : infarctus antérieur, péricardite
\item RX pulmonaire si cause pleurale, pulmonaire
\item Echo si suspicion bilio-pancréatique, gynéco, urinaire, infection sous-abdo
\item \emph{Scanner abdo} : 1ere intention si diverticulite sigmoïdienne, occlusion par
obstruction, sd péritonéal
\end{itemize}
\subsection{Principaux tableaux}
\label{sec:org01a622d}
Douleur biliaire ou colique hépatique
\begin{itemize}
\item épigastre/hypochrondre droit (irradie épaule/omoplate droite)
\item forte intensité, plusieurs heures
\item aggravée par inspiration
\item signe de Murphy
\item causes : \emph{complications lithiase bilaire}, K vésicule/voie biliaire
principale, parasite, hémobilie
\end{itemize}
Douleur gastrique ou duodénale
\begin{itemize}
\item épigastre, torsion sans irradiation
\item parfois très intense, 30min à plusieurs heures
\item calmée par aliments, anti-acides, pansements gastrique
\item EC normal ou douleur provoquée du creux épigastrique
\item causes : maladie ulcéreuse gastrique/duodénale, K gastrique, dyspepsie fonctionnelle
\end{itemize}
Douleur colique
\begin{itemize}
\item épigastre/en cadre/fosses illiaque,/hypogastre (irradie le long du cadre
colique)
\item qq minutes-qq heures
\item calmée par selles/gaz++, antispasmodique
\item examen : douleur en cadre (colique)
\item causes : troubles fonctionnels intestinaux, K côlon, colites
inflammatoires/infectieuses/ischémiques
\end{itemize}
Douleur pancréatique
\begin{itemize}
\item épigastre/sus-ombilical, crampe (irradie dos)
\item très intense, "coup de poignants", pluiseurs heures
\item déclenchée par repas gras, alcool
\item soulagée par antéflexion, aspirine
\item examen : douleur provoquée épigastrique/périombilicale
\item causes : pancréatite aigüe/chronique, K pancréas
\end{itemize}
Ischémie intestinale aigüe = urgence avec pronostic vital \footnote{Diagnostic difficile\label{org2da56b0}}
\begin{itemize}
\item y penser si terrain vasculaire
\item \emph{douleur abdo} : inaugurale aigǜe ou angor mésentérique puis diffuse rapidement
à tout l'abdomen. Intensite \inc{} sans répit
\item et \emph{terrain à risque}
\item angioscanner multibarretes en urgence
\end{itemize}
Ischémie intestinale chronique \textsuperscript{\ref{org2da56b0}}
\begin{itemize}
\item artérite oblitérante, athéromateuse++, inflammoire/radique
\item angor mésentérique avec douleurs abdo chroniques diffuses postprandiales
précoces 1-3h
\item peur alimentaire
\item perte poids
\item âgé, terrain CV
\end{itemize}
\subsection{Grandes causes}
\label{sec:org9868973}
Douleur épigastriques :
\begin{itemize}
\item ulcère (hyperalgique, perforation), pancréatite aigüe
\item biliaire (colique hépatique, migration lithiase, cholécystite)
\item autres : aorte \footnote{Dissection/anévrisme}, cardiaque \footnote{Péricardite, infarctus postéro-inf}, pulmonaire \footnote{Pneumopathie infeciteuse, pleurésie}, digestive \footnote{Gastrite, \oe{}sophagite, appendicite aigüe}
\end{itemize}
Douleur de l'hypochondre droite :
\begin{itemize}
\item hépatobilaire : colique hépatique, cholécystite, angiocholite, tumeur/abcès du
foie, affections héaptique
\item ulcère perforé, appendicite sous-hépatique, abcès sous-phrénique,
pulmonaire, urinaire
\end{itemize}
Douleurs de l'hypochondre gauche (rare)
\begin{itemize}
\item queue du pancréas, ulcère gastrique, gastrite aigǜe
\item sd de l'intestin irritable, diverticulite de l'angle colique gauche
\item splénique, pleuropulmonaire, urologique, abcès sous-phrénique
\end{itemize}
Douleurs de l'hypogastre :
\begin{itemize}
\item gynéco, urologique, colique
\item appendicite pelvienne, diverticule de Meckel, sd de l'intestin irritable
\end{itemize}
Douleurs de la fosse illiaque droite :
\begin{itemize}
\item chirurgicale : appendicite, diverticule de Meckel, diverticulite (côlon
droit/sigmoïde), hernie étranglée, grossesse extra-utérine, torsion
d'annexe/fibrome utérin, anévrisme artériel iliaque
\item médicale : sd de l'intestin irritable, adénolymphite mésentérique, torsion de
frange épiploïque, iléite, salpingite, kyste ovarien, cystite, colique
néphrétique, abcès/hématome du psoas/grand droit
\end{itemize}
Douleurs de la fosse iliaque gauche
\begin{itemize}
\item sd de l'intestin irritable, colite diverticulaire, colite, K côlon gauche
compliqué, fécalome
\item grossesse extra-utérine, torsion d'annexe/fibrome, salpingite, colique
néphrétique, pyélonéphrite, cystite
\item anévrisme artérial iliaque, abcès/hématome du psoas/grand droit
\end{itemize}
Douleurs lombaires :
\begin{itemize}
\item urologique, appendicite rétrocaecale, abcès/hématome psoas, fissuration anévrisme de l'aorte, douleur rachis
\end{itemize}
Douleurs abdominales diffuses
\begin{itemize}
\item péritonite, occlusion, ischémie/infarctus mésentérique, médicales (cf supra)
\end{itemize}
\subsection{Douleurs pièges}
\label{sec:orgc1b1e69}
\begin{itemize}
\item IDM : douleur épigastrique, FR coronaire \thus ECG
\item Insuffisance surrénale : contexte, douleurs intenses diffuse, abdo souple, TR
indolore. HyperK, hypoglycémie. Urgence
\item Hypercalcémie : urgence
\item Acidocétose diabétique : diabète connu/situation révélatrice. Sd
polyuropolydipsique/trouble neur/Kussmau et haleine cétosique \thus
hyperglycémie, cétonurie, acidose
\item Acidocétose alcoolique : alcool et jeûne. Acidose métabolique, \inc corps
cétoniques, glycémie \dec
\item Maladie périodique (fièvre méditerranéenne) : jeune, ACTD crises. Sd
inflammatoire bio \thus mutation gène de la marénostrine
\item TRAPS sd \thus mutation gène TNFRSF1A
\item Sd hyper-IgD \thus doser IgD
\item Périhépatite : femme, péritonique, vénérienne. Sd inflammatoire, écho
hépatobiliaire normale.
\item Porphyrie hépatique aigüe intermittente : femme jeune avec
infection/médic. Urine rouge porto \thus doser acide delta aminolévulinique et PBG
\item Oedème angioneurotique : \oe{}dème récidivant dans l'enfants \thus diag = \dec
inhibiteur C1-estérase, C4, C3 normal
\item Sevrage opiacés, ingestion teoxiques, amphétamines, dérivés ergo de seigle,
intoxication au plomb
\item Purpura rhumatoïde
\item Autre vascularite : y penser si purpura
\item Drépanocytose : stress, effort physique, soleil. Anémie, hyperleucocytose
\item Phéochromocytome : crise brutale avec douleurs montantes et se finit par envie
impérieuse d'uriner abondamment
\item Douleurs rachidiennes projetées : zona, sd de Cyriax (compression du nerf intercostal)
\end{itemize}
\section{268 : Reflux gastro-\oe{}sophagien}
\label{sec:orgb56dc4c}
\gls{RGO} = passage à travers le cardia d'une partie du contenu gastrique hors
effort. Pathologique = symptômes/lésions d'oesophagite
20-40\% des adultes ont un pyrosis
Mécanismes :
\begin{itemize}
\item défaillance du sphincter inférieur de l'\oe{}sophage
\item hyper pression abdo, stase gastrique
\item hernie hiatale = glissement ou roulement mais pas de lien avec RGO
\end{itemize}
Signes fonctionnels :
\begin{itemize}
\item pyrosis, régurgitations = quasi pathognomonique
\item extra-digestifs (pulmonaire, ORL, cardiaque)
\item RGO compliqué\footnote{Sévérité des symptômes indépendantes de l'intensité des lésions !} : ulcérations du bas \oe{}sophage (étendues,
confluentes/circonférentielles) \thus risque = hémorragi digestive, sténose
\oe{}sophagienne
\end{itemize}
Endobrachy\oe{}sophage : épithelium normal de l'\oe{}sophage remplacé par épithelium
métaplastique intestinal \thus surveillance régulière (risque d'ulcère,
dysplasie, adénocarcinome)
\subsubsection{CAT}
\label{sec:org47a2b34}
Interrogatoire : éliminer sd de rumination (pas de brûlure, nausée,
vomissement).
< 50 ans, pyrosis ou régurgitation, 0 dysphagie, 0 amaigrissement, 0 anémie :
pas d'examen complémentaire
Sinon : endoscopie OGD
\begin{itemize}
\item 1ere intention > 50 ans ou atypique
\item affirme diagnostic si perte de substance épithéliale, peu profonde
\item sans anomalies et (pré-chirurge ou persistance ou extradigestive), faire
ph-métrie des 24h
\end{itemize}
Autres : impédancemétrie \oe{}sophagienne (reflux persistant), manométrie
\oe{}sophagienne (si opération)
\subsubsection{Traitement}
\label{sec:org6e7373f}
Anti-acides, inhibiteurs de la sécrétion gastrique (IPP), protection de la muqueuse
\oe{}sophagienne (alginates)
\dec{} poids, arrêt tabac et alcool, tête de lit à 45\(^{\circ}\), 3h entre diner
et coucher
\begin{itemize}
\item RGO sans \oe{}sophagite: anti-acides/alginates/anti-H2 si < 1/semaine. Sinon
IPP demi-dose puis long cours
\item RGO avec \oe{}sophagite : IPP demi dose (ou pleine si sévère) 4 semaines
(ou 8) puis long cours
\item RGO principalement extra-digestif : pas d'IPP
\item RGO résistants IPP : non acide, erreur diag, \inc dose. Sinon chir
\item Sténose peptique : IPP pleine dose
\item Endobrachy\oe{}sophage : IPP si symptomatique ou \oe{}sophagite
\end{itemize}
\subsubsection{Chirurgie}
\label{sec:org34208aa}
Fundoplicature complète (Nissen)
\section{269 : Ulcère gastrique et duodénal}
\label{sec:orgdafa4e6}
\subsection{Ulcère gastrique et duodénal}
\label{sec:org18bdddb}
Déf: perte de substance en profondeur (jusque musculeuse). Chronique si socle
scléro-inflammatoire
\begin{itemize}
\item ulcères gastriques = altération des mécanismes de défense
\item ulcères duodénaux = altération des mécanismes de défense ou hypersécrétion
\end{itemize}
\subsubsection{Types}
\label{sec:org2b73141}
\begin{itemize}
\item \bact{helicobacter} :
\begin{itemize}
\item oro-orale/féco-orale, pendant l'enfance
\item pays en voie de développement. Incidence \dec dans pays développés.
\item Gastrite aigüe \thus chronique. Complications (rare) : ulcère G ou D,
(adénocarcinome gastrique, lymphome)
\end{itemize}
\item AINS (inhibition de COX-1), aspirine faible dose
\item Sd Zollinger-Ellison : sécrétion tumorale de gastrine (exceptionnel)
\item Autre (20\%) : gastrotoxique, tabac, Chron, vascularite
\end{itemize}
Autre facteur : génétique possible mais pas de stress, ni facteurs psycho
Épidémio : 0.2\% en France. Sex ratio H/F = 2 (UD) ou 1 (UG). 10\% de mortalité
des complications. 1/3 liés à l'aspirine/AINS
\subsubsection{Diagnostic}
\label{sec:orgc93ebea}
Symptômes :
\begin{itemize}
\item typique : douleur épigastrique sans irradiation, crampe/faim. Calmée par
aliments/anti-acides. Rythmée par repas. Poussées de qq semaines avec périodes asymptomatiques
\item atypique (+ fréquent) : sous-costal/postérieur, hyperalgique/frustre, non
rythmé par l'alimentation
\item asymptomatique
\item complication inaugurale
\end{itemize}
EC normal (si pas de complications)
Endoscopie digestive haute\footnote{Anesthésie locale pharyngée/générale. Morbidité et mortalité faibles} :
\begin{itemize}
\item perte de substance profonde, branchâtre, ovalaire, à bords régulieurs
\item gastrique : surtout antre. Biopsies systématiques
\item duodénal : buble, pas de biopsie de l'ulcère
\end{itemize}
\begin{tcolorbox}
Quelque soit l'ulcère, biopsie de l'antre, angle et fundus pour \bact{helicobacter}
\end{tcolorbox}
Recherche de \bact{helicobacter} :
\begin{itemize}
\item biopsie gastrique = référence
\item autre : teste respiratoire à l'urée = contrôle d'éradication hors endoscopie
\end{itemize}
\subsubsection{DD}
\label{sec:orgb4ef521}
\begin{itemize}
\item avant endoscopie : adénocarcinome/lymphome gastrique, douleur
pancréatique/biliaire, insuffisance coronarien, péricardite, ischémie
mésentérique, douleur vertébrale projetée, dypepsie non ulcéreuse
\item endoscopie : adénocarcinome, lymphome, Crohn
\item ulcère de stresse : en réa avec \(\ge\) 1 défaillance viscérale
\end{itemize}
\subsubsection{Complication}
\label{sec:orgdaae5c4}
\begin{itemize}
\item hémorragie digestive (fréquente) : à bas bruit ou aigüe, mortalité 10\% \thus
endocscopie \textpm{} hémostase
\item perforation ulcéreuse : plutôt en péritoine libre : douleur épigastrique en "coup de
poignard", choc, contracture épig. puis généralisée, cul-de-sac de Douglas
douloureux au TR, pneumopéritoine au scanner. CI à l'endoscopie \danger
\item sténose ulcéreuse (exceptionnelle) : clapotage gastrique à jeun, ondes
péristaltiques \thus évacuer stase puis diagnostic sur endoscopie
\item gastrite aigüe - atropie / métaplasie - dysplasie - cancer invasif
\end{itemize}
\subsubsection{Traitement UGD non compliqué}
\label{sec:org52cb0b0}
Associé à H. pylori
\begin{itemize}
\item éradication :
\begin{itemize}
\item si sensibilité : IPP matin et soir et amoxicilline 10j et clarithromycine (ou
lévoflaxicine si résistance)
\item sinon métronidazole, tétracycline, sous-citrate de bismuth et oméprazole
\end{itemize}
\item IPP en curatif avant éradication \emph{et} (6 semaines en curatif si ulcère ou AINS
ou persistance des douleur ou ulcèse GD compliqué) \emph{et} 6 semaines en préventif
\item Surveillance à +4 esmaines par teste respiratoire (UD) ou biopsie gastrique
(UG).
\begin{itemize}
\item Si réussite : pas d'IPP long cours
\item Si échec : quadrithérapie ou endoscopie et ABTgramme. Si échec : IPP long
cours
\end{itemize}
\item Chir exceptionnelle : ()éliminer sd Zollinger-Ellison) vagotomie \textpm{} hémostase
\end{itemize}
Induite par AINS/aspirine
\begin{itemize}
\item curatif : 4 semaines (UD) ou 8 (UG). Maintenir IPP si AINS/aspirine
continué. Contrôle endoscopique
\item préventif si FR = > 6) ans, ATCD UGD, AINS avec antiagrégant/corticoïdes/anticoagulants
\end{itemize}
Autre
\begin{itemize}
\item éliminer Zollinger-Ellison, Crohn, lymphome, K gastrique
\item UD = IPP 4 semaines \textpm{} IPP long cours
\item UG = IPP 4-8 semaines \textpm{} IPP voire chir si échec
\end{itemize}
\subsubsection{Traitement UGD compliqué :}
\label{sec:orgf1748ee}
\begin{itemize}
\item Hémorragique, perforcé : ch chap "Hémorragie digestive", "Péritonite aigüe"
\item Sténose ulcéreuse pylorobulbaire :
\begin{itemize}
\item évacuer stage, correction torubles hydroélectriques, IPP
\item si échec : dilatation sténose et endoscopie. Si échec : chir
\end{itemize}
\end{itemize}
\subsection{Gastrite}
\label{sec:orgb95904d}
Définition : atteinte inflammatoire
Pas de corrélation histologie - symptômes
\subsubsection{Chronique à \bact{helicobacter}}
\label{sec:org4ae93bc}
20-50\% population. Évolution selon :
\begin{itemize}
\item sujet hypersécréteur : gastrite antrale, risque UD
\item sujet hyposécréteur : pangastrite, risque UG, adénocarcinem gastrique
\item lymphome gastrique MALT
\end{itemize}
Diag = biopsise de l'antre et du corps. Ttt = éradication (cf supra)
\subsubsection{Chronique de mécanisme immunitaire}
\label{sec:org5de089c}
\begin{itemize}
\item Auto-immune : si atrophie fundique sévère :
\begin{itemize}
\item carence facteur intrinsuqèe \thus
anémie macrocytaire arégénérative, glossite, neuro
\item carence martiale
\item risque adénocarcinome, tumeurs endocrine \thus surveillance 3 ans si < 70
ans et bon état général
\item corriger carence B12 et fer
\end{itemize}
\item Lymphocytaire : souvent asymptomatique
\item Granulomateuse : granulomes épithélioïdes
\item À éosinophiles
\item Avec maladie de Crohn (30\% des atteints)
\end{itemize}
\subsubsection{Gastrite aigüe}
\label{sec:org4332836}
\begin{itemize}
\item \bact{helicobacter}
\begin{itemize}
\item immédiatement après contaminale, souvent asymptomatique, lésions de l'antre.
\item Diag = biopsie : \bact{helicobacter}, PNN
\end{itemize}
\item Phlegmoneuse : exceptionnelle, ID
\item Virale : ID
\end{itemize}
\subsubsection{DD}
\label{sec:orga1b4f0f}
\begin{itemize}
\item Gastropathie induite par AINS
\item Gastropathie chimique : excès d'alcool, post-gastrectomie (reflux)
\item Gastropathie congestive : hypertension portale ou ectasies vasculaires
atnrales
\item Gastropathies hypertrophiques : échoendoscoie si muqueuse épaissie
\begin{itemize}
\item maladie de ménétrie (exceptionnelle, étiologie inconnue) : exsudative, sd
\oe{}démateux
\item sd de Zollinger-Ellison
\end{itemize}
\item Gastropathie radique (> 45 Gy) : multiples biopsies, chronicité possible
\end{itemize}
\section{270 : Dysphagie}
\label{sec:org719aea7}
Déf : sensation de gêne/obstacle à la progression du bol alimentaire
(déglutition). \(\ne\) odynophagie, striction cervicale (anxiété), anorexie, satiété
précoce
2 types : oropharyngé (cervicale) et \oe{}sophagienne (rétrosternal)
\subsection{Dysphagie \oe{}sophagienne}
\label{sec:org6a2e44b}
\begin{enumerate}
\item Interrogatoire :
\begin{itemize}
\item anorexie, asthénie, \emph{amaigrissement}, \emph{localisation}, solides
ou liquide, brutal ou progressif, évolution, terrain (âge, \emph{tabac-alcool},
agents irritants, affection maligne), symptômes
\item score d'Eckart pour quantifier
\end{itemize}
\item Chercher lésion organique de l'\oe{}sophage :
\begin{itemize}
\item endoscopie OGD 1ere intention (toujours biopsie pour \oe{}sophagite à
éosinophiles !)
\item autres : scanner thoracique (lésions médiastin), échoendoscopie (paro
\oe{}sophage), transit baryté de l'\oe{}sophage (K de l'\oe{}sophage,
diverticule, achalasie)
\end{itemize}
\item Si endoscopie normale, chercher trouble moteur : manométrie \oe{}sophagienne
\end{enumerate}
(haute résolution)
\subsection{Dysphagies lésionnelles}
\label{sec:org8e61c67}
Prédomine sur les solides, s'aggrave, retentit état général. Sténoe organique en
majorité.
Principales lésions organiques :
\begin{itemize}
\item sténoses tumorales
\begin{itemize}
\item carcinome épidermoïde (terrain alcool-tabac)
\item adénocarcinome \oe{}sophagien sur endobrachy\oe{}sophage
\item tumeurs bénignes de la paroi
\item compression extrinsèque (tumeur, ADP médiastinale, carcinome bronchopulmonaire)
\end{itemize}
\item sténoses non tumorales
\begin{itemize}
\item peptique
\item caustique
\item post-radique
\item après \oe{}sophagectomie
\item après résection endoscopique étendue
\item pendant \oe{}sophagite
\item anneaux de Schatzki (aspect de diaphragme)
\item sd de Plummer-Vinson/Kelly-Paterson
\item compression extrinsèque (ADP, anomalie artérielle)
\end{itemize}
\item \OE{}sophagite sans sténoe : médicaments, à éosinophiles\footnote{Endoscopie peut être normale !}, infectieuses
(ID)
\item Diverticule de Zenker
\end{itemize}
\subsection{Dysphagies non lésionnelles}
\label{sec:org8f6011b}
Liquides et solides, fluctue dans le temps. Endoscopie souvent normales
\begin{itemize}
\item Achalasie : trouble moteur d'origine inconnue avec relaxation du sphincter
inférieur de l'\oe{}sophage et sans contractions péristaltiques
\begin{itemize}
\item surtout les liquides, capricieuse, régurgitations. Endoscopie : \oe{}sophage
dilaté (stade évolué !), méga-\oe{}sophage, cardia en "bec d'oiseau"
\item Anomalies manométriques \oe{}sophagienne : type I (défault relaxation de la
joncion), type II (pressurisation \oe{}sophage), type III (contractions
\oe{}sophagiennes prématurées)
\item DD : toujours endoscopie (néoplasie !) : tumeur infiltrante du cardia
\end{itemize}
\item Autres troubles moteurs :
\begin{itemize}
\item douleurs thoraciques peudo-angineuses : spasmes \oe{}sophagiens, \oe{}sophage
hypercontractile
\item RGO et clairance oesophage \dec : péristaltisme inefficace ou absent
\end{itemize}
\end{itemize}
\section{271 : Vomissements}
\label{sec:org322168c}
Nausées et vomissement : souvent activation des SN sympathiques et
parasympathiques
DD : régurgitations (remontée sans effort), rumination/mérycisme (remontée
volontaire)
Physio:
\begin{itemize}
\item centre = substance réticulée du tronc cérébral
\item stimulation : plancher 4eme ventricule, cortex cérébral, vestibulaire, nerfs
vagues et sympathiques
\item efférences motrice
\end{itemize}
Complications :
\begin{itemize}
\item troubles hydroélectriques : déshydratation puis IR, hypochlorémie, alcalose
métabolique, hypoK
\item sd de Mallory-Weiss\footnote{Déchirurge longitudinale du cardia} : vomissement puis hématémèse
\item rupture de la paroi de l'\oe{}sophage : exceptionnel, urgence . Dyspnée,
emphysème SC, odynophagie \thus diag par TDM thoracique
\item inhalation bronchique avec pneumopathie
\item \oe{}sophagite
\item hémorragie sous-conjonctivale, fracture de côte, dénutrition, interrution ttt
oraux
\item encéphalopathie Gayet Wernicke : urgence, femmes enceintes
\end{itemize}
Aigus si \(\ge\) 7 jours
\subsection{Diagnostic}
\label{sec:org4993d75}
Sémiologie :
\begin{itemize}
\item matin, à jeun, liquide un peu glaireux, haut-le-c\oe{}ur : alcool, médic,
tabac, grossesse
\item matin, en jets, sans nausée ni haut-le-c\oe{}ur : HTIC (rare)
\item postprandial, répétés, aliments nauséabonds partiellement digérés :
obstruction chronique GD organique/fonctionnelle
\item fécaloïdes : obstruction basse, fistule gastrocolique (exceptionnel)
\item perprandiaux/juste après repas : psychogène (par élimination !)
\item fin de journée : sd obstructif, avec nausées, balonnements, satiété, crampes
\end{itemize}
Médicaments : antimitotiques, dérivés théophylline, digitaliques
\begin{tcolorbox}
Toujours penser à : grossesse, surdosage, intolérance médicaments/toxique, métabolique, HTIC
\end{tcolorbox}
Chercher complications, dénutrition, toxiques
Si déshydratation, perte de poids, AEG, vomissement ou personnes à risque :
\begin{itemize}
\item iono sanguin, NFS, urée, créat, iono urinaire
\item albuminémie, préalbuminuméie
\end{itemize}
Si vomissements chronique : endoscopie EOG. Éventuellement : scinti de vidange
gastrique, scanner (opacification digestive haute), IRM cérébrale
\subsubsection{Vomissements aigüs}
\label{sec:org453d311}
Causes :
\begin{itemize}
\item abdominopelviennes :
\begin{itemize}
\item medicale : \emph{gastroentérite virale, toxi-infection alimentaire}, hépatite
aigüe, sténose du pylore, colique hépatique/néphrétique
\item chir : douleur biliaire, pancréatite aigüe, infarctus mésentérique, torsion
kyste de l'ovaire, grossesse extra-utérine
\end{itemize}
\item médic
\item neuro : vestibulaire, migraine, trauma cérébral, méningite, HTIC, hémorragie
méningée
\item métabolique : acidocétose diabétique, IR aigüe\footnote{Piège !\label{org450d505}}, hyperCa, hypoglycémie/malaise
vagal, insuf. surrénale aigüe, hypoNa, hyperthyroïdie
\item autre : \emph{grossesse}, postop, mal des transports, glaucome aigue\textsuperscript{\ref{org450d505}}, IDM
inférieur\textsuperscript{\ref{org450d505}}, radiothérapie, psychogène
\end{itemize}
\subsubsection{Vomissements chronique}
\label{sec:orgc1dae74}
\begin{itemize}
\item Digestif supérieur :
\begin{itemize}
\item mécanique : ulcère, K gastrique/duodénal, K pancréas, compression par
pseudo-kyste pancréatique
\item fonctionnelle : gastroparésie, chir gastrique, vagotomie
\end{itemize}
\item Intestion, côlon :
\begin{itemize}
\item obstruction mécanique tumorale
\item sténose mécanique non tumorale
\item fonctionnelle
\end{itemize}
\item SNC : HTIC, épilepsie
\item Psychogène
\item Autres : cataméniaux\footnote{Pendant menstruations}, sd des vomissements cyclique\footnote{Sans organicité ni toxiques}, sd d'hyperemesis aux cannabinoïdes
\end{itemize}
Grossesse
\begin{itemize}
\item 1er trimestre : fréquents, physiologique si pas d'AEG. Hyperemesis gravidarum
(forme grave) : anomalies disparaissent à l'arrêt
\item 3eme trimestre : non lié ou \{stéatose aigüe gravidique, prééclampsie\} =
urgences
\end{itemize}
Chimio : aigü (< 24h), retardés, anticiéps
\subsection{Traitement}
\label{sec:org1611ee8}
Hospitalisation urgrente : urgence médicale/chir/obstétricale, trouble
hydroélectriques, trouble conscience, réhydratation orale impossible, ttt oral
indispensible impossible, décompensation, complication
Symptomatique :
\begin{itemize}
\item réhydratation per os/IV
\item sonde gastrique si risque d'inhalation
\item surveillance (déshydratation, FC, PA, diurèse, iono sanguin)
\item médic:
\begin{itemize}
\item métoclopramide (neuroleptique, \(\in\) benzamides) : CI : dyskinésie des
neuroleptiques, phéochromocytome, alcool, lévodopa
\item dompéridone (neuroleptique, \(\in\) butyrophénones)
\item métopimazine (\(\in\) phénothiazines)
\end{itemize}
\item chimio : anti-5-HT3, aprépitant, corticoïdes, métoclopramide, alizapride
\end{itemize}
\section{273 : Hépatomégalie, masse abdo}
\label{sec:orgb23be14}
\subsection{\gls{HMG}}
\label{sec:orgde77426}
Projection ligne médio-claviculaire > 12cm\footnote{Entre limite supérieure (percussion) et bord inférieur (palpation)}. Écho abdominable si besoin.
DD : tumeur du rein/angle colique droit/estomac/pancreas => mobile avec
respiration échographie
\begin{table}[htbp]
\caption{Causes d'HMG}
\centering
\begin{tabular}{ll}
\toprule
Augmentation de volume & Causes\\
\midrule
diffuse, homogène & hépatite, cirrhose\\
& stéatose, stéatohépatique \hfill [foie hyperéchogène, alcool/sd métabolique]\\
& cholestase prolongée \hfill [ictère cholestatique/voie biliaires dilatées]\\
& foie cardiaque \hfill [veines hépatiques dilatées]\\
& sd Budd-Chiari, surcharge en fer, abcès du foie, autres\\
sectorielle, homogène & cirrhose, autres\\
hétérogène & cirrhose, tumeurs bénignes (kyste biliaire simple/hydatique)\\
& polykystose hépatique, abcès du foie\\
& tumeurs malignes (métastases foie, CHC, autres)\\
\bottomrule
\end{tabular}
\end{table}
\subsubsection{Moyens diagnostiques :}
\label{sec:org2844cfa}
\paragraph{Clinique}
\label{sec:orge92f6e0}
ATCD, symptômes, FR maladie du foie. Et :
\begin{itemize}
\item foie douloureux, sd inflammaatoire
\item angiomes stellaires, hypertension portale\footnote{Maladie chronique du foie}
\item reflux hépatojugulaire, expansion systolique du foie
\end{itemize}
NB foie cirrhotique = dur
\paragraph{Écho}
\label{sec:orgf9a7293}
sans attendre ! : diffuse/sectorielle, homogène/hétérogène, cirrhose,
stéatose, insuf cardiqaue droite, dilatation voies biliaires intrahépatiques
\paragraph{Autres :}
\label{sec:orga548179}
\begin{itemize}
\item hémogrammes, \{transaminases, phosphatases alcalines, \(\gamma\)-GT, TP,
bilirubinémie, électrophorèse des protéines plasmatique\footnote{Et si besoin : hépatetites virales/auto-immunes, surcharge en fere,
amibiases (abcès), hydatidose (kyste)}
\item écho Doppler/contraste, TDM, IRM, écho cardiaque si besoin
\item ponction-biopsie hépatique si cause introuvable \footnote{Pas pas voie transpariétale/transcapulaire si troubles de l'hémostase
non corrigés/dilatation diffues des voies biliaires intra-hépatiques/ascite}
\end{itemize}
\subsubsection{Démarche : HMG hétérogène}
\label{sec:orgfe293df}
\begin{enumerate}
\item Maladie chronique du foie ?
\item Si oui, CHC ? (centre spécialisé)
\item Sinon :
\begin{itemize}
\item lésion kystique : si liquidienne sans paroi ni cloison \thus kyste biliaire
symple. Sinon centre spécialisé
\item tumeur solide :
\begin{itemize}
\item rehaussement périphérie - centre : hémangiome bénin
\item rehaussement périphérie (temps artériel) : abcès/tumeur nécrosée
\item rehaussement : métastase/adénome hépatocellulaire
\item rehaussement (temps artériel) : CHCH ou autre \thus milieu spé
\end{itemize}
\end{itemize}
\end{enumerate}
\subsection{Masse abdominale}
\label{sec:org86a8b16}
Interrogatoire : découverte, date et évolution, SF, ATCD med et chir, ttt
(anticoag)
Examen : éliminer éventration, hernies, distension abdo. Localisation, taille,
forme, contours, consistante, mobile, percussion, auscultation (souffe).
Cherche métastase
Imagerie : écho abdo en 1ere intention. \emph{TDM = examen clé} \footnote{Éliminer grossesse !}
\subsection{Hypothèses}
\label{sec:org31e5f9f}
Épigastre :
\begin{itemize}
\item tumeur gastrique : masse pierreuse, AEG, signes digestifs hauts \thus diag =
endoscopie + biopsies
\item tumeur pancréatique : tête = ictère, prurite, corps = douleurs solaires, queu
= masse épigastrique/hypochondre gauche. AEG
\item pseudo-kyste du pancréas : contexte pancréatite
\end{itemize}
Hypochondre droit
\begin{itemize}
\item HMG
\item Grosse vésicule \footnote{Non palpable à l'état normal} : tumeur maligne pancréatique (ictère précédé d'un
prurit, hydrocholécyste (écho = diag), cholécystite aigüe (fébrile), tumeur
maligne d la vésicule (masse dure, fixée, irrégulière)
\item Autre : lésion angle colique D, rein D, surrénale D
\end{itemize}
Hypochondre gauche :
\begin{itemize}
\item \gls{SMG} : s'abaisse à l'inspiration, bord antérieur crénelé
\item queue du pancréas, angle colique gauche, grosse tubérosité gastrique, rein
gauche
\end{itemize}
Fosse iliaque droite :
\begin{itemize}
\item tumeur du c\ae{}cum : masse abdo, anémie ferriprive, méléna \thus diag =
coloscopie + biopsie
\item appendicite : si abcès, tuméfaction douloureuse fixée, fébrile. TDM si besoin
\item Crohn avec abcès
\item kyste de l'ovaire
\end{itemize}
Fosse iliaque gauche
\begin{itemize}
\item sigmoïdite avec abcès périsigmoïdien : douleur fosse iliaque gauche, troubles
transit, fièvre \thus diag = TDM
\item tumeur sigmoïdienne, kyste de l'ovaire
\end{itemize}
Région ombilicale
\begin{itemize}
\item anévrisme de l'aorte abdo : tuméfaction, battante, souffle systolique \thus
diag angioscanner
\item K côlon transverse, tumeurs du grêle, tumeur mésentérique
\end{itemize}
Flancs : lésions rénale, psoas
Hypogastre : éliminer fécalome, globe vésical, grossesse
\begin{itemize}
\item fibromyome utérine : ménorragie, pesanteur pelvienne, pollakiurie. Masse
régulière, bien limitée, ferme indolore \thus diag = écho pelvienne
\item K endomètre : métrorragie post-ménopausique \thus diag = gynéco + biopsie
\item tumeur de l'ovaire : douleur pelvienne, pesanteur, ascite, palpation masse
pelvienne
\end{itemize}
Ubiquitaire : tuméfaction pariétale, nodules de carcinose péritonéale, ADP, corps étranger
\section{274 : Lithiases biliaires}
\label{sec:orgb6a93b9}
Fréquence : 20\% (Occident) et 60\% après 80 ans.
3 types :
\begin{itemize}
\item calculs cholestéroliques :
\begin{itemize}
\item favorisés par \inc sécrétion biliaire de
cholestérol, défaut des facteurs le solubilisant, rétention vésiculaire
\item FR : âge, \female, surpoids, multiparité, jeûne prolongé, ethines, hyperTG,
certains médic
\end{itemize}
\item pigmentaire : déconjugaison bilirubine. FR = \inc production bilirubine,
infection ou obstacles biliaires
\item mixtes
\end{itemize}
\emph{Pas de dépistage}
\subsection{Lithiase vésiculaire symptomatique}
\label{sec:org6df10ef}
Typique = colique hépatique : douleur brutale, permanente, épigastre ou
hypochondre droit, irradiant vers l'épaule/fosse lombaire droite, qq min à qq
heures. Chercher un signe de Murphy
Bio = RAS. \emph{Échographie}
\subsection{Lithiase vésiculaire compliquée}
\label{sec:org0c4e857}
\subsubsection{Cholécystite aigüe\footnote{Infection aigüe de la vésicule (ici par obstruction prolongée !)}}
\label{sec:orga04f1b6}
Sd infectieux, douleur hypochondre droit \uline{> 6h} (> 24h), frissons \textpm{} défense,
contracture (= grave)
Bio : hyperleucocytose à PNN, hépatique normal
Imagerie : écho : paroi vésiculaire > 4mm
Complications :
\begin{itemize}
\item gangrène paroi vésiculaire \thus perforation dans le foie ou
péritoine
\item ileus biliaire\footnote{Fistule biliodigestive \thus occlusion tube digestif par le calcul}, sd Mirizzi\footnote{Gros calcul dans le collet vésiculaire/canal cystique. Ictère,
dilatation voies biliaires, perturbation bilan hépatique}, K vésiculaire
\end{itemize}
\subsubsection{Migration lithiasique}
\label{sec:orgabde85b}
Douleur colique sans fièvre. \inc \uline{transitoire} transaminases
\subsubsection{Angiocholite aigüe}
\label{sec:org9f562eb}
Infection aigùe \gls{VBP} (généralement calcul, parfois parasite). Sous 48h :
\emph{douleur biliaire, fièvre, ictère}.
Sd infectieux parfois sévère
Bio : \uline{\inc bilirubine conjugée, \inc transaminases}, hyperleucocytose PNN
Écho (moyennement sensible) : cholangio-IRM, échoendoscopie (sensibles)
Complications : choc septique, + IR
\subsubsection{Pancréatite aigüe (cf chap)}
\label{sec:org5a66e78}
\subsection{Traitement}
\label{sec:org074ed90}
\begin{itemize}
\item Asymptomatique : non
\item Colique hépatique : \danger urgence : antispasmodique, antalgiques,
anti-inflammatoire. Puis cholécystectomie < 1 mois
\item Cholécystite aigüe : remplissage vasc, ATB proba (germe digestif : (amoxicilline+
acide clavulanique) ou (CG3 + imidazolé)) puis adaptée. antalgique.
Cholécystectomie < 72h
\item Angiocholite : immédiatement ATB proba, décompression dans 24h (voire urgente si
ne répond pas) \thus \gls{CPRE} 1ere intention (extraction du calcul par
sphinctérotomie, 5-10\% de complications)
\item Calculs VBP hors angiocholite : calculs prédictifs, différentes approches
\item Pancrétite aigüe biliaire : si angiocholite aigüe en plus, ATB et extraction
calculs < 24h
\end{itemize}
\section{275 : Ictère}
\label{sec:orge11d20a}
Coloration jaune quand bilirubinémie > 40\$\(\mu\)\$mol/L
Physiopatho :
\begin{itemize}
\item dégradation hémoglobine -> bilirubine dans le plasma (non conjugée surtout)
\item transportée par l'albumine dans les hépatocytes puis conjugée par \gls{BGT}
\item puis sécrétée dans la bile (mais une partie revient dans le plasma)
\end{itemize}
\begin{figure}[htpb]
\centering
\resizebox{0.5\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
edges={nodes={fill=white, align=center}},
patho/.style={rectangle, draw=black},
h path/.style = {to path={ - (\tikztotarget)}},
layered layout]
{
"" -> {
"Urine claire\\b. non conjuguée" ->
"Ictère à bilirubine\\non conjugée" [patho] ->
"\inc{} réticulocyte \dec{} haptoglobine ?"[level distance=50pt] -> {
Hémolytique [>"oui", patho];
"Non hémolytique" [>"non", patho];
};
"Urine brune\\b. conjuguée" -> "Ictère à bilirubine\\conjugée"[patho] -> {
"Prurit\\ \inc{} phosphatases alcalines, $\gamma$ -GT" -> {
"Cholestatique" [>"oui", patho] -> Imagerie -> {
"Avec obstacles\\sur gros canaux"[patho];
"Sans obstacles\\sur gros canaux"[patho];
};
"Non cholestatique" [>"non", patho];
};
};
};
};
}
\caption{Orientation devant un ictère}
\end{figure}
\subsection{Étiologies}
\label{sec:org10df51e}
\begin{itemize}
\item Ictère à bilirubinie non conjugée
\begin{itemize}
\item hémolyse, dysérythropoïèse\footnote{Destruction intra-médullaire des nouvelles hématies :}
\item \dec conjugaisons par la BGT
\begin{itemize}
\item sd de Gilbert : bénin, fréquent \thus diagnostic = ictère non persistant,
tests hépatiques \emph{normaux} et élimination autres causes
\item sd Crigler-Najjar : exceptionnel, très grave : ictère néonatal marqué permanent
\end{itemize}
\end{itemize}
\item Ictère à bilirubine conjugée
\begin{itemize}
\item cholestase++ (\dec sécrétion biliaire)
\begin{itemize}
\item obstruction canaux biliaires
\begin{itemize}
\item \gls{VBP} (freq) : \emph{K pancréas} (ictère, AEG), \emph{K primitif VBP} (ictère),
\emph{litihiase VBP} (précédée douleurs), sténose post-op voie biliaire,
pancréatite chronique calcifiante (par compression), ADP
\item atteinte des petits/moyens canaux : cirrhose biliaire primitive
(auto-immune, rare), cholangite immunoallergique (amox-acide
clavulanique, sulfamide, macrolide, allopurinol), cholangite scérosante
primite (rare, faire cholangio-IRM)
\end{itemize}
\item sans obstacle : génétique (très rare : infantile, "récurrente béningne" ou
gravidique") ou acquises (hépatite aigües, infections bactériennes, angiocholite)
\end{itemize}
\item transport canaliculaire de bilirubine conjugée (rarissime) : sd de Rotor,
maladie Dubin-Johnson
\item multiples mécanismes
\end{itemize}
\end{itemize}
Mnémotech: la bilirubine non conjuguée ne passe pas les urines \thus urine claire
\subsection{Urgences}
\label{sec:orgd6d11a6}
\begin{itemize}
\item Encéphalopathie bilirubinique du nouveau-né : séquelles cognitives/motrices
graves \thus ttt par UV/échanges pasma en urgence
\item Angiocholite : cf table \ref{tab:org8a00f57}. Traitement :
\begin{enumerate}
\item ATB ASAP (bactéries intestinales), corrections désordres généraux
\item drainage endoscopique : sous 48h si aggravation ou en urgence si choc
septique
\end{enumerate}
\item Insuffisance hépatique :
\begin{itemize}
\item cirrhose
\item K foie en phase terminale : confort du patient
\item insuf. hépatique aigüe :
Quick et facteur V < 50\%
\begin{itemize}
\item transaminases > 20N \thus diagnostic = \dec taux
\item risque = insuf hépatique grave : 80\% mortalité
\item chercher paracétamol systématiquement \thus N-acétylcystéine en urgence
\item si grave : transplantation
\end{itemize}
\end{itemize}
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:org8a00f57}
Diagnostic d'angiocholite}
\centering
\begin{tabular}{lll}
\toprule
Suspicion & Diagnostic & DD\\
\midrule
triade "douleur-fièvre-ictère" & cholestase & infections bactériennes sévères\\
& sd inflammatoire systémique marqué & sd inflammatoires de lymphomes\\
& obstruction voies biliaire : \emph{échographie} & hépatite herpétique/virale A\\
\bottomrule
\end{tabular}
\end{table}
\subsection{Imagerie}
\label{sec:org0697a26}
\begin{itemize}
\item Échographie : diagnostic pour lithiase biliaire, obstruction VBP (et siège de l'obstacle)
\item TDM : plus sensible que l'écho pour pancréas
\item cholangio-pancréatio-oRM
\item échoendoscopie \footnote{Anesthésie générale\label{org2249f26}}: litihase VBP++
\item \gls{CPRE} \textsuperscript{\ref{org2249f26}} (\danger pancréatite aigüe) : pas en diagnostic
\item cholangiographie percutanée transhépatique \textsuperscript{\ref{org2249f26}} : si échec CPRE mais risque
hémopéritoien, bilio-péritoine, angiocholite
\end{itemize}
\end{document}
Oestrogène (à partir de la puberté) :
- stimule la croissance des ovaires, utérus, organes génitaux
externes + prolifération de endomètre
[[ECN]{.underline}]{.underline}: forte exposition aux oestrogène =\>
plus de risque que la prolifération donne des cellules cancéreuses donc
****K endomètre****, ****K des ovaires****
- stimule la croissance des seins
[[ECN]{.underline}]{.underline}: forte exposition aux oestrogènes =\>
risque de ****K du sein**** **Attention**: le tamoxifène a des effets
anti-oestrogénique sur le sein (donc ****protection du K du sein****) et
oestrogénique sur l\'utérus( donc risque de ****K de l\'endomètre****)
- stimule ostéoblaste pour croissance du squelette
[[ECN]{.underline}]{.underline}: à la ménopause `> **ostéoporose**
- secrété par les ovaires. À la ménopause, ce sont les tissus graisseux qui prennen le relais de la production via l'aromotase (`{.verbatim}
enzyme) [[ECN]{.underline}]{.underline}: d\'où les
****anti-aromatase**** seulement chez la femme ménopausée pour le cancer
du sein
Progestérone (pro-gestation)
- prépare l\'utérus pour l\'implantation de l\'oeuf fécondé
- stimule développement sein pour lactation
[[ECN]{.underline}]{.underline}: la contraception hormonale est
principalement liée à la progestérone. Il y a donc 2 effets :
1. \"périphériques\" (tous) : atrophie de l\'endomètre, diminution de
la glaire cervicale \[par régulation négative !\]
2. \"central\" (sauf les microprogestatif) par suppression du pic de LH
Cycle menstruel :
1. Prolifération de l\'endomètre par oestrogène (secrété par les
ovaires)
2. Ovulation déclenchée par pic LH
3. Développement \"sécrétoire\" de l\'endomètre par progestérone (et
augmentation de l\'oestrogène)
4. 2 jours la fin du cycle, s\'il n\'y a pas eu de fertilization, chute
de la progestérone + oestrogène =\> règles
digraph {
"Ag vWF" -> vWFpp [label="indétectable"];
vWFpp -> "Type 3" [label="absent"];
vWFpp -> "Type 1 sévère" [label="présent"] ;
"Ag vWF" -> "activité/Ag vWF"[label="sinon"];
"activité/Ag vWF" -> "FVIII/ag vWF"[label="> 0.7"];
"FVIII/ag vWF" -> "Type 1 et 2M" [label="> 0.7"];
"FVIII/ag vWF" -> "vWF:FVIIIb" [label="< 0.7"];
"vWF:FVIIIb" -> "2N"[label="diminuée"];
"vWF:FVIIIb" -> "Hémophilie A"[label="normal"];
"activité/Ag vWF" -> "Type 2"[label="< 0.7"];
"Type 2" -> { "2B\nPT-VWD\nsi RIPA\naugmenté", "2A\nsi HPM\nabsents"; "2B sinon";}
// "diminué" -> "type 2N" ;
// "normal" -> "Hémophilie A";
// "multimère" -> {"HPM absent" -> "Type 2A";
// "HPM présents" -> "Type 2M3 }
// }
}
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<polygon fill="black" stroke="black" points="302.01,-170.62 298.51,-160.62 295.01,-170.62 302.01,-170.62"/>
<text text-anchor="middle" x="313.13" y="-214.35" font-family="Times,serif" font-size="14.00">< 0.7</text>
</g>
<!-- 2N -->
<g id="node9" class="node">
<title>2N</title>
<ellipse fill="none" stroke="black" cx="243.51" cy="-18" rx="27" ry="18"/>
<text text-anchor="middle" x="243.51" y="-12.95" font-family="Times,serif" font-size="14.00">2N</text>
</g>
<!-- vWF:FVIIIb->2N -->
<g id="edge8" class="edge">
<title>vWF:FVIIIb->2N</title>
<path fill="none" stroke="black" d="M290.63,-122.51C281.5,-102.46 266.35,-69.19 255.7,-45.79"/>
<polygon fill="black" stroke="black" points="258.98,-44.53 251.65,-36.88 252.61,-47.43 258.98,-44.53"/>
<text text-anchor="middle" x="292.01" y="-57.2" font-family="Times,serif" font-size="14.00">diminuée</text>
</g>
<!-- Hémophilie A -->
<g id="node10" class="node">
<title>Hémophilie A</title>
<ellipse fill="none" stroke="black" cx="352.51" cy="-18" rx="63.63" ry="18"/>
<text text-anchor="middle" x="352.51" y="-12.95" font-family="Times,serif" font-size="14.00">Hémophilie A</text>
</g>
<!-- vWF:FVIIIb->Hémophilie A -->
<g id="edge9" class="edge">
<title>vWF:FVIIIb->Hémophilie A</title>
<path fill="none" stroke="black" d="M306.25,-122.51C315.11,-102.69 329.75,-69.93 340.18,-46.58"/>
<polygon fill="black" stroke="black" points="343.28,-48.22 344.17,-37.66 336.89,-45.36 343.28,-48.22"/>
<text text-anchor="middle" x="357.01" y="-57.2" font-family="Times,serif" font-size="14.00">normal</text>
</g>
<!-- 2B\nPT-VWD\nsi RIPA\naugmenté -->
<g id="node12" class="node">
<title>2B\nPT-VWD\nsi RIPA\naugmenté</title>
<ellipse fill="none" stroke="black" cx="423.51" cy="-140.83" rx="48.97" ry="52.33"/>
<text text-anchor="middle" x="423.51" y="-160.53" font-family="Times,serif" font-size="14.00">2B</text>
<text text-anchor="middle" x="423.51" y="-144.03" font-family="Times,serif" font-size="14.00">PT-VWD</text>
<text text-anchor="middle" x="423.51" y="-127.53" font-family="Times,serif" font-size="14.00">si RIPA</text>
<text text-anchor="middle" x="423.51" y="-111.03" font-family="Times,serif" font-size="14.00">augmenté</text>
</g>
<!-- Type 2->2B\nPT-VWD\nsi RIPA\naugmenté -->
<g id="edge11" class="edge">
<title>Type 2->2B\nPT-VWD\nsi RIPA\naugmenté</title>
<path fill="none" stroke="black" d="M478.61,-245.85C471.8,-232.99 462,-214.49 452.55,-196.65"/>
<polygon fill="black" stroke="black" points="455.84,-195.38 448.06,-188.18 449.65,-198.66 455.84,-195.38"/>
</g>
<!-- 2A\nsi HPM\nabsents -->
<g id="node13" class="node">
<title>2A\nsi HPM\nabsents</title>
<ellipse fill="none" stroke="black" cx="532.51" cy="-140.83" rx="41.54" ry="40.66"/>
<text text-anchor="middle" x="532.51" y="-152.28" font-family="Times,serif" font-size="14.00">2A</text>
<text text-anchor="middle" x="532.51" y="-135.78" font-family="Times,serif" font-size="14.00">si HPM</text>
<text text-anchor="middle" x="532.51" y="-119.28" font-family="Times,serif" font-size="14.00">absents</text>
</g>
<!-- Type 2->2A\nsi HPM\nabsents -->
<g id="edge12" class="edge">
<title>Type 2->2A\nsi HPM\nabsents</title>
<path fill="none" stroke="black" d="M493.86,-245.6C499.24,-231.16 507.21,-209.75 514.53,-190.11"/>
<polygon fill="black" stroke="black" points="517.76,-191.46 517.97,-180.86 511.2,-189.01 517.76,-191.46"/>
</g>
<!-- 2B sinon -->
<g id="node14" class="node">
<title>2B sinon</title>
<ellipse fill="none" stroke="black" cx="636.51" cy="-140.83" rx="44.19" ry="18"/>
<text text-anchor="middle" x="636.51" y="-135.78" font-family="Times,serif" font-size="14.00">2B sinon</text>
</g>
<!-- Type 2->2B sinon -->
<g id="edge13" class="edge">
<title>Type 2->2B sinon</title>
<path fill="none" stroke="black" d="M508.75,-248.57C528.65,-235.08 558.92,-213.78 583.51,-193.15 593.62,-184.67 604.18,-174.7 613.19,-165.81"/>
<polygon fill="black" stroke="black" points="615.63,-168.33 620.22,-158.78 610.67,-163.38 615.63,-168.33"/>
</g>
</g>
</svg>
# Interprétation d\'un spermogramme
Hypospermie : volume\<1,5mL Polyspermie : Num\>250M/mL Oligospermie :
Num\<15M/mL ou 40M/éjaculat
Azoospermie : absence totale de spz Asthénospermie : \<32% Spz mobiles
Tératospermie : \<4% de Spz forme normale ph : ≈ 7.2
Nécrospermie : \>42% de Spz morts
```{=latex}
\def\dec{$\searrow{}$}
```
```{=latex}
\def\inc{$\nearrow{}$}
```
```{=latex}
\setlist{nolistsep}
```
```{=latex}
\titlespacing*{\subsection}{0pt}{1ex}{1.3ex}
```
```{=latex}
\titlespacing*{\subsubsection}{0pt}{0.5ex}{0.5ex}
```
## Tuberculose maladie
Dissémination bronchogène. Décès sans traitement.
### Clinique
- Toux prolongée, expectoration muco-purulente ou hémoptoïque
- ± Douleurs thoraciques, dyspnée
- AEG: amaigrissement, asthénie, fièvre souvent vespérale, sueurs
nocturnes
### Examens
RX et scanner thorax
- infiltrats des sommets uni/bilatéraux (****excavés****), caverne(s),
nodule isolé (tuberculome)
****Diagnostic de certitude = bactériologique****
- Prélèvements :
- bronchiques : expectorations si toux productive (3 j de suite),
tubages gastriques le matin à jeun (3 j de suite) sinon , LBA si
nécessaire
- biopsiques
- Techniques :
- examen microscopique
- Dépistage rapide par PCR : différencie rapidement Mycobacterium
tuberculosis d\'une autre mycobactérie, gène de résistance au
ttt
- culture (LowensteinJensen = 3-4 semaines)
- ****antibiogramme****
- PCR
### Evolution
- Non traitée : mortelle (50 %), guérison spontanée (25%), chronique
(25%)
- Traitée : guérison quasi constante
Complications : extra-pulmonaire, miliaire
## Tuberculose miliaire
Dissémination par voie hématogène + multiples granulomes de la taille
d\'un grain de mil.
### Clinique
- Fièvre prolongée, sueurs nocturnes,
- SDRA,
- neuro-méningés (nourrissons),
- péricardite
### Examens
- RX thorax et TDM : images micronodulaires (1 à 2 mm) disséminées
- Biologie : pancytopénie (infiltration médullaire), cholestase
anictérique
- BK sur culture:
- Hémocultures sur milieux spéciaux
- Sécrétions bronchiques
- LCS
- Biopsie(s) : hépatique, BOM
Décès en l\'absence de ttt précoce
## Extra-pulmonaire (25%)
****histologie**** : granulome épithélioïde et gigantocellulaire avec
nécrose caséeuse
### Ganglionnaire
- basicervicales \>\> médiastinale
- adénites souvent volumineuses, fistulisation
- Biopsie/ponction
- BAAR au microscope + culture
- complications: fistule
### Osseuse
- Spondylodiscite
- Radiographie osseuse, IRM rachis
- Ponction-biopsie
- complications: épidurite, compression médullaire
### Pleurésie (rare)
- Insidieux, sd pleural (toux, douleur pleurale)
- RX thorax + ponction : liquide clair exsudatif lymphocytaire
- Biopsie pleurale
- complications : fibrose pleurale
### Péricardite (rare)
- Subaigu : fièvre, douleur tho, tamponnade
- ECG: anomalies diffuses
- RX thorax et echo cardiaque
- Culture liquide péricardite
- complication: tamponnade, chronique
### Neuroméningé
- AEG puis progessif
- sd méningé, déficit focaux
- Hyponatrémie( SIADH)
- PL: méningite lymphocytaire avec hyperprot et hypogly
- complications : décès, séquelles neruo sévères
### Urinaire
- \***leucocyturie aseptique**
- fréquent, asympto/dysurie douleur les flancs,
- urines 3j de suite
- complications : néphrite interstitielle granulomateuse,
hydronéphrose, rétraction vésicale
### Génitale
- homme: prostatite, épididydmite, masse scrotale
- femme : trouble menstruels, douleur abdo
- calcifications chez l\'homme, culture sur frottis/menstruations chez
femme
### Digestive
- fibro OGD, colonoscopie + biopsie
### Laryngé (rare)
- ulcération douloureuse, toux, dysphagie
- prélèvement local
% Created 2021-04-16 Fri 16:27
% Intended LaTeX compiler: pdflatex
\documentclass[a4paper,11pt,twoside,twocolumn]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{grffile}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{amssymb}
\usepackage{capt-of}
\usepackage{hyperref}
\usepackage{tabularx}
\usepackage{booktabs}
\usepackage{enumitem}
\usepackage{titlesec}
\usepackage[margin=1cm]{geometry}
\usepackage{adjustbox}
\date{}
\title{Tuberculose}
\hypersetup{
pdfauthor={Alexis},
pdftitle={Tuberculose},
pdfkeywords={},
pdfsubject={},
pdfcreator={Emacs 27.2 (Org mode 9.5)},
pdflang={English}}
\begin{document}
\def\dec{$\searrow{}$}
\def\inc{$\nearrow{}$}
\setlist{nolistsep}
\titlespacing*{\subsection}{0pt}{1ex}{1.3ex}
\titlespacing*{\subsubsection}{0pt}{0.5ex}{0.5ex}
\section*{Tuberculose maladie}
\label{sec:orga73a050}
Dissémination bronchogène. Décès sans traitement.
\subsection*{Clinique}
\label{sec:org16afab4}
\begin{itemize}
\item Toux prolongée, expectoration muco-purulente ou hémoptoïque
\item \textpm{} Douleurs thoraciques, dyspnée
\item AEG: amaigrissement, asthénie, fièvre souvent vespérale, sueurs nocturnes
\end{itemize}
\subsection*{Examens}
\label{sec:org8d29c62}
RX et scanner thorax
\begin{itemize}
\item infiltrats des sommets uni/bilatéraux (\textbf{\textbf{excavés}}), caverne(s), nodule isolé (tuberculome)
\end{itemize}
\textbf{\textbf{Diagnostic de certitude = bactériologique}}
\begin{itemize}
\item Prélèvements :
\begin{itemize}
\item bronchiques : expectorations si toux productive (3 j de suite), tubages gastriques le matin à jeun (3 j de suite) sinon , LBA si nécessaire
\item biopsiques
\end{itemize}
\item Techniques :
\begin{itemize}
\item examen microscopique
\item Dépistage rapide par PCR : différencie rapidement Mycobacterium tuberculosis d'une autre mycobactérie, gène de résistance au ttt
\item culture (LowensteinJensen = 3-4 semaines)
\item \textbf{\textbf{antibiogramme}}
\item PCR
\end{itemize}
\end{itemize}
\subsection*{Evolution}
\label{sec:orgb057e45}
\begin{itemize}
\item Non traitée : mortelle (50 \%), guérison spontanée (25\%), chronique (25\%)
\item Traitée : guérison quasi constante
\end{itemize}
Complications : extra-pulmonaire, miliaire
\section*{Tuberculose miliaire}
\label{sec:orgbe6feaf}
Dissémination par voie hématogène + multiples granulomes de la taille d'un grain de mil.
\subsection*{Clinique}
\label{sec:org2ed3d81}
\begin{itemize}
\item Fièvre prolongée, sueurs nocturnes,
\item SDRA,
\item neuro-méningés (nourrissons),
\item péricardite
\end{itemize}
\subsection*{Examens}
\label{sec:org93ccf1f}
\begin{itemize}
\item RX thorax et TDM : images micronodulaires (1 à 2 mm) disséminées
\item Biologie : pancytopénie (infiltration médullaire), cholestase anictérique
\item BK sur culture:
\begin{itemize}
\item Hémocultures sur milieux spéciaux
\item Sécrétions bronchiques
\item LCS
\item Biopsie(s) : hépatique, BOM
\end{itemize}
\end{itemize}
Décès en l'absence de ttt précoce
\section*{Extra-pulmonaire (25\%)}
\label{sec:org047807f}
\textbf{\textbf{histologie}} : granulome épithélioïde et gigantocellulaire avec nécrose caséeuse
\subsection*{Ganglionnaire}
\label{sec:orgaee8db8}
\begin{itemize}
\item basicervicales >> médiastinale
\item adénites souvent volumineuses, fistulisation
\item Biopsie/ponction
\item BAAR au microscope + culture
\item complications: fistule
\end{itemize}
\subsection*{Osseuse}
\label{sec:org0500cde}
\begin{itemize}
\item Spondylodiscite
\item Radiographie osseuse, IRM rachis
\item Ponction-biopsie
\item complications: épidurite, compression médullaire
\end{itemize}
\subsection*{Pleurésie (rare)}
\label{sec:orgf3f21d2}
\begin{itemize}
\item Insidieux, sd pleural (toux, douleur pleurale)
\item RX thorax + ponction : liquide clair exsudatif lymphocytaire
\item Biopsie pleurale
\item complications : fibrose pleurale
\end{itemize}
\subsection*{Péricardite (rare)}
\label{sec:orga2a4bc1}
\begin{itemize}
\item Subaigu : fièvre, douleur tho, tamponnade
\item ECG: anomalies diffuses
\item RX thorax et echo cardiaque
\item Culture liquide péricardite
\item complication: tamponnade, chronique
\end{itemize}
\subsection*{Neuroméningé}
\label{sec:org77905c4}
\begin{itemize}
\item AEG puis progessif
\item sd méningé, déficit focaux
\item Hyponatrémie( SIADH)
\item PL: méningite lymphocytaire avec hyperprot et hypogly
\item complications : décès, séquelles neruo sévères
\end{itemize}
\subsection*{Urinaire}
\label{sec:orgd1b69f4}
\begin{itemize}
\item \textbf{*leucocyturie aseptique}
\item fréquent, asympto/dysurie douleur les flancs,
\item urines 3j de suite
\item complications : néphrite interstitielle granulomateuse, hydronéphrose, rétraction vésicale
\end{itemize}
\subsection*{Génitale}
\label{sec:orgeaea2f2}
\begin{itemize}
\item homme: prostatite, épididydmite, masse scrotale
\item femme : trouble menstruels, douleur abdo
\item calcifications chez l'homme, culture sur frottis/menstruations chez femme
\end{itemize}
\subsection*{Digestive}
\label{sec:org57bccff}
\begin{itemize}
\item fibro OGD, colonoscopie + biopsie
\end{itemize}
\subsection*{Laryngé (rare)}
\label{sec:org2d2e6e4}
\begin{itemize}
\item ulcération douloureuse, toux, dysphagie
\item prélèvement local
\end{itemize}
\end{document}
```{=latex}
\def\dec{$\searrow{}$}
```
```{=latex}
\def\inc{$\nearrow{}$}
```
```{=latex}
\newcommand{\tabitem}{~~\llap{\textbullet}~~}
```
```{=latex}
\newcommand{\ttabitem}{~~~~~~\llap{$\square$}~~}
```
```{=latex}
\newcommand{\tttabitem}{~~~~~~~~\llap{-}~~}
```
```{=latex}
\setlist{nolistsep}
```
# Diagnostic
- Risque CV athéromateux : LDL haut, HDL bas et selon hyperTG
(facteurs associés: surpois, diabète, HDL bas)
- Bila lipidique (EAL) selon formule de Friedwal : LDL = CT - HDL -
TG/5 (en g/L) ou TG/2.2 si mmol/L
- Normal = **LDL \< 1.6g/L, HDL \< 0.4g/L, TG \> 1.5g/L**
## Hyperlipidémies secondaires :
- Hypothyroïdie
- Cholestase
- Syndrome néphrotique
- Insuffisance rénale chronique
- Alcoolisme
- Diabète
- iatrogène: œstrogènes, corticoïdes, rétinoïdes, antirétroviraux,
ciclosporine, diurétiques, bêtabloquants
# Types
::: table
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
------------------------------------ -------------------------------------------------------------------
Hypercholestérolémies familiales *mutation du gène du LDL-récepteur* (fréquent++)
monogéniques \- hétérozygote : fréquente (1/500), LDL-C : 2 - 4 g/L,
**xanthomes tendineux, arc cornéen prématuré**, risque CV élevé
\- homozygote : **exceptionnelle** , LDL-C : \> 5 g/L
xanthomes dès l\'enfance, **grave** (RA... dès la 1re décennie)
*Mutation gène apolipoprotéine B* (apoB) (rare)
/Mutation gène proétine *PCSK9* (rare)
Hypercholestérolémies polygéniques **Très fréquente**, LDL augmenté
+/- hyperTG. Risque CV selon LDL et autres fR
Hyperlipidémie familiale combinée fréquente (1 à 2 % )
hypercholestérolémie/hyperTG/mixte, risque CV variable
Dysbêtalipoprotéinémie ( III) rare, prédispos génétique + surpoids, diabète, hypothyroïdie, ttt
LDL et TG élevé
**xanthomes plans palmaires**
**xanthomes tubéreux jaune orangé**
risque CV élevé
Hypertriglycéridémie familiale rare, risque athérogène incertain.
Hyperchylomicronémies primitives très rares. TG \> 10 g/L voire 100. Pancréatite aiguë++
------------------------------------ -------------------------------------------------------------------
```{=latex}
}
```
:::
# Traitement
::: table
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
Risque Critère Objectif LDL TTT
------------ --------------------------------------------------------------- ------------------------ ------------
Faible SCORE \< 1%\< \< 1.15g/L Diététique
Modéré 1% ≤ SCORE \< 5%\< \< 1.15g/L (3 mmol/L) Diététique
Diabète de type 1/2 avant 40 ans sans atteinte d'organe cible
Elevé 5% ≤ SCORE \< 10%\< \< 1g/L (2.6 mmol/L) \+ médic
Diabète de type 1 ou 2:
Avant 40 ans avec au moins un FdRCVou atteinte d'organe
Après 40 ans sans atteinte d'organe cible ou FdRCV
IRC modérée
PA ≥ 180/110mmHg
Très élevé SCORE ≥ 10%
Diabète de type 1 ou 2 ≥ 40 ans avec au moins un FdRCV \< 0.7g/L (1.8 mmol/L) \+ médic
IRC sévère
Maladie CV documentée
```{=latex}
}
```
:::
## Diététique :
- diminuer acides gras saturés, augmenter mono/poly-insaturés
- augmenter fruits, légumes céréales
- diminuer cholestérol alimentaire
- huile d\'olive, fruits à coque
- \+ limiter alcool, controle poids, sédentarité
Pour hyperTG modérée : diminuer poids, alcool et sucres simples
## Médicamenteux
- Risque faible/modéré : diététique 3 mois puis médic si échec
- Sinon médic d\'emblée
- statines contre-indiquées en cas de grossesse.
--------------------------------------------- ---------------------------------------------------------------
Hypercholestérolémies pures **statine** → echec: augmenter dose → echec : ajout ézétimibe
et hyperlipidémies mixtes si intolérance statine: ézétimibe
Hypertriglycéridémies pures TG \< 5 g/L: diététique seul. sinon ajout fibrate
hypercholestérolémie familiale hétérozygote dépistage (1er degré). Cf hypercholestérolémie pure
--------------------------------------------- ---------------------------------------------------------------
## Surveillance:
- EAL à 12 semaine puis à 8-12 après chaque changement.
- **myalgies** (statines++) =\> surveillance musculaire clinique
(dosage CPK si risque)
- hépatique: avant puis à 8-12 semaines. Si ALAT \> 3 N,
arrêter/diminuer statine
Nouveautés thérapeutiques: immunoglobuline monoclonales humaines = Ac
anti-PCSK9, alirocumab, évolocumab
% Created 2021-02-23 Tue 23:54
% Intended LaTeX compiler: pdflatex
\documentclass[11pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{grffile}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{amssymb}
\usepackage{capt-of}
\usepackage{hyperref}
\usepackage{tabularx}
\usepackage{booktabs}
\usepackage{enumitem}
\usepackage[margin=1cm]{geometry}
\usepackage{adjustbox}
\date{}
\title{Dyslipidémies}
\hypersetup{
pdfauthor={Alexis},
pdftitle={Dyslipidémies},
pdfkeywords={},
pdfsubject={},
pdfcreator={Emacs 27.1 (Org mode 9.5)},
pdflang={English}}
\begin{document}
\maketitle
\def\dec{$\searrow{}$}
\def\inc{$\nearrow{}$}
\newcommand{\tabitem}{~~\llap{\textbullet}~~}
\newcommand{\ttabitem}{~~~~~~\llap{$\square$}~~}
\newcommand{\tttabitem}{~~~~~~~~\llap{-}~~}
\setlist{nolistsep}
\section{Diagnostic}
\label{sec:org4956287}
\begin{itemize}
\item Risque CV athéromateux : LDL haut, HDL bas et selon hyperTG (facteurs associés: surpois, diabète, HDL bas)
\item Bila lipidique (EAL) selon formule de Friedwal : LDL = CT - HDL - TG/5 (en g/L) ou TG/2.2 si mmol/L
\item Normal = \textbf{LDL < 1.6g/L, HDL < 0.4g/L, TG > 1.5g/L}
\end{itemize}
\subsection{Hyperlipidémies secondaires :}
\label{sec:org4295502}
\begin{itemize}
\item Hypothyroïdie
\item Cholestase
\item Syndrome néphrotique
\item Insuffisance rénale chronique
\item Alcoolisme
\item Diabète
\item iatrogène: \oe{}strogènes, corticoïdes, rétinoïdes, antirétroviraux, ciclosporine, diurétiques, bêtabloquants
\end{itemize}
\section{Types}
\label{sec:org2cfb23f}
\begin{table}
\centering
\adjustbox{max width=\linewidth}{
\begin{tabular}{ll}
Hypercholestérolémies familiales & \emph{mutation du gène du LDL-récepteur} (fréquent++)\\
monogéniques & - hétérozygote : fréquente (1/500), LDL-C : 2 - 4 g/L,\\
& \textbf{xanthomes tendineux, arc cornéen prématuré}, risque CV élevé\\
& - homozygote : \textbf{exceptionnelle} , LDL-C : > 5 g/L\\
& xanthomes dès l'enfance, \textbf{grave} (RA\ldots{} dès la 1re décennie)\\
& \emph{Mutation gène apolipoprotéine B} (apoB) (rare)\\
& \emph{Mutation gène proétine /PCSK9} (rare)\\
\hline
Hypercholestérolémies polygéniques & \textbf{Très fréquente}, LDL augmenté\\
& +/- hyperTG. Risque CV selon LDL et autres fR\\
\hline
Hyperlipidémie familiale combinée & fréquente (1 à 2 \% )\\
& hypercholestérolémie/hyperTG/mixte, risque CV variable\\
\hline
Dysbêtalipoprotéinémie ( III) & rare, prédispos génétique + surpoids, diabète, hypothyroïdie, ttt\\
& LDL et TG élevé\\
& \textbf{xanthomes plans palmaires}\\
& \textbf{xanthomes tubéreux jaune orangé}\\
& risque CV élevé\\
\hline
Hypertriglycéridémie familiale & rare, risque athérogène incertain.\\
Hyperchylomicronémies primitives & très rares. TG > 10 g/L voire 100. Pancréatite aiguë++\\
\end{tabular}
}
\end{table}
\section{Traitement}
\label{sec:orgc26b6f9}
\begin{table}
\centering
\adjustbox{max width=\linewidth}{
\begin{tabular}{llll}
Risque & Critère & Objectif LDL & TTT\\
\hline
Faible & SCORE < 1\%< & < 1.15g/L & Diététique\\
\hline
Modéré & 1\% ≤ SCORE < 5\%< & < 1.15g/L (3 mmol/L) & Diététique\\
& Diabète de type 1/2 avant 40 ans sans atteinte d’organe cible & & \\
\hline
Elevé & 5\% ≤ SCORE < 10\%< & < 1g/L (2.6 mmol/L) & + médic\\
& Diabète de type 1 ou 2: & & \\
& Avant 40 ans avec au moins un FdRCVou atteinte d’organe & & \\
& Après 40 ans sans atteinte d’organe cible ou FdRCV & & \\
& IRC modérée & & \\
& PA ≥ 180/110mmHg & & \\
\hline
Très élevé & SCORE ≥ 10\% & & \\
& Diabète de type 1 ou 2 ≥ 40 ans avec au moins un FdRCV & < 0.7g/L (1.8 mmol/L) & + médic\\
& IRC sévère & & \\
& Maladie CV documentée & & \\
\end{tabular}
}
\end{table}
\subsection{Diététique :}
\label{sec:orgaa45c5e}
\begin{itemize}
\item diminuer acides gras saturés, augmenter mono/poly-insaturés
\item augmenter fruits, légumes céréales
\item diminuer cholestérol alimentaire
\item huile d'olive, fruits à coque
\item + limiter alcool, controle poids, sédentarité
\end{itemize}
Pour hyperTG modérée : diminuer poids, alcool et sucres simples
\subsection{Médicamenteux}
\label{sec:org8fdc33c}
\begin{itemize}
\item Risque faible/modéré : diététique 3 mois puis médic si échec
\item Sinon médic d'emblée
\item statines contre-indiquées en cas de grossesse.
\end{itemize}
\begin{center}
\begin{tabular}{ll}
Hypercholestérolémies pures & \textbf{statine} \(\rightarrow\) echec: augmenter dose \(\rightarrow\) echec : ajout ézétimibe\\
et hyperlipidémies mixtes & si intolérance statine: ézétimibe\\
\hline
Hypertriglycéridémies pures & TG < 5 g/L: diététique seul. sinon ajout fibrate\\
\hline
hypercholestérolémie familiale hétérozygote & dépistage (1er degré). Cf hypercholestérolémie pure\\
\end{tabular}
\end{center}
\subsection{Surveillance:}
\label{sec:org504fa77}
\begin{itemize}
\item EAL à 12 semaine puis à 8-12 après chaque changement.
\item \textbf{myalgies} (statines++) => surveillance musculaire clinique (dosage CPK si risque)
\item hépatique: avant puis à 8-12 semaines. Si ALAT > 3 N, arrêter/diminuer statine
\end{itemize}
Nouveautés thérapeutiques: immunoglobuline monoclonales humaines = Ac anti-PCSK9, alirocumab, évolocumab
\end{document}
```{=latex}
\def\dec{$\searrow{}$}
```
```{=latex}
\def\inc{$\nearrow{}$}
```
```{=latex}
\newcommand{\tabitem}{~~\llap{\textbullet}~~}
```
```{=latex}
\newcommand{\ttabitem}{~~~~~~\llap{$\square$}~~}
```
```{=latex}
\newcommand{\tttabitem}{~~~~~~~~\llap{-}~~}
```
::: table
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
Déshydratation extracellulaire (DEC) Hyperhydratation extracellulaire
------------ ----------------------------------------------------------------------------------------------- -------------------------------------------------------------------------
Mécanisme Perte de sodium (peut être iso-osmotique) Gain de sodium
Étiologie [Pertes extrarénales]{.underline} (natriurèse adaptée \< 20 mmol/24 h) **Insuffisance cardiaque** ;
`\tabitem`{=latex} digestive : vomissements, diarrhées... **Cirrhose ascitique** ;
`\tabitem`{=latex} cutanée : sudation (fièvre, exercice physique ), **Syndrome néphrotique**
exsudation cutanée (brûlure, dermatose bulleuse), Rénal: GN aiguës, IR aiguë et chronique
mucoviscidose. Hypoprotidémies secondaires
[Perte rénales]{.underline} (natriurèse inadaptée \> 20 mmol/24 h) (dénutrition, entéropathies exsudatives)
`\tabitem`{=latex} maladie rénale intrinsèque : Vasodilatation périphérique excessive (grossesse, Paget..)
néphropathie interstitielle (perte de sel)
IRC sévère, régime désodé,
syndrome de levée d'obstacle.
`\tabitem`{=latex} défaut de réabsorption tubulaire du sodium :
`\tabitem`{=latex} polyurie osmotique (diabète sucré, mannitol)
`\tabitem`{=latex} hypercalcémie,
`\tabitem`{=latex} utilisation de diurétiques,
`\tabitem`{=latex} insuffisance surrénale aiguë.
[\"Troisième secteur\"]{.underline} (péritonites, pancréatites aiguës,
occlusions intestinales, rhabdomyolyses traumatiques)
Clinique Perte de poids Interstitiel :
diagnostic Signe du pli cutané. `\tabitem`{=latex} œdèmes périphériques généralisés, déclives,
HypoTA orthostatique, puis décubitus. blancs, mous, indolores et donnant le signe du godet
Tachycardie compensatrice réflexe. Séreuses : épanchement péricardique, pleural, ascite
(Choc hypovolémique) Plasmatique :
Aplatissement des veines superficielles. `\tabitem`{=latex} élévation de la pression artérielle
Baisse de la pression veineuse centrale. `\tabitem`{=latex} OAP
Oligurie avec concentration des urines si extra-rénal Prise de poids.
Sécheresse de la peau dans les aisselles.
Soif, moins marquée que DIC
Biologie `\tabitem`{=latex} hémoconcentration: `\inc`{=latex} protidémie, `\inc`{=latex} Ht Hémodilution (anémie, hypoprotidémie)
`\tabitem`{=latex} Natriurèse effondrée (UNa \< 20 mmol/24 h) (si perte extrarénale de Na) :
`\tabitem`{=latex} Conséquences de l'hypovolémie : IR fonctionnelle, hyperuricémie
`\tabitem`{=latex} Alcalose métabolique de \"contraction\"
Traitement Oral (sel de table + gélules de NaCl) ou IV soluté salé isotonique 9g/L Bilan sodé négatif :
Selon fonction cardiqaue, **Surveillance clinique** `\tabitem`{=latex} Régime alimentaire désodé (\< 2 g/24 h)
Déficit extracellulaire (en litre) = 20 % x poids actuel x (\[Ht actuel/0,45\] -- 1) `\tabitem`{=latex} diurétiques d'action rapide
DIC HIC
Mécanisme Perte d\'eau Excès d'eau
Étiologie [Avec hypernatrémie]{.underline} Potomanie, sd \"tea and soast\"
`\tabitem`{=latex} Une perte d'eau non compensée d'origine : Seuil de sécrétion d\'ADH anormalement bas (grossesse.)
`\ttabitem`{=latex} extrarénale Altération du pouvoir maximal de dilution des urines.
`\tttabitem`{=latex} cutanée : coup de chaleur, brûlure ; `\tabitem`{=latex} ADH basse : IRC avancée (DFG ≤ 20 mL/min),
`\tttabitem`{=latex} respiratoire : polypnée, hyperventilation prolongée, hyperthermie ; `\tabitem`{=latex} ADH élevée :
`\tttabitem`{=latex} digestive : diarrhée osmotique. `\ttabitem`{=latex} hypovolémie vraie (cf DEC)
`\ttabitem`{=latex} rénale : `\ttabitem`{=latex} hypovolémie \"efficace\"
`\tttabitem`{=latex} polyuries osmotiques : diabète, mannitol etc., IC congestive, cirrhose, syndrome néphrotique,
`\tttabitem`{=latex} polyurie hypotonique (U/P osm ≤ 1) : diabète insipide `\ttabitem`{=latex} SIADH
`\tabitem`{=latex} Déficit d\'apport d\'eau (anomalies hypothalamiques,
pas d'accès libre à l'eau )
`\tabitem`{=latex} Apport massif de sodium :
[Sans hypernatrémie]{.underline}: mannitol...
Bio Posm \> 300 mOsm/kg d'eau. Posm \< 280 mOsm/kg.
diagnostic \[Na+\] \> 145 mmol/L. \[Na+\] \< 135 mmol/L
Clinique Soif Nausées, confusion, céphalées
Troubles neurologiques ( somnolence, asthénie... coma, HSD...) Comitialité, trouble CS, coma
Sécheresse des muqueuses, en particulier à la face interne des joues.
Syndrome polyuro-polydipsique en cas de cause rénale.
Perte de poids.
Traitement **Eau** **Restriction hydrique** (500 à 700 mL/j) +/-
`\tabitem`{=latex} Déshydratation globale: soluté salé hypotonique à 4,5 g/L `\tabitem`{=latex} Si DEC, NaCL oral ou soluté isotonique
`\tabitem`{=latex} DIC: eau pure (*jamais par voie IV*) `\tabitem`{=latex} Si SIADH, +/- urée per os ou diurétique anse
`\tabitem`{=latex} DIC + HEC : eau pure + diurétique ou soluté hypotonique (IV). `\tabitem`{=latex} Si HEC : restriction sodée et diurétiques de l'anse.
**Si ancien ne pas dépasser 10 mmol/L/j (œdème cérébral, convulsions)** **Correction ≤ 10 mmol/L/j sur 24h puis 8 mmol/L**
La quantité d'eau à administrer peut être estimée par la formule suivante : **Hyponatrémie sévère** (Na \< 120 mOsm/kg H2O)
-Déficit en eau = 60 % x poids x (\[Natrémie/140\] -- 1) \- Perfusion rapide de NaCl hypertonique 3%
\- Puis NaCl 9 ‰ (≤ +10 mmol/L de natrémie sur 24h puis 8 mmol/L
Si correction trop rapide soluté glucosé 5 % desmopressine
\- Corriger hypokaliémie associée !
```{=latex}
}
```
:::
% Created 2021-04-22 Thu 11:27
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\documentclass[11pt]{article}
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\author{Alexis}
\date{\today}
\title{Anomalie bilan eau sodium}
\hypersetup{
pdfauthor={Alexis},
pdftitle={Anomalie bilan eau sodium},
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pdfcreator={Emacs 28.0.50 (Org mode 9.4.4)},
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\begin{document}
\maketitle
\tableofcontents
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\newcommand{\tabitem}{~~\llap{\textbullet}~~}
\newcommand{\ttabitem}{~~~~~~\llap{$\square$}~~}
\newcommand{\tttabitem}{~~~~~~~~\llap{-}~~}
\begin{table}
\centering
\adjustbox{max width=\linewidth}{
\begin{tabular}{lll}
\hline
& Déshydratation extracellulaire (DEC) & Hyperhydratation extracellulaire\\
\hline
Mécanisme & Perte de sodium (peut être iso-osmotique) & Gain de sodium\\
Étiologie & \uline{Pertes extrarénales} (natriurèse adaptée < 20 mmol/24 h) & \textbf{Insuffisance cardiaque} ;\\
& \tabitem digestive : vomissements, diarrhées\ldots{} & \textbf{Cirrhose ascitique} ;\\
& \tabitem cutanée : sudation (fièvre, exercice physique ), & \textbf{Syndrome néphrotique}\\
& exsudation cutanée (brûlure, dermatose bulleuse), & Rénal: GN aiguës, IR aiguë et chronique\\
& mucoviscidose. & Hypoprotidémies secondaires\\
& \uline{Perte rénales} (natriurèse inadaptée > 20 mmol/24 h) & (dénutrition, entéropathies exsudatives)\\
& \tabitem maladie rénale intrinsèque : & Vasodilatation périphérique excessive (grossesse, Paget..)\\
& néphropathie interstitielle (perte de sel) & \\
& IRC sévère, régime désodé, & \\
& syndrome de levée d’obstacle. & \\
& \tabitem défaut de réabsorption tubulaire du sodium : & \\
& \tabitem polyurie osmotique (diabète sucré, mannitol) & \\
& \tabitem hypercalcémie, & \\
& \tabitem utilisation de diurétiques, & \\
& \tabitem insuffisance surrénale aiguë. & \\
& \uline{"Troisième secteur"} (péritonites, pancréatites aiguës, & \\
& occlusions intestinales, rhabdomyolyses traumatiques) & \\
\hline
Clinique & Perte de poids & Interstitiel :\\
diagnostic & Signe du pli cutané. & \tabitem \oe{}dèmes périphériques généralisés, déclives,\\
& HypoTA orthostatique, puis décubitus. & blancs, mous, indolores et donnant le signe du godet\\
& Tachycardie compensatrice réflexe. & Séreuses : épanchement péricardique, pleural, ascite\\
& (Choc hypovolémique) & Plasmatique :\\
& Aplatissement des veines superficielles. & \tabitem élévation de la pression artérielle\\
& Baisse de la pression veineuse centrale. & \tabitem OAP\\
& Oligurie avec concentration des urines si extra-rénal & Prise de poids.\\
& Sécheresse de la peau dans les aisselles. & \\
& Soif, moins marquée que DIC & \\
\hline
Biologie & \tabitem hémoconcentration: \inc protidémie, \inc Ht & Hémodilution (anémie, hypoprotidémie)\\
& \tabitem Natriurèse effondrée (UNa < 20 mmol/24 h) (si perte extrarénale de Na) : & \\
& \tabitem Conséquences de l’hypovolémie : IR fonctionnelle, hyperuricémie & \\
& \tabitem Alcalose métabolique de "contraction" & \\
\hline
Traitement & Oral (sel de table + gélules de NaCl) ou IV soluté salé isotonique 9g/L & Bilan sodé négatif :\\
& Selon fonction cardiqaue, \textbf{Surveillance clinique} & \tabitem Régime alimentaire désodé (< 2 g/24 h)\\
& Déficit extracellulaire (en litre) = 20 \% x poids actuel x ([Ht actuel/0,45] – 1) & \tabitem diurétiques d’action rapide\\
& & \\
& & \\
& & \\
\hline
& DIC & HIC\\
\hline
Mécanisme & Perte d'eau & Excès d’eau\\
\hline
Étiologie & \uline{Avec hypernatrémie} & Potomanie, sd "tea and soast"\\
& \tabitem Une perte d’eau non compensée d’origine : & Seuil de sécrétion d'ADH anormalement bas (grossesse.)\\
& \ttabitem extrarénale & Altération du pouvoir maximal de dilution des urines.\\
& \tttabitem cutanée : coup de chaleur, brûlure ; & \tabitem ADH basse : IRC avancée (DFG ≤ 20 mL/min),\\
& \tttabitem respiratoire : polypnée, hyperventilation prolongée, hyperthermie ; & \tabitem ADH élevée :\\
& \tttabitem digestive : diarrhée osmotique. & \ttabitem hypovolémie vraie (cf DEC)\\
& \ttabitem rénale : & \ttabitem hypovolémie "efficace"\\
& \tttabitem polyuries osmotiques : diabète, mannitol etc., & IC congestive, cirrhose, syndrome néphrotique,\\
& \tttabitem polyurie hypotonique (U/P osm ≤ 1) : diabète insipide & \ttabitem SIADH\\
& \tabitem Déficit d'apport d'eau (anomalies hypothalamiques, & \\
& pas d’accès libre à l’eau ) & \\
& \tabitem Apport massif de sodium : & \\
& \uline{Sans hypernatrémie}: mannitol\ldots{} & \\
\hline
Bio & Posm \textgreater{} 300 mOsm/kg d’eau. & Posm \textless{} 280 mOsm/kg.\\
diagnostic & [Na+] \textgreater{} 145 mmol/L. & [Na+] \textless{} 135 mmol/L\\
\hline
Clinique & Soif & Nausées, confusion, céphalées\\
& Troubles neurologiques ( somnolence, asthénie\ldots{} coma, HSD\ldots{}) & Comitialité, trouble CS, coma\\
& Sécheresse des muqueuses, en particulier à la face interne des joues. & \\
& Syndrome polyuro-polydipsique en cas de cause rénale. & \\
& Perte de poids. & \\
\hline
Traitement & \textbf{Eau} & \textbf{Restriction hydrique} (500 à 700 mL/j) +/-\\
& \tabitem Déshydratation globale: soluté salé hypotonique à 4,5 g/L & \tabitem Si DEC, NaCL oral ou soluté isotonique\\
& \tabitem DIC: eau pure (\emph{jamais par voie IV}) & \tabitem Si SIADH, +/- urée per os ou diurétique anse\\
& \tabitem DIC + HEC : eau pure + diurétique ou soluté hypotonique (IV). & \tabitem Si HEC : restriction sodée et diurétiques de l’anse.\\
& \textbf{Si ancien ne pas dépasser 10 mmol/L/j (œdème cérébral, convulsions)} & \textbf{Correction \(\le\) 10 mmol/L/j sur 24h puis 8 mmol/L}\\
& La quantité d’eau à administrer peut être estimée par la formule suivante : & \textbf{Hyponatrémie sévère} (Na < 120 mOsm/kg H2O)\\
& -Déficit en eau = 60 \% x poids x ([Natrémie/140] – 1) & - Perfusion rapide de NaCl hypertonique 3\%\\
& & - Puis NaCl 9 ‰ (\(\le\) +10 mmol/L de natrémie sur 24h puis 8 mmol/L\\
& & Si correction trop rapide soluté glucosé 5 \% desmopressine\\
& & - Corriger hypokaliémie associée !\\
\end{tabular}
}
\end{table}
\end{document}
\graphicspath{{../../pictures/medecine/}}
\usetikzlibrary{quotes}
\section{Définitions}%
\label{sec:definitions}
\begin{figure}
\centering
\includegraphics[width=0.8\linewidth]{160_macule_papule}
\includegraphics[width=0.8\linewidth]{160_purpura_placard}
\includegraphics[width=0.8\linewidth]{160_vesicule}
\end{figure}
Morbiliforme = avec intervalles de peau saine\\
Scarlatiniforme = sans intervalles de peau saine
\section{4 - Sécurité du patient}%
\label{sec:ue_1_item_4_securite_du_patient}
Infection nosocomiale : > 48h post-admission ( > 30 j après opération, > 1 an si
pose de matériel étranger)
Agents infectieux : \bact{ecoli}, \bact{dore}, \bact{aeruginosa}
\begin{table}[htpb]
\centering
\caption{Précautions}
\begin{tabular}{ccc}
\toprule
Air & Gouttelettes & Contact \\
\midrule
masque FFP2 & masque chir & tablier \\
tuberculose, rougeole & grippe, ménigocoque & BMR, SARM, varicelle...\\
varicelle & coqueluche, mycoplasme, rubéole, & \\
& oreillons, parvorvirus B19, VRS & \\
\bottomrule
\end{tabular}
\end{table}
ATB :
\begin{itemize}
\item prophylaxie pour Altemeier 1-2 (\{pas de, faible\} rupture d'asepsie
resp.)
\item curatif pour Altemeier 3-4 (\{trauma < 4h contamination digestive,
trauma > 4h, contamination fécale\},
\end{itemize}
Cathéter : changer 72h
\section{UE2 - 26 : Prévention des risques foetaux}%
\label{sec:ue2_item_26_prevention_des_risques_foetaux}
\begin{table}[htpb]
\centering
\caption[dummy]{Dépistage obligatoire.\\
\dag: pas de sérologie (hémoc + PL chez NN)}
\begin{tabular}{*{4}{c}}
\toprule
Infection & Dépistage & Prévention primaire & Prev. secondaire \\
\midrule
Toxoplasmose & 10 SA & Hygiène & Spiramycine ou Pyriméthamine\\
& mensuel si non immun & & \\
\midrule
Rubéole & < 10 SA, 20 SA & ROR & \\
& & Pas de vaccin pendant grossesse & \\
\midrule
VHB & 6M & lamivudine/ténofovir & vaccin \\
strept.\dag B & 34-38 SA & amoxicilline & \\
syphilis & 1er trimestre & &pénicilline G retard\\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htpb]
\centering
\caption[dummy]{Dépistage non obligatoire.\\
\dag: pas de sérologie (hémoc)}
\begin{tabular}{*{3}{c}}
\toprule
Infection & Prévention primaire & Prev. secondaire \\
\midrule
VIH & & antirétroviral, AZT (foetus)\\
CMV (frequent) & hygiène & \\
HSV & & (val)aciclovir (césarienne ?)\\
Rougeole & ROR & Ig (sous 6 j) \\
Varicelle & vaccin & Ig (sous 96h) \\
Listériose & hygiène & amoxicilline \\
\bottomrule
\end{tabular}
\end{table}
\paragraph{Autres} : paludisme [urgence (quinine-artésunate IV)], IU, \bact{burnetii}
[pas de lait cru], parvovirus B19 [surveillance], vaginose [métronidazole],
arbovirus
\section{143 - Vaccination}%
\label{sec:item_143_vaccination}
Vaccins acellulaire : coqueluche\\
Vaccins anatoxine : diphtérie-tétanos\\
Vaccins entier: polio,grippe, VHA, rage
\subsection{Enfant}%
\label{sub:enfant}
\begin{table}[htpb]
\centering
\caption{Vaccins obligatoires pour l'enfant}
\begin{tabular}{*{7}{c}}
DTP + Coqueluche & 2M & 4M & 11M & & 6A & 11-13A\\
\bact{influenzae} & 2M &4M & 11M \\
VHB & 2M & 4M & 11M \\
Pneumocoque & 2M & 4M & 11M \\
Méningocoque C & & 5M & 12M\\
ROR & & & 12M & 16-18M\\
\end{tabular}
\end{table}
Rattrapages :
\begin{itemize}
\item VHB : 3 doses (16M - 11A), 2 doses (11-15A)
\item Méningocoque C : 1 dose (16M - 24A)
\item HPV : 3 dose (15-19A)
\item ROR : nb doses manquantes (11A)
\end{itemize}
\subsection{Adulte}%
\label{sub:adulte}
\begin{table}[htpb]
\centering
\caption{Vaccins recommandés pour l'adulte}
\begin{tabular}{*{5}{c}}
DTP & 25A & 45A & 65A & 75, 85...A\\
Coqueluche & 25A \\
Grippe& & & & 65,66...A\\
Zona& & & & 1 dose (65-74A)\\
\end{tabular}
\end{table}
Post-exposition : tétanos [vaccin +/- Ig], VHA, méningocoque (A,B,C,Y ou W135), rage [vaccin +/-
Ig], rougeole (72h, sauf femme enceinte = Ig)
Contre indications :
\begin{itemize}
\item permanente : allergie oeuf (fièvre jaune, grippe), immunodéprimé
\item temporaire : infection aigüe grave, pas de vaccin vivant pour la femme
enceinte, 3 mois après Ig
\end{itemize}
Réactions :
\begin{itemize}
\item bénigne : vivant = infection retardée, inerte = inflammation locale
immédiate
\item grave : anaphylactique, maladie infectieuse, dysimmunitaires
\end{itemize}
\subsection{Grossesse}%
\label{sub:grossesse}
Recommandé : grippe
Possible : inactivé (tétanos, diphtérie, VHA, VHB, méningo, pnemoc...), vivant
atténué (fièvre jaune si voyage obligatoire)
Contre-indiqué : Varicelle, ROR (2 mois avant grossesse mais possible en début)
\section{144 - Fièvre aigüe}
Fièvre : \(\ge 38^{o}\) matin, \(38.3^{o}\) soir [+0.5$^{o}$ si axillaire/buccal]
\begin{itemize}
\item aigüe si \textless{} 5 jours
\item prolongée si \textgreater{} 20 jours
\end{itemize}
\danger fièvre \(\neq\) infection
\begin{figure}[htpb]
\centering
\resizebox{\linewidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
Point d'appel évident -> {
oui -> {
Virose banale -> Ttt symptomatique [draw] -> "Réévalution 48-72h";
Foyer bactérien -> Ttt étiologique [draw] -> "Réévalution 48-72h";
};
non -> {
"Sepsis grave\\Choc septique ?"[level distance=1.8cm] ->["oui"]
"ATB probabiliste\\Remplissage vasc.\\TDM, TAP urgence" [draw];
"Sepsis grave\\Choc septique ?" ->["non"]
"Réévaluation\\Hospitalisation \\si terrain à risque";
"Neutropénie\\asplénie" -> "Hémocultures\\ATB probabiliste" [draw];
non infectieux -> {Hyperthermie, Autres};
};
};
};
}
\caption{Démarche diagnostique}
\end{figure}
Signes de gravité :
\begin{itemize}
\item
neuro: angoisse, agitation, confusion, troubles du comportement, coma
\item
cardiovasc : FC > 120/min, TA systol < 90 mmHg,
PAM < 65 mmHg
\item
cutané : purpura, extrémités froides et cyanosées, marbrures
\item
respiratoire : polypnée > 24/min, tirage, balancement
thoraco-abdominal, polypnée superficielle, \(SaO_2 < 90 \%\)
\end{itemize}
Peut décompenser une comorbidité :
\begin{itemize}
\tightlist
\item
neurologique
\item
\(37 + n^\circ\) =\textgreater{} \(+400\cdot n\) mL/j pertes hydriques
\item
\(37 + n^\circ\) =\textgreater{} \(+10 \cdot n\) battements/min pour
FR et FC
\item
augmentations des besoins en oxygène
\end{itemize}
Terrain à risque : femme enceinte, immunodépression
\danger ATB sans diagnostic seulement pour sepsis/grave, choc septique,
neutropénie (\(< 500 PNN/mm^3\)), asplénie, pupura fulminans
Traitement sympotmatique :~antipyrétiques seulement si fièvre mal
tolérée/terrain particulier =\textgreater{} paracétamol (aspirine, AINS
non recommandés)
\section{145 - Infections naso-sinusiennes}%
\label{sec:item_145_infections_naso_sinusiennes}
Rhinopharyngite virale = 99\%. Contagieux++ (goutelettes)
\paragraph{Clinique} rhume banal + fièvre, myalgie + inflammation muqueuses respiratoire
Peut rarement se compliquer en sinusite bactérienne (\bact{pneumocoque},
\bact{influenzae})
\begin{itemize}
\item maxillaire++
\item frontale, ethmoïdale, sphénoïdale (complication possible)
\end{itemize}
Y penser si
\begin{itemize}
\item fièvre $\ge 3$ jours
\item 2 parmi 3 critères : douleurs $\ge 48$h, douleur unilatérale,
augmentation rhinorrhée et purulence
\end{itemize}
\paragraph{Traitement}%
\label{par:traitement}
\begin{itemize}
\item paracétamol, sérum phys. (pas d'AINS !)
\item ATB seulement pour les sinusites bactériennes = amoxicilline ou
amoxicilline-acide clavulanique si échec ou non maxillaire
\end{itemize}
\section{146 - Angines}%
\label{sec:item_146_angines}
Diagnostic clinique : fonctionnel (odynophagie, otalgie réflexe), physique
(fièvre, inflammation oropharynx + amygdale, adénopathies satellites sensibles)
Traitement ATB : seulement pour SGA\footnote{streptocoque $\beta$-hémolytique du groupe A}, l'angine de Vincent, diphtérie, gonocoque,
chancre syphilitique
\subsection{Érythémateuse/érythémato-pultacées}%
\label{sub:erythemateuse_erythemato_pultacees}
80-90\%
Étiologie = EBV, VIH (virus) ou SGA
Score de McIsaac : 1 point pour fièvre $> 38^{\circ}$, pas de toux, adénopathie
cervicale sensible, atteinte amygdale. -1 point si $\ge 45$ ans.
\begin{figure}[htpb]
\centering
\caption{Prise en charge}
\tikz \graph[
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
tree layout]
{
"" -> {
"McIsaac < 2" -> ttt symptomatique [level distance=2cm];
"Enfant\\ou McIsaac $\ge$ 2" -> TDR [level distance=2cm]-> {
"Dépistage VIH ?" -> ttt symptomatique [>"négatif"];
"Amoxicilline\\(C2G/C3G)" [>"positif", draw];
};
};
};
\end{figure}
\subsection{Pseudo-membraneuse}%
\label{sub:pseudo_membraneuse}
\paragraph{Mononucléose infectieuse} : fréquent, évolution bénigne
Examens : MNI-test et sérologie si négatif (IgM anti-VCA)
\paragraph{Diphtérie} : rare mais urgence
Clinique :
\begin{itemize}
\item voyage en Europe en l'Est/développement, pas de vaccins, < 7 jours
\item fausses membranes envahissant la luette
\end{itemize}
Examens : prélèvement puis ED + culture (corynébactéries) + PCR
Traitement : sérum puis vaccins + amoxicilline. Précautions gouttelettes
\subsection{Vésiculeuses}%
Toujours virales. Bénignes
\subsection{Ulcéreuses/ulcéro-nécrotiques}
Angine de Vincent (fréquent++)
\begin{itemize}
\item clinique puis confirmé par association fusospirillaire (ED).
\item risque de complications locales
\item amoxicilline
\end{itemize}
Chancre syphilitique : cf~\nameref{sub:syphilis}
Agranulocytose
\section{147 - Otites}%
\label{sec:otites}
\subsection{Otite moyenne aigüe}%
\label{sub:otite_moyenn_aigue}
Oedème de la trompe d'Eustache $\to$ otite congestive $\to$ otite purulente
\bact{pneumocoque}, \bact{influenzae}
Diagnostic : fièvre, signes généraux + otoscopie surtout (épanchement
rétro-tympanique si purulente, congestion si congestive)
Traitement :
\begin{itemize}
\item ATB seulement pour OMA purulente chez enfant $\le 2$ ans ou adulte si
symptomatologie bruyante
$\rightarrow$ amoxicilline per os (+acide clavulanique si otite et conjonctivite)
\item paracétamol (pas d'AINS, corticoïdes !)
\end{itemize}
Suivi 48-72h : échec si persistance des symptôme $\rightarrow$ amoxicilline +
acide clavulanique (si 1er traitement = amoxicilline). Au 2eme échec :
spécialiste
\subsection{Otite externe nécrosante}%
\label{sub:otite_externe_necrosante}
Bénigne : traitement local + antalgique\\
Nécrosante chez immunodéprimé + polype $\to$ avis ORL en urgence
\subsection{Otite séromuqueuse}%
\label{sub:otite_seromuqueuse}
Inflammation chronique $\rightarrow$ épanchement non purulent. Fréquent chez
l'enfant. Adulte: chercher tumeur du cavum.
Diagnostic : hypoacousie, tympans mats
Guérison spontanée, pas d'ATB.
\subsection{Otites cholesteatomateuse}%
\label{sub:otites_choestatomateuse}
Non infectieux.
Diagnostic : otorrhée fétide chronique, intermittente.
Traitement chirurgical, pas forcément réversible.
\section{148 - Méningites, méningo-encéphalites}
Signes de gravité :
\begin{itemize}
\item purpura extensif
\item trouble de la conscience (Glasgow \textless{}= 8)
\item signes de focalisation neuro
\item signes de souffrance du tronc cérébral
\item état de mal convuslif
\item instabilité hémodynamique
\end{itemize}
Contre-indication à la PL :
\begin{itemize}
\item
anomalie de l'hémostase {[}PL dès stabilité{]}
\item
instabilité hémodynamique {[}PL dès stabilité{]}
\item
signe d'engagement cérébral (mydriase unilatérale, hoquet, trouble
ventilatoire, enroulement) {}
\item
crise convulsive récente
\item
risque d'engagement cérébral (localisation neuro, trouble vigilance +
Glasgow \textless{}= 11) {}
\end{itemize}
\subsection{Méningite}
Épidémio : virale dominent < 65 ans. Bactérienne dominent > 65 ans (70\% de
pneumocoque > 40 ans, 50\% sinon). Herpétique :
80\% < 20 ans ou > 50 ans
\begin{figure}[htpb]
\centering
\begin{subfigure}{0.4\textwidth}
\resizebox{\textwidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Signes de localisation, crises comitiales, Glasgow $\le$ 11 ?" [level
distance=2cm ]
%->["oui"] "Hémocultures" [draw]-> "DXM+ATB" [draw] -> scanner [draw]-> PL[draw] ;
->["oui"] "Hémocultures\\DXM+ATB\\scanner" [draw]->["pas CI"] PL[draw] ;
"Signes de localisation, crises comitiales, Glasgow $\le$ 11 ?"
->["non"] "CI PL ?";
"CI PL ?" [level distance=2cm] ->[left, "résolution"] PL [align here];
PL-> {
"bactérien ?" -> "ATB + DXM" [draw];
"viral ?" -> {
"méningo-\\encéphalite" -> aciclovir [draw];
méningite -> symptomatique [draw];
};
"autres ?";
};
};
}
\caption{Traitement}
\end{subfigure}
\begin{subfigure}{0.58\textwidth}
\resizebox{\textwidth}{!}{
\tikz \graph [
% Labels at the middle
%edge quotes mid,
% Needed for multi-lines
nodes={align=center},
%edges={nodes={fill=white}},
layered layout]
{
PL [draw] ->
"ED Gram\\culture + antibiogramme\\Coloration Ziehl-Neelsen $\rightarrow$
PCR BK" [draw, align=left]
-> {
"Suspicion méningite\\ bactérienne" [level distance=2cm ]
->["forte"] "Ag\\pneumocoque" [draw, level distance=2cm ]
-> ["négatif"] "PCR méningocoque" [draw];
"Suspicion méningite\\ bactérienne"
->["faible"] "PCR\\entérovirus LCS" [draw];
"Autres" -> {"cryptocoque (ID), Lyme,\\VDRL-TPHA, leptospirose"};
}
};
}
\caption{Orientation}
\end{subfigure}
\end{figure}
\begin{figure}[htpb]
\centering
\begin{minipage}{0.42\textwidth}
\resizebox{\textwidth}{!}{
\tikz \graph [
layered layout]
{
LCS -> {
purulent [level distance=1.5cm] -> {bactérien; "début viral"; };
clair ->["normo",swap] viral ;
clair ->["hypoglycorachie"] "Listeria, BK";
}
};
}
\end{minipage}
\begin{minipage}{0.69\textwidth}
\resizebox{\textwidth}{!}{
\tikz \graph [
nodes={align=center},
layered layout]
{
ED LCS -> {
positif ->
{"diplocoque\\Gram+" -> pneumocoque -> "C3G + DXM" [draw];
"diplocoque\\Gram{-}" -> méningocoque -> "C3G + DXM" [draw];
"bacille\\Gram+" -> Listeria -> "amoxicilline\\+gentamicine" [draw];
};
negatif -> C3G + DXM [draw];
negatif ->["Listeria ou signes de gravité"] "C3G + DXM\\(+ amoxicilline\\+
gentamicine)"[draw];
};
};
}
\end{minipage}
\end{figure}
\begin{figure}[htpb]
\centering
\includegraphics[width=0.8\linewidth]{../../pictures/medecine/148_antibio}
\caption{Début des antibiotiques}
\end{figure}
\begin{table}[htpb]
\centering
\caption{Aspect LCS}
\begin{tabular}{*{4}{c}}
\toprule
&normal & purulent & liquide clair \\
\midrule
Aspects & clair & trouble & clair \\
Elements & < 5/\(mm^3\) & > 20/\(mm^3\) & 5-100/\(mm^3\)
\\
& & PNN > 50\% & Lymphocytes > 50\% \\
Glycorachie & 2/3 glycémie & < 0.4 glycémie & 2/3 glycémie (viral)\\
& & & < 0.4 glycémie (Listéria/BK) \\
\midrule
Protéinorachie & < 0.4 g/L & > 1 g/L & < 1 g/L (viral)\\
& & & 1-2 g/L (batérien) \\
Lactatorachie & < 3.2 mmol/L & > 3.2 mmol/L & <
3.2 mmol/L \\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htpb]
\centering
\caption{Méningites purulentes}
\begin{tabular}{*{4}{c}}
\toprule
Bactérie & Clinique & Traitement & Précautions \\
\midrule
Méningocoque & Début brutal & C3G parentérale & Gouttelettes \\
Gram+ grains de café & Sd méningé franc & puis amoxicilline & ATB
prophylaxie \\
& Pas de signe de localisation & si sensible & Vaccins \\
& \textbf{Purpura} & 4-7 j & Déclaration obligatoire \\
\hline
Pneumocoque & Début brutal & C3G & Vaccins \\
Diplocoque Gram+ & Sd méningé franc & 10-14j & Chercher porte d'entrée \\
& (Purpura) & & (ORL, pulmonaire) \\
& Signes de localisation & & \\
\hline
Listéria & Rhombencéphalite + sd méningé & Amoxicilline & Hygiène alimentaire \\
Bacille Gram+ & (début \textbf{progressif} & + gentamicine & \\
& Atteinte du tronc cérébral & 3 semaines & \\
& (nerfs crâniens) & & \\
\hline
Bacilles Gram+ & Souvent trompeur & C3G & \\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htpb]
\centering
\caption{Méningites lymphocytaires hypoglycorachiques : tuberculeuse}
\begin{tabular}{*{3}{c}}
\toprule
Clinique & Traitement & Prévention \\
\midrule
Début \textbf{progressif} & Quadrithérapie 2 mois & Vaccins \\
Sd méningé frustre & (isoniazide, rifampicine, ethambutol, pyranizamide) & \\
Détections infections latentes & Bithérapie 10 mois & \\
Fébricule, sueurs &(isoniazide, rifampicine) & \\
AEG & & \\
Neuropsy, localisation neuro & & \\
\bottomrule
\end{tabular}
\end{table}
Méningites lymphocytaires normoglycorachiques
\begin{longtable}[]{@{}lll@{}}
\toprule
\endhead
\begin{minipage}[t]{0.24\columnwidth}\raggedright
Virale\\
Syphilis, Lyme\\
Leptospirose\strut
\end{minipage} & \begin{minipage}[t]{0.39\columnwidth}\raggedright
Allure bénigne\\
Sd méningé intense, brutal\\
Fièvre élevée\\
Signes extra-mémingés Pas de signes neuro centraux\strut
\end{minipage} & \begin{minipage}[t]{0.23\columnwidth}\raggedright
Symptomatique\\
ou VIH\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}
\danger Dexaméthasone inutile si ATB parentéral avant \danger
Surveillance :
\begin{itemize}
\item efficacité : fièvre, signes neuro
\item si évolution négative 48-72h : imagerie médicale puis PL de
contrôle si pas de CI
\item suivi prolongé neuropsycho + audiométrique
\end{itemize}
\subsection{Méningo-encéphalite à liquide clair}
Causes :
\begin{itemize}
\item 50\% inconnues
\item virus : HSV, entérovirus, VIH
\item bactéries : \bact{tuberculose}, \bact{listeria}, Lyme, syphilis
\end{itemize}
À évoquer devant : fièvre, sd méningé, signes neuro centraux \\
Traitement :~aciclovir si encéphalite + méningite lymphocytaire normoglycorachique
Clinique de la méningo-encéphalite herpétique
\begin{itemize}
\item fièvre
\item installation sur qq jours
\item Localisation temporale $\to$ troubles du comportement,
troubles mnésiques, aphasie, crises convulsives temporales
\end{itemize}
\subsection{Abcès}
Contamination :~contiguïté, hématogènes, post-traumatique,
post-chirurgical \\
Polymicrobien :~streptocoques (oraux, mileri), anaérobies
\section{149 - Endocardite infectieuse}
\begin{table}[htpb]
\centering
\caption{Principaux agents infectieux et porte d'entrée}
\begin{tabular}{cc}
\toprule
Agent & Porte d'entrée \\
\midrule
\bact{dore} & Cutanée\\
Streptocoques oraux & Bucco-dentaire\\
\bact{gallolyticus} & Digestive\\
Entérocoques & Digestive, urinaire\\
\bottomrule
\end{tabular}
\end{table}
Diagnostic =
\begin{itemize}
\item fièvre + souffle cardiaque (nouveau/modifié)
\item agent infectieux identifié
\item anomalie intracardiaque
\end{itemize}
\begin{figure}[htpb]
\centering
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
%sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
Clinique[draw] // [layered layout] {
"\textit{Général}" // [layered layout] {"Fièvre\\AEG"[fill=gray!20];};
"\textit{Cardiaque}" // [layered layout] {"Nouveau/modif\\souffle cardiaque"[fill=gray!20];};
"\textit{Extra-cardiaque}" // [layered layout] {
"Emboles" -> {
Coeur gauche -> {
"cérébral\\rate,reins,foie\\membres\\peau\\anévrisme inf."[fill=gray!20];
};
Coeur droit -> pulmonaires[fill=gray!20];
};
Immuno -> {
"Purpura vasc.\\
Faux panaris d'Osler\\
Erythème palmoplantaire\\de Janeway"[fill=gray!20];
}
};
}
-> "Hémocultures\\Echographie TT, TO"[draw]
-> "Gravité ?" [level distance=2cm]
-> ["oui"] "ATB proba.\\Amoxicilline+(cl)oxacilline+gentamicine (> 1
an)\\Vancomycine+gentamicine+rifampicine (< 1 an)" [draw]
-> "Chirurgie ?\\ATB\\Ttt porte d'entrée"[draw];
"Gravité ?" -> ["non"] "scanner TAP\\IRM cérébral"[draw]
-> "ATB adaptée"[draw] -> "Chirurgie ?\\ATB\\Ttt porte d'entrée";
};
\caption{Démarche}
\end{figure}
\begin{table}[htpb]
\centering
\caption{$\beta$-lactamine (remplacer par glycopeptide si allergie)}
\begin{tabular}{cc}
\toprule
Agent infectieux & $\beta$-lactamine \\
\midrule
\bact{dore} & Pénicilline M IV \\
Streptocoques oraux & Amoxicilline IV ou ceftriaxone IV $\pm$ gentamicine\\
\bact{gallolyticus} & Amoxicilline IV ou ceftriaxone IV $\pm$ gentamicine\\
Entérocoques & Amoxicilline + gentamicine \\
\bact{faecalis} & Amoxicilline + ceftriaxone \\
\bottomrule
\end{tabular}
\end{table}
\danger Fièvre inexpliquée chez valvulopathe = EI par défaut
\danger Signe neuro. fébrile $\to$ chercher EI (auscult + hémoc.)
\begin{table}[htpb]
\centering
\caption{Cardiopathies à risque}
\begin{tabular}{cc}
\toprule
Risque élevé & Risque moyen \\
\midrule
Prothèse valvulaire & Valvulopathie\\
Cardiopathies congénitales cyanogène & Cardiomyopathie obstructive \\
(+ shunt persistant + dérivation chir.) & Cardiopathie non cyanogène\\
& \quad (sauf communication intraauricul.)\\
ATCD d'EI & Bicuspidie aortique\\
\bottomrule
\end{tabular}
\end{table}
ATB adaptée :
\begin{itemize}
\item
Staph. aureus : penicilline M IV
\item
Strept. oraux :~amoxicilline IV, ceftriaxone IV
\item
Strept. gallolyticus :~amoxicilline IV, ceftriaxone IV
\item
Enteroccocus spp. : amoxicilline + gentamicine IV \emph{ou}
amoxicilline + ceftriaxone (Si allergie/résistance : glycopeptide)
\end{itemize}
Critères de Duke : certitude = 2 majeurs / 1 majeurs + 3 mineurs / 5
mineurs
\begin{longtable}[]{@{}ll@{}}
\toprule
Majeurs & Mineurs\tabularnewline
\midrule
\endhead
hémocultures + (typique/compatible) & cardiopathie/toxico\tabularnewline
écho caractéristique & Fièvre \textgreater{} 38\tabularnewline
nouveau souffle & Phénomènes vasc, immuno\tabularnewline
& Microbiologique\tabularnewline
& Échographie\tabularnewline
\bottomrule
\end{longtable}
\section{150 - Surveillance des porteurs de valve et prothèses vasculaires}
Haut risque d'endocardite infectieuse (prothèses valvulaire) + anévrisme
infectieux si prothèse vasculaire.
Prévention amont, péri-, post-opératoire :
amoxicilline 1h avant geste dentaire à risque (clindamycine si allergie)
\section{151 - Infections broncho-pulmonaires communautaires}
\subsection{Bronchite aigüe}
Clinique : toux (sèche ?) sur plusieurs semaines, brûlure
rétro-sternale, râles bronchiques\\
Évolution favorable spontanément
\subsection{Pneumonie aigüe communautaire}
Diagnostic :
\begin{itemize}
\item signes fonctionnels respiratoires (toux, expector, dyspnée, douleur
thoracique)
\item fébrile
\item radio (atteinte parenchyme) $\to$ pneumonie
alvéolaire/interstitielle/micronodulaire
\end{itemize}
\begin{figure}[htpb]
\centering
\caption{Démarche diagnostique}
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Clinique"[draw] // [layered layout] {
Auscultatoire ->
"\textbf{Sd de condensation pulmonaire}\\
$\searrow$ murmure vésiculaire\\
râles crépitants\\
souffle tubaire\\
matité\\
$\nearrow$ vibration vocales" ;
"\textbf{Signes de gravité}" -> {
"Trouble conscience\\
FR > 30 cycles/min\\
TA systol < 90 mmHg\\
FR > 120 bat./min\\
T < 36 ou $\ge 40^{\circ}$)\\" ;
"Cyanose\\
Tirage\\
Marbrures";
}
}
-> Radio [draw]
-> Terrain [draw] // [layered layout] {
Immunocompétent -> {
"Tabac\\
Ethylisme chronique\\
Contexte post-grippal\\
> 65 ans\\
Comorbidités";
};
Immunodéprimé -> {
"Splénectomie\\
VIH\\
Transplantés\\
Patho auto-immune sous IS";
};
"Circonstances part." -> {
"Institution\\
Trouble déglutition\\
Isolement social\\
Socio-économique\\
Inobservance thérapeutique";
};
};
};
\end{figure}
Facteurs de risque de mortalité :
\begin{itemize}
\item 65 ans
\item Comorbidités :
\begin{itemize}
\item insuffisance cardiaque
\item AVC/AIT
\item insuffisance rénale chronique
\item maladie hépatique
\item broncho-pneumopathie chronique + trouble ventilatoire obstructif
\item diabète sucré non équilibré
\item drépanocytose
\item néoplasie associté
\end{itemize} \item
Immunodépression
\item ATCD pneumonie bactérienne
\item Hospitalisation dans l'année
\item Institution
\end{itemize}
\begin{table}[htpb]
\centering
\captionsetup{singlelinecheck=off}
\caption[dummy]{Prise en charge. \\NB:
\begin{itemize}
\item \dag = Coxiella burnetti
\item pneumonie franche lobaire aigüe : début brutal, douleur thoracique
``coup de poignard'', touche sèche $\to$ expector.
purulentes/rouille, frissons intenses, fièvre 39-40, malaise général
\end{itemize}
}
\resizebox{\textwidth}{!}{
\begin{tabular}{ccccc}
\toprule
& Streptococcus pneumoniae& Atypique& Legionella& Post-grippal \\
\midrule
&Cocci Gram+& Intracellulaires& Bacille Gram-& S. pneumoniae, S. aureus\\
&&&&, H. influenza, S. pyogenes\\
\midrule
Début& brutal& progressif (\dag{} brutal)& progressif& Grippal fébrile préalable\\
Temp.& 39-40& faible (\dag{} élevée)& 40& \\
Radio& opacité alvéolaire systématisée& & opacité alvéolaire non systématisée& \\
Clinique& pneumonie franche lobaire aigüe && Signes non spécifiques&
+5-7j: réapparation + toux,\\
&&&&expector. muco-purulentes \\
\bottomrule
\end{tabular}
}
\end{table}
Complications:~
\begin{itemize}
\tightlist
\item
respiratoire : plèvre, parenchyme, voies aériennes, fonctionnelle
\item
générales : décompensation, complication infectieuses à distance, choc
septique, décès
\end{itemize}
\begin{figure}[htpb]
\centering
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
%sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
%\node (proba1) {proba};
Pneumocoque[draw] // [layered layout] {
"\faHospital Examen direct/Ag" -> Amoxicilline;
"\faAmbulance ?" -> Amoxicilline;
} -> "Réévaluation 48-72h";
Legionella[draw] // [layered layout] {
"\faHospital Ag Legionella" -> Macrolide;
"\faAmbulance Intracellulaire ?" -> Macrolide;
}
-> "Réévaluation 48-72h" -> {
"\faAmbulance" [level distance=2cm] -> ["échec"] Échange;
"\faHospital" ;
"\faHospital" -> ["échec"] "Amoxicilline + macrolide\\(+ acide clavulanique\\si agé/comorbid)";
"\faHospital" -> ["non"] "Amoxicilline\\(+ acide clavulanique\\si agé/comorbid)";
}
};
\caption{Traitement probabiliste PAC (Pneumonie aigüe communautaire)}
\end{figure}
\begin{figure}[htpb]
\centering
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
%sibling distance=40cm,
edges={nodes={fill=white, align=center}},
level 2/.style={sibling distance=6cm},
layered layout]
{
"Signes cliniques de gravité ou circonstances part" [level distance=2cm]
-> ["oui"] Hospitalisation;
"Signes cliniques de gravité ou circonstances part"
-> ["non"] "Facteurs de risque\\de mortalité";
"Facteurs de risque\\de mortalité" [level distance=3cm, sibling distance=50cm]
-> ["$\le 65$ ans, FR $\ge 2$\\$> 65$ ans, FR $\ge 1$"]
"Hospitalisation\\recommandée";
"Facteurs de risque\\de mortalité"
-> ["$\le 65$ ans, FR $\le 1$\\$> 65$ ans, FR $= 0$"]
Ambulatoire;
};
\caption{Hospitalisation des PAC}
\end{figure}
\begin{table}[htpb]
\centering
\caption{ATB pour l'exacerbation de bronchopneumopathie obstructive}
\begin{tabular}{ccc}
\toprule
Sans EFR& EFR& ATB\\
\midrule
\(\emptyset\) dyspnée& VEMS \textgreater{} 50\%& \(\emptyset\)\\
Dyspnée d'effort& VEMS \textless{} 50\%& Si expectoration purulente verdâtre :
Amoxicilline\\
Dyspnée de repos& VEMS \textless{} 30\%& Amoxicilline/acide clavulanique\\
\bottomrule
\end{tabular}
\end{table}
\section{152 - Infections cutanéo-muqueuses}%
\label{sec:ue_6_152_infections_cutaneo_muqueuses}
\subsection{Bactériennes}%
\label{sub:bacteriennes}
\bact{dore} ou \bact{pyogenes} -> pénicilline M ou amoxicilline (resp.)
\paragraph{Impétigo} Diagnostic clinique : vésicol-bulle $\rightarrow$ érosion.\\
Autres formes : impétigo péri-anal, impétiginisation, ecthyma. \\
Bénignes, complications très rares.\\
Traitement : hygiène + pommade ATB si < 2\% surface, sinon amoxicilline-acide clavulanique
7j per os.
\paragraph{Folliculite} \bact{dore}. \\
Clinique : papule érythmateuses autour des poils $\rightarrow$ pustules\\
Traitement : hygiène (ATB si formee profuses (amox.+acide clav.))
\paragraph{Furoncle} Folliculite profonde, nécrosante. \bact{dore}\\
Complications :
\begin{itemize}
\item locale = staphylococcie maligne de la face \danger urgence \faHospital{}.
\item globale = bactériéme
\end{itemize}
Traitement : hygiène, ATB si risque de complication ou si furonculose (7j)
\paragraph{Érysipèle}
\danger Ne pas passer à côté d'une DB nécrosante
Clinique : placard inflammatoire, bourrelet, fièvre\\
Diagnostic différentiel : dermo-hypodermite de {stase, nécrosante, à
\bact{dore}}, infection du site opératoire, morsure/griffure\\
ATB : amoxicilline en 1ere intention, traitement de la porte d'entrée
\paragraph{Dermohypodermite bactérienne nécrosante} urgence médico-chirurgicale
\\
Clinique : érysipèle + sepsis grave, douleur intense
\subsection{Mycoses}%
\label{sub:mycoses}
Diagnostic clinique, traitement local sauf teignes, onyxis, onyxis
candidosiques\\
Candida ou dermatophyte $\to$ azolés local ou griséofulvine (teignes)
\paragraph{Candida}
\begin{itemize}
\item Intertrigo des grands plis
\item Périonyxis, onyxis à Candida
\item Balanite
\item Candidose buccale
\end{itemize}
\paragraph{Malasseiza furfur}
\begin{itemize}
\item Pityriasis versicolor
\item Dermite séborrhéique (fréquent)
\end{itemize}
\paragraph{Dermatophytes}
\begin{itemize}
\item Intertrigo des petits plis
\item Intertrigo des grands plis (extension à distance contrairement à Candida)
\item Onyxis dermatophytique : verins antifongique ou terbinafine si atteinte
étendue
\item Dermatophytie cutanée
\item teignes tondantes : azolé + griéofulvine
\item teignes suppurées
\end{itemize}
\section{153 - Infections ostéo-articulaires}%
\label{sec:ue_6_153_infections_osteo_articulaires}
Fréquentes et coûteuses\\
Étiologie : \bact{dore} sur os natif, staphylocoques coagulase négative sur
prothèses\\
Infection :
\begin{itemize}
\item aigüe : \danger urgence = isoler agent puis ATB
\item chroniques : argumenter diagnostic, isoler agent
\item arthrite septique/bactériémie/sepsis grave/choc septique : ATB
probabiliste $\beta$-lactamine $\pm$ gentamicine $\pm$ glycopeptitde
\end{itemize}
\subsection{Arthrite septique (os natif)}
Hématogène ou inoculation (morsure)\\
Arthrite = septique par défaut. \\
Urgence : ponction articulaire, hémoculture puis ATB probabiliste
(penicilline M + gentamicine) puis ATB adaptée\\
Complications : bactériémie, atteinte articulaire\\
Échographie rapidement (radio pour référence, IRM/TDM si localisaion)\\
DD : non purulentes, réactionnelle, inflammatoire microcristalline ou systémique
\subsection{Spondylodiscite}
Adulte > 50 ans. Syndrome rachidien d'horaire inflammatoire \\
Cherche porte d'entrée, agent, localisation secondaire (endocardite ?)\\
\danger complications : si signes neuro radiculaires/médullaire -> IRM urgence\\
IRM\\
Hémoculture : si stériles, ponction-biopsie discovertébrales \\
DD : tassement, spondylarthropathie inflammatoire, myélome, métastase\\
Bactériémie/sepsis grave/choc septique : traitement probabiliste\\
Pas de chirurgie
\subsection{Ostéite}
Inoculation directe ou post-opératoire. Clinique : fistule (pathognomonique)\\
Radio (retardé) ou IRM\\
Ponction-biopsie osseuse puis ATB\\
Traitement médico-chirurgical
\subsection{Infection sur prothèse ostéoarticulaire}
\begin{itemize}
\item Post-opératoire précoce / infection aigüe hématogène : radio/écho si
hématogène. Prélèvement puis chirurgie rapidement
\item Post-op chronique : diagnostic difficile. Radio,TDM,IRM, écho.
Changement en 1-2 temps de la prothèse
\end{itemize}
\subsection{Infection du pied diabétique}
Plaie infectée chez diabètique $\to$ avis spécialisé\\
Ostéite : contact osseux + infection = bonne VPP\\
Souvent polymicrobien (\bact{dore})\\
ATB adaptée (2 semaines)
\section{154 - Bactériémie, fongémie}%
\label{sec:ue_6_154_bacteriemie_fongemie}
\subsection{Diagnostic}%
Fièvre $\pm$ frissons $\rightarrow$ hémocultures (avant ATB !)
\begin{itemize}
\item plusieurs positives : si même bactérie, OK. Sinon, chercher terrain
\item 1 seule positive : toujours chercher \bact{dore}, Candida. Conclusion si
2 hémoc de 2 paires
\end{itemize}
\subsection{CAT}%
\label{sub:cat}
\paragraph{Signes de gravité}%
\label{par:signes_de_gravite}
Sepsis : "quick SOFA" = 2 parmi \{FR $\ge 22$/min, Glasgow $\le 13$, PA systolique $\le
100mmHg$\}\\
Choc septique : sepsis + vasosuppresseurs pour $PA_{moy} \ge 65$mmHg, lactate
> 2 mmol/L, malgré correction hypovolémie
Défaillances d'organes (les + précoces) :
\begin{itemize}
\item CV : PA syst < 100mmHg (ou -40mmHg)
\item Cutané : marbrures, extr. froides et cyanosées
\item Métab : acidose lactique
\item Rénale : oligo-anurie < 0.5 ml/kg/h
\end{itemize}
Chercher porte d'entrée + localisation secondaire (echographie pour endocardite
si agent, fond d'oeil si candidémie)
\danger Bactériéme + sepsis = urgence
Prélèvement $\rightarrow$ ATB probabiliste si suspicion de bactériémie + sepsis/grave/choc
septique/neutropénie/asplénie
\begin{itemize}
\item digestif/urinaire : céfotaxime/ceftriaxone + imidazolé $\pm$ aminoside
\item pneumonie communautaire : céfotaxime/ceftriaxone + lévofloxacine ou macrolid
\item 0 foyer, communautaire : céfotaxime/ceftriaxone $\pm$ aminoside
\item 0 foyer, nosocomial : céfépime/ceftazidime/imipénème + amikacine $\pm$
vancomycine $\pm$ echinocandine
\end{itemize}
Sinon :
\begin{itemize}
\item CG+ : pénicilline M si cutané à \bact{dore}, amoxicilline sinon
\item CG- : cefotaxime/ceftriaxone (méningocoque)
\item BG+ : amoxicilline (Listeria)
\item BG- : cefotaxime/ceftriaxone (+ imidazolé si voie dig/bilaire ou pas de
foyer)
\end{itemize}
Traiter porte d'entrée \danger
\vspace*{1cm}
\bact{dore} : avis spécialisé + echo (endocardite). Négativation hémoc à J3
Fongémies (Candida) : souvent soin + terrain. Grave .\\
Localisation secondaire : fond d'eil, echo (endocardite), controle hémoc. 14j
\section{155 - Tuberculose}%
\label{sec:tuberculose}
Bacille Acido-Alcool résistant. Plus fréquent = \bact{tuberculose}\\
Pathognomonique : granulome épithélioïde giganto-cellulaire centré par de la
nécrose caséeuse\\
Infection $\rightarrow$ latente (ITL) ou primaire. L'ITL peut se réactiver. Si
symptômes : tuberculose maladie\\
Multi-résistance : à isoniazide + rifampicine
\subsection{Tests}%
\label{sub:tests}
IDR ou interféron $\gamma$ : positif = primo-infection mais sans date.
Sensibilité dimunée par immunodépression\\
\danger spécificité de 70\%
IDR positive =
\begin{itemize}
\item \diameter $\ge 5$mm si ID ?
\item \diameter > 10mm si vaccin > 10 ans ou non vacciné
\item \diameter > 15mm si vaccin < 10 ans
\item virage (+10mm à > 2 mois)
\item réaction bulleuse
\end{itemize}
\begin{table}[htpb]
\centering
\caption{Indication des tests}
\begin{tabular}{*{6}{c}}
\toprule
& < 5 ans & < 79 ans & $\ge 80$ ans & Migrant < 15 ans & Migrant $\ge$ 15 ans \\
\midrule
IDR & X & X & & & X \\
IFN$\gamma$ & & X & X & X & X \\
\bottomrule
\end{tabular}
\end{table}
\subsection{Diagnostic}%
\begin{tcolorbox}
Primo-infection: virage tuberculinique ou IFN gamma\\
Tuberculose maladie : isolement BK dans tissus
\end{tcolorbox}
Mises en évidence du bacille :
\begin{itemize}
\item 3 prélèvement (ECBC/tubage). Si miliaire : +hémocultures, ECBU
\item direct, culture, identification et ATBgramme
\item Granulomes épithélioïdes gigantocellulaires avec nécrose caséeuses,
coloration Ziehl Neelsen (> $10^3$bacilles/mL)
\end{itemize}
\paragraph{Pulmonaire} Clinique = toux prolongée, expector muco-purulente,
{asthé, anorexie, amaigrissement, fébricule (nocture), sueurs nocturnes}.\\
Radio thorax = nodules, infiltrats, cavernes (lob sup, post)\\
Diag = prélèvements bactério (sécrétion/tubage) = examen direct, culture
\paragraph{Miliaire} Après primo-infection ou phase terminale.
Clinique : fièvre prolongée, sueurs nocturnes, SDRA\footnote{Syndrome de
détresse respiratoire aigüe}, neuro-méningés,
péricardite.\\
Radio thorax : interstitiel diffus micronodulaire\\
Diag : culture (hémoculture, LCS, biopsie)
\paragraph{Autres manifestations pulmonaires} pleurésie (épanchement unilat, exsudative lymphocytaire), pneumonie aigüe
\paragraph{Extra-pulmonaire}
\begin{itemize}
\item ganglionnaire : clinique = adénite, fistulisation. Biopsie (ED+culture)
\item osseux : spondylodiscite. Radio, ponction (culture)
\item pleurésie : rare en france. Radio thorax (épanchement pleural), PL
(lymphocytaire), biopsie pleurale
\item péricardite : rare en France. Clinique = fièvre, douleurs thoracique,
dyspnée. Anomalies CG, radio thorax, écho cardiaque, culture liquide
péricardique
\item neuro-méningé : AEG, progressif, sd méningé, rhombencéphalite, déficits
focaux. PL (lymphocytair, hyperprot, hypoglyco), arachnoïdite de la base
(IRM), culture LCS
\item urinaire : leucocyturie aseptique. Urine 3j
\item génitale : Clinique = \male{} prostatite, épididymite, masse scrotale. \female{}
trouble mestruels, douleur abdomino-pelvienne. \male{} calcifications.
\female{} culture sur menstruations/frottis
\item digestive : fibro, colonoscopie
\item laryngé : rare. Clinique = ulcération douloureuse, toux, dysphagie,
odynophagie, wheeing. Prélèvement local
\end{itemize}
\paragraph{Infection tuberculeuse latente}
Diagnostic (\danger pas pour tuberculose active):
\begin{itemize}
\item IDR (non spécifique, faux négatifs !) : +72h : \diameter > 10mm (15 si vaccination) ou +10mm en 3 mois : suspicion ITL
\item IGRA\footnote{Interferon Gamma Release Assay} : > 15 ans ou migrant < 15 ans
\end{itemize}
Traitement :
\begin{itemize}
\item primaire si < 2 ans, secondaire si < 18 ans ou ID ou ITL < 1 an ou séquellaire
\item INH 9 mois ou INH + RMP 3 mois
\end{itemize}
\subsection{Traitement}%
ITL : ttt si immunodérimé, infection < 2 an, enfant < 15 ans.\\
Primo-infection : oui si symptomatique, sinon au cas par cas
EI (\texttt{PERI}):
\begin{itemize}
\item isoniazide : cytolyse hépatique, neuropatie périph (examen réflexes
OT\footnote{ostéo-tendineux})
\item rifampicine : cytolyse hépatique, urines orange
\item éthambutol : névrite optique
\item pyrazinamide : hépatite toxique
\end{itemize}
Toujours + vitamine B6.\\
Corticothérapie si neuro-méningé ou péricardique
\begin{table}[htpb]
\centering
\caption{Traitement tuberculose}
\begin{tabular}{*{3}{c}}
\toprule
& Primo/tuberculose maladie & ITL \\
\midrule
isoniazide & 6 mois & 9 mois ou 3 mois\\
rifampicine & 6 mois & rien ou 3 mois \\
ethambutol & 2 mois &\\
pyrazinamide & 2 mois\\
\bottomrule
\end{tabular}
\end{table}
\subsection{Cas particuliers}
Grossesse : INH (+vit. B6) + RMP (+vit. K1) + EMB\\
Insuf. rénale :
$ \begin{cases}
[15,30] \text{mL/min} : & \text{diminuer EMB, PZA}.\\
< 15 \text{mL/min} : & \text{diminuer INH, EMB, PZA}\\
\end{cases} $
Insuf. hépatique :
$\begin{cases}
[3,6N] : & \text{arrêt PZA}\\
> 6N : & \text{arrêt INH, PZA}\\
\end{cases}$
ID, VIH : penser tuberculose si fièvre
Si anti-TNF, bilan tuberculose
\subsection{Déclaration obligatoire}
\subsection{Vaccination}
Sauf VIH, déficits immunitaires
\section{156 - Tétanos}
\begin{table}[htpb]
\centering
\caption{Traitement tétanos}
\begin{tabular}{ccc}
\toprule
Blessure& Vaccins à jour& Non à jour\\
\midrule
Mineure, propre& ∅ injection& Vaccin immédiat\\
Majeure/contamination& pas d'injection& Ig 250 UI dans 1
bras, vaccin dans l'autre\\
tellurique possible&&\\
\bottomrule
\end{tabular}
\end{table}
\section{157 - Infections urinaires}%
\label{sec:item_157_infections_urinaires}
\begin{table}[htpb]
\centering
\caption{Résistances pour les infecitons urinaires}
\begin{tabular}{ccc}
\toprule
Antibiotiques & Résistance (\%) & Probabiliste ? \\
\midrule
Fosfomycine-trométamol & < 5 & oui \\
Nitrofurantoïne & &\\
Aminosides & &\\
\midrule
C3G & 5 & éviter \\
Aztréonam&&\\
Fluoroquinolones (IU simple)&&\\
\midrule
Fluoroquinolones (IU à risque)& 10-20& éviter\\
Pivmécillinam & & oui (E. coli) \\
\midrule
Amoxicilline & > 20 & non\\
Amoxicilline- acide clavulanique &\\
Cotrimoxazole &\\
\bottomrule
\end{tabular}
\end{table}
\subsection{BU-ECBU}%
\label{sub:bu_ecbu}
BU :
\begin{itemize}
\item négative chez la femme $\rightarrow$ chercher autre diagnostic
\item négative chez l'honme $\rightarrow$ inconclusif
\end{itemize}
Pas d'ECBU de contrôle si évolution favorable
Leucocyturie : $> 10^4/ml$\\
Bactériurie : $\ge 10^3/ml$ ($10^4$ chez la femme pour bactéries autres que
\bact{ecoli}, \bact{saprophyte})
\danger Ne pas chercher/traiter de colonisation, sauf chez la femme enceinte
\subsection{Cystite}%
\label{sub:cystite}
\paragraph{Cystite simple}
Clinique : pollakurie, brûlures+douleur à la miction, miction impérieuse\\
Diagnostic : BU\\
DD: pyélonéphrite (fièvre, frissons, douleurs abdo/lombaire)
\begin{figure}[htpb]
\begin{subfigure}{0.49\linewidth}
\centering
\begin{tikzpicture}
\graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center, draw},
edges={nodes={fill=white}},
layered layout]
{
"Fosfomycine-trométamol" -> Pivmécillinam ->
"Fluoroquinolone\\Nitrofurantoïne";
};
\end{tikzpicture}
\caption{Traitement de la cystite simple}
\end{subfigure}
\begin{subfigure}{0.49\linewidth}
\begin{tabular}{*{4}{c}}
\toprule
& PNA simple & PNA à risque & PNA grave \\
\midrule
Hémocultures & si doute & si doute & oui \\
CRP, urée, créat & & oui & oui \\
Imagerie & oui & oui \\
ATB & mono & mono & bi \\
\bottomrule
\end{tabular}
\caption{Examens complémentaires PNA}
\end{subfigure}
\end{figure}
Surveillance: clinique, par la patiente
\paragraph{Cystite à risque}
Diagnostic : BU + ECBU
\begin{figure}[htpb]
\centering
\begin{tikzpicture}
\graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Traitement différé ?"[level distance=2cm]
-> ["oui"] "Selon antibiogramme\\
\textit{l'Amoureux Pivert}\\\textit{Niche dans un Très}\\
\textit{Comfortable Fauteuil}" [draw]
-> "Nitrofurantoïne\\(ou céfixime ou FQ)"[draw];
"Traitement différé ?" ->["non"] "Nitrofurantoïne\\(ou céfixime ou FQ)";
};
\end{tikzpicture}
\caption{Traitement de la cystite à risque}
\end{figure}
\paragraph{Cystite récidivante}%
\label{ssub:cystite_recidivante}
Si $\ge 4$ épisodes/an : triméthoprime ou fosfomycine-trométamol
\subsection{Pyélonéphrite aigüe}%
\label{sub:pyelonephite_aigue}
Clinique : cystite + lombalgie fébrile\\
Diagnostic : BU + ECBU\\
Surveillance : clinique si favorable, ECBU + uroscanner à 72h sinon
\begin{figure}
\begin{subfigure}[b]{0.4\linewidth}
\centering
\resizebox{\textwidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
ATB probabiliste // [layered layout] {
"Facteur de risque ?" -> {
FQ [>"non", draw];
C3G parentérales [>"oui", draw];
};
};
FQ -> "ATB adaptée (7j)" [draw];
C3G parentérales -> "ATB adaptée (10-14j
)" [draw];
};
}
\caption{PNA à risque}
\end{subfigure}%
\begin{subfigure}[b]{0.4\linewidth}
\resizebox{\textwidth}{!}{
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
level distance=2cm,
edges={nodes={fill=white}},
layered layout]
{
Probabiliste // [layered layout] {
"Choc septique + ATCD IU 6 mois ?" -> {
"C3G IV + amikacine\\
(aztréonam+ amikacine si allergie)" [>"non", draw];
"carbapénème\\+ amikacine" [>"oui", draw];
};
} -> "ATB adapté\\(PNA non grave)";
};
}
\caption{PNA grave}
\end{subfigure}
\end{figure}
\subsection{IU masculine/prostatite aigüe}%
\label{sub:iu_masculine_prostatite_aigue}
Clinique :
\begin{itemize}
\item fièvre élevée, sueurs, frissons
\item brûlures mictions, dysurie, pollakurie
\item douleurs pelviennes
\item toucher rectal
\end{itemize}
Diagnostic : BU + ECBU
\begin{figure}[htpb]
\centering
\begin{tikzpicture}
\graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
sibling distance=3cm,
%level distance=2cm,
edges={nodes={fill=white}},
layered layout]
{
Probabiliste [draw] // [layered layout] {
"Sepsis grave\\ drainage" -> "PNA grave";
"Rétention urine\\ID profonde" -> "PNA à risque";
"Fièvre\\mauvaise tolérance" -> "PNA simple";
"Autre" -> "pas de probabiliste";
} -> Fluoroquinolones;
};
\end{tikzpicture}
\caption{Traitement de la PNA grave}
\end{figure}
\subsection{Personne âgée}%
\label{sub:personne_agee}
Fièvre + bactériure + leucocyturie = pas forcément IU
\subsection{Grossesse}%
Dépistage systémitaque des colonisation (BU) à partir du 4eme mois.
BU positive $\rightarrow$ ECBU
\danger Traitement de la colonisation
\begin{figure}[htpb]
\centering
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center, draw},
sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"" -> {
"Cystite aigǜe" -> {
"Probabiliste\\
1. fosfomycine-trométamol\\
2. pivmécillinam\\
3. nitrofurantoïne"
->
"Adapté\\
1. amoxicilline\\
2. fosfomycine-trométamol ou pivmécillinam\\
3. triméthoprime";
};
Colonisation -> "Adapté\\
1. amoxicilline\\
2. pivmécillinam\\
3. fosfomycine-trométamol";
PNA simple -> {
"Probabiliste\\
C3G IV (aztreonam si allergie)"
-> "Adapté\\
amoxicilline\\
amoxicilline-acide clavulanique\\
céfixime";
};
};
};
\caption{Traitement si grossesse}
\end{figure}
\danger Contrôle 8-10 après l'arrêt
\section{158 - IST}%
\label{sec:item_158_ist}
Chancre mou = \bact{ducreyi}\\
Gonocoque = \bact{gonocoque}\\
Syphilis = \bact{syphilis}
\subsection{Urétrites, cervicites}%
Clinique :
\begin{itemize}
\item ulcération = herpès génital, syphilis primaire, chancre mou, donovanose,
lymphogranulomatose vénérienne (\bact{chlamydia})
\item \male{} urétrite, orchite, prostatite
\item \female{} : infections hautes ( endométrite, salpingite), basses (vaginites, cercivites)
\item extra-génitale possible
\end{itemize}
\begin{table}[htpb]
\centering
\caption{Explorations}
\begin{tabular}{*{4}{c}}
\toprule
Clinique & Ulcération & Écoulement, irritation & Rectite \\
\midrule
Agents ? & \bact{syphilis} & \bact{chlamydia} & \bact{chlamydia} \\
& HSV & \bact{gonocoque} & (HSV)\\
& \bact{ducreyi} & \bact{trichomonose} \female & (\bact{gonocoque})\\
& \bact{granulomatis} & &\\
\midrule
Explorations & TPHA-VDRL & PCR \bact{chlamydia} & PCR \bact{chlamydia} \\
& HSV ? & PCR/culture \bact{gonocoque} & PCR/culture \bact{gonocoque}\\
& culture \bact{ducreyi} ? & sur \male{} écoulement/urines & PCR HSV ?\\
& culture \bact{granulomatis} ? & \female{} écouvillonage & \\
\bottomrule
\end{tabular}
\end{table}
\danger Si gonocoque, Chlamydia ou syphilis : dépistage des 2 autres
\begin{figure}[htpb]
\centering
\caption{Traitement IST \female}
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
%sibling distance=3cm,
edges={nodes={fill=white, align=center}},
layered layout]
{
"" -> {
"Cervicite/urétrite franche" ->
"\bact{gonocoque}\\\bact{genitalium}" ->
"Probabiliste\\
Ceftriaxone IM\\
+ Azithromycine/doxycycline PO 7j" [draw]-> {
"Ceftriaxone IM\\\bact{gonocoque}\\\bact{genitalium}" [draw];
"Azithromycine\\Doxycycline PO\\\bact{chlamydia}" [draw];
};
"Orchite" -> {
IST -> "\bact{gonocoque}\\\bact{chlamydia}" ->
"Probabiliste\\
Ceftriaxone IM\\
+ Azithromycine/doxycycline PO 7j";
IU -> "Probabiliste\\C3G IV/FQ" [draw] -> "FQ ou CTM"[draw] ;
};
"Vaginite\\sans cervicite\\hors IST" ->
"\bact{trichomonose}\\\bact{gardnerella}\\candidose" ->
"Métronidazole PO" [draw];
"Salpingite, endométrite" ->
"Doxycycline\\+ métronidazole" [draw];
};
};
\end{figure}
\subsection{Syphilis}%
\label{sub:syphilis}
Clinique :
\begin{itemize}
\item syphilis primaire = chancre d'inoculation
\item syphilis secondaire = roséole $\rightarrow$ syphilides, alopécie, plaque
muqueuse (+ tous les organes potentiellement). Neurosyphilis
\item syphilis tertiaire (rarissime) = granulomatose, viscérale, osseuse...
\end{itemize}
Diagnostic : TPHA (nombre d'infections) - VDRL (si infection active)
Traitement : péncilline G (doxycycline 14 j si allergie) jusque VDRL / 4 à 6 mois
\subsection{HPV}%
\danger Dépistage \female : frottis régulier après 25 ans
Clinique : asymptomatique/condylomes
Traitement : local (laser)
\label{sub:hpv}
\section{159 - Coqueluche}
\subsection{Général}
Toux (adulte/enfant anciennement vacciné) \textgreater{} 1 semaine
=\textgreater{} penser coqueluche Transmission interhumaine stricte
(aérosol, gouttelettes) Grave chez le nourrisson
\subsection{Diagnostic}
Contagiosité maximale pendant la catharre. Toux :
\begin{itemize}
\tightlist
\item
quinte paroxistique (``chant du coq'' chez nourrison = forme grave)
\item
nocture
\item
(émétisant)
\end{itemize}
Évolution
\begin{figure}[htpb]
\centering
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every node/.style = {align=center},
Line/.style = {-angle 90, shorten >=2pt},
Brace/.style 2 args = {
semithick, decorate,
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% 2mm = 1j
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\coordinate[right=30mm of catharre] (quinte);
\coordinate[right=30mm of quinte] (contagFin);
\coordinate[right=60mm of quinte] (fin);
\draw[Line] (a) -- (fin) node[below left] {t};
% % Draw special brace
\def\offset{10pt}
\draw[Brace={\offset}{}]
(a) -- node [above=\offset] {Incubation} (catharre);
\draw[Brace={\offset}]%{mirror}]
(catharre) -- node[above=\offset] {Catharre (7-15j)} (quinte);
\draw[Brace={\offset}]%{mirror}]
(quinte) -- node[above=\offset] {Quintes (30-45j} (fin);
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\draw[Brace={\offset}{mirror}]
(contagDebut) -- node[below=\offset] {Contagiosité} (contagFin);
%\def\offset{15pt}
%\draw[<->, transform canvas={yshift=-\offset}]
%(incub) -- node[below] {Invasion (1-2j)} ( invas);
%\def\offset{10pt}
%\draw[Brace={\offset}{}]
%(invas) -- node [above=\offset] {Eruption} (contagFin);
% draw vertical lines
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\draw (\x) -- ([yshift=-1mm] \x);
}
\foreach \x/\y in {a/0, catharre/+7-21j}{%, quinte/+7-15j} {
\draw node at ([yshift=-3mm] \x) {\y};
}
\end{tikzpicture}
\end{figure}
Si suspicion clinique, confirmation par
\begin{itemize}
\tightlist
\item
PCR (référence) si \textless{} 21 j
\item
culture (peu sensible) si \textless{} 15 j
\end{itemize}
Différentiel : toux infectieuse, pneumo-allergique, mécanique,
iatrogène, psychogène
\subsection{Traitement}
Curatif/préventif : macrolides (cotrimoxazole si CI) Éviction (durée
dépendant du traitement)
\section{160 - Exanthèmes fébrile de l'enfant}
\begin{table}[htpb]
\centering
\begin{tabular}{cc}
\toprule
Morbiliforme & Scarlatiniforme\\
\midrule
Rougeole & Scarlatine\\
Rubéole & Intolérance médicamenteuse\\
Roséole infantile & Sd de Kawasaki\\
Mégalérythème épidémique & Toxic-shock sd\\
Monoculéose infectieuse & \\
Entéro-, adénoviroses & \\
VIH (primo) & \\
Zika & \\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htpb]
\centering
\caption{Éruptions cutanées virales}
\begin{tabular}{cc}
\toprule
(papulo-)Maculeuses & Vésiculeuses\\
\midrule
Rougeole & Varicelle, Zona\\
Mégalérythème épidémique (virus B19) & Herpes simplex\\
Rubéole & Poxviridae \\
EBV &\\
CMV &\\
Exathème subit (HHV-6) & \\
Entérovirus (virus coxsackie) VIH & \\
\bottomrule
\end{tabular}
\end{table}
\subsection{Virales (papulo-)maculeuses}
\paragraph{Morbiliforme}
Rubéole :
\begin{itemize}
\item contagieuse, contamination aérienne \item immunisante, bénigne sauf grossesse
\item phase d'état : éruption morbiliforme (inconstante, souvent discrète 20\%)
\item complications : polyarthrite, thrombopénie, encéphalite \item embryon/foetus : risque du sd malformatif de Gregg
\item diagnostic : clinique trompeuse, sérologie (IgM), NFS\\ \item traitement préventif : vaccin vivant atténué ROR (12M, 16-18M)
\end{itemize}
Rougeole
\begin{figure}[htpb]
\centering
\caption{Rougeole : aspect (gauche), signe de Köplick (droite)}
\includegraphics[width=0.3\linewidth]{160_rougeole}
\includegraphics[width=0.5\linewidth]{160_rougeole_koplik.pdf}
\end{figure}
\begin{itemize}
\item
très contagieux, contamination aérienne
\item
diagnostic :~clinique++, NFS, PCR, sérologie
\begin{itemize}
\item
catarrhe occulo-naso-bronchique fébrile
\item
signe de Köplick, exanthème maculopapuleux
\end{itemize}
\item
complications :
\begin{itemize}
\item
respiratoires :~surinfections bactériennes (otites, laryngites,
bronchites), pneumonies bactériennes/viral
\item
encéphalites : encéphalomyélite aigüe post-éruptive, encéphalite
aigüe progressive, panencéphalite sclérosante subaigüe (PESS)
\end{itemize}
\item
traitement préventif : vaccin vivant atténué ROR (12M, 16-18M)
\end{itemize}
\begin{figure}
\caption{Timeline: rougeole (gauche), rubéole (droite)}
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\coordinate[right=18mm of a] (contag);
\coordinate[right=32mm of a] (incub);
\coordinate[right=4mm of incub] (invas);
\coordinate[right=38mm of contag] (contagFin);
\coordinate[right=10mm of contagFin] (fin);
\draw[Line] (a) -- (fin) node[below left] {t};
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\draw[Brace={\offset}{}]
(a) -- node [above=\offset] {Incubation (10-12j)} (incub);
\def\offset{35pt}
\draw[Brace={\offset}{mirror}]
( contag) -- node[below=\offset] {Contagiosité (10j)} ( contagFin);
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(incub) -- node[below] {Invasion (1-2j)} ( invas);
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\draw[Brace={\offset}{}]
(invas) -- node [above=\offset] {Eruption} (contagFin);
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\foreach \x in {a, contag, incub, invas, contagFin} {
\draw (\x) -- ([yshift=-1mm] \x);
}
\foreach \x/\y in {a/0, invas/14j, contagFin/19j} {
\draw node at ([yshift=-3mm] \x) {\y};
}
\end{tikzpicture}
\begin{tikzpicture}[
every node/.style = {align=center},
Line/.style = {-angle 90, shorten >=2pt},
Brace/.style 2 args = {
semithick, decorate,
decoration={
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\coordinate (a) at (0,0);
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\coordinate[right=4mm of incub] (invas);
\coordinate[right=20mm of contag] (contagFin);
\coordinate[right=5mm of contagFin] (fin);
\draw[Line] (a) -- (fin) node[below left] {t};
\draw[Line] ([ys=9mm] invas) node[above] {Eruption} -- (invas);
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\def\offset{10pt}
\draw[Brace={\offset}{}]
(a) -- node [above=\offset] {Incubation (16j)} (incub);
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\draw[Brace={\offset}{mirror}]
( contag) -- node[below=\offset] {Contagiosité (10-18j)} ( contagFin);
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\draw[<->, transform canvas={yshift=-\offset}]
(incub) -- node[below] {Invasion (1-2j)} ( invas);
% draw vertical lines
\foreach \x in {a, contag, incub, invas, contagFin} {
\draw (\x) -- ([yshift=-1mm] \x);
}
\foreach \x/\y in {a/0, incub/16j} {
\draw node at ([yshift=-3mm] \x) {\y};
}
\end{tikzpicture}
\end{figure}
Mégalérythème épidémique
\begin{itemize}
\item
contagion respiratoire
\item
clinique : rash maculopapuleux (joue $\to$ tronc
$\to$ extrémités), arthralgies
\item
diagnostique : sérologie, PCR
\end{itemize}
Exanthème subit~:(HHV-6)?
\begin{itemize}
\item
enfant 6 mois - 4 ans
\item
clinique :
\begin{itemize}
\item
fièvre 3-4 jours
\item
exanthème maculo-papuleux rose pâle + enanthème voile du palais
(éruption 24h)
\end{itemize}
\item
traitement symptomatique
\item
complications : celles de la fièvre
\end{itemize}
Autres exanthèmes :
\begin{itemize}
\item
adénovirus
\item
zika
\item
VIH
\end{itemize}
\paragraph{Scarlatiniforme}
Scarlatine :
\danger angine + vomissements = scarlatine par défaut
\begin{itemize}
\item
clinique :~
\begin{itemize}
\item
début brutal (fièvre, céphalées, maux gorge, vomissements)
\item
exanthème se généralisant, marqués aux plis de flexion (8j)
$\to$ desquamation
\item
enanthème orop-pharyngé-lingual (lange framboisée)
\end{itemize}
\item
traitement :~
\begin{itemize}
\item
pénicilline V ou amoxicilline 10j
\item
antibioprophylaxie
\end{itemize}
\end{itemize}
Syndrome de Kawasaki
\begin{itemize}
\item
vascularite systémique aigüe
\item
clinique :
\begin{itemize}
\item
fièvre prolongée, exanthème, glossite
\item
adénopathies cervicales volumineuses
\item
desquamation en doigts de gants
\end{itemize}
\item
jeunes enfants
\item
traitement : Ig IV 2j puis aspirine 14j {}
\end{itemize}
Sd du choc toxique
\begin{itemize}
\item
Tampon périodique \textgreater{} 8h
\item
Clinique : fièvre, état de choc, érythrodermie généralisée,
desquamation tardive
\item
traitement : clindamycine + gentamicine IV
\end{itemize}
\subsection{Virales vésiculeuses}
\paragraph{Vésiculeuses}
Varicelle : cf ~\nameref{subsec:varicelle}
Zona, Herpès : cf~\nameref{sec:item164}
Coxsackie : sd pieds-mains-bouche (vésicules ovalaires). Contagion par
les selles (10j). Clinique : vésicules fesses, pieds, bouche, lèvre
\paragraph{Pustuleuses} Poxviridae, variole
\subsection{Bulleux} Erythème polymorphe (lésion en cocarde). Toxidermies bulleuses :~sd de
Stevens-Johnson, sd de Lyell
\section{161 :~Oreillons}
Bénigne, contagieuse à réservoir humain. Diagnostic principalement
clinique :
\begin{itemize}
\item incubation 19j
\item invasion 24-48h
\item état : parotidite ourliennes (70\%) unilatérale puis bilatérale
\end{itemize}
Guérison spontanée 8-10j. Autres formes :
\begin{itemize}
\tightlist
\item
neuroméningé++ : méningite lymphocytaire (pas de séquelles),
encéphalite (décès 1-5\%, surdité possible)
\item
orchite/épidymite ourlienne, atrophie testiculaire 50\%
\item
pancréatie ourlienne : rare, guérison spontanée sans séquelle
\end{itemize}
Traitement symptomatique\\
Prévention :~vaccin ROR
\section{162 - Grippe}
\label{sec:item_162_grippe}
Transmission inter-humaine (gouttelettes)
\subsection{Diagnostic}%
\paragraph{Clinique}%
\label{par:clinique}
\danger Toux fébrile brutale novembre-févier en Europe \textit{ou} contact
grippe = grippe par défaut
\begin{figure}[htpb]
\centering
\begin{tikzpicture}[
every node/.style = {align=center},
Line/.style = {-angle 90, shorten >=2pt},
Brace/.style 2 args = {
semithick, decorate,
decoration={
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ys/.style = {yshift=#1}
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\linespread{0.8};
\coordinate (a) at (0,0);
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\coordinate[right=6mm of a] (incub);
\coordinate[right=4mm of a] (contagDebut);
\coordinate[right=14mm of incub] (symptome);
\coordinate[right=14mm of contagDebut] (contagFin);
\coordinate[right=10mm of contagFin] (fin);
\draw[Line] (a) -- (fin) node[below left] {t};
% % Draw special brace
\def\offset{10pt}
\draw[Brace={\offset}{}]
(a) -- node [above=\offset] {Incubation (1-3j)} (incub);
\def\offset{30pt}
\draw[Brace={\offset}]%{mirror}]
(incub) -- node[above=\offset] {Symptômes (7-15j)} (symptome);
\def\offset{15pt}
\draw[Brace={\offset}{mirror}]
(contagDebut) -- node[below=\offset] {Contagiosité 7j} (contagFin);
% draw vertical lines
\foreach \x in {a, incub, symptome} {
\draw (\x) -- ([yshift=-1mm] \x);
}
%\foreach \x/\y in {a/0, incub/+7-21j}{%, quinte/+7-15j} {
%\draw node at ([yshift=-3mm] \x) {\y};
%}
\end{tikzpicture}
\end{figure}
Sd grippal :
\begin{itemize}
\item
Local : ORL (rhinorrhée, pharyngolaryngite), trachéo-bronchique (toux sèche, irritative)
\item Systémique : sd algique (céphalée, arthromyalgies, courbatures)
\end{itemize}
\paragraph{Complications}%
\label{par:complications}
\begin{itemize}
\item respiratoires
\begin{itemize}
\item surinfection bactérienne : OMA, sinusite aigüe, surtout pneumonie aigüe =
grippe maligne primaire (rare, $$) et secondaire
\end{itemize}
\item extra-respiratoire
\end{itemize}
Examens microbiologie : seulement pour les grippes compliquées. Référence = PCR
Influenza
Hospitalisation :
\begin{itemize}
\item saisonnière : à risque, complications
\item pandémie : forme grave/compliquée
\end{itemize}
\subsection{Traitement}%
Symptomatique.
Antigrippal = inhibiteurs de la neuramidase (oseltamivir, zanamivir)
\begin{itemize}
\item curatif : < 48h !
\item prophylaxie (pré- ou post-exposition)
\end{itemize}
\section{163 : Hépatites virales}
\begin{figure}[htpb]
\begin{subfigure}{0.49\textwidth}
\resizebox{\textwidth}{!}{
\begin{tabular}{*{5}{c}}
\toprule
& Orofécale & Parentérale & Sexuelle & Maternofoetale\\
\midrule
A & + & (+) & (+) & \\
B & & + & + & + \\
C & & + & (+) & (+) \\
D & & + & (+) & (+) \\
E & + & (+) & & \\
\bottomrule
\end{tabular}
}
\caption{Transmission}
\end{subfigure}
\begin{subfigure}{0.49\textwidth}
\resizebox{\textwidth}{!}{
\begin{tabular}{*{5}{c}}
\toprule
& Guérison & Fulminante & Chronique \\
\midrule
A & 100\% & < 5\textperthousand & non\\
B & 90\% (adulte) & 1\% & 10\% \\
& 5\% (petite enfance) & & 95\% \\
C & 15-30\% & Exceptionelle & 70-85\% \\
D & si co-infection VHB & 5\% & si surinfection\\
E & si IC & < 5\textperthousand & si ID \\
\bottomrule
\end{tabular}
}
\caption{Évolution}
\end{subfigure}
\caption{Hépatites virales}
\end{figure}
\subsection{Diagnostic}%
Élévation transaminases $\pm$ clinique (asthénie, anorexie, hépatalgie)\\
\paragraph{Aigüe} \danger Y penser si fébrile aigüe + ictère/hypertransaminasémie
1ère intention : VHA, VHB.\\
Si négative : VHC si risque, VHE si zone tropicale ou porc, sd mononucléosique,
dengue/arboviroses si zone tropicale
\paragraph{Chronique} VHB, VHC si risque
\begin{table}[htpb]
\centering
\caption{Suivi}
\label{tab:suivi}
\begin{tabular}{*{4}{c}}
\toprule
& Aigüe & Chronique & Guérison \\
\midrule
A & Augmentation T. & non & normalisation T.\\
& IgM & & \\
\midrule
B & Augmentation T. & Ag HBs+ > 6 mois, & normalisation T. \\
& Ag HBs +, Ac anti-HBc + & Ac anti-HBs- & Ac anti-HBs+\\
& IgM anti-HBc+, Ac anti HBs- & &\\
& PCR élevée & & \\
\midrule
C & Augmentation T. & & normalisation T. \\
& IgG anti-VHC+ \danger & idem & PCR neg.\\
& PCR élevée & \\
\midrule
D & Augmentation T. & & PCR nég. \\
& IgM & IgG & \\
\midrule
E & Augmentation T. ? & idem & normalisation T. \\
& IgM & & PCR neg.\\
\bottomrule
\end{tabular}
\end{table}
\subsection{Prise en charge}
Symptomatique : pas de paracétamol, AINS, alcool
Urgence = hépatite fulminante : sd hémorragique + signes d'encéphalite
(confusion, inversion rythme nycthéméral, somnolence, astérixis)
\paragraph{VHB+VHC} bilan biologique, histologique (sauf cirrhose évidente)
directe (score METAVIR) ou indirecte, imagerie (échographie abdo puis IRM),
fibro (varices oeosphage/cardia)
\paragraph{VHB} Interférons pégylée $\alpha{}2a$, $\alpha{}2b$ (tolérance
médiocre), analogue nucléosidique (entécavir [toxicité musculaire]), nucléotidique (ténéfovir
[tox. rénale].
\paragraph{VHC} si fibrose $\ge F2$, manif. extra-hépatique. Ribavirine ou
antiviraux d'action directe (++).
\subsection{Prévention}
Hygiène, vaccination VHA (autour d'un cas), VHB
\section{164 - Infections à herpès virus du sujet immunocompétent}
\label{sec:item164}
Herpesvirinae
\begin{itemize}
\tightlist
\item
Alpha- : HSV1 et 2, VZV
\item
Beta : CMV, HHV-6 (roséole), HHV-7
\item
Gamma- :~EBV (MNI), HHV-8 (sarcome de Kaposi)
\end{itemize}
Primo-infection puis latente à vie (récurrence)
\begin{table}[htpb]
\centering
\begin{tabular}{*{4}{c}}
\toprule
& & Immunocompétent& Immunodéprimé\\
\midrule
\multirow{2}{*}{Aciclovir IV} & HSV &
\begin{tabular}{c}
grave : méningoencéphalite,\\~oculaire sévère,
\\gingivostomatite sévère
\end{tabular}&primo-infection, réactivation\\
& VZV& grave : encéphalite, pneumopathie& varicelle, zona\\
\midrule
\multirowcell{2}{ Valaciclovir PO,\\Famciclovir PO} & HSV &
\begin{tabular}{c}
génital, cutanéomuqueux,\\oculaire non sérèves
\end{tabular} & \\
& VZV&
\begin{tabular}{c}
ophtalmique,risque d'algie\\post-zostérienne
\end{tabular}&\\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htpb]
\centering
\caption{Traitement HSV}
\begin{tabular}{*{4}{c}}
\toprule
& & Immunocompétent& Immunodéprimé\\
\midrule
Aciclovir IV& HSV&
\begin{tabular}{c}
grave : méningoencéphalite,\\~oculaire sévère,
\\gingivostomatite sévère
\end{tabular}&primo-infection, réactivation\\
& VZV& grave : encéphalite, pneumopathie& varicelle, zona\\
\midrule
\begin{tabular}{c}Valaciclovir PO,\\Famciclovir PO
\end{tabular}& HSV&
\begin{tabular}{c}
génital, cutanéomuqueux,\\oculaire non sérèves
\end{tabular}
& \\
& VZV&
\begin{tabular}{c}
ophtalmique,risque d'algie\\post-zostérienne
\end{tabular}&\\
\bottomrule
\end{tabular}
\end{table}
\subsection{CMV}
Transmission par contact direct Immunodéprimé :~greffe de CSH,
transplantation d'organe, SIDA
\subsection{EBV}
Contamination salivaire. Primo infection = VCA IgG +/- \footnote{viral capsid antigen}
, VCA Ig +, EBNA IgG-\footnote{Epstein Barr Nuclear Antigen}
Contexte: MNI, allogreffe CSH, VIH
\subsection{HSV1, 2}
Transmission :~directe, cutanéomuqueuse, transplacentaire
\begin{table}[htpb]
\centering
\begin{tabular}{*{4}{c}}
\toprule
Type& Localisation& Primo& Récurrence\\
\midrule
HSV1& plutôt orale&
\begin{tabular}{c}
enfance,~asymptomatique\\
(ou gingivostomatite aigüe)
\end{tabular} &
\begin{tabular}{c}
Vésicules unilatérales\\(narines, menton).\\
Kératite possible
\end{tabular}
\\
\midrule
HSV2& plutôt génitale&
\begin{tabular}{c}
Érythémato-vésiculeuses\\+ exsudat blanchâtre
\end{tabular} &
\begin{tabular}{c}
Prodromes puis\\~Lésions :~vésicules,\\guérison 7-10j
\end{tabular}\\
\bottomrule
\end{tabular}
\end{table}
Traitement :\\
\begin{itemize}
\item gingivostomatite aigüe : spontanément favorable
\item ophtalmologique :~aciclovir pommade (+ IV ?), pas de corticothérapie \danger
\item préventif si > 6 récurrences/an (valaciclovir quotidien 6-12 mois)
\end{itemize}
\subsection{Varicelle}
\label{subsec:varicelle}
90\% chez l'enfant, plus grave chez l'adulte Diagnostique clinique
\begin{itemize}
\tightlist
\item
incubation (14j)
\item
état : (maculo-papule) $\to$ vésicules (prurit+++)
$\to$\_érosion + pseudo-ombilication $\to$ croûtes
(J4) $\to$ cicatrisation (J10)
\item
spontanément favorable (10-15j)
\end{itemize}
Complications :
\begin{itemize}
\item surinfection bactérienne fréquente (grattage)
\item terrains, état infectieux sévère, respiratoie neuro, purpura
thrombopénique aigu
\end{itemize}
Traitement :
\begin{itemize}
\item symptomatique (pas d'aspirine, ni AINS ⚠)
\item ATB si surinfection cutanée, antiviral si formes graves/compliquées
\item pas d'éviction scolaire
\item vaccination : ado, \female en âge de procréer, contact avec ID, professionnel.
pas la femme enceinte !
\end{itemize}
NB : toxicité rénale pour l'aciclovir
\subsection{Zona}
Réactivation du VZV. Gravité : douleurs post-zostériennes,
immunodépression, localisations
Diagnostic : clinique
\begin{itemize}
\item prodrome
\item état :~éruption (érythémateux roses vifs $\to$ vésicules en
bouquets $\to$ érosives $\to$ croûtes
$\to$ cicatrices dépigmentées (rosées $\to$
blanchâtres) + fébricule
\item poussées sur 2-3 semaines, douleurs plusieurs mois
\end{itemize}
Complications : principalement DPZ (rarement neurologique)
Traitement
\begin{itemize}
\item local : symptomatique, douleur (antalgique phase aigüe)
\item ATB si surinfection cutanée, antiviral en prévention DPZ (valaciclovir
per os 7 jours)
\item prévention vaccination (entre 65 et 74 ans)
\end{itemize}
\subsection{Complications}
HSV1, 2 :
\begin{itemize}
\item nouveau-né (périnatale++) :~mortalité très élevée, séquelle
très lourdes
\item femme enceinte : maladie chez nouveau-né
\item atopique : Kaposi-Juliusberg VZV
\end{itemize}
\section{165 - VIH}
Transmission : sexuel, sang, mère $\to$ enfant Prévention
:~TasP (Treat as Prevention), TPE (Traitement Post-Exposition),
traitement pré-exposition, prévention de la transmission mère-enfat
\subsection{Sérologie}
\begin{figure}[htpb]
\centering
\caption{Fenêtre diagnostique}
\includegraphics[width=0.8\linewidth]{165_diag}
\end{figure}
Tests diagnostics
\def\mminus{\large\textbf{-}}
\def\pplus{\large\textbf{+}}
\begin{figure}[htpb]
\centering
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
level distance=2cm,
%sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Elisa (Ac, Ag p24)" -> {
"> 6 semaines ?" [>"\mminus"] -> {
"Elisa (2eme)" [>"non"];
};
"Western-Blot" [>"\pplus"] -> {
"Elisa" [>"\pplus"];
};
};
};
\end{figure}
\begin{table}[htpb]
\centering
\begin{tabular}{cc}
\toprule
Infection non-opportuniste& Prévention\\
\midrule
Pneumonie à S. pneumonia& Vaccin\\
Infections digestions& Hygiène alimentaire\\
Grippe& Vaccin\\
IST (syphilis, gonococcies, C. trachomatis, HPV)& Préservatif, dépistage, vaccin VHA, VHB (homosexuel hommes)\\
VHB, VHC& Surveillance, vaccination\\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htpb]
\centering
\begin{tabular}{cccc}
\toprule
Infection opportuniste& Seuil CD4& Diagnostic& Prévention\\
\midrule
Tuberculose & $\emptyset$ & BK, anatomopath. & ITL par IGRA\\
Candidose oesophagienne &< 200& Clinique& $\emptyset$\\
Pneumocystose pulmonaire &< 200& Radio thorax, prelev. respi& CTM si CD4 < 200\\
Toxoplasmose cérébrale &< 200& TDM/IRM $\to$ sérologie $\to$ PCR LCS \\
&& $\to$ test thérapeutique $\to$ biopsie& CTM (CD4 $\to$ 100)\\
CMV & < 100& PCR& \danger rétinite\\
Cryptococcose& < 100& LCS& \\
LEMP& < 100& IRM, PCR LCS& \\
Mycobactérioses atypiques& < 100& Hémocultures, prélèvement& \\
\bottomrule
\end{tabular}
\caption{VIH : infecions opportunistes. BK=bacille de Koch, CMT =
Cotrimoxazole. Mnémo: "quand les pneus sont toxiques" pour < 200}
\end{table}
🔥 = fréquents
\begin{longtable}[]{@{}ll@{}}
\toprule
Cancers classant SIDA & Cancers non classants\tabularnewline
\midrule
\endhead
Lymphome malin non hodgkinien & Cancer du canal anal\tabularnewline
Maladie de Kaposi & Hépatocarcinome\tabularnewline
Cancer du col de l'utérus &\tabularnewline
\bottomrule
\end{longtable}
\subsection{Traitement}
Toxicité long-terme : lipodystrophie, CV, rénale, osseuse, métabolique
\begin{figure}[htpb]
\centering
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
%sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"\textbf{2 inhibiteurs nucléosidiques de la transcriptase inverse}\\
Abacavir + lamivudine
ou ténéfovir + emtricitabine" -> {
"\textbf{1 INNTI}\\Rilpivirine";
"\textbf{1 inhibiteur de la protéase}\\Darunavir";
"\textbf{1 inhibiteur de l'intégrase}\\Dolutégravir/Raltégravir/Elvitégravir";
}
};
\end{figure}
\subsection{Vaccins}
Grippe, fièvre jaune, tétanos, diphtérie, VHB, VHA, HPV, pneumocoque
\section{166 - Paludisme}
Fièvre + retour zone d'endémie palustre = paludisme par défaut
Géographie
\begin{figure}[htpb]
\centering
\includegraphics[width=0.8\linewidth]{palu_map_2016.jpg}
\end{figure}
Démarche
\begin{figure}[htpb]
\centering
\tikz \graph [
% Labels at the middle
edge quotes mid,
% Needed for multi-lines
nodes={align=center},
%sibling distance=3cm,
edges={nodes={fill=white}},
layered layout]
{
"Fièvre\\
Céphalée, myalgies\\
Troubles digestif\\
(Splénomégalie)"
->
"Frottis sanguin\\
+goutte épaisse\\
+/- Ag circulants" [draw] -> {
"P. vivax/ovale\\/malariae" -> "Chroloquine PO" [draw];
"P. falciparum\\/knowlesi" -> {
"Signes de gravité ?" [level distance=40pt] -> ["oui"] "\faHospital{} urgence\\artésunate IV" [draw];
"Signes de gravité ?" ->["non"] "\faAmbulance{} possible ?" -> "Vomissements ?"
};
};
"Vomissements ?" [level distance=50pt] -> {
"Quinine IV" [>"oui", draw];
"Dihydroartémisinine\\-pipéraquine PO\\
\textit{ou} artéméther\\-luméfantrine PO" [>"non", draw];
};
};
\end{figure}
\begin{table}[htpb]
\centering
\caption{Signes de gravité du paludisme}
\begin{tabular}{cc}
\toprule
Critère& Seuil\\
\midrule
Défaillance neuro& \\
Défaillance respi& Ventilé:~\(PaO_2/FiO_2 < 300\) mmHg\\
& Non ventilé : \(PaO_2 < 60\) mmHg\\
& ou \(SpO_2 < 92\) \% ou FR > 30/min. \\
&Radio (interstitelle, alvéolaire)\\
Défaillance CV& PA systol. < 80 mmHg + signes insuffisance circulatoire\\
Hémorragie& clinique\\
Ictère& clinique / bilirubine \(> 50 \mu{}mol/L\)\\
Hémoglobuinurie macroscopique& \\
Anémie& Hg < 5 g/dL, Ht < 20\%\\
Hyoglycémie& glycémie < 2.2 mmol/L\\
Acidose& bicarbonates plasma. < 15 mmol/L ou ph < 7.35\\
Hyperlactémie& > 2 mmol/L\\
Hyperparasitémie& > 4\%\\
Insuffisance rénale& créat. \(> 65 \mu{}mol/L\) ou urée sanguine > 20 mmol/L\\
\bottomrule
\end{tabular}
\end{table}
\section{167 - Gale et pédiculose}
Ectoparasitoses humaines strictes, très contagieuses. Prurit++
\subsection{Gale}
\paragraph{Clinique} 5j-1mois incubation.\\
Prurit avec contage, collectif, nocturne, pas sur le dos ni visage\\
Sillons épidermiques, vésicules perslé, nodules scabieux, lésions de grattage
Diagnostic : paralistologique (visuel ou grattage). Penser IST
\paragraph{Traitement}
Indivuel et collectif\\
Ivermectine 1ere intention (> 15kg) ou benzoate de benzyle\\
Traitement linge, précautions contact, surinfection bactérienne
\subsection{Pédiculose}
Porteur de \bact{typhus}, \bact{tranchees}, \bact{recurrente}
\begin{itemize}
\item Corporelle : précarité. Clinique=dos, thorax. Ttt = vêtements, literie
\item Cuir chevelu : enfants. Clinique = prurit diurne, nocturne sur
cheveux. Lentes visibles. Ttt = malathion ou dimeticone. Décontamination
\item Pubien : clinique = lésions de gratage. Déister IST !. Ttt = pyréthrinoïde
\end{itemize}
\section{168 - Parasitoses digestives}
Protozoaires (unicellulaires) : amoebose, giardiose\\
Helmintes (pluricellulaires) :
\begin{itemize}
\item plathelminthes = téniasis, cysticercose, hydatidose,
\item nemathelminthes = asciridiose, oxyurose
\end{itemize}
Traitement : métronidazole pour protozoaires, albendazole pour helmintes\\
En france : giardiose, oxyurose\\
Transmission féco-orale sauf téniasis
\paragraph{Giardiose} Formes : végétatives/kystique. \\
Souvent asymptomatique. EPS (biopsie jéjunale si végétative)\\
Controle EPS. Hygiène
\paragraph{Téniasis} \bact{saginata} (boeuf) et \bact{solium} (porc).\\
Adulte ou cysticercose (enkystement)\\
Diagnostic =
\begin{itemize}
\item adultes : anneaux dans les selles, EPS
\item cysticercose : épidémio, scanner, calcifications musculaires
\end{itemize}
\paragraph{Ascaridiose} fréquent pays en développement. Souvent asymptomatique.
Diagnostic : EPS
\paragraph{Oxyurose} Asymptomatique, prurit anal nocture. Diagnostic : oeil nu,
scotch test. Contrôle par EPS
\paragraph{Amoebose}
\begin{itemize}
\item intestinale aigüe : diag = pas de fièvre, sd dysentérique (subaigüe
souvent). 3 EPS. Rectoscopie éventuelle : ulcérations en "boutons de chemise"
\item hépatique : diag = fièvre, douleur hypochondre droit, hépatomégalie.
Radio, échographie éhaptique. Sérologie Ac anti-amibiens
\end{itemize}
\section{169 - Zoonoses}%
\label{sec:ue_6_169_zoonoses}
\paragraph{Pasteurellose} morsure, griffure animale/végétale
Clinique: inflammation majeure en 3-6h autour de la plaie\\
Diagnostic : prélèvement plaie -> culture\\
Traitement: amoxicilline
\paragraph{Maladie des griffes de chat} Griffure de chat (jeune)\\
Clinique : locorégionale + au moins une adénobathie. 2-3 semaines incubation
Endocardite à hémoc. négatives\\
Diagnostic : sérologie (PCR si doute)\\
Traitement : si systémique et viscérale, azithromycine
\paragraph{Maladie de Lyme} Piqûre de tique\\
Clinique :
\begin{itemize}
\item primaire : érythème migrant $\pm$ signes généraux
\item secondaire :
\begin{itemize}
\item neurologique = ménigoradiculite (sensitif, liquide clair
lymphocytaire, normoglyco, hyperprot), méningite, encéphalite/myélite
\item articulaire = oligoarthrite sur grosses articulaires
\item cardiaque = myocardite (ECG ?)
\item cutanée = lymphocytome borrélien
\item oculaires
\end{itemize}
\item tertaire : cutanées (acrodermatite chronique atrophiante = quasi
pathognomonique), neurologique, articulaires
\end{itemize}
Diagnostic :
\begin{itemize}
\item érythème migrant
\item OU clinique + épidémio + sérologique (Elisa + WB) + pas de DD
\end{itemize}
Traitement : amoxicilline/doxycycline (primaire), ceftriaxone/doxycycline
(secondaire/tertaire)
\paragraph{Fièvre Q} Digestive ou inhalation\\
Clinique :
\begin{itemize}
\item aigüe : hépatite fébrile/pneumopathie/fièvre isolée. 3 semaines d'incubation
\item chronique : endocardite infectieuse à hémoc. négatives
\end{itemize}
Diagnostic : sérologie\\
Traitement : doxycycline
\paragraph{Tularémie} Contact lagomorphes/piqûre de tique\\
Clinique : après 4 j, fièvre + adénopathies inflammatoires (satellites lésions)
Diagnostic : Sérologie + PCR\\
Traitement : doxycycline
\paragraph{Rickettsioses}
\begin{itemize}
\item \bact{conorii} : tiques du chien. Clinique : fièvre + tâche noire +
éruption maculo-papuleuse
\item \bact{typhus} poux du corps. Clinique : fièvre + éruption
maculo-papuleuse
\end{itemize}
Diagnostic : sérologie + PCR\\
Traitement : doxycycline
\paragraph{Brucellose} Contaminations à l'étranger (ruminant/porcins)\\
Clinique :
\begin{itemize}
\item aigüe : fièvre ondulante sudoro-algique, arthromyalgie, adénopathies,
hépatosplénomégalie
\item subaigüe/chronique
\end{itemize}
Diagnostic : sérologie (+ hémoc. si aigüe)\\
Traitement : doxycycline + gentamicine/rifampicine
\paragraph{Toxoplasmose} Alimentation\\
Clinique : asthénie, fièvre modérée, polyadénopathie. Si ID : kyste
cérébraux/oculaires\\
Diagnostic : infection aigüe, sérologie, PCR\\
Traitement : aucun, évolution bénigne. Femme enceinte : spiramycine. ID :
pyriméthamine + acide folinique + sulfadiazine
\paragraph{Leishmaniose} Piqûre de phléobotome (nuit), zones tropicales
\begin{itemize}
\item forme cutanée : lésion.
\item forme viscérale : fièvre hectique, anémie, amaigrissement,
hépatosplénomégalie, adénopathies.
\end{itemize}
Diagnostic : ED, culture, PCR (sérologie si viscérale)\\
Traitement : cutané (local), amphotéricine B liposomale (viscérale)
\paragraph{Hydatidose (échinococcose hydatique)} Contact chien/aliments
souillés.
Clinique : asymptomatique\\
Diagnostic : sérologie.\\
Traitement : pas de ponction-biopsie du kyste \danger. Chir + albendazole
\paragraph{Rage}
Risque élevée (chauve-souris, zone de rage, animal porteur): vaccination
curative + sérothérapie\\
Risque quasi-nul : rien\\
risque non nul : vaccination curative
\section{170 - Pathologies chez les migrants}%
\label{sec:ue_6_170_pathologies_chez_les_migrants}
\subsection{Diagnostic}
\begin{table}[htpb]
\centering
\caption{Risque majeur suivant la géographie}
\begin{tabular}{*{5}{c}}
\toprule
& Afrique subsaharienne & Afrique du N & Asie SE & Amérique latine \\
\midrule
Tuberculose & X & X & X\\
VHB
& X & X & X\\
VIH & X \\
Téniasis & X & X & X\\
Bilhariozes & X \\
Paludisme & X & & X \\
Hydatidose & & X & & X\\
Gale & X & X & X & X \\
\bottomrule
\end{tabular}
\end{table}
\paragraph{Étiologies}
Parasitose
\begin{itemize}
\item paludisme (fièvre + zone endémie)
\item parasitoses amoebiose, giardiose, ascaridiose, ankylostomose,
anguillolose [dépistage si immunosuppresseur], hydatidose, tédiasis
[penser neurcysticercose si comitialité]
\item filariose : loase, filarioses lymphatiques, (onchocercose)
\item schistosomoses
\item leishmanioses
\item trypanasomoses africhaine, américaine
\item gale
\end{itemize}
Mycoses : dermatophyties (histoplasmoses)\\
Bactéries : tuberculose + VIH, lépre\\
Viral : VIH\\
\subsection{Protection maladie}
Aide Medicale del'Etat : $\ge 3$ mois + pas titre séjour + faibles ressources \\
Couverture Maladie Universelle : régulière $\ge 3$ mois
\subsection{Préventions}
\danger Penser paludisme en premier\\
Vaccins : méningocoque (La Mecque), {VHA, VHB, typhoïde (fièvre jaune)} si
retour au pays
\section{171 - Voyage en pays tropical}%
\subsection{Vaccins}%
Routine : DTP, coqueluche, rougeole, VHB, BCG (enfant), grippe (> 65 ans)\\
Obligatoire : fièvre jaune (Amazonie, Afrique intertropicale), méningocoque
(Arabie Saoudite)\\
Recommandés :
\begin{itemize}
\item VHA : bas niveau d'hygiène
\item typhoïde : prolongé (Inde)
\item cholérique : personnel médical + épidémie
\item rage: prolongé + risque
\item méningite ("ceinture" africain)
\item encéphalite japonaise
\item encéphalite tiques (Europe central, Est, Nord)
\end{itemize}
\subsection{Fièvre, diarrhée, lésions cutanées}
\begin{table}[htpb]
\centering
\caption{Fièvre}
\begin{tabular}{*{4}{c}}
\toprule
Durée & Étiologie & Clinique & Confirmation \\
\midrule
< 7 j & dengue, chikungunka & Myalgies, arthralgie & PCR (< 5 j)\\
& & Rash J3-J5 & Sérologie sinon\\
\midrule
< 2 semaines & typhoide & Céphalées++, SMG & Hémocultures\\
& rickettsioses & &\\
\midrule
1sem - 2 mois& paludisme & Digestif, neuro, SMG & Frottis/goutte épaisse\\
> 10j & hépatites virales & Digestif, ictère & Sérologies \\
mois/années & amoebose hépatique & HMG douloureuse, fièvre & écho foie $\pm$ TDM\\
& & & Sérologie\\
2-6 sem & schistosomose & Prurit, arthralgie, HMG & Sérologie, EPS\\
\bottomrule
\end{tabular}
\end{table}
Diarrhée :
\begin{itemize}
\item fébrile : paludisme puis shigellose, salmonelle, Campylobacter
$\rightarrow$ coproculture
\item sinon parasitaire $\rightarrow$ EPS. Giardose = + fréquente
\end{itemize}
Lésions cutanées :
\begin{itemize}
\item fréquent = pyodermites \bact{dore}/\bact{pyogenes}
\item escarre : rickettsiose
\item exanthème fébrile : arbovirose, leptospirose, syphilis, VIH,
rickettsiose, médicament
\item urticaire : schistosomose, hépatite virale, rickettsiose, médicament
\end{itemize}
Typhoïde : \bact{salmonelle} (para)typhi. Hémocultures $\pm$ coproculture. ATB :
C3G parentéral (proba) puis documenté (FQ). Vaccin disponible (60\%)
\vspace{10pt}
Arboviroses : transmission arthropode. Guérison 7eme jour ou
hémorragie/encéphalite. PCR puis sérologie
\begin{itemize}
\item dengue = 2eme cause fièvre tropicale
\item chikungunya : dengue-like + arthralgie persistante
\item fièvre jaune
\item zika : généralement bénin
\item encéphalite
\end{itemize}
\section{172 - Diarrhées infectieuses}%
\label{sec:ue_6_172_diarrhees_infectieuses}
\begin{table}[htpb]
\centering
\caption{Étiologies infectieuses des diarrhées aigües}
\begin{tabular}{ccc}
\toprule
& Syndrome cholériforme & Entéro-invasif\\
\midrule
& Virus & Shigelloses \\
& & Salmonelloses non typhi \\
& & Campylobacter \\
& & Yersinia \\
& & E. coli entéropathogène\\
\midrule
Diarrhée post-ATB & & \bact{difficile}\\
\midrule
TIAC & \bact{dore} & Salmonelloses mineures\\
& \bact{cereus} & Shigelloses\\
& \bact{perfringens} & \bact{jejuni}\\
& & \bact{ecoli} entéro-hémorr./aggr.\\
\midrule
Voyage & Virus & Amoebose colique \\
& Cryptosporidies \\
& \bact{ecoli} entérotoxin. \\
& Choléra\\
\bottomrule
\end{tabular}
\end{table}
\bigskip
\danger Urgences : Déshydratation, sepsis gravie, sd pseudo-occlusif, diarrhée fébrile + retour
endémie
\subsection{Examens}
Coproculture : si diarrhée aigüe/TIAC fébrile $\rightarrow$ SSYC
Recherche virus\\
EPS \\
Toxine \bact{difficile}\\
Hémoc si fièvre
\subsection{Traitement}
FQ ou azithromycine + symptomatique
\subsection{TIAC}
\begin{table}[htpb]
\centering
\caption{Causes de TIAC}
\begin{tabular}{ccc}
\toprule
Agent & Incubation & Clinique\\
\midrule
\bact{dore} & 2-4h & vomissements, douleurs abdo\\
& & diarrhé, pas de fièvre\\
\bact{perfringens} & 8-24h & Diarrhée sans fièvre\\
\bact{salmonelle} no typhi & 12-24h & Diarrhée aigüe fébrile\\
Noroviris & 24-48h & idem \bact{dore}\\
\bottomrule
\end{tabular}
\end{table}
\section{173 - Prescription des antibiotiques}
\begin{table}[htpb]
\hspace*{-3cm}
%\centering
\caption{Pénicillines}
\begin{tabular}{*{5}{c}}
\toprule
Peni. G/V & Amoxicilline & Amox. + inhib $\beta$ &
Péni. M & Carboxy\\
& & & /uréïdo-peni.\\
\midrule
Streptocoques & Idem peni G+ & Idem amox + & Staph. meti-S & idem amox + \\
\bact{diphterie} & Pneumocoques péni-S & Staph. meti-S & & bacilles G- \\
Fusobacterium & \bact{faecalis} & \bact{influenzae}\\
Treponema & \bact{listeria} & \bact{catarrhalis} \\
& \bact{meningocoque} & \bact{ecoli} et autres entérobact. \\
& Borrelia & produisant pénicillinase\\
& Entérobactérie grp I & Baccilles G- anaérobies\\
\midrule
\multicolumn{2}{c}{Réactions allergiques}\\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htpb]
\centering
\caption{Céphalosporines}
\begin{tabular}{*{3}{c}}
\toprule
C2G & C3G orales & C3G IV\\
\midrule
Cocci G+ & Idem C2G + & Ceftriaxone, cefotaxime : strept.\\
(strepto, staph. méti-S) & Entérobactérie grp II & Neisseria, entérobact, Haemophilus\\
Entérobactérie grp I & & Ceftazidime, céfépime : \\
& & \bact{aeruginosa} \\
\midrule
\multicolumn{2}{c}{Allergies cutanées}\\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htpb]
\centering
\caption{Autres ATB}
\begin{tabular}{*{4}{c}}
\toprule
Carbapénèmes & Aminosides & Fluoroquinolones & Cotrimoxazole \\
\midrule
\textbf{large} & \textbf{En association} & \textbf{Après doc} & Entérobactéries\\
Entérobactéries & Staph. méti-S & Entérobactéries & \bact{listeria} \\
\bact{aeruginosa} & \bact{listeria} & intracellulaires & Staph.\\
Staph méti-S, anaérobies & Bactéries Gram- & Staph. méti-S & \bact{jirovecii}\\
& & \bact{influenzae}\\
& & \bact{aeruginosa}\\
& & \bact{catarrhalis}\\
\midrule
Allergie cutanée & Néphrotoxique & Neuropsy & Allergies\\
Neuro & Toxicité cochléovestibulaire & Hépatites & Cytopénies\\
& & Phototoxicité & IR\\
& & Tendinopathie\\
& & Allongement QT\\
\bottomrule
\end{tabular}
\end{table}
\begin{table}[htpb]
\centering
\caption{Autres ATB (2)}
\begin{tabular}{*{4}{c}}
\toprule
Macrolides & Lincosamides & Imidazolés & Glycopeptides \\
& (Clindamycine) & (Métronidazole) & Vancomycine\\
\midrule
Intracellulaires & Strepto, staph & Anaérobies & Gram+ : strept\\
Strep. staph méti-S & \bact{toxoplasmose} & (sauf Actinomyces, Propionibacterium) & Pneumocoq, entérocoq\\
\bact{helicobacter} & & \bact{helicobacter} & Staph méti-S et méti-R\\
\bact{toxoplasmose} & & Parasites & Listeria \\
& & & \bact{difficile} \\
\midrule
Inhib. enzymatique & Troubles digestifs & Antabuse avec alcool & Phlébite\\
Troubles digestif & & Troubles digestifs & Érythrodermie \\
Réactions cutanées & & glossite, stomatite, goût métallique & si perf trop
rapide\\
Hépatites immunoallegiques & & Céphalées & Néphrotoxicité\\
Allongement QT & & Neuropathie\\
\bottomrule
\end{tabular}
\end{table}
%\paragraph{Synthèse}
%Action sur enveloppe de la bactérie
%\begin{longtable}[]{@{}llllll@{}}
%\toprule
%\begin{minipage}[b]{0.10\columnwidth}\raggedright
%Famille\strut
%\end{minipage} & \begin{minipage}[b]{0.16\columnwidth}\raggedright
%Mode d'action\strut
%\end{minipage} & \begin{minipage}[b]{0.10\columnwidth}\raggedright
%Spectre\strut
%\end{minipage} & \begin{minipage}[b]{0.16\columnwidth}\raggedright
%Pharmacologie\strut
%\end{minipage} & \begin{minipage}[b]{0.22\columnwidth}\raggedright
%Effets secondaires\strut
%\end{minipage} & \begin{minipage}[b]{0.09\columnwidth}\raggedright
%Suffix\strut
%\end{minipage}\tabularnewline
%\midrule
%\endhead
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Beta-lactamines\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Inhibe synthèse de la paroi par fixation aux PLP\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Variable (diffusion extra-cellulaire)\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Absorption digestive médiocre, demi-vie courte, élimination rénale\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%Réactions immuno-allergiques, troubles digestifs, impact sur le
%microbiote\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%pénicillines : -ciline ~ céphalosporines: cef- ~monobactames: *Aztréonam
%~carbapénèmes: -pénem\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Fosfomycine\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Inhibe synthèse de la paroi\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Large (cocci Gram+ {[}certains SARM{]}, bacilles Gram- {[}certaines
%entérobactéries BLSE, P. aeruginosa{]})\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Bonne diffusion tissulaire -\textgreater{} infections méningées,
%endocardites, ostéo-articulaire (en association)\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%\emph{Fosfomycine}\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Glycopeptides\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Inhibe synthèse de la paroi\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%large sur bactéries Gram+ (cf mécanisme). Staphylocoques SARM +++. Usage
%raison pour éviter sélection de résistances\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Élimination rénale (adapter posologie!)\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%\emph{Vancomycine}\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Polymyxines\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Perméabilise la membrane\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Nombreux bacciles Gram-\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Absorption digestive très limitée. Diffusion tissulaire faible.
%Élimination rénale (prodrogue)\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%Toxicité rénale (+neuromusculaire)\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Lipopeptides\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Dépolarise la membrane\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Large sur bactéries Gram+. Bonne efficacité infections de la peau/tissus
%mous, bactériémies à SARM. Pas d'effication pour infection
%pulmonaire\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%Rhapdomyolyse (arrêt statines, surveillance CPK)\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%\emph{Daptomycine}\strut
%\end{minipage}\tabularnewline
%\bottomrule
%\end{longtable}
%Inhibe synthèse des protéines
%\begin{longtable}[]{@{}llllll@{}}
%\toprule
%\begin{minipage}[b]{0.10\columnwidth}\raggedright
%Famille\strut
%\end{minipage} & \begin{minipage}[b]{0.16\columnwidth}\raggedright
%Mode d'action\strut
%\end{minipage} & \begin{minipage}[b]{0.10\columnwidth}\raggedright
%Spectre\strut
%\end{minipage} & \begin{minipage}[b]{0.16\columnwidth}\raggedright
%Pharmacologie\strut
%\end{minipage} & \begin{minipage}[b]{0.22\columnwidth}\raggedright
%Effets secondaires\strut
%\end{minipage} & \begin{minipage}[b]{0.09\columnwidth}\raggedright
%Suffix\strut
%\end{minipage}\tabularnewline
%\midrule
%\endhead
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Aminoside\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Rapidement bactéricides, concentration dépendant. Le plus souvent en
%association (beta-lactamines, glycopeptides, FQ)\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Infection sévère, bactéries multi-résistantes\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Élimination rénale\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%Néphrotoxicité, toxicité cochléovestibulaire\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%-cine ?\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Cycline\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Bactéries intracellulaires++. Prophylaxie paludisme\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%CI:~grossesse, jeune enfant. Photosensibilisation,
%hypersensibilité\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%-cycline\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Macrolides\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Bactéries intracellulaires. Azithromycine:~fièvre typhoïde, diarrhées du
%voyageur. Pristinamycine, clindamycine:~infections cutanées à
%staphylocoque\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Acide fusidique\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Cocci à Gram+ (SARM++). Parentéral pour infections systémiques sévères à
%SARM. Association (glycopeptide) pour éviter émergence de
%résistances\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%\strut
%\end{minipage}\tabularnewline
%\bottomrule
%\end{longtable}
%Nitrofurane \textbar{} Cystite \textbar{} \emph{Nitrofurantoïne}
%\textbar{}
%Action sur les acides nucléiques
%\begin{longtable}[]{@{}llllll@{}}
%\toprule
%\begin{minipage}[b]{0.10\columnwidth}\raggedright
%Famille\strut
%\end{minipage} & \begin{minipage}[b]{0.16\columnwidth}\raggedright
%Mode d'action\strut
%\end{minipage} & \begin{minipage}[b]{0.10\columnwidth}\raggedright
%Spectre\strut
%\end{minipage} & \begin{minipage}[b]{0.16\columnwidth}\raggedright
%Pharmacologie\strut
%\end{minipage} & \begin{minipage}[b]{0.22\columnwidth}\raggedright
%Effets secondaires\strut
%\end{minipage} & \begin{minipage}[b]{0.09\columnwidth}\raggedright
%Suffix\strut
%\end{minipage}\tabularnewline
%\midrule
%\endhead
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Rifamycine\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Bloque transcription ADN -\textgreater{} ARN\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Rifampicine: tuberculose, staphylocoque\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Pas de monothérapie en curatif ! (résistance)\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%Interfactions médicamenteuses fréquentes (induction enzymatique)\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%rifa-ine\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%(Fluoro)Quinolones\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Inhibe l'élongation ADN\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Infections systémiques\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Biodisponibilité élevée et excellente diffusion tissulaire\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%Tendinopathie, toxicité hépatique/cardiaque/neuro-psychique\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%-floxacine\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Sulfamides\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Inhibe synthèse bases puriques/pyrimidiques\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Infection bactériennes (documentée), fongique, parasitaire. Plus
%fréquent: infection urinaire (documentée ou prophylaxie si récidive),
%pneumocystose si ID (traitement, prophylaxie)\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Bénins mais parfois grave (épidermolyse toxique)\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%sulfa-\strut
%\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright
%\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.10\columnwidth}\raggedright
%Imidazolés\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%Inhibe synthèse acides nucléiques\strut
%\end{minipage} & \begin{minipage}[t]{0.10\columnwidth}\raggedright
%Bactéries anaérobies strictes (digestives, génitales féminines),
%parasites {[}protozoaires{]} (amoebose, trichomonose, giardose)\strut
%\end{minipage} & \begin{minipage}[t]{0.16\columnwidth}\raggedright
%-nidazole\strut
%\end{minipage} & \begin{minipage}[t]{0.22\columnwidth}\raggedright
%\strut
%\end{minipage}\tabularnewline
%\bottomrule
%\end{longtable}
%\paragraph{Spectre}
%Aérobie
%Gram+
%Gram-
%Cocci
%Bacci
%Cocci
%Bacci
%~
%Staphylocoque
%Streptocoque
%Pneumocoque
%Entérocoque
%Listeria
%C. diphteria
%Neisseria
%M. catarrhalis
%Entérobactéries
%Haemophilus
%Autres
%~
%Autres~
%Meti-S
%Meti-R
%~
%~
%~
%~
%~
%~
%~
%I
%II
%III
%Peni G/V
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%Peni A
%~
%~
%~
%~
%~
%E. faecalis
%monocytogenes
%~
%menigitidis
%~
%~
%~
%~
%~
%~
%~
%Peni A + inhibβ
%~
%~
%~
%~
%~
%~
%monocytogenes
%~
%menigitidis
%~
%pénicillinase
%influenza pénicillinase
%~
%~
%Peni M
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%Carbo/Uréïdo
%~
%~
%~
%~
%~
%~
%monocytogenes
%~
%~
%~
%~
%~
%~
%~
%~
%~
%C2G
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%C3G O
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%C3G IV (ceftriaxone, cefotaxime)
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%C3G IV (ceftazidime, céfépime)
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%certaines
%~
%~
%Carbapénèmes
%~
%~
%~
%~
%~
%sauf ertapénème
%~
%~
%~
%~
%~
%~
%~
%~
%Aminosides
%~
%~
%~
%~
%~
%~
%monocytogenes
%~
%~
%~
%~
%~
%~
%~
%Fluoroquinolones
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%influenza
%~
%~
%Cotrimoxazole
%~
%~
%~
%~
%~
%~
%monocytogenes
%~
%~
%~
%~
%~
%~
%~
%Macrolides
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%H. pylori
%Lincosamide
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%H. pylori
%Imidazolés
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%H. pylori
%Glycopeptides
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%Anaérobie
%Gram+
%Gram -
%~
%Spirochètes
%Champignons
%Bactéries intracellullaires
%Parasites
%~
%~
%Fusobacterium
%Autres
%Pseudomonas aeruginosas
%Treponema
%Borrelia
%Pneumocystis jirovecii
%Toxoplasma gondii
%Autres
%Peni G/V
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%Peni A
%~
%~
%~
%~
%~
%~
%Lincosamide
%~
%~
%Peni A + inhibβ
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%Carbo/Uréïdo
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%C3G IV (ceftazidime, céfépime)
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%Carbapénèmes
%~
%~
%~
%sauf ertapénème
%~
%~
%~
%~
%~
%~
%Fluoroquinolones
%~
%~
%~
%ciprofloxacine
%~
%~
%~
%~
%~
%~
%Cotrimoxazole
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%Macrolides
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%Lincosamide
%~
%~
%~
%~
%~
%~
%~
%~
%~
%~
%Imidazolés
%sauf Actinomyces, Propionibacterium
%~
%~
%~
%~
%~
%~
%Glycopeptides
%Clostridium difficile
%~
%~
%~
%~
%~
%~
%~
%~
%~
%\subsection{Antiviraux}
%\begin{longtable}[]{@{}lll@{}}
%\toprule
%\begin{minipage}[b]{0.24\columnwidth}\raggedright
%Groupe\strut
%\end{minipage} & \begin{minipage}[b]{0.30\columnwidth}\raggedright
%Objectif\strut
%\end{minipage} & \begin{minipage}[b]{0.37\columnwidth}\raggedright
%Médicaments\strut
%\end{minipage}\tabularnewline
%\midrule
%\endhead
%\begin{minipage}[t]{0.24\columnwidth}\raggedright
%HSV, VVZ\strut
%\end{minipage} & \begin{minipage}[t]{0.30\columnwidth}\raggedright
%Contrôle de l'infection\strut
%\end{minipage} & \begin{minipage}[t]{0.37\columnwidth}\raggedright
%aciclovir, penciclovir (prodrogue:~valaciclovir, famciclovir\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.24\columnwidth}\raggedright
%VIH(1,2)\strut
%\end{minipage} & \begin{minipage}[t]{0.30\columnwidth}\raggedright
%Suspensif\strut
%\end{minipage} & \begin{minipage}[t]{0.37\columnwidth}\raggedright
%2 INRT + 1 INNRT/anti-protéase/anti-intégrase\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.24\columnwidth}\raggedright
%Influenza\strut
%\end{minipage} & \begin{minipage}[t]{0.30\columnwidth}\raggedright
%Curatif/prophylaxique\strut
%\end{minipage} & \begin{minipage}[t]{0.37\columnwidth}\raggedright
%inhibiteurs de la neuramidase\strut
%\end{minipage}\tabularnewline
%\bottomrule
%\end{longtable}
%INRT:~inhibiteurs nucléosidiques de la transcriptase inverse
%INNRT:~inhibiteurs non-nucléosidiques de la transcriptase inverse
%\subsection{Antifongiques}
%Candida : echinocandine (probabiliste) -\textgreater{} fluconazole si
%possible Aspergillus : Voriconazole (1ere intention) , amophétiricine B
%(2e intention)
%\subsection{Antiparasitaires}
%Anti-helminthes (regroupé par catégorie mais n'est pas forcément actif
%pour toute la catégorie)
%\begin{longtable}[]{@{}ll@{}}
%\toprule
%\begin{minipage}[b]{0.52\columnwidth}\raggedright
%Molécule\strut
%\end{minipage} & \begin{minipage}[b]{0.42\columnwidth}\raggedright
%Spectre\strut
%\end{minipage}\tabularnewline
%\midrule
%\endhead
%\begin{minipage}[t]{0.52\columnwidth}\raggedright
%Flubendazole\strut
%\end{minipage} & \begin{minipage}[t]{0.42\columnwidth}\raggedright
%\emph{nématodes} (oxyurose, ankylosotomose, ascaridiose)\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.52\columnwidth}\raggedright
%Albendazole ~\textbackslash{}\strut
%\end{minipage} & \begin{minipage}[t]{0.42\columnwidth}\raggedright
%\emph{nématodes} (oxyurose, ankylosotomose, ascaridiose, anguillulose),
%\emph{cestodes} (taeniasis, hydatitose, échinococcose, cysticercose),
%trichinose\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.52\columnwidth}\raggedright
%Praziquantel\strut
%\end{minipage} & \begin{minipage}[t]{0.42\columnwidth}\raggedright
%\emph{plathelminthes} (schistosomiose, distomatose, taeniasis,
%cysticercose\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.52\columnwidth}\raggedright
%Ivermectine\strut
%\end{minipage} & \begin{minipage}[t]{0.42\columnwidth}\raggedright
%\emph{nématodes} (anguillulose, ankylosotomose, filariose)\strut
%\end{minipage}\tabularnewline
%\begin{minipage}[t]{0.52\columnwidth}\raggedright
%Diethylcarbamazine\strut
%\end{minipage} & \begin{minipage}[t]{0.42\columnwidth}\raggedright
%filariose\strut
%\end{minipage}\tabularnewline
%\bottomrule
%\end{longtable}
\section{174 - Risques émergents}%
\label{sec:item_174_risques_emergents}
Maladie hautement transmissible: transmission inter-humaine, létalité
potentielle, contagiosité élevée, traitement inexistant, pas de vaccins
Toxines à savoir : \bact{botulisme}, \bact{charbon}, Variole
\section{186 - Fièvre prolongée}
\label{sec:org0f8d15e}
T \(\ge 38^{\circ}\) (\(38.3^{\circ}\) le soir) \(\ge 3\) semaines\\
Infections (40\%)
\begin{itemize}
\item bactériennes : endocardites infectieuses++, tuberculose++, foyers suppurés++, bactéries intracellulaires
\item virales : VIH, EBV, CMV
\item fongique : candidoses, crptococcose, histoplasmose, aspergillose
\item parasitaire : autochtones, tropicale
\end{itemize}
Malignes (20-30\%) : cancers solides, lymphomes, leucémies aigües\\
Inflammatoires systémiques (10\%) : Horton, arthropathies microcristallines,
MICI\footnote{Maladies inflammatoires chroniques de l'intestin}\\
Autres : médicaments, endocrinopathies, maladie thrombo-embolique, hématome profonds, fièvre factice, dysrégulation thermique autonome
Fièvre récurrente : infection canalaire, foyer infection profond, infection sur matériel étranger
\section{187 - Fièvre chez l'immunodéprimé}
\label{sec:org3e1654b}
Fièvre aigüe chez l'ID = urgence
\begin{table}[htbp]
\caption{Agents pour l'immunsuppression}
\centering
\begin{tabular}{ll}
Agent & Étiologie\\
\hline
Neutropénie & Chimiothérapie\\
Hypo\(\gamma\) & Myélome, chimio\\
Aspéline & Post-chir, fonctionnelle\\
Déficits compléments & Congénital\\
Déficits immunité cellulaire & VIH, IS\\
\end{tabular}
\end{table}
\subsection{Fièvre chez neutropénique}
\label{sec:org077134a}
Fièvre + PNN \(< 500/mm^3\) urgence
Neutropénie = déficit phagocytose
Fièvre = souvent seul facteur.
Risque inversement proportionnel taux PNN, proportionnel durée
Traitement :
\begin{itemize}
\item faible risque : amoxicilline-acide clavulanique + ciprofloxacine PO
\item sinon urgent, probabiliste, après hémocultures, large spectre, bactéricide : \(\beta\)-lactamine antipyocyanique \(\pm\) amikacine (sepsis grave, baccile G- MR) \(\pm\) vancomycine (infection cutanée/cathéter, sepsis)
\end{itemize}
\subsection{Autres}
\label{sec:org8c06c0e}
Asplénie (déficit immunité humorale) :
\begin{itemize}
\item urgente, active sur bactéries encapsulées (pneumocoque) après prélèvements
\item fièvre inexpliquée : céfotaxime/ceftriaxone
\end{itemize}
Autres : urgence diagnostique seulement
\section{211 - Purpuras}
\label{sec:orga164eae}
\danger Purpura + fièvre = urgence
\danger Purpura avec 1 élements ecchymotique $\ge 3$ mm / nécrotique $\to$ C3G
IV en urgence
\section{213 - Syndrome mononucléosique}%
\label{sec:syndrome_mononucleosique}
Définition : NFS = {> 50\% leucocytes mononuclés et > 10\% de lymphocytes T
activés (\nearrow taille, coloration)
Principales étiologies :
\begin{itemize}
\item EBV : MNI test ou sérologie (IgM anti-VCA +, IgG anti-VCA et anti-EBNA -)
\item CMV : sérologie
\item VIH : sérologie $\pm$ charge virale
\item \bact{toxoplasmose} : sérologie
\item médicaments
\end{itemize}
\section{214 - Éosinophilie}
\label{sec:org4e42b49}
Cytotoxique, défense antiparasitaire
Définition : PNE > 0.5G/L
\faHospital{} si signes de gravité
\subsection{Étiologies}
\label{sec:orgdb9b717}
Parasitaires :
\begin{itemize}
\item helminthoses++ : élévation IgE, EPS 2-3mois plus tard, sérologie délicate
\item si voyage : anguillulose (ondulante), filarioses (ondulante), schistosomoses (aigüe), distomatoses tropicales (aigües), gnathostomoses (aigüe)
\item hors séjour : asciridiose (aigüe), trichinellose (aigüe), toxocarose (ondulante), distomatose (aigüe), taeniasose, oxyuroses, échinococcoses
\end{itemize}
Non parasitaires : médicaments++, atopie, onco-hématologiques, système,
vascularites\ldots{}
\section{216 - Adénopathies superficielles}%
\label{sec:adenopathies_superficielles}
Définition : ganglion palpable > 1cm. Causes : infectieuse, tumorale (,
inflammatoire, médicamenteuse)
Diagnostic différentiel : tumeur, lipome, hernie inguinale, masse vasculaire,
hidrosadénite
Localisée :
\begin{itemize}
\item cervicale : si aigü, infection tête+cou, EBV, CMV, VIH, toxplasmose. Sinon,
\item EBV, CMV, VIH, toxolpasmose, syphilis, tuberculose, griffes du chat, lymphome,
\item cancer
\item sus-claviculaire : néoplasie
\item axillaire : griffes du chat, cancer du sein
épitrochlée : infection locale, griffes du chat, syphilis
\item inguinale : cancer, infection, IST
\end{itemize}
Polyadénopathie :
\begin{itemize}
\item bactérienne : mycobactérie (tuberculose),
\item virale : EBV, CMV, VIH
\item parasitaire : toxoplasmose
\item non infectieux : lymphome/leucémies, lupus
\end{itemize}
% Examens complémentaires
% \begin{itemize}
% \item si AEG, > 2cm, pas d'étiologie
% \item sérologie VIH, EBV, CMV, toxoplasmose, maladie des griffes du chat,
% syphilis
% \item NFS, CRP
% \end{itemize}
% Polyadénopathies
% 1ère intention :
% \begin{itemize}
% \item radio thorax (tuberculose)
% \item sérologie VIH EBV, CMV, toxoplasmose
% \item NFS, CRP
% \item bilan hépatique, LDH
% \end{itemize}
% 2eme intention :
% \begin{itemize}
% \item sérologie syphilis
% \item AAN (lupus)
% \item TDM TAP
% \item ponction/biopsie si négatif (lymphome)
% \item myélograme (leucémie aigüe)
% \end{itemize}
% Polyadénopathies + splénomégalie :
% \begin{itemize}
% \item infectieux : bactérien (tuberculose, brucellose), viral (EBV, VIH),
% parasitaire (leishmaniose)
% \item hématologique, inflammatoire
% \end{itemize}
\section{252 - Péritonite aigüe}
ATB : C3G + métronidazole ou amoxicilline-acide clavulanique + gentamicine
\section{362 - Exposition accidentelle aux liquides biologiques}
\subsection{Exposition au sang}
Déclaration d'accident du travail < 48h
Sérologie VIH, VHC
\paragraph{VIH}
TPE = ténéfovir + emtricitabine + rilpivirine < 4h si
\begin{itemize}
\item exposition importante sauf si sérologie inconnue et groupe à prévalence
faible
\item exposition intermédiarie sauf si CV indétectable ou groupe à prévalence faible
\end{itemize}
\paragraph{VHB, VHC}
\begin{table}[htbp]
\caption{VHB}
\centering
\begin{tabular}{lll}
& Ag HBs + ou prévalence élevée & Prévalence faible\\
\hline
Non vacciné & Ig + vaccin & Vaccin\\
Ne répond pas à la vaccination & Ig & \\
\end{tabular}
\end{table}
\paragraph{Exposition sexuelle}
TPE si
\begin{itemize}
\item anal réceptif sauf si prévalence faible
\item CV détectable ou prévalence élevée ou viol
\end{itemize}
\section{Annexe}
\input bacteries
`\setlist{noitemsep}`{=latex}
Source: Vidal
# Cardiovasculaire
## Antagoniste du calcium
- *Action* : diminue contractilité musculaire (muscles lisse, coeur)
en bloquant canaux Ca2+
- *Indications* :
- amlodipine : HTA, angor
- verapamil : idem + IDM, tachycardies
## Glucoside cardiotonique : digoxine
- *Action*: augmente contractilité myocarde, ralentit conduction dans
le noeud AV
- *Indications*: insuf. cardiaque, FA, flutter
## Antiarythmiques
- Classe I : flécaine (Ic)
- *Action*: augmente période réfractaire du noeud AV
- *Indications* : TdR ventriculaire, prévention tachy.
supra-ventriculaire
- Classe II : beta-bloquant
- *Action*: diminue activité sino-atriale et AV.
- *Indications* :
- Angor, IDM : diminue FC et contractilité donc diminue
consommation O2
- glaucome : diminue production d\'humeur aqueuse
- HTA: diminue débit cardique et rénine
- hyperthyroïdie : diminue symptoe (diminution FC,
tremoblements)
- hypertrophie cardiqaue : diminue FC donc soulage obstruction
- tachy. supra-ventriculaire : diminue conduction AV
- hémorragie variqueuse : diminue gradient pression veineuse
hépatique et hypertension portable
- Classe III : amiodarone
- *Action*: allonge potentiel d\'action (bloque canaux K+),
augmente période réfractaire auriculaire+nodale+ventriculaire
- *Indications*: tachy. (supra) ventriculaires, fibrillation
ventriculaire
- Classe IV : vérapamil
- *Action*: ralentit la vitesse de conduction, allonge période
réfractaire du noeud AV (bloque canaux Ca2+)
- *Indications*: angor, HTA, IDM, tachycardie
## Ivabradine :
- *Action*: prolonge dépolarisation (noeud sinusal)
- *Indications* : angor, insuf. cardiaque
TdR = troubles du rythme
```{=latex}
\def\dec{$\searrow{}$}
```
```{=latex}
\def\inc{$\nearrow{}$}
```
```{=latex}
\newcommand{\tabitem}{~~\llap{\textbullet}~~}
```
```{=latex}
\newcommand{\ttabitem}{~~~~~~\llap{$\square$}~~}
```
```{=latex}
\newcommand{\tttabitem}{~~~~~~~~\llap{-}~~}
```
::: table
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
LCS Couleur Elements Glycorachie Protéinorachie Lactatorachie ED Etiologie
------------------ --------- ------------- ----------------------- ------------------------- --------------- ------------------ -------------------------------
normal claire \< 5/mm^3^ \> 2/3 gly \< 0.40g/L \< 3.2mmol/L négatif
****Purulent**** trouble \> 20/mm^3^ ≤ 0.4 gly \> 1g/L \> 3.2mmol/L positif (60-80%) ****Bactérienne****
(PNN) (\> 1000) (pneumo, méningo)
PNN \> 50% Virale (début)
****Clair**** clair 5-100/mm^3^ viral: \>2/3 gly viral: \> 1g/L \< 3.2mmol/L négatif ****Normogly: virale****
(Ly) Ly \> 50% Listera/BK \< 0.4 gly Listeria/BK: \< 0.4 gly (Listeria/BK : ****Hypogly: Listeria, BK****
parfois positif)
```{=latex}
}
```
:::
# Syndrome néphrotique
= tout ce qui est **-ose** + tout ce qui sclérose
## Syndrome néphrotique à lésons glomérulaires minimes
- rien
## Hyalinose segmentaire et focale (HSF)
- prolifération: fibrose qui va piéger les protéines plasmatiques
(dépôts hyalins)
- dépôts immuns: non, pas immun !
## Glomérulonéphrite extramembraneuse
- dépôts immuns: oui, le long de la membrane baso-glomérulaire
- prolifération: ces dépôts vont épaissir la MBG (spicules)
## Amylose
- dépôts immuns: oui, c\'est immun
- prolifération: oui, rouge Congo
## Diabète
- prolifération: oui, sclérose du mésangium
- dépôts immuns: non, pas immun
# Syndrome hématurique
= le reste, sans compter les infections
## Glomérulonéphropathie à dépôts d\'IgA (fréquente++)
- dépôts immuns: oui, c\'est dans le nom (mésangium)
- prolifération: partout (mésangium, endo et extracapillaire)
## Syndrome d\'Alport
- rien
## GN rapidement progressive
- prolifération : nécrose qui va rompre la MBG et prolifération en
croissant extracapillaire à partir de là
- dépôts immuns : non si ANCA, granuleux si lupus/PR, linéaire le long
de la MBG (Goodpasture si atteinte pulmonaire en plus ou GN à Ac
anti-MBG seule)
# Syndrome néphritique
Post-infectieu
- prolifération: endocapillaire (les PNN qui circulent à cause de
l\'inflammation) + des *humps* en extramembraneux (pas
d\'explications)
- dépôts immuns : oui, de complément et partout (endo+
extramembraneux)
\section{UE5 - Item 132 : Thérapeutiques antalgiques médicamenteuses et non
médicamenteuses}%
\label{sec:ue5_item_132}
\subsection{Médicaments}%
\paragraph{Analgésiques}%
Palier 1 :
\begin{itemize}
\item Paracétamol : < 4g / jour. Toxicité hépatique
\item Aspirine : < 500mg-1g toutes les 6-8h. Toxicité gastro-intestinale. Risque allergique, effet antiagrégant
\item Néfopam (Acupan\copyright) < 20-120mg/j. CI : ATCD convulsion, adénome
\item prostatique, glaucome angle fermé
\end{itemize}
Palier 2
\begin{itemize}
\item Codéine : posologie suivant paracétamol. ES: opioïdes
\item Tramadol : alternative codéine. Associer au paracétamol. < 400mg/j. ES : opioïdes
\item Lamaline\copyright : < 10 comprimés/jour
\end{itemize}
Palier 3
\begin{itemize}
\item Anta-agonistes morphiniques : buprénorphine
\item Agonistes morphiniques : morphine, oxycodone, hydromorphone, fentanyl
\end{itemize}
Antidote : naloxone (urgence seulement)
\paragraph{Douleurs neurogènes}%
Antiépileptiques : prégabaline (Lyrica\copyright), carbamazépine
Antidépresseur : 1ère intention : tricycliques (Laroxyl\copyright). Puis : inihibiteur de la recapture de la sérotonine
\subsection{Non médicamenteux}%
\label{sub:non_medicamenteux}
Neurochirugie, neurostimulation cutanée, suivi psy, thérapies physiques, ttt non
conventionnels, médico-social.
# Anomalies biologiques
On représente la même information sous 2 approches différentes
## Par maladie
### Cytopénies
**Syndrome myélodysplasique** anomalie des précurseurs =\> défaut de
production de globules rouges +/- plaquettes et neutrophile
### Prolifération
**Myéloprolifératif** : attention, on a souvent les leucocytes et les
plaquettes qui augmentent ensemble...
- Vaquez = [excès de GR]{.underline}, leucocytes et plaquettes
- Thrombocytémie = [excès de mégacaryocyte]{.underline} et leucocytes
- Leucémie myéloïde chronique = [excès de neutrophiles]{.underline} et
plaquettes, baisse de GR (wtf)
**Lymphoprolifératif**
- Leucémie lymphoïde chronique = excès lymphocytes
- Lymphomes = excès de cellules du *tissu lymphoïde*
- Leucémie aigüe = excès de blastes
Les 3 vont envahir la moelle et bloquer les 3 lignées (globules rouges,
plaquettes, leucocytes) [sauf la LLC qui ne bloque pas les leucocytes
!]{.underline} Les 3 vont envahissement les organes lymphoïdes :
adénopathie, splénomégalie.
## Par anomalie biologique
Note:
- lymphoprolifératif = leucémie lymphoïde chronique/leucémie
myéloïde/lymphome
- myéloprolifératif = Vaquez, leucémie myéloïde chronique,
thrombocytémie
**Splénomégalie** : hypeproduction \<= syndrome myéloprolifératif,
lymphoprolifératif
**Anémie**
- défaut de production : syndrome myélodysplasique
- envahissement : syndrome lymphoprolifératif, leucémie myéloïde
chronique ([le seul des syndromes myéloprolifératif]{.underline})
**Thrombopénie**
- défaut de production : syndrome myélodysplasique
- envahissement : syndrome lymphoprolifératif, sd myéloprolifératif
[aigü]{.underline} (attention !)
**Neutropénie** (fièvre !)
- anomalie des précuseurs =\> syndrome myélodysplasique
- envahissement médullaire =\> leucémie aigùe, lymphomes (pas les
autres syndrome prolifératifs, cf plus haut)
Tumeurs bénignes Tumeurs malignes
------------------------------------------------- -------------------------------------
Bien limitée Mal limitée
Encapsulée Non encapsulée
Histologiquement semblable au tissu d'origine Différenciation variable
Cellules régulières Anomalies du cytoplasme et du noyau
Croissance lente Croissance rapide
Refoulement sans destruction des tissus voisins Envahissement des tissus voisins
Pas de récidive locale après exérèse complète Récidive possible après exérèse
Pas de métastase Métastases
: Tumeurs bénignes/malignes.
Cellule ou tissu d'origine Tumeur bénigne Tumeur maligne
---------------------------- ---------------------- ------------------------
Épithélium malpighien Papillome malpighien Carcinome épidermoïde
Épithélium urothélial Papillome urothélial Carcinome urothélial\*
Épithélium glandulaire Adénome Adénocarcinome
: Tumeurs épithéliales.
Cellule ou tissu d'origine Tumeur bénigne Tumeur maligne
------------------------------ ---------------- ------------------
Fibroblastes Fibrome Fibrosarcome
Cellules musculaires lisses Leiomyome Leiomyosarcome
Cellules musculaires striées Rhabdomyome Rhabdomyosarcome
Adipocytes Lipome Liposarcome
Cellules endothéliales Angiome Angiosarcome
Cellules cartilagineuses Chondrome Chondrosarcome
Cellules osseuses Ostéome Ostéosarcome
: Tumeurs conjonctives.
Cellule ou tissu d'origine Tumeur bénigne Tumeur maligne
---------------------------- ----------------------------------------- -----------------------------------
Lymphocytes Lymphomes Leucémies aiguës lymphoblastiques
Myéloïdes Syndromes myéloprolifératifs chroniques Leucémies aiguës myéloïdes
: Tumeurs des tissus hématopoïétiques.
Cellule ou tissu d'origine Tumeur bénigne Tumeur maligne
---------------------------- ---------------------- ---------------------------------------------------
Mélanocyte Nævus nævocellulaire Mélanome
Mésothélium Mésothéliome bénin Mésothéliome malin
Tissu méningé Méningiome Méningiome malin
Nerf périphérique Schwannome Tumeur maligne des gaines nerveuses périphériques
Cellules gliales Astrocytome\* Glioblastome
: Tumeurs dérivées d'autres tissus.
Cellule ou tissu d'origine Tumeur bénigne Tumeur maligne
----------------------------- ------------------------ ---------------------------
Gonies Séminome
Sac vitellin tumeur vitelline
Placenta Mole hydatiforme Choriocarcinome
Disque embryonnaire Carcinome embryonnaire
Complexes (pluritissulaire) Tératome mature Tératome immature (malin)
: Tumeurs du tissu germinal et des annexes embryonnaires.
Tissu embryonnaire Tumeur bénigne Tumeur maligne
-------------------- ---------------- ----------------
Nerveux Neuroblastome
Renal Néphroblastome
Hépatique Hépatoblastome
: Tumeurs du blastème embryonnaire.
% Created 2019-01-15 Tue 12:04
% Intended LaTeX compiler: lualatex
\documentclass[11pt]{article}
\usepackage[hidelinks]{hyperref}
\usepackage{booktabs}
\input{header}
\usepackage[linesnumbered,ruled,vlined]{algorithm2e}
\usepackage[nonumberlist]{glossaries}
\makeglossaries
\newacronym{RPM}{RPM}{Réflexe photomoteur}
\newacronym{DMLA}{DMLA}{Dégénérescence maculaire liée à l'âge}
\newacronym{PEV}{PEV}{Potentiels évoqués visuels}
\def\ttt{\hspace*{1cm}Ttt: }
\newacronym{NOIA}{NOIA}{Neuropathie optique ischémique antérieure}
\newacronym{GPAO}{GPAO}{Glaucome primitif à angle ouvert}
\newacronym{GNV}{GNV}{Glaucome néovasculaire}
\author{Alexis Praga}
\date{\today}
\title{Ophtalmologie}
\hypersetup{
pdfauthor={Alexis Praga},
pdftitle={Ophtalmologie},
pdfkeywords={},
pdfsubject={},
pdfcreator={Emacs 26.1 (Org mode 9.1.9)},
pdflang={English}}
\begin{document}
\maketitle
\tableofcontents
\section{1 Sémiologie oculaire}
\label{sec:org8900ef6}
\subsection{Globe}
\label{sec:org75c6c69}
Membranes (d'avant en arrière)
\begin{itemize}
\item externe = \{cornée (avant), conjonctive (sur sclère antérieure), sclère\}
\item intermédiaire (uvée) = \{iris, corps ciliaires, choroïde\}
\item interne (rétine) = \{épithelium pigmentaire, neurosensorielle (photorécepteurs,
fibres optiques\}\}. NB : phototransduction = pigment visuel
(épithelium) \(\rightarrow\) photorécepteurs (bâtonnets = \{vision périphérique,
nocturne\}, cône = \{détails, couleurs\} \(\in\) macula)
\end{itemize}
Contenu :
\begin{itemize}
\item humeur aqueuse \(\in\) chambre antérieure, évacuée dans l'angle iridocornéen. P
normale si \(\le\) 22 mmHg.
\item cristallin : biconvexe, convergente, déformation par zonule \thus accomodation
\item corps vitré : 4/5e cavité oculaire \thus segment antérieur vs postérieur
\end{itemize}
Voies optiques :
\begin{itemize}
\item nerf optique - chiasma - bandelettes optiques - corps genouillés externes - radiations optiques - cortex occipital
\item mydriase "sensorielle"\footnote{Plus de voie afférente \thus \gls{RPM} direct et consensuel aboli pour l'\oe{}il atteint} vs "paralytique"\footnote{Plus de voie efférente \thus \oe{}il atteint : RPM direct aboli. \OE{}il sain : RPM consensuel aboli}
\item voie efférente sympathique : si atteinte, sd Claude-Bernard-Horner (myosis, ptosis)
\end{itemize}
Annexes
\begin{itemize}
\item oculomoteur : nerf IV = \{oblique supérieur\}, VI = \{droit externe\} et III =
\{droit sup, droit inf, droit médial, oblique inf\}
\item protection : paupière (muscle orbiculaire, tarse), conjonctive (face interne
paupière, globe antérieur), film lacrymal
\end{itemize}
\subsection{Examen}
\label{sec:org8716406}
Interrogatoire :
\begin{itemize}
\item baisse d'acuité visuelle (BAV), fatigue visuelle, myodésopsies, métamorphopsies, héméralopie, scotome/amputation champ visuel,
\item mode d'installation : urgence si brutal
\item douleur superficielles/profondes
\item diplopie mono/bi-noculaire
\item évolution : aggration rapide = grave
\end{itemize}
Acuité visuelle : échelle de Monoyer (à 5m), de Parinaud (33cm)
Segment antérieur : "lampe à fente"
\begin{itemize}
\item conjonctive : rougeur (diffuse/localisée/culs-de-sac inférieure/avec
sécrétions/cercle périkératique/paupière), chemosis\footnote{\OE{}dème conjonctival}
\item cornée (transparence)
\item iris : myosis/mydriase
\item chambre antérieure : inflammation (Tyndall\footnote{Cellules inflammatoires, protéines dans l'humeur aqueuse}, précipités rétro-cornéens,
synéchies iridocristaliniennes), hypopion (pus), hyphéma (sang)
\end{itemize}
Pression intraoculaire par tonomètre à air pulsé. Hypertonie si \(\ge\) 22 mmHg
Gonioscopie : angle iridocornéen
Fond d'\oe{}il
\begin{itemize}
\item direct, indirect (apprentissage++), biomicroscopie
\item aspect : pôle postérieur = \{papille, vaisseaux rétitiens, macula\}, rétine
périphérique (si besoin)
\item lésions : microanévrisme (points rouges), hémorragie (intravitréennes,
prérétiniennes, sous-rétiniennes, intra-rétiniennes\footnote{Punctiformes, flammèches, profondes}), nodules cotonneux,
exsudats profonds, \oe{}dème papillaire\footnote{Si BAV, vasculaire probable. Sinon HTIC}
\end{itemize}
Oculomotricité
\subsection{Complémentaires}
\label{sec:org30acd9d}
Fonctions visuelles
\begin{itemize}
\item Champ visuel :
\begin{itemize}
\item sensibilité lumineuse \dec périphérie, papille = zone aveugle
\item périmétrie cinétique (Goldman : trace isoptères) ou statique (dépistage glaucome)
\end{itemize}
\item Vision des couleurs : si dépistage anomalie congénitale (planches colorées) ou
\end{itemize}
affection acquise (Farnsworth = classer couleurs). Utile pour antipaludéens de
synthèse ou \{éthambutal, isoniazide\}
Angiographie du fond d'\oe{}ils : fluorescine ou vert d'indocyanine (\gls{DMLA}++)
Électrophysio : électrorétinogramme (si lésion rétiniennes étendues), \gls{PEV} (cortex occipital) (SEP++), électro-oculogramme (épithelium pigmentaire)
Echographie : mode A (longueur globe oculaire) ou B (décollement rétine, corps
étranger intraoculaire, tumeur)
Tomographie en cohérence optique (OCT) : affection maculaire (trou, DMLA),
dépistage glaucome chronique
\section{2 Réfraction}
\label{sec:org259641b}
\OE{}il \(\approx\) 60 dioptries (cornée = 42, cristallin = 20)
Emmétrope = \oe{}il normal. Amétrope = anomalie de réfraction
Punctum remotum (PR) : point le plus éloigné visible \emph{sans} accomoder. Punctum
proximum (PP) = point le plus proche visible \emph{en} accomodant.
Acuité visuelle = \(\frac{1}{\alpha}\) où \(\alpha\) = pouvoir séparateur de
l'\oe{}il. Mesurée par l'échelle de Monoyer (de loin) en 10eme (!) et de Parinaud
(de près)
\subsection{Accomodation}
\label{sec:org5a076a5}
Amplitude \dec jusque 0 (79 ans) \thus presbytie (BAV vision de près). Compensée
par verres sphériques convexes progressifs ou implant cristallinien
Sinon, \dec vision de près par : médicaments, paralysie III, maladie générale,
spasmes de l'accomodation
\subsection{Anomalies de la réfraction}
\label{sec:orgfcd2f13}
Différencier maladie de l'\oe{}il/voie optique et anomalie réfraction !
Examen : réfractomètres automatiques \thus réfraction, kératométrie\footnote{Courbure de la cornée}. \footnote{Chez l'enfant, cycloplégique}
\subsubsection{Myopie}
\label{sec:org25c9aca}
\OE{}il trop convergent. \(\approx\) 20\% population occidentale. PR à distance finie,
PP plus proche.
Types : myopie d'indice (\inc indice de réfraction), de courbure (courbure
cornée \inc) ou axile (longueur axiale \inc)
Myopie
\begin{itemize}
\item faible : < 6 dioptrie
\item forte : > 6 dioptries ou longueur axiale \(\ge\) 26mm. Héréditaire, \(\in\) [1/10,
5/10] \emph{après} correction. Complications : glaucome chronique à angle ouvert,
cataracte, décollement de la rétine++
\end{itemize}
Correction : verres sphériques concaves.
Chirurgie par photoablation au laser excited dimer\footnote{Abrasion épithelium cornéen ou volet dans cornée.}. Chirurgie du cristallin
possible.
\subsubsection{Hypermétropie}
\label{sec:orge728fd4}
Fréquent (enfant++). Pas assez convergent. PR = virtuel à l'arrière. Correction
par verres sphériques convexes, lentilles ou chir.
\subsubsection{Astigmatisme}
\label{sec:org552aa74}
Rayons de courbures différents pour les méridiens. Régulier si 2 méridiens
principaux \bot{}.
1 point à l'infini = 2 droite perpendiculaire (= focales) \thus myopique,
hypermétropique ou mixtes\footnote{Focales en avant/arrière/des 2 côtes de la rétine resp.}
Correction par verres cylindriques convexes/concaves, lentilles ou chir
\section{3 Suivi d'un nourisson}
\label{sec:orgb0dd1a4}
Déficits mineurs (amétropie, strabisme) ou sévères (grave !) (milieux transparents,
malformation, rétinopathie, atteintes neuro centrales)
20\% d'enfant < 6 ans avec anomalie visuelle. Si non traitée, amblyopie\footnote{BAV par altération précoce de l'expérience visuelle.} ,
définitive après 6ans !
Développement :
\begin{itemize}
\item 1ere semaine : réflexe lumière, RPM
\item 2-4e semaine : reflexe de poursuite
\item 4-12e semaine : reflexe de poursuite
\item 3e mois : vision des formes
\item 4-5e mois : coordinatio \oe{}il-tête-main
\item > 2 ans : AV mesurable
\end{itemize}
Examens obligatoires pour \{strabisme, nystagmus, anomalie organique, trouble
comportement visuel\}: \emph{dépistage anténal - S1 - 4M - 9M - 2A - 3 à 6A}
Dépistage : leucocorie, glaucome congénital, malformations, infections
maternelles, maladies enfants secoués, rétinopathie des prématurés
\section{4 Strabisme de l'enfant}
\label{sec:org550d080}
Position de l'\oe{}il anormale et altération vision binoculaire. Due à une perturbation de la fusion.
Conséquences :
\begin{itemize}
\item Si aigu : diplopie possible. Si ancien : corrigé par cerveau \thus vision binoculaire non acquise si strabisme dans premiers mois de vie !. Amblyopie possible
\item Perturbation vision stéréoscopie (3D)
\end{itemize}
Souvent dans l'enfance. 4\% population. \textbf{Dépistage avant 2 ans}
\subsection{Dépistage}
\label{sec:org144ddd9}
Jamais normal, toujours symptôme
Interrogatoire :
\begin{itemize}
\item date d'apparition
\item horizontal : \emph{eso-} si convergent, \emph{exo-} si divergent. Vertical : \emph{hyper-},
\emph{hypo-}. Si divergent < 9 mois, examen neuroradio
\item intermittent ?
\item \oe{}il dominé
\end{itemize}
Examen :
\begin{itemize}
\item motilité : strabisme paralytique ?
\item segment antérieur et FO (fond d'\oe{}il) : perte transparence, patho rétinienne ? Si nystagmus : électrorétinogramme, PEV, IRM
\item mesure de réfraction sous collyre cycloplégique : amyotropie ? Hypermétropie fréquente
\item acuité visuelle : amblyopie ? (> 2/10 entre 2 yeux)
\item mesure de l'angle de déviation (si chir), vision binoculaire (pronostique)
\end{itemize}
\subsection{Traitement}
\label{sec:org3fe45af}
Correction optique. Si amblyopie, occlusion de l'\oe{}il dominant (jusque 6-8ans)
Chir si angle résiduel avec correction. Correction optique après opération
\section{5 Diplopie (binoculaire)}
\label{sec:org27b125a}
Binoculaire : disparaît à l'occlusion d'un \oe{}il\footnote{Monoculaire : disparaît à l'occlusion de l'oeil \emph{atteint}. Cause cornéenne, irienne, cristalinienne \(\ne\) urgence.}. Souvent une urgence
\danger
Noyaux des nefs oculomoteurs \(\in\) tronc cérébral - racine - troncs -
muscle. Voies supranucléaires (latéralité, verticalité), internucléraires.
\begin{table}[htbp]
\caption{Champ d'action (\danger \(\ne\) action) avec l'innervation}
\centering
\begin{tabular}{ll}
\toprule
oblique inférieur (III) & droit supérieur (III)\\
\midrule
droit médial (III) & droit latéral (VI)\\
\midrule
oblique supérieur (IV) & droit inférieur (III)\\
\bottomrule
\end{tabular}
\end{table}
Mouvement bilatéraux : synergie des muscles
Vision binoculaire :
\begin{itemize}
\item loi de Hering : même influx nerveux pour muscles antagonistes. Loi de
Sherrington : muscle antagonistes se relâchent quand muscles synergistes se
contractent.
\item si correspondance rétinienne anormale (yeux non \(\parallel\)) : diplopie
\end{itemize}
\subsection{Diagnostic}
\label{sec:orgf46569f}
\begin{itemize}
\item Signes fonctionnels : dédoublement toujours même direction\footnote{\danger méconnu si ptosis/\oe{}dème palpébral}, disparaît à
\end{itemize}
l'occlusion
\begin{itemize}
\item Interrogatoire : terrain, circonstance, brutal/progressif, \{douleurs, vertiges,
\end{itemize}
céphalées, nausées\}, \{horizontale, verticale, oblique\}, moment journée
\begin{itemize}
\item Attitude vicieuse ? Chercher déviation en position primaire par reflets
cornéens
\end{itemize}
Examens :
\begin{itemize}
\item motilité
\item cover-test (\oe{}il dévié puis se redresse)
\item au verre rouge (dissociation point rouge et blanc)
\item test de Lancaster (superposer flèches de couleurs différentes) \thus diagnostic
paralysie oculomotrie
\item RPM, inégalité pupillaire
\end{itemize}
\subsection{Sémiologie}
\label{sec:orgd4b1f1b}
\begin{itemize}
\item Paralysie du III : totale (ptosis total, mydriase aréflective, 0 accomodation) ou partielle
\item Paralysie du IV : diplopie verticale oblique
\item Paralysie du VI : convergence \oe{}il atteint, déficit abduction
\item Formes particulières :
\begin{itemize}
\item paralysie supranucléaire : sd Foville (latéralité), sd Parinaud (verticalité
et cv \thus pinéalome++)
\item paralysie intranucléaire : ophtalmoplégie intranucléaire (parallélisme OK mais
déficit adduction) \thus SEP
\item paralysie intraxiale : (atteinte fonction et diplopie) ou (diplopie et signe neuro
controlatéraux)
\end{itemize}
\end{itemize}
\subsection{DD}
\label{sec:org0a3487b}
Diplopie monoculaire, simulation, hystérie
\subsection{Étiologie}
\label{sec:orgaa99d9d}
\begin{itemize}
\item Traumatique : fracture du plancher de l'orbite (élévation globe douleureuse),
hémorragie méningé traumatique
\item Tumeurs : HTIC, de la base du crâne
\item Vasculaires : AVC, insuf vertébrobasilaire, \textbf{anévrisme
intrâcranien} (Y penser si atteinte partielle, signes
pupillaires, sujet jeune, 0 FR vasc, céphalée \thus angioscanner urgence
), fistule carotidocaverneuse
\item Avec exophtalmie : Basedow, tumeurs de l'orbite
\item douleureuse : penser \{anévrisme intracrânnien, dissection carotidienne, fistule
carotidocaverneuse\} = urgences . Maladie de Horton. Sd Tolosa-Hunt
\item SEP : paralysie VI, ophtalmoplégie internucléaire
\item Myasthénie : diag = \{test Prostigmine, Ac anti récepteur acétylcholine, électromyographie\}
\end{itemize}
\subsection{CAT}
\label{sec:org8eab1ca}
\begin{itemize}
\item Récente : étiologie++ (neuro, imagerie cérébrale)
\item Phase précoce : occlusion oeil paralysé, prismation, toxine botulique
\item Phase tardive : attendre régénérescen nerveuse (6 mois-1an)
\end{itemize}
\section{6 \OE{}il rouge/douloureux}
\label{sec:org12b83bc}
\subsection{Examen}
\label{sec:orge3d3376}
Interrogatoire : mode d'apparition, douleur superficielle/profonde, BAV
?, ATCD ophtalmo et généraux, signes locaux associés
Examen à lampe à fente (bilatéral) :
\begin{itemize}
\item acuité visuelle
\item conjonctive : rougeur en nappe hémorragique (hémorragie
sous-conjonctivale\footnote{Cherche plaie conjonctivale !}, diffuse (conjonctivite), secteur (épisclérite),
cercle (kératite aigüe, uvéite antérieure)
périkératique
\item cornée : perte de transparence, dépôts rétro-cornéens
\item collyre à fluorescine pour ulcération cornéenne : unique (trauma), localisée
avec zone blanche (kératite bactérienne), dendritique (kératite herpétique),
petites et disséminées (kératite à adénoviruse, sd sec oculaire, corps
étranger)
\item iris et pupille : synéchie iridocristallinienne (uvéite), atrophie iris
(herpès), myosis (kératite aigüe, uvéite aigüe), semi-mydriase
aréflexique (glaucome aigü)
\item chambre antérieure : étroite, plate (glaucome aigü, plaie perforante), signes inflammatoires
\item tonus oculaire : hypertonie (glaucome aigu par fermeture de l'angle, glaucome
néovasculaire), hypotonie (plaie oculaire transfixiante)
\item conjonctive palpébrale : follicules (conjonctivite virale), papilles
(conjonctivite allergique), corps étranger
\item FO
\end{itemize}
\subsection{Étiologies}
\label{sec:orgd272705}
\begin{table}[htbp]
\caption{Étiologies résumées d'\oe{}il rouge}
\centering
\begin{tabular}{ll}
\toprule
Non douloureux sans BAV & Douloureux avec BAV\\
\midrule
hémorragie ss-conjonctivale & kératite aigüe\\
conjonctivite & uvéite antérieure aigüe\\
(épi)sclérite & crise aigüe de glaucome par fermeture d'angle\\
& glaucome néovasculaire\\
\bottomrule
\end{tabular}
\end{table}
\subsubsection{\OE{}il rouge, non douloureux, sans BAV}
\label{sec:orgec5e8a7}
\begin{itemize}
\item \emph{hémorragie sous-conjonctivale spontanée} : chercher HTA, trouble
coagulation. Penser corps étranger, plaie sclérale \danger
\item \emph{conjonctivite} : sensation de "grain de sable", prurit
\item \emph{conjonctivite bactérienne} : sécrétions mucopurulentes (paupières collées le
matin). Germe Gram+.
\end{itemize}
\ttt hygiène des mains, lavage sérum phy, collyre antiseptique (pas forcément ATB !!)
\OE{}il rouge unilatéral, douloureux, sans BAV
\begin{itemize}
\item \emph{épisclérite} (sous conjonctive) : rougeur disparaissant avec collyre
vasoconstricteur.
\end{itemize}
\ttt corticothérapie locale
\begin{itemize}
\item \emph{sclérite} : douleur \inc mobilisation du globe. Ne disparait pas au
collyre. Cherche maladie de système (articulaire, vasc, granulomateuse,
infectieuse).
\end{itemize}
\ttt AINS générale et cause.
\subsubsection{Yeux rouges bilatéraux, douloureux, sans BAV}
\label{sec:orge1c403c}
\begin{itemize}
\item \emph{conjonctivite virale} : fréq++, contagieux. Sécrétion claires, ADP prétragienne
douloureuses à palpation.
\end{itemize}
\ttt inutile
\begin{itemize}
\item \emph{conjonctivite allergique} : terrain, prurit, chemosis\footnote{\OE{}dème conjonctival}, sécrétion claire,
volumineuses papilles.
\end{itemize}
\ttt bilan allergique, éviction, collyre antiallergique
\begin{itemize}
\item \emph{conjonctivite à \bact{chlamydia}} : tiers-monde++
\item \emph{sd sec oculaire} : fréq++. Diag = test Schirmer (quantité sécrétion lacrymale),
qualité film lacrymal, surfarce cornéenne, surface conjonctivale\}. Cause :
involution (âge), sd Gougerot-Sjögren.
\end{itemize}
\ttt substituts lacrymaux, évictions
facteurs irritants, occlusion points lacrymaux
\begin{itemize}
\item autres : Basedow, malpositions palpébrale, conjonctivite d'irritation
\end{itemize}
\subsubsection{\OE{}il rouge, douloureux, BAV}
\label{sec:orgcb24bf0}
\begin{itemize}
\item \emph{Kératite aigüe} : BAV, douleurs
superficielles importantes, larmoiement, photophobie,
blépharospasme. Érosion/ulcérationsc cornée, \dec transparence cornée,
cercle périkératique
\begin{itemize}
\item \emph{kératite à adénovirus} : petite ulcérations disséminées. Évolution favorable
(?)
\item \emph{kératite herpétique} : ulcération en "feuille de fougère".
\end{itemize}
\end{itemize}
\ttt
valaciclovir \textpm{} aciclovir en pommade. Jamais de corticothérapie locale
sans avoir éliminé une ulcération cornéenne
\begin{itemize}
\item \emph{kératite zostérienne} : zona ophtalmique \thus (?) kératite superficielle ou
neuroparalytique (grave).
\end{itemize}
\ttt valaciclovir et protecteurs locaux
cornéens
\begin{itemize}
\item \emph{kératite bactérienne, parasitaire, mycosique} : plage blanchâtre. Prélèver
sur l'abcès.
\end{itemize}
\ttt collyre ATB (si important : "collyre fortifiés"). \danger
évolution : endophtalmie, perforation cornéenne, taie cornéenne cicatricielle
\begin{itemize}
\item \emph{kératite sur sd sec}
\item \emph{kératite d'exposition} (paralysie faciale) :
\end{itemize}
\ttt protecteurs cornéens en prévention, tarsorraphie (=suture)
\begin{itemize}
\item \emph{Uvéite antérieure} : cercle périkératique, transparence cornée OK, myosis,
(synéchies iridocristalliniennes ou iridocornéennes), Tyndall, précipités
rétro-cornéens. FO systématique !
\begin{itemize}
\item Causes : inconnue, spondylarthrite ankylosante (diag = \{sacro-iléite, rachis,
Ag HLA B27), uvéite herpétique, arthrite juvénile idiopathique, sarcoïdose,
Behçet, lupus erythémateux disséminé.
\end{itemize}
\end{itemize}
\ttt collyre mydriatique, collyres corticoïdes
\begin{itemize}
\item \emph{Glaucome aigu par fermeture de l'angle} : rare, pronostic sévère.
\begin{itemize}
\item prédisposition anatomique, pendant une mydriase
\item humeur aqueuse ne peut plus passer dans la chambre antérieure, s'accumule
dans chambre postérieure et bloque le trabeculum\footnote{Entre la cornée et l'iris !}.
\item signes fonctionnels .: douleurs profondes++ irradiant dans trijumeau,
souvent nausées, vomissement, BAV
\item examen : douleurs intenses, \oe{}il rouge, transparence cornée \dec diffuse,
semi-mydriase aréflexique, angle iridocornéen fermé, hypertonie oculaire++
\item cécité en qq jours sans ttt \danger
\end{itemize}
\end{itemize}
\ttt antalgique, inhibiteurs de l'anhydrase carbonique \footnote{\dec production d'humeur aqueuse. Acétazolamide IV + potassium.}, solutés hyperosmolaires\footnote{Déshydratation du vitré}, collyre hypotonisants,
collyres myotiques\\
post-crise : iridotomie périphérique sur \textbf{les deux yeux} (laser ou chir)
\begin{itemize}
\item \emph{Glaucome néovasculaire} : VEGF crée néovaisseux qui empêche la résorption de
l'humeur aqueuse
\begin{itemize}
\item néovaisseaux sur l'iris
\end{itemize}
\end{itemize}
\ttt hypotonisants locaux et généraux, photocoagulation ou injection anti-VEGF
\begin{itemize}
\item \emph{Endophtalmie post-opératoire} : douleur intense, \oe{}dème palpébral, hyalite
\end{itemize}
\begin{tcolorbox}
Uvéite : penser maladie générale (rhumatismal, sarcoïdose, MICI, arthrite juvénile idiopathique [enfant++])
\end{tcolorbox}
\section{7 Altération de la fonction visuelle}
\label{sec:orga7c5003}
\subsection{Examen}
\label{sec:org6067a53}
Interrogatoire : BAV objective, altération CV (myodésopsies, phosphènes,
métamorphopsies, éclipse visuelle (qq secondes) ou cécité monoculaire
transitoire (qq min-heures), aura visuelle), installation, unilatéral ?, douleur
? ATCD, ttt, traumatisme ?
Examen ophtalmo : AV (avec correction), RPM, segment antérieur, tonus oculaire,
\{cristallin, vitré, rétine, vaisseaux, nerf optique\}
\subsection{BAV progressive \footnote{Cf chapitre suivant pour BAV brutale}}
\label{sec:org80b3258}
Si améliorée par correction optique, trouble de réfraction. Sinon :
\subsubsection{Transparence anormale}
\label{sec:org101974d}
\emph{Cataracte} : BAV bilatérale, photophobie, myopie d'indice, diplopie
monoculaire. Perte de transparence du cristallin (opalescent). Étiologie : âge
surtout.\\
\ttt chir
Autres : \emph{cornée, vitré} (hyalite des uvéite)
\subsubsection{Transparence normale: atteinte nerf optique}
\label{sec:org6e8e93b}
\emph{Glaucome chronique à angle ouvert} (GCAO) : longtemps asymptomatique. Diag =
\{\inc tonus oculaire, altération CV, excavation glaucomateuse de la
papille\}. \\
\ttt collyre hypotonisants, trabéculoplastie (laser/chir)
Autres : \emph{neuropathie toxiques} (alcool-tabac, médic), \emph{héréditaires, compressive}
\subsubsection{Transparence normale: atteinte de la rétine/macula}
\label{sec:org6984df6}
Dystrophies rétiniennes héréditaires :
\begin{itemize}
\item \emph{maculopathies héréditaires} : maladie de Stargardt = débute vers 7-12 ans,
1/10e en fin d'évolution (!), en "\oe{}il de b\oe{}uf"
\item \emph{rétinopathies pigmentaires} : héméralopie, rétrécissement progressif du CV
(débute dans l'enfance), aspect réticulé "en ostéoblastes"
\end{itemize}
"Interface vitréomaculaire" = \emph{séparation vitré-région maculaire}
\begin{itemize}
\item membranes épi-/pré-maculaire (par tissu fibreux). "reflet" cellophane". OCT
maculaire. Chir possible
\item trous maculaires : OCT
\end{itemize}
\emph{Dégénérescence maculaire liée à l'âge}
\emph{\OE{}dème maculaire} : en "pétales de fleur" si important. Causes :
\begin{itemize}
\item rétinopathie diabétique : \emph{ttt} : injection IV anti-VEGF ou corticoïdes
\item occlusion veine centrale de la rétine : \emph{ttt} idem
\item chir cataracte
\item uvéite postérieures : \emph{ttt} : cause ou corticoïdes retard
\end{itemize}
\emph{Maculopathies toxiques aux antipaludéens de synthèse} : potentiellement cécité
irréversible. Pas avant 5 ans ? Commence par périfovéolopathie \thus arrêt
immédiat du ttt \danger
\subsection{Altération du CV}
\label{sec:org0ef0e97}
= altération vision périphérique
\subsubsection{Affections rétiniennes}
\label{sec:orgb34fac9}
Scotomes (para)centraux , déficits périphériques
\subsubsection{Atteinte des voies optiques}
\label{sec:org0283737}
Atteinte nerf optique : cécité unilatérale (trauma, tumeur)
\begin{itemize}
\item scotome central unilatéral ou caecocentral uni-/bi-latéral
\item déficicit fasciculaire possible
\item déficit altitudinal si \gls{NOIA}
\item étiologies :
\begin{itemize}
\item SEP (névrite optique rétrobulbaire)
\item NOIA
\item toxiques et métabolique : bilatéral, progressive. \{alcool-tabac, médicament,
professionnelle, métabolique\}, tumoral (tumeurs intraorbitaires, étage
antérieur du crâne)\}
\end{itemize}
\end{itemize}
Lésion du chiasma optique : hémianopsie/quadranopsie bitemporale (décussation
!). Étiologies : adénome hypophyse surtout
Lésions rétrochiasmatique : hémianopsie latérale homonyme. Si atteinte des
radiaton optiques, quadranopsie latérale homonymes. Étiologies vasc, tumoral,
trauma
Cécité corticale : bilatérale, brutale. Examen ophtalmo OK, RPM OK,
désorientation, hallucination visuelles, anosognosie
\section{8 Anomalies de la vision d'apparition brutale}
\label{sec:org4c5aa65}
\subsection{Diagnostic}
\label{sec:org86e1015}
Interrogatoire : BAV ? altération CV ? myodésopsies, phosphènes,
métamorphopsies ? rapidité, latéralité, type de douleurs, ATCD, ttt, trauma ?
Examen ophtalmo ( 2 yeux) : AV, RPM, segment antérieur, tonus oculaire, FO
\subsection{Étiologie}
\label{sec:orgaed12f6}
\subsubsection{BAV, \oe{}il rouge et douloureux}
\label{sec:org4e48ca5}
\begin{itemize}
\item \emph{kératite aigüe} : douleur superficielles importantes, photophobie,
blépharospasme. \dec transparence cornée, cercle périkératique, ulcération(s)
cornéenne(s)
\item \emph{glaucome aigü par fermeture de l'angle} : douleurs profondes, intense,
irradiant dans trijumeaux. \inc\inc tonus oculaire ("bille de bois" à la
palpation)
\item \emph{uvéites}
\begin{itemize}
\item \emph{antérieure aigüe} : BAV, douleurs, cercle périkératique, myosis par synéchies
iridocristalliniennes. Tyndall, chercher uvéite postérieure
\item \emph{postérieure} : toxoplasmose oculaire le plus souvent. Myodésopsies, BAV. FO =
foyer blanchâtre puis cicatrice. \\
\end{itemize}
\end{itemize}
\ttt antiparasitaire si AV menacée
\begin{itemize}
\item autres : glaucome néovasculaire, endophtalmie (contexte post-op)
\end{itemize}
\subsubsection{BAV, \oe{}il blanc indolore}
\label{sec:orgd9a604e}
\begin{itemize}
\item FO non visible
\begin{itemize}
\item \emph{hémorragie intravitréenne} : précédée d'une "pluie de cendre", BAV
variable. Écho. B pour éliminer un décollement de la rétine. Causes :
rétinopathie diabétique proliférante, occlusions ischémique de la veine
centrale de la rétine, déchirure rétinienne, sd de Terson\footnote{Hémorragie intravitréenne uni-/bi-latérale et hémorragie méningée par
rupture d'anévrisme intracrânien}, plaie
perforante
\item \emph{uvéite intermédiaire} (dans le vitré) : cellules inflammatoires
\end{itemize}
\item FO visible anormal
\begin{itemize}
\item \emph{occlusion de l'artère centrale de la rétine} : BAV brutale, mydriase
aréflexique et RPM direct aboli, \dec diffuse du calibre artériel, \oe{}dème
blanc rétinien ischémique de la rétine (macula rouge cerise)
\item \emph{occlusion de la veine centrale de la rétine} : BAV variable, \{\oe{}dème
papillaire, hémorragie rétiniennes disséminées, nodules cotonneux,
tortuosités veineuse\}. Préciser si ischémique
\item \emph{DMLA} : BAV et métamorphopsies brutales, décollement exsudatif de la rétine
maculaire \textpm{} hémorragies, exsudats profonds
\item \emph{décollement de la rétine rhegmatogène} : après une déhiscence, le vitré va
sous la rétine.
\begin{itemize}
\item causes : idiopathique (âgé), myopie (forte), chir cataracte
\item évolution spontanée = cécité
\item \emph{ttt} chir (semi-urgence \danger)
\item clinique : myodésopsies, phosphènes, amputation CV périphérique, BAV
\item diag par FO : rétine en relief, mobile, avec des plis
\item toujours examiner \oe{}il controlatéral (ttt préventif par photocoagulation)
\danger
\end{itemize}
\item \emph{neuropathie optique ischémique antérieure} : BAV unilatérale brutale, \dec
RPM direct, \oe{}dème papillaire, déficit fasciculaire pour CV. Cause : surtout
artériosclérose mais penser à Horton (urgence )
\end{itemize}
\item FO visible normal
\begin{itemize}
\item \emph{névrite optique rétrobulbaire} : BAV unilatérale progresse en qq jours (!),
douleur \inc mouvement oculaires, RPM direct \dec, FO normal, scotome
(caeco)-central
\item \emph{atteinte des voies (rétro)chiasmatiques} : tumorale (si progressive), vasc (si brutale)
\end{itemize}
\end{itemize}
Anomalies transitoire
\begin{itemize}
\item \emph{cécité monoculaire transitoire} (qq minute) = amarause. FO pour embole
rétinien. Urgence . Chercher athérome carotidien, cardiopathie embolinogène
\item insuf vertébrobasilaire, éclipses visuelle, scotome scintillant
\end{itemize}
\section{9 Prélèvement de cornée}
\label{sec:org9e0085a}
Le médecine prélèveur \(\ne\) celui qui a fait le constat de mort
Sérologies à faire : HIV, HTLV, hépatite B et C, syphilis
CI :
\begin{itemize}
\item locale : chir sur segment antérieure, uvéite, conjonctivite, tumeur,
rétinoblastome, mélanome choroïdien
\item infectieuses (Sida, rage, Creutzfeld-Jakob, hépatite..),
\item neuro inexpliquée, démence
\end{itemize}
Prélèvement \textbf{in situ}
\section{10 Greffe de cornée}
\label{sec:orgaaa8828}
Couches (depuis l'extérieur) = épithelium, couche de Bowman, stroma, membrane
de Descemet, endothelium
Techniques
\begin{itemize}
\item kératoplastie transfixiante = toute les couches
\item kératoplastie lamellaire antérieure = épithelium, Bowman et stroma seulement
\item kératoplastie endothéliale : membrane de Descemet et endotheliale seulement.
\end{itemize}
Indications : trauma perforant de la cornée, brûlures chimiques, dégénérescence
cornéenne (kératocône), kératite (herpétique), dystrophie bulleuse chez âgé
Bon pronostic dans \(\frac{2}{3}\)
Complications rares (retard d'épithélialisation, \oe{}dème cornéen précoce, rejet
immunitaire, récivide de maladie causale, hypertonie oculaire, astigmatisme post-op)
\section{11 Traumatismes oculaires}
\label{sec:org20ae531}
\subsection{Globe fermé (contusions)}
\label{sec:org383585c}
Dangerosité inversement \(\propto\) taille agent.
Interrogatoire : douleurs, AV, heure dernier repas, lésions associées.
Examen :
\begin{itemize}
\item contusions du segment antérieur
\begin{itemize}
\item cornée : \emph{ttt} lubrifiant cicatrisant
\item conjonctive : plaie ou hémorragie sous-conjonctivale. Toujours chercher plaie
sclérale, corps étranger
\item chambre antérieure : hyphéma. Résorption spontanée
\item iris : iridodyalise \footnote{Désinsertion de la base de l'iris}, rupture sphincter irien, mydriase post-trauma
\item cristallin : (sub)luxation, cataracte contusive (plusieurs mois après\ldots{})
\item hypertonie oculaire : si lésions de l'angle iridocornée, hyphéma, luxation
antérieure du cristallin
\end{itemize}
\item contusions du segment postérieur
\begin{itemize}
\item \oe{}dème rétinien du pôle supérieur : guérison spontanée
\item hémorragie intravitréenne : résorption spontanée. Écho B si décollement de
rétine (DR) suspecté
\item déchirure rétiniennes périph. Photocoagulation prophylactique possible
(contre DR)
\item rupture de la choroïde : BAV définite si macula
\end{itemize}
\end{itemize}
\subsection{Globe ouverts}
\label{sec:org9a9d4c3}
Rupture du globe : pronostic plus péjoratif si postérieur
Trauma perforant :
\begin{itemize}
\item AVP, accidents domestique, bricolage, agression.
\item plaies : larges (mauvais pronostic) ou petites (cornée ou sclère)
\item risque : méconnaître plaie, corps étranger. Si doute, scanner !
\end{itemize}
\subsection{Corps étrangers}
\label{sec:org1b68e8c}
Diagnosic évident :
\begin{itemize}
\item superficiel
\begin{itemize}
\item circonstance, symptôme de conjonctivite ou kératite superficielle. Corps étranger souvent visible
\item bon pronostic, ttt lubrifiant et antiseptique/ATB local
\end{itemize}
\item intraoculaire : circonstance, porte d'entrée et trajet visible
\end{itemize}
Délicat si trauma non remarqué, pas de porte d'entrée, trajet et corps non visible
Examens : TDM si doute. Pas d'écho B si transfixiante. Pas d'IRM \danger
Complications (si intraoculaire) : endophtalmie (grave++), DR, cataracte traumatique
Complications tardives : ophtalmie sympathique \footnote{Uvéite auto-immune sévère}, sidérose (fer), chalcose (cuivre)
\section{12 Brûlures oculaires}
\label{sec:orged6a084}
Accident industriels (graves), domestiques, aggression
Brûlures
\begin{itemize}
\item thermique : peu grave (brûlure par cigarette). Cicatrisation rapide, sans séquelles
\item acides : gravité modérée-moyenne, grave si très concentré
\item basiques : grave !
\end{itemize}
Classification de Roper-Hall
\begin{enumerate}
\item bon pronostic
\item bon pronostic : opacité cornéenne mais détails iris, ischémie < 1/3 \diameter
\item pronostic réservé : désépithélialisation cornéenne totale, opacité cornéenne
, ischémie \(\in\) [1/3, 1/2] \diameter
\item pronostic péjoratif
\end{enumerate}
Ttt d'urgence par lavage (20-30min) par sérum phy (ou eau), puis collyre
corticoïde ASAP
Autres :
\begin{itemize}
\item brûlures des UV (ski, UV) : guérison en 48h, sans séquelles
\item soudure à l'arc sans lunette : idem
\item phototraumatisme (éclipse) : BAV définitive !
\end{itemize}
\section{13 Cataracte}
\label{sec:orga20513d}
Déf: opacification (partielle ou non) du cristallin.
\subsection{Diagnostic}
\label{sec:orge896af5}
Découvert sur BAV (progressive, vision de loin), photophobie, (diplopie
monoculaire), jaunissement
Examen clinique :
\begin{itemize}
\item interrogatoire : âge, profession, ATCD (diabète, corticoïdes), myodésopsies,
métamorphopsies
\item AV (\oe{}il par \oe{}il, bionculaire)
\item lampe à fente :
\begin{itemize}
\item cristallin (caracte \{nucléaire, sous-capsulaire postérieure, corticale, totale\})
\item éliminer autre patho (cornée, iris, vitré, rétine (DMLA, glaucome))
\item mesure tonus oculaire (hypertonie, glaucome)
\end{itemize}
\end{itemize}
Diagnostic clinique mais en complémentaire :
\begin{itemize}
\item écho en mode B si décollement de rétine/tumeur intraoculaire
\item pour le cristallin artificiel : kératométrie, longeur axiale
\end{itemize}
Étiologies :
\begin{itemize}
\item âge++
\item traumatique (contusion violent, trauma perforant)
\item secondaire à uvéites chroniques (postérieures), myopie forte, rétinopathie
pigmentaires, chir oculaire
\item secondaire à diabète, hypoparathyroïdie
\item secondaire aux corticoïdes locaux/généraux au long cours, à radiothérapie
orbitaire
\item secondaire à dystrophie myotonique de Steinert, trisomie 21
\item congénitales
\end{itemize}
\subsection{Traitement = chir}
\label{sec:org6a497aa}
Anesthésique topique/locorégionale\footnote{Voire générale}, en ambulatoire. Sous dilatation
pupillaire.
Technique = extraction extracapsulaire automatique par phacoémulsification. Puis
collyre anti-inflammatoire+ATB (1 mois).
Correction optique : implant de chambre postérieure (rarement antérieure)
\begin{itemize}
\item monofocal = sphérique (hypermétropie/myopie) ou torique (idem + astigmatisme)
\item multifocaux : corrige vision de loin et de près
\item si implant impossible : lentilles de contact/ ou lunettes (exceptionnel)
\end{itemize}
Indication : quand BAV = 5/10.
Complications :
\begin{itemize}
\item opacification de la capsule postérieure
\item endophtalmie\footnote{Infection intraoculaire sévère.} : à J2-J7. Ttt : ATB local, intravitréenne et générale
\item décollement de la rétine
\item \oe{}dème maculaire : semaines/mois. ttt : anti-inflammatoire
(local/locorégional)
\item kératite bulleuse
\end{itemize}
\section{14 Glaucome chronique}
\label{sec:org692bbbe}
= \gls{GPAO}. Neuropathie optique progressive altérant la fonction/structure.
FR : âge, hypertonie oculaire (\(\ne\) cause !!), ATCD familaux directs, noirs
d'origine africaine, myopie
Physio : perte accélérée des fibres optiques liée à l'âge
\subsection{Formes cliniques :}
\label{sec:org2e97f49}
GPAO à pression élevée (> 21 mmHg) (70\% des pop. occidentales)
\begin{itemize}
\item anomalies de structures visibles cliniquement : papille = \{\dec surface,
hémorragies péripapillaires en flammèches, atrophie péripapillaire de type \(\beta\), \inc
excavation papillaire\}. Rapport de taille entre papilles des 2 yeux > 0.2
\thus suspect
\item autres anomalies de structures : OCT
\item anomalies de foncton : champ visuel mais AV touchée très tardivement
\end{itemize}
GPAO à pression normale (70\% pop. asiatique) : plutôt femmes, migraine, acrosyndromes
DD :
\begin{itemize}
\item hypertonie oculaire : pression intraoculaire > 21mmHg, angle ouvert (gonio),
\(\emptyset\) neuropathie optique. Pas forcément de ttt.
\item glaucomes à angles ouvert secondaires
\item glaucomes par fermeture de l'angle
\item crise aigüe de fermeture de l'angle : douleur, urgence
\item neuropathie optiques non glaucomateuses
\end{itemize}
\subsection{Traitement}
\label{sec:org0d15942}
Dépistage : seulement ATCD familaux de GPAO, myopie, > 40 ans
Ttt : \dec pression intra oculaire
Médicaments :
\begin{itemize}
\item à vie
\item 1ere intention : collyre à base de prostaglandines \footnote{EI : rougeur, irrit. oculaire. Puis iris plus sombre, \inc pousse cils.}(\inc élimination humeur
aqueuse) ou collyre betabloquant
(\dec sécrétion humeur aqueuse)
\item association possible mais \(\le\) 3
\item rarement : acétazolamide par voie générale
\end{itemize}
Trabéculoplastie au laser = photocoagulation de l'angle. Effet modeste, non durable.
Chir : trabéculectomie. Complications (rare) = cataracte, hypotonie précoce
avec décollement choroïdien, infection globe oculaire. Principal échec :
fermeture de la voie par fibrose sous-conjonctivale.
\section{15 Dégénérescence maculaire liée à l'âge}
\label{sec:org8e69b43}
1ere cause de malvoyance après 50 ans (pays industrialisés).
Atteinte de la macula chez > 50 A. Débutante/intermédaire : drusen, altération
pigmentaire, AV normale ou peu \dec. Évoluée : atrophique ou exsudative
Prévalence : 18\% après 50 ans, 37\% à 85 ans.
FR : âge, pop européennes, polymorphisme facteur H du complément, tabac, régime
pauvre en anti-oxydant/riches en (acide gras saturés et cholestérol)
\subsection{Diagnostic}
\label{sec:org55a703b}
\begin{itemize}
\item Mesure AV (loin et près), recherche scotome central ou métamorphopsies (grille d'Amsler)
\item FO (drusen, altération pigmentaires, atrophie épithelium pigmentaire, forme
exsudative [cf \emph{infra} ].
\item OCT : suivi, ou diagnostic si + FO
\item Angiographie
\end{itemize}
\subsection{Formes cliniques}
\label{sec:org2d774e2}
\begin{itemize}
\item débutante : \emph{drusen} = résidus de phagocytose des photorécepteurs. Petites
lésions profondes jaunâtre. OCT
\item atrophique : disparition de l'épithelium pigmentaire. FO : atrophie de
l'épithelium pigmentaire et choroïde. BAV sévère avec scotome centrale
\item exsudative (néovaisseaux sous rétine) : \oe{}dème intrarétinien, hémorragies,
décollement maculaire exsudatif (BAV, métamorphopsies brutales). Sans ttt :
BAV sévère, scotome central définitif. BAV + drusen = urgence
\end{itemize}
\subsection{Ttt}
\label{sec:orgd614e37}
\begin{itemize}
\item débutante : vitamine E, C, zinc, lutéine, zéaxantine
\item atrophique : \(\emptyset\)
\item exsudative : injection d'anti-VEGF : ranibizumab,
aflibercet, bévacizumab. Stoppent néovaisseux, font régresser l'\oe{}dème. 40\%
ont amélioration visuelle à 2 ans.
\end{itemize}
Laser possible mais risque thrombose
\section{16 Occlusions artérielles rétiniennes}
\label{sec:orgf1904fd}
Artères ciliaires postérieure alimente les couches profondes (épithelium
pigmentaire de la rétine, photorécepteurs).
Artère centrale de la rétine = couche internes (cellules bipolaires,
ganglionnaires, fibres optiques).
Arrêt circulatoire \thus lésions définitives en 90min \danger
\subsection{Occlusion de l'artère centrale de la rétine}
\label{sec:org767be22}
Diagnostic :
\begin{itemize}
\item BAV brutale (amaurose transitoires précédentes possibles)
\item Oeil blanc indolore, AV effondrée, mydriase aréflective (RPM direct aboli)
\item FO : dans les heures : oedème ischémique rétinien blanchâtre, tache "rouge
cerise de la macula")
\end{itemize}
Étiologie :
\begin{itemize}
\item embolies : athérome carotidien++, cardiopathie embolinogène, ( fractures des os
long ou emboles tumoraux)
\item thromboses : maladie de Horton (urgence , à rechercher), (maladies de systèmes)
\item troubles coagulation : anomalie primitive, sd antiphospholipides, hyperhomocystéinémie
\end{itemize}
\emph{Très mauvais pronostic fonctionnel} (régression \oe{}dème,
atrophie rétine et papille)
CAT : urgence \danger (fonction visuelle et patho sous-jacente)
\begin{itemize}
\item bilan étio : athérome, carotidien, cardiopathie embolinogène, dissection
carotidienne (si jeune), horton
\item ttt décevant : hypotonisant (acétazolamide IV/per os), vasodilatateur,
anticoagulant si besoin, fibrinolytique
\item bilan cardio
\item Aspirine dans tous les cas. Si jeune, bon état général, ttt max.
\item selon étio : antiagrégant plaquettaire (athérome carotidien), anti-vit K (emboles
cardiaques), endartériectomie
\end{itemize}
\subsection{Occlusion de branche de l'artère centrale de la rétine}
\label{sec:orge1f0f36}
Amputation du CV. BAV possible. FO : \oe{}dème rétinien ischémique en secteur
Évolution : \inc AV en qq semaines, pronostic visuel bon mais amputation
persiste.
Même étio, sauf Horton. Même ttt.
\subsection{Nodules cotonneux}
\label{sec:org6edabad}
Occlusion d'artérioles rétiniennes précapillaire \thus nodules cotonneux =
petites lésions blanches superficielles d'aspect duveteux.
Étio : HTA, diabète, occlusions veineuses rétiniennes, sida, lupus érythémateux
disséminé, périartérite noueuses, embolies graisseuses, pancréatite aigüe, sd Purtscher
\section{17 Occlusions veineuses rétiniennes}
\label{sec:org367216b}
\subsection{Occlusion de la veine centrale de la rétine}
\label{sec:org1b4c7c7}
SF : vision trouble brutalement, BAV variable, \oe{}il blanc indolore
FO :
\begin{itemize}
\item diagnostic = \{\oe{}dème papillaire, veines rétitiennes tortueuses et dilatées,
hémorragies sur la surface rétitienne, nodules cotonneux\}
\item formes non ischémiques (freq) : AV > 2/10, hémorragies en flammèches, ischémie
peu étendue
\item formes ischémiques\footnote{Différence avec l'angiographie fluorescinique} : AV < 1/10, réflexe pupillaire direct diminué, hémorragies
plus volumineuses, en tache
\end{itemize}
\begin{tcolorbox}
Diag facile car tableau typique : BAV brutale, dilatation veineuse, nodules cotonneux,
hémorragies disséminées, oedème papillaire
\end{tcolorbox}
Suivi par OCT
Étiologie inconnue
\begin{itemize}
\item mais > 50 ans avec FR vasc \thus recherche \{tabac, HTA, diabète, hypercholestérolémie, SAS\}, hypertonie oculaire++
\item si < 50 ans, 0 FR ou OVCR bilatérale, chercher anomalie primitive de la
coagulation, sd antiphospholipides, hyperhomocystéinémie, contraception, hyperviscosité
\end{itemize}
Évolution :
\begin{itemize}
\item formes non ischémiques : normalisation AV en 3-6 mois. Sinon : conversion en
forme ischémique, persistance d'un \oe{}dème maculaire cystoïde (BAV permanente !)
\item formes ischémiques :
\begin{itemize}
\item pas de récupération fonctionnelle.
\item Pire complication = néovascularisation irienne \thus progression rapide vers glaucome
\end{itemize}
néovasculaire (3 mois) \thus prévention par photocoagulation panrétinienne
\begin{itemize}
\item néovascularisation prérétiniennes ou précapillaire (hémorragie intravitréenne)
\end{itemize}
\end{itemize}
Ttt
\begin{itemize}
\item formes non ischémique : injection d'anti-VEGF/triamcinolone si \oe{}dème
maculaire cystoïde avec BAV persistante. Surveillance tous les mois
\item formes ischémiques : photocoagulation panrétinienne (PPR) pour éviter glaucome
néovasculaire
\item glaucome néovasculaire : PPR en urgence après hypotonisant local \danger
\end{itemize}
\subsection{Occlusion de branche veineuse rétinienne}
\label{sec:orgf1a3e05}
Identique à OVCR mais territoire plus limité.
Signe du croisement (cf chap 23) \thus > 60 ans, FR d'artériosclérose
Clinique : BAV variable, FO identique OVCR
Évolution favorable en majorité. Défavorable si maculopathie ischémique,
\oe{}dème maculaire persistante, néovaisseaux prérétiniennes \thus hémorragie du
vitré mais \textbf{pas} de \gls{GNV}
Ttt similaire.
\begin{itemize}
\item Si \oe{}dème maculaire persistant : injection intravitréenne
\item photocoagulation maculaire en grille (si \(\ge\) 3 mois, \oe{}dème maculaire
persistante, AV ɇ 5/10)
\item photocoagulation sectorielle
\end{itemize}
\section{18 Pathologies des paupières}
\label{sec:orgdc03251}
Anatomie : plan antérieur cutanéomusculaire, plan postérieur : tarse,
conjonctive (papébrale, cul-de-sac, bulbaire). Sécrétion des larmes par la
glande lacrymale principale, évacuées par les voies lacrymales excrétrices
Fermeture paupière : nerf VII, ouverture par nerf III
\subsection{Pathologies}
\label{sec:org1b5bdfb}
Orgelet : furoncle du bord libre, centré sur follicule du cil.
\begin{itemize}
\item infection bactérienne (\bact{dore}), tuméfaction rouge autour point blanc
\item ttt : ATB 8 jour
\end{itemize}
Chalazion : granulome inflammatoire sur glande de Meibomius (tarse)
\begin{itemize}
\item tuméfaction douloureuses
\item Ttt : pommade corticoïde locale, massage des paupières. Éventuellement
incision
\end{itemize}
\subsection{Autres}
\label{sec:org3258698}
Malformation palpébrales :
\begin{itemize}
\item entropion : bascule vers l'intérieur. Sénile, cicatriciel
\item ectropion : sénile, cicatriciel, paralytique
\item ptosis : neurogène, myogène, sénile, traumatique
\item lagophtalmie (inoclusion palpébrale) : anesthésie générale, coma prolongé,
paralysie faciale
\end{itemize}
Tumeurs palpébrales :
\begin{itemize}
\item bénignes : papillome, hydrocystome (kyste lacrymal), xanthélesmas (dépôts
cholestérol). Ttt : chir
\item malignes :
\begin{itemize}
\item épithéliale : carcinome basocellulaire surtout (nodule perlé,
télangiectasise; peut menacer globe oculaire, pas de métastases), carcinome
épidermoide (métastase)
\item mélaniques : pronostic peut être effroyable. suspecter si tuméfaction
(pigmentée) des paupières
\item carcinomes sébacés, lymphomes MALT
\end{itemize}
\end{itemize}
Trauma : vérifier septum orbitaire, globe oculaire, canalicules lacrymaux
arrachés (urgence )
\section{19 SEP}
\label{sec:orgbdad651}
Névrite optique rétrobulbaire \(\in\) SEP (20\% = inaugurale). Atteint adulte \(\in\)
[20,40]ans, surtout \female
Neuropathie optique :
\begin{itemize}
\item BAV variable sur qq jours, douleurs rétro oculaires (80\%)
\item pupille de Marcus gunn (dilatation paradoxale). Si inflammation intraoculaire,
penser syphilis, sarcoïdose
\item Complémentaire :
\begin{itemize}
\item examen du CV : scotome (caeco)central.
\item dyschromatopsie d'axe rouge-vert
\item IRM encéphalique systématique (SEP)
\end{itemize}
\item régression en 3-6 mois. Risque de SEP = 50\% à 15 ans (75\% si lésions
encéphaliques à l'IRM). Phénomène d'Uhthoff possible\footnote{BAV transitoire quand température \inc}
\item ne pas confondre avec neuromyélite de Devic ! Inflammation (\(\ne\) auto-immune) du
SNC, BAV profonde rapide. IRM : pas d'inflammation cérébrale mais médullaire
\item ttt : corticothérapie parentérale 3-5j (1g/j) puis oral court (11 j). Retarde
un nouvel épisde. Si SEP, ttt de fond (immunomodulateur [interférons, acétate
de glatiramère] ou natalizumab, fingolimod)
\item pronostic fonctionnel souvent favorable
\item DD : autres neuropathies optiques
\end{itemize}
Autres :
\begin{itemize}
\item oculomotrice : paralysie du VI, internucléaire (penser SEP si bilatérale chez jeune)\footnote{Pas d'adduction de l'\oe{}il atteint mais adduction des yeux OK à la
convergence. Nystagmus pendulaire en abduction de l'\oe{}il sain !}
\item nystagmus : 1/3 patient avec SEP > 5 ans
\item périphlibite rétiniennes (5\%)
\end{itemize}
\section{20 Neuropathie optique ischémique antérieure}
\label{sec:org265270c}
Ischémie de la tête du nerf optique (artères ciliaire postiérieures)
Diagnostic clinique :
\begin{itemize}
\item BAV unilatérale brutale indolore
\item AV variable, \dec RPM direct, FO = \oe{}dème papillaire++, papille souvent
pâle, hémorragie en flammèche sur le bord papillaire
\item complémentaire : examen CV++ = \{déficit fasciculaire, altitudinal\},
angiographique du fond d'\oe{}il
\end{itemize}
Étiologie :
\begin{itemize}
\item maladie de Horton = urgence (cécité bilatérale définitive) \thus
\begin{itemize}
\item signes systémique, modif artères temporale
\item signes oculaire : amaurose fugace, défaut de remplissage choroïdien (angiographie)
\item bio : VS \inc (non systématique), CRP \inc
\item biopsie de l'artère temporale (ne doit pas retarder les soins !)
\end{itemize}
\item artériosclérose (fréq) : FR (tabac, HTA, diabète, hypercholestérolémie)
\end{itemize}
Évolution : résorbtion de l'\oe{}dème en 6-8 semaines (atrophie). Pas de récup
visuelle. Bilatéralisation possible en qq jours \danger
DD : causes d'\oe{}dème papillaire (HTIC)
Ttt :
\begin{itemize}
\item artéritique = urgence ! Corticothérapie générale à forte dose puis per os
1mg/kg/j
\item non artéritique : pas de ttt efficace
\end{itemize}
\section{21 Rétinopathie diabétique}
\label{sec:org3ee8da8}
30\% diabétique en ont une. Diabète 1 : 90\% après 20 ans. Diabète 2 : 60\% à 15
ans
Physiopatho : hyperglycémie \thus \{accumulation sorbitol, glycation, stress
oxydatif\} \thus \{inflammation, activation rénine-angiotensine, modif flux
sanguin rétinien, production VEGF\} puis
\begin{itemize}
\item occlusion capillaire et néovascularisation
\item \oe{}dème maculaire
\end{itemize}
\subsection{Diagnostic}
\label{sec:org4061a34}
Photographie du FO = référence et dépistage
\begin{itemize}
\item microanévrisme rétitiens : dilatations punctiformes rouges (postérieure)
\item hémorragie rétiniennes punctiformes
\item nodules cotonneux
\item signes d'ischémie : hémorragies intrarétiniennes "en taches" ou en flammèche, anomalies
microvasculaire intrarétinienne, dilatations veineuses "en chapelet",
néovaisseaux prérétiniens et précapillaires, hémorragie prérétiniennes/intravitréennes
\item complications : hémorragie intravitréenne, décollement de la rétine \emph{par
traction}, néovascularisation irienne (\thus glaucome néovasculaire !)
\item signes maculaires : \oe{}dème maculaire (cystoïde), exsudats lipidiques
(souvent en couronne)
\end{itemize}
Complémentaire : OCT pour diagnostic et suivi \oe{}dème maculaire, echo en mode B
pour décollement de rétine par traction
\subsection{Dépistage RD}
\label{sec:org9524e43}
Diabète 1 : photo FO à la découverte puis surveillance annuelle
\begin{itemize}
\item enfant: pas avant 10 ans
\item grossesse : avant puis tous les 3 mois (tous les mois si RD !)
\end{itemize}
Diabète 2 : dès découverte
Surveillance :
\begin{itemize}
\item \(\emptyset\) RD on non proliférante minime : annuelle
\item sinon tous 4 à 6 mois
\item renforcé si puberté, adolescence, si équilibrage trop rapide de la glycémie,
chir bariatrique, diabète ancien mal équilibré, chir de la cataracte,
\oe{}dème maculaire
\end{itemize}
Classification :
\begin{itemize}
\item \(\emptyset\) RD
\item RD non proliférante : minime, modérée, sévère (hémorragie rétiniennes dans 4
quadrants ou dilatations veineuses 2 quadrants ou AMIR 1 quadrant)
\item RD proliférante (néovaisseaux): minime, sévère, compliquée (décollement de
rétine par traction, \gls{GNV})
\end{itemize}
Progression lente, aggravations rapides possibles. \danger prolifération néovasc
peut donner cécité
\subsection{Traitement}
\label{sec:org6231bed}
Médical :
\begin{itemize}
\item équilibre glycémique et hypertension pour 2 diabètes !
\item pas de ttt médicamenteux
\end{itemize}
RD proliférante
\begin{itemize}
\item photocoagulation panrétinienne : régression dans 90\%. Indication : RD
proliférante ou (RD non proliférante sévère si grossesse, sujet jeune
diabétique 1 avec normalisation rapide glycémie, chir cataracte)
\item injection intravitréenne anti-VEGF (pour néovasc. iridienne, glaucome
néovasculaire)
\item chir si RD proliférante avec hémorragie intravitréenne persistante/décollement
de rétine tractionnel
\end{itemize}
\OE{}dème maculaire
\begin{itemize}
\item photocoagulation au laser si exsudats lipidiques ou liquides
\item injection anti-VEGF mensuelle. Dexaméthasone retard possible mais cataracte,
risque d'hypertonie oculaire (30\%)
\end{itemize}
\section{22 Orbitopathie dysthyroïdienne}
\label{sec:org6339015}
Surtout maladie de Basedow (ou thyroïdite auto-immune d'Hashimoto
Thyrotoxicose : \{palpitations, tachycardie\}, \{nervosité, tremblement, insomnie\},
thermophobie, \{amaigrissement, fatigue\}
Classification :
\begin{itemize}
\item gravité = NOSPECS\footnote{No sign, Only lid retraction, Soft tissues, Proptosis \(\ge\)
3mm, Extraocular muscle, Corneal}
\item inflammation = CAS (clinical activity score)
\end{itemize}
Manifestation :
\begin{itemize}
\item exophtalmie : bilatérale (75\%), axile, non pulsatile, réductible, indolore,
> 21 mm
\item rétraction paupière, asynergie oculopalpébrale vers le bas, \dec fréquence
clignement
\item trouble oculomoteur : myosite \thus diplopie
\end{itemize}
Complications :
\begin{itemize}
\item cornée : kératite, peforation
\item neuropathie optique compressive (3\%) \thus méthylprednisolone forte dose ou
décompression rapide !
\end{itemize}
Complémentaire : TSH effondrée (hyperthyroïdie), scanner et IRM pour conforter,
\{pupille, champ visuel, couleurs, PEV\}
DD : infection orbitaire, fistules artériocaverneuses, tumeurs, orbitopathies
inflammatoires
Traitement
\begin{itemize}
\item médical :
\begin{itemize}
\item traiter thyrotoxicose (\danger iode radioactif peut aggraver orbitopathie) arrêt tabac, ttt locaux (symptômes), sélénium si forme modérée
\item CAS \(\ge\) 3 \thus anti-inflammatoire (méthylprednisolone)
\end{itemize}
\item chir : décompression orbitaire, muscles oculomoteurs, paupières
\end{itemize}
\section{23 Rétinopathie et choroïdopathie hypertensive}
\label{sec:orgbfd2b06}
Bien différencier modifications liée à l'HTA (réversible par ttt de l'HTA) et
celles irréversibles liées à l'artériosclérose
\inc Pa \thus vasoconstriction artérieur active (autorégulation)
\subsection{Rétinopathie hypertensive}
\label{sec:org69a5704}
AV normale. Signes oculaires seulement si sévère :
\begin{itemize}
\item barrière hématorétinienne rompue \thus hémorragies rétiniennes superficielles,
\oe{}dème maculaire et exsudat secs, \oe{}dème papillaire
\item occlusion artérioles précapillaires \thus nodules cotonneux, hémorragies
rétiniennes profondes
\item hémorragies en flammèches péripapillaire (superficielles) ou rondes sur toute
la rétine (profondes)
\end{itemize}
\thus non spécifiques mais évocateurs d'HTA si associés. Pas de BAV
\subsection{Choroïdopathie hypertensive}
\label{sec:orgf71b23a}
Pas d'autorégulation pour les vaisseaux choroïdiens. Occlusion \thus ischémie et
nécrose de l'épithelium pigmentaire. cicatrices en petite taches pigmentées
("d'Elschnig").
Formes plus sévères : décollement de rétine exsudatif (post) avec
BAV. Normalisation avec ttt
\subsection{Artériosclérose}
\label{sec:org2ab2842}
Lésions chroniques irréversibles mais asymptomatiques :
\begin{itemize}
\item accentuation du reflet artériolaire
\item signe du croisement\footnote{Veine "écrasée" sur le croisement avec l'artère, dilatée en amont}
\end{itemize}
Classification de Kirkendall
\begin{itemize}
\item rétinopathie hypertensive : I (rétrécissement artériel sévère et disséminé),
II (idem + hémorragies rétiniennes, exsudats secs, nodules cotonneux), III
(idem + \oe{}dème papillaire
\item artériosclérose : I (croisement), II (idem plus rétrécissement marqué), III
(idem plus occlusion de branche)
\end{itemize}
\printglossaries
\end{document}
Postural Motricité fine Langage Social Alimentation Sommeil
------------ -------------------------- --------------------------------------- ----------------------------------- ------------------------------ ---------------------------
2 mois Soulève la tête Serre le doigt Réponse à la sollicitation Sourire réponse Dort 18h/j
Suit des yeux
3-4 mois **Tenue de tête droite** Joue avec les mains Vocalise Rit aux éclats 15h/j
4 repas/j
6 mois Assis avec appui Passe un objet d\'une main à l\'autre Babillage (\"ma-ma\") Reconnaît un visage familier
8 mois **Assis sans appui** **Pince pouce-index** **Répète syllabe** **Réagit à son prénom**
Debout avec appui Peur de l\'étranger
12-18 mois Marche seul Autonomie verre-cuillère \"non\" Joue avec d\'autres enfants 2 siestes (12mois)
Empile 2 cubes
24 mois Court Trait 3 mots en phrase Consigne simple Propre le jour
(accidents possibles)
Début de propreté la nuit
36 mois Tricycle Rond Dit une petite histoire Se lave les mains seul
Monte les escaliers
4 ans Appui monopodal Carré Raconte des histoires 13-14h/j
Additions simples
5-6 ans Vélo sans les Triangle (5 ans) Dessus, dessous, devant, derrière
petites roues Losange (6 ans) Après-midi, soir
\begin{figure}[ht]
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/alveolaire1.png}
\caption{Image en "nuage"}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/alveolaire2.png}
\caption{Bronchogramme aérique}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/alveolaire3.png}
\caption{Bronchogramme aérique}
\end{subfigure}
\caption{Alvéolaire = diffus et avec bronchogramme aérique}
\end{figure}
\begin{figure}[ht]
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/interstitiel1.png}
\caption{réseaux de lignes ("réticulaire" )}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/interstitiel2.png}
\caption{Nodules}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/interstitiel3.png}
\caption{Rétulaire + nodulaire}
\end{subfigure}
\caption{Interstitel = sous forme de petits "amas", avec 3 formes possibles}
\end{figure}
\begin{figure}[ht]
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_opacite.png}
\caption{Flèche blanche}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_opacite2.png}
\caption{Flèche blanche}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_opacite3.png}
\caption{Flèche noire}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_opacite3.png}
\caption{Flèche noire (oui, ça peut donner des petits trucs comme ça !)}
\end{subfigure}
\caption{Signe 1: opacités}
\end{figure}
\begin{figure}[ht]
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_trachee.png}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_trachee2.png}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_trachee3.png}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_trachee3.png}
\end{subfigure}
\caption{Signe 2 : l'atélectaise attire vers elle les structures "déplaceables". Ça veut dire la trachée (flèches noires sur les 3 figures)}
\end{figure}
\begin{figure}[ht]
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/normal.png}
\caption{Radio normale}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_coeur.png}
\caption{Coeur à gauche}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_coeur2.png}
\caption{Coeur à droite}
\end{subfigure}
\caption{Signe 2 (suite) : ça peut aussi déplacer le coeur.}
\end{figure}
\begin{figure}[ht]
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/normal.png}
\caption{Radio normale}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_diaphragme.png}
\caption{diaphragme gauche remonté}
\end{subfigure}
\caption{Signe 2 (suite) : ça peut faire remoter le diaphragme.}
\end{figure}
\begin{figure}[ht]
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/atelectasie_trachee2.png}
\caption{Radio normale}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{./img/pleuresie.png}
\caption{diaphragme gauche remonté}
\end{subfigure}
\caption{ À l'ECN, il faut se rappeler qu'un poumon blanc ne veut pas forcément dire une pleurésie. Sauras-tu reconnaître l'atélectasie de la pleurésie sur ces 2 images ?}
\end{figure}
```
```
```{=latex}
```
```{=latex}
```
```{=latex}
```
```{=latex}
```{=latex}
C\'est une perte de volume d\'une partie du poumon (ou du poumon tout
entier !). Donc au lieu d\'apparaître noir, ça appaîtra blanc (opacité)
```
# Atélectasie
```
```{=latex}
```{=latex}
# Syndrome alvéolaire ou interstitiel ?
Notes sur le stage de réa
# SDRA
FiO2 = proportion d\'oxygène dans ce que respire le patient. Air ambiant
= 0.20. Ne pas trop augmenter pour éviter effets nocifs de l\'oxygène
Gravite selon PaO2 / FiO2 :
- 200-300 mmHg = léger
- 100-200 = modéré
- ≤ 100 = sévère
Traitement
1. Curare + ventilation mécanique : le curare relâche les muscles
striés =\> facilite l\'intubation.
Permet également une diminution de l\'inflammation, de la mortalité et
une augmentation de l\'oxygénation (collège de réa)
1. Monoxyde d\'azote inhalé : relaxe fibre musculaire =\> peut
améliorer oxygénation
2. ECMO = poumon artificiel (étude en cours)
# Endocrino
## Cortisol
- minimal à minuit, max à 8h. Idem pour ACTH
- Acromégalie : test de freinage au glucose. Si diabétique, suivre
cycle de GH sur
3 ans (≠ gold standard, simplement un argument !)
Acanthosis nigricans : monte insulino-résistance
## Antidiabétiques oraux
1ere intention : metformine 2eme intention : metformine + glinides ou
victoza (GLP1) 2eme intention (HAS) : metformine + sulfamides
hypoglycémiants (moins chers ?)
NB : inhib de DPP-4 et analogue de GLP1 sont redondants ! Ne pas
combiner...
## Insuline
- 50% basal 50% en rapide (sur les 3 repas) avec total = 0.5\*poids si
DT2, 0.8\*poids si DT1
- Basal bolus ou novomix (semilente + rapide) 2x / jour selon les
services
## Complications
3 stages (par gravité croissante) : hyperglycémique, cétosique,
acido-cétosique
TTT : insuline par IV avec contrôle gylcémie toutes les heures, contrôle
cétoné Adaptation l\'insuline sur la cétonémie+++ (pas la glycémie qui
est trop rapide à se corriger) Seuil : \> 3mmol/L = insuilen IV. Patho
si \> 0.5mmol/L Si besoin, ajouter glucose (si glycémie basse)
## Objectifs
- standards : 0.8-1.3g/L avan repas et 1.3-1.8 =\> risque d\'hypo mais
évite complications long terme =\> sujet jeunes
- élargies : 1-1.5 avantrepas, 1.5-2g/L sinon
## Notes
Si coronaropathie, important de baisser le diabète (athérome)
## Examen clinique
### ATCD
chir, med, gynéco, familial, perso
### Ttt
habituel, allergies (dernier repas)
### MDV
- profession, main dominante, sport
- toxiques, alcool, tabac, viral
- conditions de vie, autonome
### HDM
- anamnèse: déclenché par ? favorisé par ?
- clinique : quantifier, signes
- complications, retentissement, fièvre, AEG
### Examen physique
- constantes : TA, températeure, FR, FC, sat, poids, diurèse, CS
- hémodynamique,
- repi
- neuro
- infectieux
### Endocrino
- poids, taille, IMC, tour taille
- visag, répartition graisses, xanthome
- thyroïde, profil + face, tour cou, palpation
### Diabétique
1. Clinique
- fonctionnel : angor, AIT, claudication HTA, vision
- FR CV : ATCD, tabac, obésité
- PA couché et debout
- pieds : pouls, cutané, TRC, réflexe achilléen, sensibilité
superficiell, monofilament
- neuro
- pouls, souffle vasc
- bouches, sinus
2. Histoire
- découverte ?
- histoire du traitement
- DG (macrosome \> 4kg)
- suivi des complications : ophtalmo (FO), cardio (doppler MI,
TSA), rein
- poids, alim
- demander carnet glycémie, si autonome
### CS pré-chir bariatrique,
- ATCD, ttt, allergie,
- Grossesse, DG (macrosome \> 4kg, ttt)
- ATCD familiaux
- Histoire du poids
- Activié physique
- Comportement alimentaire (régimes précédents)
- SAOS
- Acanthosis nigricans
# Généraliste
## [DONE]{.done .DONE} J4 {#j4}
page 1 + 2 faite
## [TODO]{.todo .TODO} J5 {#j5}
## [TODO]{.todo .TODO} J6 en cours {#j6-en-cours}
## [TODO]{.todo .TODO} J7 à reprendre {#j7-à-reprendre}
TVP : rupture de kyste poplité
## [TODO]{.todo .TODO} J8 {#j8}
TVP : rupture de kyste poplité
## Dépistage
- Cancer colorectal :
- risque modéré (\> 50A, asymptomatique) = test immuno de sang
dans le selles tous les 2 ans ± coloscopie.
- risque élevé : coloscopie tous les 3 à 5 ans selon ATCD
## Examen clinique
### Hygroma
- Genou++, coude : fréquent si sollicitation professionnelle
- Douleur local, aspect inflammatoire (chaud), épanchement liquidient
palpation
- Repos, glace, anti-inflammatoire
### Réflexes archaïques (doivent avoir disparus à 4 mois)
- Moro: extension cervical (en arrière) rapide =\> extension +
abduction des bras
- stimulation palmaire =\> agrippement
- frottement des pieds =\> ébauche de marche
- succion
- stimulation péribuccal =\> tête tournée vers stimulation
- allongement croisé : stimulation plante de pied =\> flexion et
extension controlatérale
### Critères d\'Ottawa
Radio de cheville si douleur malléolaire **et**
- impossible de marcher \> 4 pas immédiatement et à l\'examen
- **ou** sensibilité 6cm distaux tibia
- **ou** sensibilité 6cm distaux
### Dorsalgie/cervicalgie
Palper épineuses (signe de la sonnette), muscles paravertébreux
### Déchirure musculaire
Douleur brutale ± hématome, voussure palpation
### Douleur pouce
Tendinite de De Quervain ? Signe de DQ = pathognomonique Rhizarthrose
## Examens
- Fracture de fatigue : scinti/TDM/IRM ou RX différée
## Médicaments
Acide fusidique : impétigo Airomir : crise d\'asthme Antadys :
rhumatismes inflammatoires, dysménorrhées(AINS) Apranax = *naproxène* :
AINS Atarax = anxiolytique Auricularum = *dexaméthasone* + *ATB* : otite
externe bactérienne, otite chronique Avodart = *dutasteride* : HBP
Bedelix : symptomes des manifestation fonctionnelles intestinale Bilaska
: rhino-conjonctivite allergique Bipreterax = *périndopril* (IEC) +
*indapamide* (diurétique) : HTA Celebrex : arthrose, PR, spondylarthrite
ankylosante Cerulyse = *xylène* : bouchons cérumène Ciclopirox =
antifongique : intertrigo, onychomycoses... Ciloxadex = *ofloxacine* +
*dexaméthasone* : otite aigüe externe Clindamycine = *macrolide*
Coversyl = *périndopril* Daily = contraceptif estroprogestatif Duplavin
= aspirine + clopidogrel : prévention secondaire chez SCA ST-, IDM ST+
Ezetimibe : +statine pour hypecholestérolémie primaire Flector =
*diclofénac* : tendinite (AINS) Fluinidone = *previscan* (AVK) Flécaïne
: TV Gibiter = *corticoïde* + *BDLA* pour l\'asthme Hamamélis :
hémorroïdes, insuf. veinolymphatiques Hamamélis : hémorroidies, insuf.
veinolymphatique (phytothérapie) Ibufetum = AINS en gel Izalgie =
*opium* + *paracétamol* (\> Lamaline) Kétoconazole =: antifongique :
dermite séborrhéqiue, candidoses Lasilix = *furosémide* = diurétique de
l\'anse Lumirelax = relaxant musculaire Micardis = *telmisartan* (ARA
II) Norset = *mirtazapine* : épisodes dépressifs majeurs Norset =
*mirtazapine* : épisodes dépressifs majeurs Optimizette = contraceptif
progestatif Pradaxa = *dabigatran* Prolia = *dénosumab* : ostéoporose (5
ans puis 1 an biphosphonates) Salbutamol : asthme, BPCO Smecta =
*diosmectite* : adsorbant intestinal (diarrhée) Spasfon : troubles
fonctionnels digestifs Spedra : dysfonction érectile Stresam :
anxiolytique Structocal = calcium + vitamine D3 Tanganil =
antivertigineux Tiorfan = *racecadtril* : complément des diarrhées aigüe
de l\'adulte Ténormine = *aténolol* Uvédose : carence vitamine d
Vogalène = *métopimazine* : antiémétique
## Orientation
- Sensation faiblesse persistante : cardio (rythme, conduction),
infection, thyroïde, pulmonaire
## Prévention risques foetaux
- Toxoplasmose : sérologie **systématique** \< 10SA =\> si négatif,
contrôle **mensuel** !
- Rubéole : sérologie **systématique** \< 10SA
- Syphilis : sérologie **systématique** \< 10SA
- VHB : sérologie **systématique** 6eme mois
- VIH
- streptocoque : prélèvement **systématique** 36-38SA
## Suivi
## Vaccins
Diphtérie, tétanos, coqueluche, polio =\> 2M, 4M et rappel à 11M et 6A
puis 11A (vaccin différent)
- Tétravac, Repevac (seulement après 3A)
Haemophilus influenzae : 2M, 4M, 11M Pneumocoque, hépatite B : idem
Ménigocoque : 5M et 12M Rougeole, oreillons, rubéole :12M et 16-18M
# Médecine nucléaire
Scinti
Isotope Vecteur
--------------------- ---------------------- ----------------------------
Technetium HDMP (diphosphonate) os
Technetium albumine perfusion pulmonaire
Technetium Technegas (carbone) ventilation pulmonaire
Technetium DMSA masse rénale fonctionnelle
Technetium HMPAO perfusion cérébrale
Iode 0 thyroïde
Indium (Octréoscan) Pentétréotide tumeurs neuroendocrines
TEP
------ ---------------
18-F FDG
18-F FCH (choline)
18-F FDOpa
------ ---------------
## Cours
### Médicaments radiopharmaceutiques : constitués d\'un radio-élement (émet le rayonnement) + un vecteur (se fixe aux organes)
- technétium : scintigraphie++. Produit directement dans le service
- F18-fluorodésoxyglucose : grande sensibilité pour la détection de
nombreux cancers (sauf prostate), certaines maladies inflammatoires
ou infectieuses
- analogues de la somatostatine + gallium 68 : certaines tumeurs
endocrines
- bisphosphonates : métastases osseuses
- Radiothérapie : hyperthyroïdes, métatastes osseuses des adénomes
prostatique
Choix du radio-élement
- scintigraphie : émissions de \*photons *γ*\*
- TEP : émissions de **positons** (électrons avec charge positive).
### Principe technique :
1. Détection des photons *γ*1. Après émissions, ils arrivent sur un
cristal. Leur énergie est transférée aux
électrons du cristal, qui émet des photons lumineux
(\"scintillation\") dans toutes les direction.
1. Conversion en signal électrique et amplification dans des tubes
photomultiplicateurs
2. NB: Les premiers photons γ peuvent interagir avec les tissus
biologiques et diffuser d\'autres photons (source d\'erreur) =\>
filtrage
3. NB: Dans l\'étape 1, comment savoir d\'où vient le photon
**lumineux** si émis dans des direction aléatoire ? Le nombre de
photons reçus est inversement proportionnel à la distance de la
source =\> comparaison des différents tubes
*Comment retrouver la position du photon initial depuis le cristal ?
Collimation physique (scinti) ou électronique (TEP)*
2. Gamma caméra : collimation physique
- canaux parallèle : filtre les photons arrivant
perpendiculairement au cristal
- \"pinhole\" : bonne résolution mais mauvaise sensibilité =\>
Thyroïde
- Il faut trouver un compromis entre résolution spatiale et
sensibilité
- Acquisition planaire ou tomoscintgraphie (le détecteur
tourne autour du patient, 15min donc sur un seul organe...)
3. TEP
- Annihilation d\'un position génère une paire de photons gamma
partant à 180°.
Grâce à des détecteurs en \"couronne\", détection simultanée (enfin
presque, fenêtre de 10ns)
- Contrairement à la scinti, plusieurs cristaux sur chaque
récepteur
- Meilleure sensibilité et résolution spatiale que la scinti
- souvent combiné à une TDM en même temps
4. Correction des biais de quantification
Imprécise en tomoscintigraphie, meilleure en TEP
5. Évolution
- Cristaux semi-conducteur pour gamma-caméra : améliore
sensibilité et résolution spatiale
- Tube PM =\> photodiodes plus compact pour TEP
## Stage
Choline : adénome parathyroïdien Scinti : utile pour algodystrophie
Ganglion sentinelle : opération du sein++, pour aider le chirurgien à
repérer le ganglion (injection la veille/le jour même)
### Cancers
1. Prostate
- Scinti : bilan d\'extension de K de la prostate
- Classif selon PSA et score Gleason (histo), mais cinétique
importante
- Méta = os, ganglions de l\'abdomen et du bassin
### Lymphome
Classif d\'Ann Arbor : I= 1 territoire, II = N territoires du même côté,
III = sus et sous-diaphragmatique, IV = viscérale
### Scinti thyroide
- Basedow : diffus
- De Quervain : pas de fixation
- Hashimoto : hyperthyroïde puis hypothyroïde : fixation faible
hétérogène
### Scinti cardiaque
- Effort et repos, sans et avec correction à chaque fois (sert à
corriger
l\'atténuation corporelle)
- Déficit réversible = ischémie, sinon nécrose
## ECNI
Scinti thyroïdienne, éventuellement pulmonaire peuvent tomber
# Gynéco
- Diabète gestationnel :
déclenchement pour éviter macrosomie et d\'aggraver le diabète (à vérif)
- HELLP (completer)
- SHAG
- GUE : methotrexate possible (sauf si à la base des trompes)
# Urgences
Douleurs abdo : urgence = torsion testiculaire (1 testicule remonté,
voire gonglé et rouge). Y penser même sans douleurs...
# Gardes
## 1. Urgences : ABCDE
<https://www.resus.org.uk/resuscitation-guidelines/abcde-approach/>
[WHO](https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=12&ved=2ahUKEwjqre3gkezkAhWPohQKHWVxAygQFjALegQIBBAC&url=https%3A%2F%2Fwww.who.int%2Femergencycare%2Fpublications%2FBEC_ABCDE_Approach_2018a.pdf&usg=AOvVaw3Cu1L7fniTpCUwq9PwOeap)
Éliminer les risques vitaux en 30s
### A : airway
[corps étranger, brûlure, anaphylaxis, trauma ?]{.underline} Peux parler
?
- oui :
- difficilement ? cherche obstruction, fluide
- Corps étranger : si visible, enlever. Si toux, encourager.
Sinon frappes dans le dos (par 5)
- anaphylaxie : adrénalie IM
- non : dégager voies respi
### B : breathing
[pneumothorax, overdose, asthme, BPCO ?]{.underline} Très rapide, très
lent ? Muscles accessoires, tirage, balancement thoraco-abdominal
### C : circulation
[0 pouls, chock, hémorragie sévère, tamponnande cardiaque ?]{.underline}
Perfusion : extrémités froides, TRC \> 2s, hypotension, tachypnée,
tachycardie, pas de pouls Saignement ? Poitrine, abdomen, fractures
Tamponnade ? hypotension, veines du cous, bruits du coeur étouffés
Pression sanguine
### D : disability
[Hypoglycémie, HTIC, convulsion ?]{.underline} Conscient ? Glasgow
Hypoglycémie ? Pupille ?
- myosis : opiodes ? =\> naloxone
- inégales : HTIC ? lever la tête
- sinon : trauma ?
Convulsion ?
### E : exposure
Autres blessures, réactions allergiques Protéger de l\'hypothermie,
enlever vêtements/bijous \"constricteurs\"
## 2. Si non, reste de l\'examen
### Examen clinique
- Genou : tiroir antérieur postérieur, laxité latéral, épanchement ?
(bilatéral !!), Zohlen, amplitude passive
- plaie : infectée, oedème, lymphangite (trainée rouge ?)
### Enfant
- examen de la bouche : bras en arrière de la tête
- trauma crânien : si a pleuré, pas de perte de conscience !
Surveillance simple à domicile si pas de point d\'appel. Les parents
doivent le réveiller régulièrement et surveiller : vomissements,
céphalées, troubles cognitifs....
# Footnotes
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\begin{document}
\tableofcontents
\section{Endocrino}
\label{sec:org7ea4546}
\subsection{Cortisol}
\label{sec:org8ed4be4}
\begin{itemize}
\item minimal à minuit, max à 8h. Idem pour ACTH
\item Acromégalie : test de freinage au glucose. Si diabétique, suivre cycle de GH sur
\end{itemize}
3 ans (\(\ne\) gold standard, simplement un argument !)
Acanthosis nigricans : monte insulino-résistance
\subsection{Antidiabétiques oraux}
\label{sec:orge555e85}
1ere intention : metformine
2eme intention : metformine + glinides ou victoza (GLP1)
2eme intention (HAS) : metformine + sulfamides hypoglycémiants (moins chers ?)
NB : inhib de DPP-4 et analogue de GLP1 sont redondants ! Ne pas combiner\ldots{}
\subsection{Insuline}
\label{sec:org6982df6}
\begin{itemize}
\item 50\% basal 50\% en rapide (sur les 3 repas) avec total = 0.5*poids si DT2, 0.8*poids si DT1
\item Basal bolus ou novomix (semilente + rapide) 2x / jour selon les services
\end{itemize}
\subsection{Complications}
\label{sec:org17418b2}
3 stages (par gravité croissante) : hyperglycémique, cétosique, acido-cétosique
TTT : insuline par IV avec contrôle gylcémie toutes les heures, contrôle cétoné
Adaptation l'insuline sur la cétonémie+++ (pas la glycémie qui est trop rapide à se corriger)
Seuil : > 3mmol/L = insuilen IV. Patho si > 0.5mmol/L
Si besoin, ajouter glucose (si glycémie basse)
\subsection{Objectifs}
\label{sec:orgb5ecd7f}
\begin{itemize}
\item standards : 0.8-1.3g/L avan repas et 1.3-1.8 => risque d'hypo mais évite
complications long terme => sujet jeunes
\item élargies : 1-1.5 avantrepas, 1.5-2g/L sinon
\end{itemize}
\subsection{Notes}
\label{sec:org8faa4ab}
Si coronaropathie, important de baisser le diabète (athérome)
\subsection{Examen clinique}
\label{sec:org78b206c}
\subsubsection{ATCD}
\label{sec:org3bd873c}
chir, med, gynéco, familial, perso
\subsubsection{Ttt}
\label{sec:orgd272fd2}
habituel, allergies (dernier repas)
\subsubsection{MDV}
\label{sec:org5f660a2}
\begin{itemize}
\item profession, main dominante, sport
\item toxiques, alcool, tabac, viral
\item conditions de vie, autonome
\end{itemize}
\subsubsection{HDM}
\label{sec:org15728f8}
\begin{itemize}
\item anamnèse: déclenché par ? favorisé par ?
\item clinique : quantifier, signes
\item complications, retentissement, fièvre, AEG
\end{itemize}
\subsubsection{Examen physique}
\label{sec:org338d661}
\begin{itemize}
\item constantes : TA, températeure, FR, FC, sat, poids, diurèse, CS
\item hémodynamique,
\item repi
\item neuro
\item infectieux
\end{itemize}
\subsubsection{Endocrino}
\label{sec:org964e22b}
\begin{itemize}
\item poids, taille, IMC, tour taille
\item visag, répartition graisses, xanthome
\item thyroïde, profil + face, tour cou, palpation
\end{itemize}
\subsubsection{Diabétique}
\label{sec:org840a4f2}
\begin{enumerate}
\item Clinique
\label{sec:org60ddc63}
\begin{itemize}
\item fonctionnel : angor, AIT, claudication HTA, vision
\item FR CV : ATCD, tabac, obésité
\item PA couché et debout
\item pieds : pouls, cutané, TRC, réflexe achilléen, sensibilité superficiell,
monofilament
\item neuro
\item pouls, souffle vasc
\item bouches, sinus
\end{itemize}
\item Histoire
\label{sec:org18d1fe3}
\begin{itemize}
\item découverte ?
\item histoire du traitement
\item DG (macrosome > 4kg)
\item suivi des complications : ophtalmo (FO), cardio (doppler MI, TSA), rein
\item poids, alim
\item demander carnet glycémie, si autonome
\end{itemize}
\end{enumerate}
\subsubsection{CS pré-chir bariatrique,}
\label{sec:org5000b09}
\begin{itemize}
\item ATCD, ttt, allergie,
\item Grossesse, DG (macrosome > 4kg, ttt)
\item ATCD familiaux
\item Histoire du poids
\item Activié physique
\item Comportement alimentaire (régimes précédents)
\item SAOS
\item Acanthosis nigricans
\end{itemize}
\section{Généraliste}
\label{sec:orgb9426bd}
\subsection{{\bfseries\sffamily DONE} J4}
\label{sec:orgc478290}
page 1 + 2 faite
\subsection{{\bfseries\sffamily TODO} J5}
\label{sec:org0397808}
\subsection{{\bfseries\sffamily TODO} J6 en cours}
\label{sec:org65bb54e}
\subsection{{\bfseries\sffamily TODO} J7 à reprendre}
\label{sec:orgcd24470}
TVP : rupture de kyste poplité
\subsection{{\bfseries\sffamily TODO} J8}
\label{sec:org4c24c01}
TVP : rupture de kyste poplité
\subsection{Dépistage}
\label{sec:org89e9210}
\begin{itemize}
\item Cancer colorectal :
\begin{itemize}
\item risque modéré (> 50A, asymptomatique) = test immuno de sang dans le selles tous les 2 ans \textpm{} coloscopie.
\item risque élevé : coloscopie tous les 3 à 5 ans selon ATCD
\end{itemize}
\end{itemize}
\subsection{Examen clinique}
\label{sec:org48c04d0}
\subsubsection{Hygroma}
\label{sec:orge8a56dd}
\begin{itemize}
\item Genou++, coude : fréquent si sollicitation professionnelle
\item Douleur local, aspect inflammatoire (chaud), épanchement liquidient palpation
\item Repos, glace, anti-inflammatoire
\end{itemize}
\subsubsection{Réflexes archaïques (doivent avoir disparus à 4 mois)}
\label{sec:org5027dc7}
\begin{itemize}
\item Moro: extension cervical (en arrière) rapide => extension + abduction des bras
\item stimulation palmaire => agrippement
\item frottement des pieds => ébauche de marche
\item succion
\item stimulation péribuccal => tête tournée vers stimulation
\item allongement croisé : stimulation plante de pied => flexion et extension controlatérale
\end{itemize}
\subsubsection{Critères d'Ottawa}
\label{sec:org801aa04}
Radio de cheville si douleur malléolaire \textbf{et}
\begin{itemize}
\item impossible de marcher > 4 pas immédiatement et à l'examen
\item \textbf{ou} sensibilité 6cm distaux tibia
\item \textbf{ou} sensibilité 6cm distaux
\end{itemize}
\subsubsection{Dorsalgie/cervicalgie}
\label{sec:orgc7de25b}
Palper épineuses (signe de la sonnette), muscles paravertébreux
\subsubsection{Déchirure musculaire}
\label{sec:org22b9cb5}
Douleur brutale \textpm{} hématome, voussure palpation
\subsubsection{Douleur pouce}
\label{sec:org0f69b45}
Tendinite de De Quervain ? Signe de DQ = pathognomonique
Rhizarthrose
\subsection{Examens}
\label{sec:orge3f312a}
\begin{itemize}
\item Fracture de fatigue : scinti/TDM/IRM ou RX différée
\end{itemize}
\subsection{Médicaments}
\label{sec:org94943d3}
Acide fusidique : impétigo
Airomir : crise d'asthme
Antadys : rhumatismes inflammatoires, dysménorrhées(AINS)
Apranax = \emph{naproxène} : AINS
Atarax = anxiolytique
Auricularum = \emph{dexaméthasone} + \emph{ATB} : otite externe bactérienne, otite chronique
Avodart = \emph{dutasteride} : HBP
Bedelix : symptomes des manifestation fonctionnelles intestinale
Bilaska : rhino-conjonctivite allergique
Bipreterax = \emph{périndopril} (IEC) + \emph{indapamide} (diurétique) : HTA
Celebrex : arthrose, PR, spondylarthrite ankylosante
Cerulyse = \emph{xylène} : bouchons cérumène
Ciclopirox = antifongique : intertrigo, onychomycoses\ldots{}
Ciloxadex = \emph{ofloxacine} + \emph{dexaméthasone} : otite aigüe externe
Clindamycine = \emph{macrolide}
Coversyl = \emph{périndopril}
Daily = contraceptif estroprogestatif
Duplavin = aspirine + clopidogrel : prévention secondaire chez SCA ST-, IDM ST+
Ezetimibe : +statine pour hypecholestérolémie primaire
Flector = \emph{diclofénac} : tendinite (AINS)
Fluinidone = \emph{previscan} (AVK)
Flécaïne : TV
Gibiter = \emph{corticoïde} + \emph{BDLA} pour l'asthme
Hamamélis : hémorroïdes, insuf. veinolymphatiques
Hamamélis : hémorroidies, insuf. veinolymphatique (phytothérapie)
Ibufetum = AINS en gel
Izalgie = \emph{opium} + \emph{paracétamol} (> Lamaline)
Kétoconazole =: antifongique : dermite séborrhéqiue, candidoses
Lasilix = \emph{furosémide} = diurétique de l'anse
Lumirelax = relaxant musculaire
Micardis = \emph{telmisartan} (ARA II)
Norset = \emph{mirtazapine} : épisodes dépressifs majeurs
Norset = \emph{mirtazapine} : épisodes dépressifs majeurs
Optimizette = contraceptif progestatif
Pradaxa = \emph{dabigatran}
Prolia = \emph{dénosumab} : ostéoporose (5 ans puis 1 an biphosphonates)
Salbutamol : asthme, BPCO
Smecta = \emph{diosmectite} : adsorbant intestinal (diarrhée)
Spasfon : troubles fonctionnels digestifs
Spedra : dysfonction érectile
Stresam : anxiolytique
Structocal = calcium + vitamine D3
Tanganil = antivertigineux
Tiorfan = \emph{racecadtril} : complément des diarrhées aigüe de l'adulte
Ténormine = \emph{aténolol}
Uvédose : carence vitamine d
Vogalène = \emph{métopimazine} : antiémétique
\subsection{Orientation}
\label{sec:org036b1fb}
\begin{itemize}
\item Sensation faiblesse persistante : cardio (rythme, conduction), infection, thyroïde, pulmonaire
\end{itemize}
\subsection{Prévention risques foetaux}
\label{sec:org49f9524}
\begin{itemize}
\item Toxoplasmose : sérologie \textbf{systématique} < 10SA => si négatif, contrôle \textbf{mensuel} !
\item Rubéole : sérologie \textbf{systématique} < 10SA
\item Syphilis : sérologie \textbf{systématique} < 10SA
\item VHB : sérologie \textbf{systématique} 6eme mois
\item VIH
\item streptocoque : prélèvement \textbf{systématique} 36-38SA
\end{itemize}
\subsection{Suivi}
\label{sec:org93cb8df}
\subsection{Vaccins}
\label{sec:org9336543}
Diphtérie, tétanos, coqueluche, polio => 2M, 4M et rappel à 11M et 6A puis 11A
(vaccin différent)
\begin{itemize}
\item Tétravac, Repevac (seulement après 3A)
\end{itemize}
Haemophilus influenzae : 2M, 4M, 11M
Pneumocoque, hépatite B : idem
Ménigocoque : 5M et 12M
Rougeole, oreillons, rubéole :12M et 16-18M
\section{Médecine nucléaire}
\label{sec:org36f70f4}
Scinti
\begin{center}
\begin{tabular}{lll}
Isotope & Vecteur & \\
\hline
Technetium & HDMP (diphosphonate) & os\\
Technetium & albumine & perfusion pulmonaire\\
Technetium & Technegas (carbone) & ventilation pulmonaire\\
Technetium & DMSA & masse rénale fonctionnelle\\
Technetium & HMPAO & perfusion cérébrale\\
\hline
Iode & 0 & thyroïde\\
\hline
Indium (Octréoscan) & Pentétréotide & tumeurs neuroendocrines\\
\end{tabular}
\end{center}
TEP
\begin{center}
\begin{tabular}{ll}
18-F & FDG\\
18-F & FCH (choline)\\
18-F & FDOpa\\
\end{tabular}
\end{center}
\subsection{Cours}
\label{sec:orga764ca9}
\subsubsection{Médicaments radiopharmaceutiques : constitués d'un radio-élement (émet le rayonnement) + un vecteur (se fixe aux organes)}
\label{sec:org8df29e6}
\begin{itemize}
\item technétium : scintigraphie++. Produit directement dans le service
\item F18-fluorodésoxyglucose : grande sensibilité pour la détection de nombreux
cancers (sauf prostate), certaines maladies inflammatoires ou infectieuses
\item analogues de la somatostatine + gallium 68 : certaines tumeurs endocrines
\item bisphosphonates : métastases osseuses
\item Radiothérapie : hyperthyroïdes, métatastes osseuses des adénomes prostatique
\end{itemize}
Choix du radio-élement
\begin{itemize}
\item scintigraphie : émissions de \textbf{photons \(\gamma\)}
\item TEP : émissions de \textbf{positons} (électrons avec charge positive).
\end{itemize}
\subsubsection{Principe technique :}
\label{sec:orgd70ab7a}
\begin{enumerate}
\item Détection des photons \(\gamma\)
\label{sec:org4e13b22}
\begin{enumerate}
\item Après émissions, ils arrivent sur un cristal. Leur énergie est transférée aux
\end{enumerate}
électrons du cristal, qui émet des photons lumineux ("scintillation") dans
toutes les direction.
\begin{enumerate}
\item Conversion en signal électrique et amplification dans des tubes photomultiplicateurs
\item NB: Les premiers photons \(\gamma\) peuvent interagir avec les tissus biologiques et
diffuser d'autres photons (source d'erreur) => filtrage
\item NB: Dans l'étape 1, comment savoir d'où vient le photon \textbf{lumineux} si émis
dans des direction aléatoire ? Le nombre de photons reçus est inversement
proportionnel à la distance de la source => comparaison des différents tubes
\end{enumerate}
\emph{Comment retrouver la position du photon initial depuis le cristal ? Collimation physique (scinti) ou électronique (TEP)}
\item Gamma caméra : collimation physique
\label{sec:orgbfc7293}
\begin{itemize}
\item canaux parallèle : filtre les photons arrivant perpendiculairement au cristal
\item "pinhole" : bonne résolution mais mauvaise sensibilité => Thyroïde
\item Il faut trouver un compromis entre résolution spatiale et sensibilité
\begin{itemize}
\item Acquisition planaire ou tomoscintgraphie (le détecteur tourne autour du
patient, 15min donc sur un seul organe\ldots{})
\end{itemize}
\end{itemize}
\item TEP
\label{sec:orgf41fbc8}
\begin{itemize}
\item Annihilation d'un position génère une paire de photons gamma partant à 180°.
\end{itemize}
Grâce à des détecteurs en "couronne", détection simultanée (enfin presque,
fenêtre de 10ns)
\begin{itemize}
\item Contrairement à la scinti, plusieurs cristaux sur chaque récepteur
\item Meilleure sensibilité et résolution spatiale que la scinti
\item souvent combiné à une TDM en même temps
\end{itemize}
\item Correction des biais de quantification
\label{sec:org29f8190}
Imprécise en tomoscintigraphie, meilleure en TEP
\item Évolution
\label{sec:orgd92ee59}
\begin{itemize}
\item Cristaux semi-conducteur pour gamma-caméra : améliore sensibilité et résolution spatiale
\item Tube PM => photodiodes plus compact pour TEP
\end{itemize}
\end{enumerate}
\subsection{Stage}
\label{sec:org3c87d59}
Choline : adénome parathyroïdien
Scinti : utile pour algodystrophie
Ganglion sentinelle : opération du sein++, pour aider le chirurgien à repérer le
ganglion (injection la veille/le jour même)
\subsubsection{Cancers}
\label{sec:orgb91803d}
\begin{enumerate}
\item Prostate
\label{sec:org0df22a4}
\begin{itemize}
\item Scinti : bilan d'extension de K de la prostate
\item Classif selon PSA et score Gleason (histo), mais cinétique importante
\item Méta = os, ganglions de l'abdomen et du bassin
\end{itemize}
\end{enumerate}
\subsubsection{Lymphome}
\label{sec:org50f625d}
Classif d'Ann Arbor : I= 1 territoire, II = N territoires du même côté, III =
sus et sous-diaphragmatique, IV = viscérale
\subsubsection{Scinti thyroide}
\label{sec:org5332196}
\begin{itemize}
\item Basedow : diffus
\item De Quervain : pas de fixation
\item Hashimoto : hyperthyroïde puis hypothyroïde : fixation faible hétérogène
\end{itemize}
\subsubsection{Scinti cardiaque}
\label{sec:org8953eba}
\begin{itemize}
\item Effort et repos, sans et avec correction à chaque fois (sert à corriger
\end{itemize}
l'atténuation corporelle)
\begin{itemize}
\item Déficit réversible = ischémie, sinon nécrose
\end{itemize}
\subsection{ECNI}
\label{sec:orgadaf12c}
Scinti thyroïdienne, éventuellement pulmonaire peuvent tomber
\section{Gynéco}
\label{sec:org745e20f}
\begin{itemize}
\item Diabète gestationnel :
\end{itemize}
déclenchement pour éviter macrosomie et d'aggraver le diabète (à vérif)
\begin{itemize}
\item HELLP (completer)
\item SHAG
\item GUE : methotrexate possible (sauf si à la base des trompes)
\end{itemize}
\section{Urgences}
\label{sec:orge8fb1a3}
Douleurs abdo : urgence = torsion testiculaire (1 testicule remonté, voire
gonglé et rouge). Y penser même sans douleurs\ldots{}
\section{Gardes}
\label{sec:org17716bc}
\subsection{1. Urgences : ABCDE}
\label{sec:orgabe5982}
\url{https://www.resus.org.uk/resuscitation-guidelines/abcde-approach/}
\href{https://www.google.com/url?sa=t\&rct=j\&q=\&esrc=s\&source=web\&cd=12\&ved=2ahUKEwjqre3gkezkAhWPohQKHWVxAygQFjALegQIBBAC\&url=https\%3A\%2F\%2Fwww.who.int\%2Femergencycare\%2Fpublications\%2FBEC\_ABCDE\_Approach\_2018a.pdf\&usg=AOvVaw3Cu1L7fniTpCUwq9PwOeap}{WHO}
Éliminer les risques vitaux en 30s
\subsubsection{A : airway}
\label{sec:orgb9972b6}
\uline{corps étranger, brûlure, anaphylaxis, trauma ?}
Peux parler ?
\begin{itemize}
\item oui :
\begin{itemize}
\item difficilement ? cherche obstruction, fluide
\begin{itemize}
\item Corps étranger : si visible, enlever. Si toux, encourager. Sinon frappes
dans le dos (par 5)
\item anaphylaxie : adrénalie IM
\end{itemize}
\end{itemize}
\item non : dégager voies respi
\end{itemize}
\subsubsection{B : breathing}
\label{sec:org495672d}
\uline{pneumothorax, overdose, asthme, BPCO ?}
Très rapide, très lent ?
Muscles accessoires, tirage, balancement thoraco-abdominal
\subsubsection{C : circulation}
\label{sec:orgb110504}
\uline{0 pouls, chock, hémorragie sévère, tamponnande cardiaque ?}
Perfusion : extrémités froides, TRC > 2s, hypotension, tachypnée, tachycardie,
pas de pouls
Saignement ? Poitrine, abdomen, fractures
Tamponnade ? hypotension, veines du cous, bruits du coeur étouffés
Pression sanguine
\subsubsection{D : disability}
\label{sec:orgaa5be4b}
\uline{Hypoglycémie, HTIC, convulsion ?}
Conscient ? Glasgow
Hypoglycémie ?
Pupille ?
\begin{itemize}
\item myosis : opiodes ? => naloxone
\item inégales : HTIC ? lever la tête
\item sinon : trauma ?
\end{itemize}
Convulsion ?
\subsubsection{E : exposure}
\label{sec:org43d7adb}
Autres blessures, réactions allergiques
Protéger de l'hypothermie, enlever vêtements/bijous "constricteurs"
\subsection{2. Si non, reste de l'examen}
\label{sec:org6c179a5}
\subsubsection{Examen clinique}
\label{sec:orgcf647d2}
\begin{itemize}
\item Genou : tiroir antérieur postérieur, laxité latéral, épanchement ? (bilatéral !!), Zohlen, amplitude passive
\item plaie : infectée, oedème, lymphangite (trainée rouge ?)
\end{itemize}
\subsubsection{Enfant}
\label{sec:org4a07d9a}
\begin{itemize}
\item examen de la bouche : bras en arrière de la tête
\item trauma crânien : si a pleuré, pas de perte de conscience !
Surveillance simple à domicile si pas de point d'appel. Les parents
doivent le réveiller régulièrement et surveiller : vomissements,
céphalées, troubles cognitifs\ldots{}.
\end{itemize}
\end{document}
::: table
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=0.8\linewidth}{
```
Si exposition au sang (AES) Si exposition sexuelle
------------ ------------------------------------------------ ------------------------------------------------
J1-J4 Séro VIH Idem
(jusque J7 Séro VHC \+ **PCR chlamydia et gonocoque** (1)
si AES) Séro VHB
\- Anti-HBs si vacciné et titre Ac inconnu
\- Ag HBs, Anti-HBc et Anti-Hbs si non vacciné
\- ALAT
\- Créatinine
\- Test de grossesse si indication de TPE
S2 ALAT, créatinine (si TPE et comorbidité ou idem
crainte de iatrogénie)
S6 \- Séro VIH \- Séro VIH si TPE ou en l'absence de TPE
\- ALAT et sérologie VHC (ARN VHC si ARN si sujet source de statut VIH inconnu ou VIH+
VHC + chez sujet source) avec charge virale détectable
\- ALAT et ARN VHC chez HSH ou si ARN VHC+
chez sujet source
\- Séro syphilis
\- **PCR chlamydia et gonocoque** (1)
S12 \- Séro VIH VIH si TEP
\- Séro VHC \- Séro VHC si HSH ou si ARN VHC+
\- Ag HBs, Anti-HBc et anti-Hbs si absence chez sujet source
d'immunité de la personne exposée et sujet \- Ag HBs, Anti-HBc et anti-Hbs si non vacciné
source Ag Hbs+ ou de statut inconnu
```{=latex}
}
```
:::
\(1\) Indications : femme \< 25 ans, homme \< 30 ans, ou HSH ou sujet
symptomatique ; Modalités : 1 à 3 sites de prélèvements selon circons-
tances (NB : absence de remboursement du test gonocoque).
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\begin{document}
\begin{table}
\centering
\adjustbox{max width=0.8\linewidth}{
\begin{tabular}{lll}
& Si exposition au sang (AES) & Si exposition sexuelle\\
\hline
J1-J4 & Séro VIH & Idem\\
(jusque J7 & Séro VHC & + \textbf{PCR chlamydia et gonocoque} (1)\\
si AES) & Séro VHB & \\
& - Anti-HBs si vacciné et titre Ac inconnu & \\
& - Ag HBs, Anti-HBc et Anti-Hbs si non vacciné & \\
& - ALAT & \\
& - Créatinine & \\
& - Test de grossesse si indication de TPE & \\
\hline
S2 & ALAT, créatinine (si TPE et comorbidité ou & idem\\
& crainte de iatrogénie) & \\
\hline
S6 & - Séro VIH & - Séro VIH si TPE ou en l’absence de TPE\\
& - ALAT et sérologie VHC (ARN VHC si ARN & si sujet source de statut VIH inconnu ou VIH+\\
& VHC + chez sujet source) & avec charge virale détectable\\
& & - ALAT et ARN VHC chez HSH ou si ARN VHC+\\
& & chez sujet source\\
& & - Séro syphilis\\
& & - \textbf{PCR chlamydia et gonocoque} (1)\\
\hline
S12 & - Séro VIH & VIH si TEP\\
& - Séro VHC & - Séro VHC si HSH ou si ARN VHC+\\
& - Ag HBs, Anti-HBc et anti-Hbs si absence & chez sujet source\\
& d’immunité de la personne exposée et sujet & - Ag HBs, Anti-HBc et anti-Hbs si non vacciné\\
& source Ag Hbs+ ou de statut inconnu & \\
\end{tabular}
}
\end{table}
(1) Indications : femme < 25 ans, homme < 30 ans, ou HSH ou sujet symptomatique ; Modalités : 1 à 3 sites de prélèvements selon circons-
tances (NB : absence de remboursement du test gonocoque).
\end{document}
# Cardiologie
## 218 Athérome
1ere cause mortalité dans monde.
Prévention : aspirine, statines, antihypertenseurs
Si rupture de plaque : aspirine, clopidogrel, héparine
Localisations : coronaires, aorte, carotides, artères MI
Prévention secondaire : aspirine/clopidogrel, statines, IEC/ARA II
## 219 Facteur de risques cardio-vasculaires
FR : LDL \> 1.6G/L, HDL \< 0.4g/L, tabac[^1], âge[^2], tension
≥ 140/90, diabète, ATCD coronaires familiaux[^3]
Objectifs : tension \< 140/90, LDL \< 1g/L
## 220 Dyslipidémies
Haut risque : maladie vasculaire/coronaire, diabète 2 et atteinte
rénale, $p(\text{evt coronaire à 10 ans}) > 0.2$
Ttt : hypercholestorémie, hyperlipidémies mixtes : statines.
Hypertriglycéridémie : fibrate si TG \> 4g/L
## 334 Syndromes coronariens aigüs
::: table
```{=latex}
\caption{SCA}
```
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
Type douleur PEC Ttt
-------------- --------------------- --------------------------------- -----------------------------------
Angor stable angineuse ECG d\'effort Dérivés nitrés (crise)
à l\'effort Aspirine, β-bloquants
trinitro-sensible
SCA sans ST angineuse `\faHospital{}`{=latex} urgente Aspirine, inhib P2Y12
spontanée \> 20min ECG, troponine , héparine, β-bloquants, statines
Angioplastie percut.
SCA ST+ angineuse ECG Angioplastie si \< 120min
repos \> 30min/jour Sinon FIV
trinitro-résistante Morphine, $O_2$, aspirine
, inhib P2Y12, héparine (crise)
```{=latex}
}
```
:::
ST- : sous-ST pendant la douleur ≥ 1 mm dans 2 dérivations contigües
ST+ : sus-ST ≥ 2*m**m* ($V_1$ à $V_6$) ou ≥ 1*m**m* (autres) dans 2
dérivations contigües
## 228 Douleur thoracique aigüe
Examens sytématiques : ECG 12 dérivation, RX pulmonaire, troponines
Urgence Caractéristiques Examens
-------------------------- ---------------------------------------------------------------------------------------------------------------------- -------------------------------------------
Péricardite (tamponnade) signes droits`\tablefootnote{Turgescence jugulaire, reflux hépatojugulaire}`{=latex}, choc avec tachy, PAs \< 90mmHg échocardio
IDM douleur spontanée de repos \> 20min ECG, troponine x2
Embolie pulmonaire terrain, douleur basithoracique + dyspnée D-dimère `\thus`{=latex} angioscan/scinti
Dissection aortique douleur déchirement, irradie dans dos echo cardio et ETO
: 4 urgences = PIED
Non CV : 4P = pneumonie, pleurésie, pneumothorax, pancréatite
## 223 Artériopathie oblitérante (aorte, MI)
AOMI : pronostic grave !
- asymptom. - claudication intermittente - douleur ischémique de
repos - ulcération/gangrène
- diag: IPS \< 0.70 ( + écho-doppler MI en pratique)
- ttt : FR, antiagrégant, statines, IEC + arrêt tabac, marche ±
revascularisation (stent/chir)
Anévrisme aorte abdominale : âge, tabac, ATCD familiaux
- scanner abdopelvien/IRM = référence
- asymptomatique : chir si ⌀ ≥ 50-55mm
- symptomatique : urgence
Ischémie aigüe des membres inférieurs = urgence (embolie/thrombose)
- diag : douleur brutale, intense, broiement avec impotence
fonctionnelle et membre froid, livide, douleur palpation musc
- ttt : anticoagulant, antalgique niv. 3, $O_2$ et revasc. chir
## 231 Rétrécissement aortique
Pronostic vital mis en jeu si symptômes !
Auscult : souffle systolique éjectionnel au foyer aortique
Diag : ETT = $V_{max} > 4m/s$, gradient moyen \> 40mmHg, surface
aortique \< 1$cm^2$
Ttt : chir si symptomatique = valve mécanique ou bio
## 231 Insuffisance mitrale
Classif. de Carpentier (I à III)
Auscult : souffle apexo-axillaire holosytolique de régurgitation dès B1
Examen : ETT ± ETO
Ttt : chir = reconstruction valve ou prothèse (bio/méca)[^4]
## 231 Insuffisance aortique
Formes : dystrophiques (valves normales mais non jointive), bicuspidie
aortique
Auscult : souffle diastolique. ETT = diagnostic
Opérer :
- urgence si chronique volumineuse symptomatique ou aigüe volumineuse
- si dystrophie et aorte dilatée[^5], si chronique volumineuse
asymptomatique et (aorte dilatée, FEVG \< 50%...)
## 150 Surveillance des porteurs de valves, prothèses vasculaires
Complications : embolie, thromboses[^6], désinsertion, EI ,
dégénérescence[^7], ttt anticoagulant
INR ∈ \[2.5,4\] à vie pour prothèse mécanique
## 149 Endocardite infectieuse
Diag = ETO. Critères de Duke : 2 majeur/1 majeur et 3 mineurs/5mineurs
- majeurs :
- hémoc = typique sur 2HC ou positive \> 12h ou *C. burnetii*
- végétation/abcès/désinsertion (écho) ou nv souffle régurgitation
valvulaire
- mineurs : cardiopathie à risque, \> 38$^\circ$, complication vasc,
immunologique
Complications : insuf cardiaque , embolie septiques, neuro , rénale Ttt
:
- streptocoques (oraux/groupe D) : amoxicilline + gentamicine
- staphylocoques : cloxacilline si sensible (sinon vancomycine)
## 236 Souffle cardiaque chez l\'enfant
Néonatale : coarctation aortique préductale (chir urgente ),
transposition des gros vaissaux, malformations complexes
Nourisson (2M - marche) : shunt gauche-droite (communication
intraventricul), tétralogie de Fallot
2A-16A : souffles fonctionnels[^8]
## 337 Malaise, perte de connaissance
- Éliminer épilepsie
- Éliminer urgence (SCA, EP....)
- ECG, clinique : cause évidente = mécanique[^9], électrique[^10],
hypotensive[^11] ?
- Sinon chercher cardiopathie (échocardio)
## 230 Fibrillation atriale
ECG indispensable : pas de P, QRS irréguliers
Risques = insuf cardiaque, thromboembolique artériel systémique
Étiologie : HTA, valvulopathies
Ttt
- 1er épisode : HNF seule
- FA persistante[^12] : 3 semaines HNF IV puis choc électrique puis 4
semaine anticoagulants oraux
- FA permanente[^13] : bradycardisants (β-bloquants)
- FA paroxystique : anti-arythmique et bradycardisants
## 234 Troubles de la conduction intracardiaque
Bradychardie grave = urgence
Ttt : tachycardisants (atropine, catécholamine)
Type Causes Diagnostic Pacemaker
------------- -------------------- ------------------ ---------------------
Dysfonction dégénérative ECG + Holter Si symptomes
sinusale médicaments, vagal
BAV hyperkaliémie ECG ± Holter/EEP BAV II symptom.
si paroxystique BAV III non curable
BdB dégénérative ECG + EEP Si symptômes
: EEP = étude électrophysiologique endocavitaire
## 229 ECG
---------------------------- ----------------------------------------- -------------------------------
Hypertrophie atriale gauche : P \> 0.12s (largeur) droite : P \> 2.5mm (hauteur)
Hypertrophie ventriculaire gauche : $SV_1 + rV_5 > 35$ mm droite +110$^\circ$
BdB gauche: QRS \> 0.12s ) droite : QRS \> 0.12s
et (rS ou QS en V~1~) et RsR\' en V~1~
Hémibloc antérieur : $S_3 > S_2$ postérieur : $S_1Q_3$
BAV I : PR \> 0.2s , II : `\inc`{=latex} PR III : aucun P
Angor sous-ST
IDM sus-ST convexe (vers le haut)
Péricardite aigüe sus-ST concave
---------------------------- ----------------------------------------- -------------------------------
Troubles supraventriculaire : FA (100-200/min), flutter atrial
(300/min), tachy. atriale, tachy. jonctionnelle, extrasystole
Troubles ventriculaires : tachy. ventricale, fibrillation ventricalure (
absolue), torsade de pointe
## 235 Palpitations
Éliminer urgences immédiates (tachy à QRS large !!)
Fréquents : fibrillation/flutters atriaux, tachy jonctionnelle
Tachy sinusale (grossesse, hyperthyroïde, SAS, alcoolisme)
## 232 Insuffisance cardiaque
Grave : 50% de DC à 5 ans
EC : dyspnée d\'effort, signes d\'IC droite[^14]
Examens : ECG, RX thorax, dosage BNP, *ETT*
Cause : ischémie, HTA, cardiomypathie
IC aigüe ≈ OAP : polypnée, sueurs, cyanose, expectorations \"mousseuses
saumon\", crépitants `\thus`{=latex} PEC immédiate
------------------- ---------------------------------------------------------
IC à FE \< 40% diurétiques + IEC + β-bloquants`\footnotemark`{=latex}.
Si échec : ivabradine puis défibrillateur auto
IC à FE conservée mal définie (idem ?)
OAP assis, furosémide, dérivés nitrés, HBPM
------------------- ---------------------------------------------------------
: Ttt insuffisance cardiaque
`\footnotetext{Pas si crise aigüe ! \danger}`{=latex}
## 221 Hypertension artérielle
3 catégories. Étiologies :
- Essentielles (90%)
- Secondaire : néphropathie parenchym., HTA rénovasculaire,
phéochromocytome, sd Conn, coarctation aortiques, SAS, médicaments,
HTA gravidique
Examens : glycémie, cholestérol, kaliémie, créat, BU, ECG
Complications : rein, neuro, CV
Ttt : objectif \< 140/90 `\thus`{=latex} hygiéno-diét et {IEC,
diurétiques thiazidiques, β-bloquants, ARA II
## 225 Insuffisance veineuse chronique
FR : varices = âge, ATC, obésité, grossesse; MTEV = immobilisation, K,
anomalies hémostase
Clinique : jambes lourdes[^15], dermite ocre, varices
Examen : echo-doppler veineux des MI
Ttt (non curatif) : contention, hygiène de vie, invasif
## 233 Péricardite aigüe
Douleur : thoracique, trinitro-résistant, `\inc`{=latex} inspiration,
`\dec`{=latex} assis en avant
Examens : ECG (4 phases[^16]), marqueurs de nécrose cardio, sd
inflammatoire, *échocardio*
Étiologie : péricardite aigüe virale, néoplasiques, tuberculeuse surtout
Ttt : AINS, colchicine
Complications : tamponnade = urgence (drainage/ponction)
## 327 Arrêt cardiocirculatoire
ABCD : maintien voies Aéoriennes, assistance respi (B), massage
Cardiaque, Défibrillation et Drogues
Ttt : adrénaline 1mg/4min et après 2eme choc amiodarone (300mg dans
30mL)
Ventilation, hypothermie
Étio : FA, bradyc, asystolie
## 264 Diurétiques
Type Molécule Indication ES
------------------------ ------------------------ ----------------------- -----------------------
de l\'anse furosémide insuf cardiaque, IR hypoK, déshydratation
œdème/ascite cirrhose
thiazidique hydrochlorothiazidique HTA hypoK
épargnant le potassium spironolactone Insuf cardiaque, HTA hyperK, IR
: Diurétiques
## 326 Antithrombotiques
::: table
```{=latex}
\caption{Antithrombotiques}
```
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
Type Action Indication Dangers
------------------- --------------------------------------------------------------------------------- ---------------------------- -------------------------------
Antiagrégants aspirine AVC, coronaropathie
/clopidogrel, prasugrel, ticagrelor/`\tablefootnote{Inhibiteurs P2Y12}`{=latex} SCA, post-angio coronaires hémorr. cérébrale (prasugrel)
Héparines HNF, HBPM, *fondaparinux* urgence : TVP, EP, SCA ☡ hémorragie, thrompopénie
Anti-vit. K Oral, relais héparine FA, TVP, EP ☡ hémorragie
valve cardiaque
Nv anticoag oraux *dabigatran, rivaroxaban, apixaban* Surv. rein
rapide, 0 antidote
Thrombolytique *-kinase*, *-téplase* EP grave, AVC \< 6h30
IDM \< 6-12h
```{=latex}
}
```
:::
# Pneumologie
## 73 Addiction au tabac
16 millions de fumeurs en France. 1 fumeur sur 2 décède d\'une malaide
liée au tabac. Cause 90% K bronchopulomaire (25% si passif)
Sevrage : TCC, éducation thérapeutique, substituts nicotiniques.
## 108 Troubles du sommeil de l\'adulte
Sd d\'apnée obstructive du sommeil :
- diagnostic : {ronflement, pause respi, nycturie et somnolence
diurne} et polysomnographie[^17]
- ttt : pression positive continue
Autres : sd d\'apnée centrale[^18] (IC cardiaque sévère !), insuf respi
chronique avec hypoventilation alvéolaire, sd obésite hypoventilation
(ttt = VNI)
## 151 Infections broncho-pulmonaires communautaires
Bronchite aigüe : virale++, diag clinique (épidémie, toux,
expectoration, pas de crépitants), ttt symptomatique
Exacerbation BPCO (cf item 205)
Pneumonie aigüe communautaires : grave. Cf table [tab:pac](tab:pac)
- Clinique : signes auscult en foyer, crépitants. RX thorax !
- Ttt : ATB urgence (pneumocoque !), réévaluation 48-72h
Pneumocoque`\tablefootnote{Pas de transmission interhumaine}`{=latex} Légionellose`\tablefootnote{Pas d'isolement}`{=latex} Atypiques
----------------------------------------------------------------------- ------------------------------------------------------- -------------------------------------------
fréquent++ progressif virale `\thus`{=latex} inhib neuramidases
début brutal, fièvre myalgies *Mycoplasmia pneumoniae*
RX: condensation systématisée macrolides *Chlamydia pneumoniae*, *psitacci*
amoxicilline `\thus`{=latex} macrolides
RX: opacités multifocales
: PAC
## 151 Tuberculose
Diag = IDR/IFN γ si primo infection. Sinon bacille de Koch sur
prélèvement Cf table [tab:tuberculose](tab:tuberculose).
Diag = ED ou culture Löwenstein `\thus`{=latex} granulome épithélioïde
gigantocellulaire avec nécrose caséeuse
Forme pulmonaire miliaire
------------- ------------------------------- ---------------------
Clinique AEG, fièvre, sueurs nocturnes idem, VIH !
RX nodules, infiltrats, cavernes sd interstitiel
Prélèvement crachat/tubage/fibro biopsie
Diag sécrétions/tubages LCS, hémoc, biopsie
: Formes pulmonaires
Ttt (PERI) : isoniazide (6M), rifampicine (6M), ethambutol (2M),
pyranizamide (2M). Vaccination !
## 180 Accidents du travail
Asthme (10-15%), BPCO (10-20%), K (mésothéliome ou bronchique primitif),
PID (hypersensibilité, silicose, bérylliose, sidérose, asbestose)
Amiante : K ou pleural
Idemnité : assurance maladie ou FIVA
## 182 Hypersensibilités et allergies respiratoires
Allergie : le plus souvent médiée par IgE. Asthme et rhinite (cf item
184)
Diag = prick test (⌀ ≥ 3 mm/témoin)
Ttt : éviction, {antihistaminique (rhinite seulement), corticoïdes[^19],
(adrénaline si choc)}, immunothérapie spécifique
## 184 Asthme, rhinite
Asthme :
- suspicion sur clinique : dyspnée, gêne, respi, siflement *variable
et réversible*
- diag[^20] : TVO (VEMS/CVF \< 0.7) réversible aux BDCA (≥ +200mL et ≥
+12%)
- ttt de fond [^21]= corticostéroïdes inhalés (voire
anti-leucotriènes, voire cortico oraux) et symptomatique =
*β*2-mimétique courte durée
- {} exacerbation grave : SAMU + β~2~-mimétique →
`\faHospital`{=latex} : β~2~-mimétique nébulisé, corticoïdes oraux,
$O_2$
Rhinite :
- PAREO : Prurit, Anosmie, Rhinorrhée, Éternuement, Obstruction nasale
- ttt : antihistaminiques/corticoïdes nasaux
## 188, 189 : Pathologies auto-immunes
Si ttt pour connectivite, vascularite, penser 1. infenction 2.
médicament 3. manifestation maladie 4. manifestation indépendante
Cf Table [tab:auto-immune](tab:auto-immune)
-------------------------------------------- -----------------------------------------------------------------------------------------
Sclérodermie systémique PID, HTAP
Lupus érythémateux Pleurésie lupique, sd hémorragie alvéolaire
Polymyosite PID chronique/aigùe
Sd Gougerot-Sjögren Toux chronique , PID
Granulomatose avec polyangéite Nodules`\tablefootnote{Évoluant vers excavation, infiltrats diffus bilatéraux}`{=latex}
Granulomatose éosinophile avec polyangéite Asthme, pneumopathie à éosinophiles
Polyangéite microscopique Sd hémorragique alvéolaire
-------------------------------------------- -----------------------------------------------------------------------------------------
: Manifestations respiratoires
## 199 Dyspnée aigüe et chronique
Examens : ECG, RX thorax, gaz du sang, D-dimère, BNP, NFS a minima
Étiologies : cf Tab [tab:dyspnee_aigue](tab:dyspnee_aigue),
[tab:dyspnee_chronique](tab:dyspnee_chronique)
Inspiratoire Expiratoire Sinon
-------------------- -------------------------------------- --------------------------------------
corps étranger (E) asthme (sibilants) EP (ascult normale)
épiglottite (E) BPCO (ATCD, sibilants) pneumothorax, épanchement pleural
laryngite (E) OAP (crépitants, expector mousseuse) pneumopathie infectieuse
œdème de Quincke OAP (crépitants, expector mousseuse)
: Étiologies de dyspnée aigüe (E = enfant)
Sibilants Crépitants Auscult normale
------------------------ ------------------------- -----------------------------
BPCO PID EP
asthme Insuf cardiaque gauche) Neuromusc
Insuf cardiaque gauche Pariétale, hyperventilation
: Étiologies de dyspnée chroniques
## 200 Toux chronique
Diagnostic principaux : rhinorrée chronique, RGO, asthme, tabac,
médicaments (IEC)[^22], coqueluche
Pas d\'orientation (dans l\'odre) : test rhinorrée post chronique, EFR
(asthme), RGO, sinon antitussif[^23]/kiné respi
Penser bronchectasies si toux productive quotidienne, hémoptysies RX
normale `\thus`{=latex} diag = TDM , ttt = drainage $\pm$ ATB si
exacerbation
## 201 Hémoptysie
Étiologies : tumeurs bronchopulomaires, bronchectasies, tuberculose,
idiopathique, (EP, ICG)
PEC : confirmer hémoptysie, angio-scanner (ou RX thorax)
Ttt 1ere intention : `\faHospital`{=latex} : $O_2$, terlipressine,
protection voie aériennes[^24]
## 202 Épanchement pleural
Clinique : douleur thoracique, toux sèche + sd pleural[^25]
RX (opacité dense, homogène, concave) et ponction (sauf ICG) !
Selon liquide, voir Tab.
[tab:epanchement_pleural](tab:epanchement_pleural)
------------------------------------------- ----------------------------------------------------
Transsudat Exsudat
(prot \< 25g/L, liquide clair: mécanique) (prot \> 35g/L, aspect variable : inflammatoire, )
*ICG* *Tumorale* : K bronchique, mésothéliome pleural
cirrhose *Tuberculose*
sd néphrotique bactérienne, virale
EP
------------------------------------------- ----------------------------------------------------
: Types d\'épanchement pleural
Si abondant/purulent/à germe : ttt anti-infectieux + évacuation du
liquide pleural
## 203 Opacités et masses thoraciques : tab. [tab:masses_thorax](tab:masses_thorax)
Nodules (⌀ \< 3 cm) Masses (⌀ \> 3cm) médiastinales
---------------------------------------------------------------------------------------- -------------------------------------------------------
\- malin si terrain, \> 1cm, morphologie[^26], fixe TEP, `\inc`{=latex} récente taille \- antérieur : goître, K thyroïdes, thymome, lymphome
\- chez 1 gros fumeur sur 2 et cancéreux 1 sur 10 \- moyen : lymphome
\- scanner, TEP-FDG. Diag = ponction transpariétale \- postérieur : neurogène
\- malignes : métastates (pulmon), primitif (bronchopulmon)
: Masses thoraciques
## 204 Insuffisance respiratoire chronique
Clinique : dyspnée, hypoxémie (PaO~2~ \< 70mmHg)
Examens : EFR, RX thorax, écho cardiaque.
Étiologies : table [tab:etio_IRC](tab:etio_IRC)
Obstructive Restrictive Mixte Pas de TV
------------- ------------- --------------- -----------
BPCO PID DDB HTP
asthme Obésité Mucoviscidose
: Étiologies IRC selon TV
TTT : arrêt tabac, $O_2$ longue durée (si *obstructif et PaO~2~ \< 55
mmHG ou restrictif et \< 60mmHg*) ou ventilation long cours (restrictif)
## 205 BPCO
Clinique : tabac++, dyspnée, toux, expectoration ± distension thoracique
Diag = VEMS/CV \< 0.70 *non réversible*
Ttt :
- broncho-dilatateur courte durée/longue durée si exacerbation. +
corticoïdes inhalés si besoin.
- Arrêt tabac, kiné respi, vaccins grippe, pneumocoque
Exacerbation BPCO : déclenché par infection
- diag : BPCO connu, `\inc`{=latex} dyspnée, toux ou expectoration
- ttt : bronchodilatateur courte durée (nébulisé) + amox-acide clav
[^27]si aggravation/`\inc`{=latex} purulence
## 206 Pneumopathies infiltrantes diffuses
Clinique : dyspnée d\'effort (apparition progressive) Orientation =
scanner thoracique++
PID aigüe : éliminer œdème cardiogénique puis LBA. Si fièvre, ATB
probabilist (sur pneumocoque ± pneumocystose, tuberculose)
PID subaigüe/chronique :
- interrogatoire, LBA (fibro), scanner thoracique 1ere intention
- sarcoïdose , insuf cardiaque gauche , médicaments , fibrose
pulmonaire idiopathique lymphangite carcinomateuse
## 207 Sarcoïdose
Manifestations:
- respi : RX thorax 4 stades[^28]
- oculaire (uvéite), peau (sarcoïdes), ADNP (superficielles), foie
(cholestase non ictérique)
Diag : clinique + histologie (granulomes sans nécrose caséuse) +
élimination autres granulomatose (ou sd Löfgren typique[^29])
Pronostic favorable 80%
Ttt : corticoïdes \> 1 an
## 222 HTA pulmonaire artérielle
Classification : HTAP, HTP cardiopathies gauches (*post-capillaire*),
HTP respiratoires chroniques, HTP post-embolique chroniques, HTP
multi-factorielle
HTAP = PAP moyenne ≥ 25mmHg (=HTP) et PAPO ≤ 15mmHg (pré-capillaire).
Pronostic sombre
Clinique : dyspnée à l\'effort
Complémentaire : ECG, RX thorax, EFR, gaz du sang normaux
Diagnostic : ETT et cathétérisme cardiaque droit
## 224 Thrombose veineuse profonde et embolie pulmonaire
### TVP
Probabilité : score de Wells (unilatéral : OMI, douleur trajet
veineux...)
Diagnostic : (D-dimère si proba faible puis) Écho-doppler veineux MI
Étiologies : congénitale (\"thrombophilie\") ou acquise (K, alitement,
contraception, chir...)
Prévention : HBPM, contention, lever
### EP
Suspicion : proba clinique, RX thorax, ECG, gaz du sang [^30]
Diagnostic : (D-dimère si proba faible puis) scanner (ETT en attendant).
Si scanner toujours non disponible et patient à haut risque, traiter !
### Ttt (TVP + EP)
Ttt :
- HBPM/fondaparinux + relais AVK ou nv anticoag 3 mois (1ere EP, TVP
proximale provoquée) ou 6 mois
- thrombolyse si EP grave
- contention si TVP ou EP + TVP
## 228 Douleur thoracique aigüe et chronique
Examens : ECG, $SpO_2$, RX thorax
1. Urgences vitales : SCA++, EP, tamponnade, dissection aortique,
pneumothorax oppressif
2. Sinon :
- rythmée par la respiration : pneumothorax, infectieuses,
péricardite, pariétales, EP, trachéobronchites
- non rythmée par la respiration : SCA, dissection aortique,
RGO++, psychogène
Chronique : paroi thoracique, plèvre
## 306 Tumeurs du poumon
K bronchique : 1ere cause de DC par K en France (17% survie 5 ans).
Cause = tabac !
Y penser si SF respi chez tabagique \> 40 ans, AEG chez tabagique. Toux
souvent révélatrice
2 types :
- non à petites cellules (80%) : chir/radio/chimio
- à petite cellule (15%) : mauvais pronostic, chimio ± radio (pas de
chir)
Diagnostique = histologique (fibroscopie). Extension = TDM
## 333 Oedème de Quincke et anaphylaxie
Réaction anaphylactique médiée par IgE ou non Diag = clinique +
contexte. Toujours doser tryptase sérique
- fortement probable : gêne respi \"haute\" ou asthme aigü ou choc
impliquant PV, {rash, urticaire, angioedème}, début brutal et
progression rapide Urgence (atteinte multiviscérale menaçant la vie)
: adrénaline [IM]{.underline}
0.01mg/kg toutes 5min, arrêt agent, allongé/PLS
Sinon : antihistaminique + corticoïdes
## 354 Corps étranger des voies aériennes
Pics : enfant, âgé
Y penser si symptôme respiratoire chronique/récidivant dans même
territoire
Clinique : mobile (sd pénétration, suffocation), expulsé (pétéchies),
enclavement
CAT : Toux/Heimlich/réa. Extraction bronchoscopie/centré spé (enfant)
## 354 Détresse respiratoire aigüe
PEC : $O_2$, VNI/VI et investigation
Diagnostic
- RX thorax anormale : urgence = pneumonie infectieuse, œdème
pulmonaire aigu, pneumothorax. Puis SDR, exacerbation path.
infiltrative
- Sinon clinique + gaz du sang : asthme aigü grave, EP, BPCO, anomalie
paroi, neuromusc, pneumothorax
SDRA : détresse respi \< 7j + anomalie RX (opacités alvéolaire bilat
diffuse) sans défaillance cardiaque
## 356 Pneumothorax
Primaire (jeune, longiligne, 0 patho, fumeur) VS secondaire (âgé, patho
connue)
Clinique : douleur pleurale (`\inc`{=latex} inspiration et otux)
Diag = RX face.
Ttt : sevrage tabac
- urgence si compressif (aiguille simple).
- Sinon (mal toléré/grande taille) : exsufflation ou drain.
Prévention récidive : pleurodèse
# Endocrinologie - Nutrition
## 32 Allaitement maternel
## 35 Contraception (gynéco)
œstroprogestatif Micro/macroprogestatifs
------------ --------------------------------------------- -----------------------------
1ère intention (Minidril), le plus efficace 2eme intention
CI K sein, HTA non contrôlée, thrombose K sein, accident TEV récent
hépatopathie sévère, diabète
Surveiller chostérole, TG, glycémie spotting
Urgence : lévonorgestrel \< 72h
## 37 Stérilité du couple (gynéco)
Infertilité : 0 conception à 1 an. Stérilité = définitif
- ♀ : anovulation (courbe de température), bilan hormonal, écho
ovarienne, hystérographie.
- ♂ : volume testiculaire, testostérone, spermogramme. Hormonal si
oligo/azoospermie
## 40 Aménorrhée (gynéco)
Primaire
- pas dév. pubertaire :
- FSH, LH `\dec`{=latex} : tumeur H-H[^31], sd de Kallmann
- FSH, LH `\inc`{=latex} : sd de Turner (45X)
- retard pubertaire simple (diag élimination)
- examen gynéco + écho : hyperplasie congénitale des surrénales,
anomalie utéro-vaginale, anomalie sensibilité androne
Secondaire :
1. hCG pour éliminer grossesse
2. prolactine `\inc`{=latex} : médicaments, IRM H-H (adénome
prolactine, tumeur/infiltration)
3. LH `\inc`{=latex} : écho ovaires (sd ovaires polykystiques)
4. estradiol, LH, FSH `\dec`{=latex} (déficit gonadotrope) :
tumeur/infiltration H-H(IRM) ou nutrition
5. `\inc`{=latex} testostérone (insuffisance ovarienne) : scanner
surrénales, écho ovarienne
## 47 Puberté (pédia)
Retard : pas de seins \> 13 ans ou pas de règle \> 15 (♀), volume
testicule \< 4mL après 14 ans(♂)
- hormonal (hypogonadotrope)
- FSH, LH `\dec [fn:34]`{=latex} : IRM H-H (infiltratif, tumoral),
nutrition, sport, sd Kallmann
- FSH, LH `\inc`{=latex} : caryotype (sd Turner si ♀, Klinefelter
♂)
- retard pubertaire simple
Précoce \< 8 ans ♀, \< 9.5 ans ♂. Table [tab:puberte](tab:puberte)
Type Diagnostic Étiologie Examens
-------------- ------------------------ ----------------------------- ---------------------------------------------
centrale FSH, LH `\inc`{=latex} ovaire/testicule, surrénale écho pelvien/testic., test stimulation GnRH
périphérique FSH, LH `\dec`{=latex} idiopathique, tumeurs SNC imagerie cérébrale
: Puberté précoce
## 48 Cryptorchidie (pédia)
Exploration : c. de Leydig, c. de Sertoli, FSH, LH +
17-hydroxyprogestérone si bilatérale
Ttt chir (sinon = infertilité, hypogonadisme, K testiculaire)
## 51 Retard de croissance (pédia)
Définition : taille \< -2DS ou ralentissement croissance ou $<<$ parents
Cf table [tab:retard_croissance](tab:retard_croissance) + bilainVS, NFS,
foie, rein.
Cause Exploration
---------------------------------- -------------------------------------------
Constitutionnelle++
RCIU
Déficit en GH, hypothyroïdie GH, {TSH, T4L}
Maladie coeliaque, mucoviscidose {IgA, IgA anti-transglutamase},test sueur
Os radio
Retard pubertaire simple
: Retards de croissance
## 69 Troubles des conduites alimentaires (à compléter)
## 78 Dopage
*Stéroïdes anabolisant*, testostérone (`\inc`{=latex} masse musculaire,
puissance)
Autres : GH (`\inc`{=latex} masse musculaire), IGF-1. Glucocorticoïdes,
ACTH (antalgique, psychostimulant)
## 120 Ménopause et andropause (gynéco, uro)
Ménopause :
- diag clinique : sd climatérique, aménorrhée ≥ 1 an (bio si doute
FSH `\inc`{=latex}, oestradiol `\inc`{=latex})
- ttt hormonale = œstrogène et progestatif. Surveiller et réévaluation
annuelle
- bénéfice : ttt sd climatérique, prévention ostéoporose
- risque : `\inc`{=latex} incidence K sein, `\inc`{=latex}
accidents TE veineux `\thus`{=latex} [CI]{.underline}
Andropause : si testostérone \< 2.3ng/mL[^32] :
- FSH, LH `\inc`{=latex} = insuf testiculaire primitive (sd
Klinefelter)
- sinon hypogonadisme hypogonadotrope `\thus`{=latex} IRM H-H pour
adénome hypophysaire
## 122 Troubles de l\'érection (uro)
Étiologies factorielles !
- psychogène (érections nocturnes) : rassurer, psychothérapie
- diabète+~~, hypogonadisme+~~, hyperprolactinémie
- vasculaire (HTA), chir pelvienne, anti-hypertenseur, neuro
dégénératif, trauma médullaire
Bilan bio : glycémie jeun, testostéronémie ± prolactine, hormones
thyroïdiennes
Ttt
- hypogonadisme confirmé : androgènes (CI nodule prostatique, PSA \>
3ng/mL)
- 1ere intention : inhibiteurs phosphodiéstérase type 5 (Viagra) +
stimulation
## 124 Ostéopathies
Ostéoporose secondaires de ♀ : endocrino++ (Table
[tab:osteoporose](tab:osteoporose)). ♂ : y penser si hypogonadisem,
hypercortisolisme
Cause Sous-cause Ttt
------------------------------- --------------------------- ------------------------------------------------------------
Hypogonadisme Anorexie mentale Pilule œstroprogestative
Activité physique intense Si aménorrhée, `\dec`{=latex} activité ou œstroprogestatif
Patho. hypophysaire Œstrogènes
Iatrogène Bisphosphonates
Sd Turner ŒStrogène + GH ou (adulte) œstroprogestatif
Hyperthyroïdie Surveillance (ttt supressif) ± bisphosphonate
Hypercortisolisme/corticoïdes Vitaminocalcique, bisphosphonates
: Causes endocriniennes d\'ostéoporose chez ♀
## 207 Sarcoidose
Penser à sarcoïdose hypothalamo-hypophysaire si diabète insipide. Diag =
défici endocrinien + infiltration HH à l\'imagerie si sarcoïdose connue.
Sinon arguments de sarcoïdose (cf [*item de pneumo*]{.spurious-link
target="207 Sarcoïdose"})
## 215 Hémochromatose
Suspicion clinique : Asthénie, Arthalgie, `\inc`{=latex} ALAT (3 A)
Atteinte : foie (cirrhose++), diabète sucré++, hypogonadisme,
chondrocalcilnose articulaire, cœur
Diag : CST `\inc`{=latex} et ferritine `\inc`{=latex} : chercher
mutation C282Y sur HFE
Ttt dès CST `\inc`{=latex} : saignées jusque ferritine \< 50g/L.
Dépistage parents 1er degré
## 221 HTA : hyperaldostorénonisme primaire, sd de Cushing
[]{#sec:Cushing} Iatrogène : œstroprogestatifs, corticoïdes, réglisse
Hyperminéralocorticisme primaire :
- suspicion : HTA (± résistante) + hypokaliémie
- diag : aldostérone `\inc`{=latex} et rénine `\dec [fn:38]`{=latex}
- TDM ou IRM :
- adénome de Conn[^33] `\thus`{=latex} chir
- idiopathique `\thus`{=latex} spironolactone, antihypertenseurs
Phéochromocytomes[^34]
- dépistage : HTA paroxystique, \"triade de Ménard\" = céphalées +
sueurs + palpitations, NEM2, NF1
- diag : métanéphrine `\inc`{=latex}
- Imagerie puis chir
Sd de Cushing
- clinique : obésité androïde et graisses facio-tronculaire +
vergétures, ostéoporose + hyperandrogénie[^35]
- diag = cortisolurie 24h `\inc`{=latex}, test freinage minute négatif
à DXM
- étiologie :
- ACTH `\dec`{=latex} `\thus`{=latex} adénome surrénalien,
cortico-surrénalome malin
- sinon : test de freinage fort à DXM, test de stimulation ACTH
`\thus`{=latex} maladie de Cushing (positif) ou sd
paranéoplasique (négatif)
## 238 Hypoglycémie
Diag : neuroglucopénie[^36] et glycémie \< 0.50g/L et correction à
normalisation[^37]
Cause :
- surdosag insuline++ chez diabétique `\thus`{=latex} sucre si CS,
sinon glucagon IM/SC (ou perf glucose)
- insulinome : diag par épreuve de jeune `\thus`{=latex} chir
## 239 Goitre, nodules thyroïdiens, cancers thyroïdiens
Goître (hypertrophie thyroïdie) : évolue en multinodulaire
(complications ?)
- étiologie : tabac, déficience iode
- diag : TSH et T4 (si TSH `\inc`{=latex}: Ac anti-TPO et anti-TG
(auto-immunité))
- ttt : ado = correction par levothyroxine , adulte = surveillance.
Chir chez l\'adulte si symptomatique, hyperfonctionnel, morphologie
suspecte (ou iode 131 si âgé)
Nodules (hypertrophie localisée thyroïdie) : doser TSH
- si signes : hématocèle (brutal + douleur), thyroïdite subaigüe
(douleur + fièvre), cancer (compressif + ADP), toxique
(hyperthyroïdie), thyroïdite lymphocytaire (hypothyroïdie)
- nodule isolé cf [tab:nodule_isole](tab:nodule_isole). Selon
cytologie : surveillance si bénin, chir
TSH `\dec`{=latex} TSH N TSH `\inc`{=latex}
--------------------- ----------------- --------------------
nodule hyperfonct ? tumeurs thyroiidite ?
scinti écho, cytologie Ac anti-TPO
: Orientation pour nodule isolé
Cancers thyroïdiens :
- types :
- différencié d\'origine vésiculaire = Papillaire (85%, excellent
pronostic), Vésiculaire (5%, très/moins bon pronostic),
Anaplasique (1%, 15% survie 1 an)
- Medullaire (5%, 80% survie 5 an)
- ttt = thyroïdectomie totale ± curage ganglionnaire
- si origine vésiculaire : iode 131 (après thyroïdectomie totale si
haut risque), L-T4 (si récidive)
- si médullaire : chercher autres lésions NEM2[^38]
## 240 Hyperthyroïdie
Clinique : sd thyrotoxicose = asthénie, amaigrissement, sueurs, CV
(tachycardie)
Diagnosic : TSH `\dec`{=latex} puis T4L `\inc`{=latex}
Étiologie Clinique Diagnostic
--------------------------------- -------------------------------- ---------------------------------------------------------------------------------------------
*maladie de Basedow* goitre, oculaire (exophtalmie) oculaire
ou écho + Ac anti récepteur TSH `\tablefootnote{Scinti: fixation homogène diffuse}`{=latex}
*goître multinodulaire toxique* Scinti: en damier
*adénome toxique* Scinti: hyperfixation (reste = \"froid\")
De quervain virale, goitre dur, douloureux clinique
: Étiologies
Ttt :
- β-bloquants, contraception, *anti-thyroidiens de synthèse*
\[Neomercazole\] (☡ agranulocytose[^39])
- spécifique :
- cardiothyréose = propranolol, anticoag, ATS, chir/radio-iode
- Crise aigüe thyrotoxique ATS, pronanolol, corticoïdes puis iode
- Orbitopathie : pas d\'ATS, ni d\'iode !
- enceinte : surveillance/ATS/thyroïdectomie selon
## 241 Hypothyroïdie
Clinique : sd myxoedemateux[^40], hypométabolisme[^41]
Diag = TSH `\inc`{=latex}. Puis doser T4. Étio : Ac anti-TPO,
échographie
Étiologies :
- atteinte thyroïde
- thyroïdite d\'Hashimoto : Ac anti-TPO. Écho = hypoéchogène,
hétérogène
- thyroïdite atrophique (pas de goitre), du post-partum
- carence iode (endémie), iatrogène (interféron)
- atteinte hypothalamo-hypophysaire `\thus`{=latex} IRM
Complications : insuf cardiaque, coma myxoedemateux
Ttt : lévothyroxine [^42]. Surveiller TSH (primaire) ou T4L (atteinte
H-H) !
## 242 Adénome hypophysaire
Découverte : sd tumoral = céphalée, hémianopsie bi-temporale, apoplexie
hypophysaire (rare mais urgence !)
IRM (référence) : microadénome (hypointense, non rehaussé à
l\'injection) ou macroadénome (\> 10mm, rehaussé injection)
Hypersécrétion par l\'hypophyse :
- prolactine : galactorrhée, spanioménorrhée. Diagnostic =
- vérifier hyperprolactinémie, éliminer grossesse, médicaments,
hypothyroïdie périph, insuf rénale
- microadénome : positif. Sinon, test agoniste dopaminergique
- GH (acromégalie) : sd dysmorphique[^43], HTA
- complication : insuf cardiaque !, diabète
- diagnostic : pas de freinage de GH à l\'HGO et `\inc{}`{=latex}
IGF-1
- glucocorticoïdes (indirectement) : cf [HTA et Cushing](sec:Cushing)
Insuffisance hypophysaire : table
[tab:insuf_hypophyse](tab:insuf_hypophyse)
-------------- ------------------------------------------------------------------
gonadotrope oestradiol/testostérone `\dec`{=latex} ou FSH, LH `\dec`{=latex}
corticotrope cortisolémie `\dec`{=latex}, synacthène (aldostérone normale !)
thyréotrope T4l `\dec`{=latex} mais TSH normale...
somatotrope (GH) stimulation GH négative
-------------- ------------------------------------------------------------------
: Insuffisance hypophysaire
## 243 Insuffisance surrénale
Chronique :
- clinique = asthénie, anorexie, hypotension. Hyperk, hypoNa[^44]
mélanodermie (surrénale), pâleur (hypophyse)
- ttt sans attendre diag : hydrocortisone, fludrocortisone [^45] +
cause
- diag : cortisol `\dec`{=latex}, ACTH `\inc`{=latex} si primaire
- étiologies :
- primaire (surrénale) = *autoimmune* 80%[^46], *tuberculose* des
surrénale 10%[^47]), VIH, iatrogène, métastases bilatérales
- secondaire (hypophyse) = interruption corticothérapie prolongé
IS aigüe = urgence
- déshydratation extracellulaire, confusion, fièvre. Bio :
hémoconcentration, hypoNa, hyperK, hypoglycémie
- hydrocortisone 100mg puis `\faHospital`{=latex} : NaCL et facteur
déclenchant (IS chronique++)
##
## 244 Gynécomastie
Palpation : ferme, mobile, centré mamelon. Si doute, mammographie pour
élimiter K et adipomastie
Physiologique : NN, ado (\< 20 ans), \> 65A (palper testicules !)
Étiologies : médicaments, idiopathique (25%), cirrhose, insuf
testiculaire/gonadotrope (8%), tumoral (rare).
- bilan hormonal si non évident
Ttt : cause. Androgène si idiopathique voire chir plastique
## 245 Diabète sucré
Glycémie jeun ≥ 1.26 g/L `\time 2`{=latex} ou (≥ 2g/L + signes
d\'hyperglycémie)
### Diabète 1
insulinopénie (destruction c. β pancréas) auto-immun++ ou idiopathique
Début brutal, sujet jeune, sd cardinal (polyuro-polydipsie,
amaigrissement, polyphagie}, acidocétose (cétonurie)
Diagnostic : hyperglycémie + triade {cétonurie, \< 35 ans} ou auto-Ac
PEC :
- insuline à vie : lent et rapide (3-4)
- objectif HbA1c \< 7%
- surveillance : glycémie 4/jour
- CS : ophtalmo 1/an, dentiste 1/an, diabétologique 3/an ± cardio 1/an
si sympto/âgé/compliqué
Dépistage pendant grossesse !
### Diabète 2 (90 %)
Insulinorésistance [et]{.underline} déficit insulinosécrétoire
Découverte fortuite (asymptomatique longtemps). Dépistage : clinique
d\'hyperglycémie, sd métabolique[^48]
PEC :
- objectif HbA1c \< 7%
- activité physique [^49], alimentation équilibrée sans sucres rapides
- metformine (sinon sulfamide, inhibiteurs DPP-4, inhibiteurs
α-glucosidase)
- \+ insuline et HGO si insulinorequérance
### Complications
Œil : voir [partie ophtalmo](sec:retinopathie_diabetique)
Rein : diabète = 1ere cause d\'IR terminale.
- dépistage 1/an chez D2 : BU (protéinure), albuminure/créatinurie
- ttt : prévention : diabète, HTA. Puis cf tab
[tab:ttt_nephro_diabete](tab:ttt_nephro_diabete)
Stade type Ttt
------- ----------------------------------- ---------------------------------------------
3 microalbuminurie Obj: HBA1c \< 7%, PA \< 140/85 mmHg
4 macroalbuminurie IEC/sart + diurétique thiazidique
5 IR avec DFG \< 30/mL/min/1.73m^2^ insuline, répaglinide, inhib. α-glucosidase
: 2 premiers stade de néphro diabètes = asymptomatique
Neuropathies
- sensorimotrice : polynévrite symétrique distale++ (hypoesthéie, 0
ROT achilléen, bilat , douleur neurogène)
- autonome : digestiv (gastroparésie), dysfonction érectile, parésie
vésicale
- dépistage : examen neuro (pied !!), ECG annuel
- ttt : préventif++ (glycémie, alcool, tabac...)
Macroangiopathie : 2/3 DC pour cause CV
- ischémie myocardite silencieuse !!, AOMI
- prévention : glycémie (metformine), activité physique, LDL
(statines), aspirine, anti-hypertenseurs, poids, 0 tabac
Mal perforant plantaire : creux autour d\'hyperkératose
- examen réguliers des pieds et chaussures quotidien
- ttt : décharge, excision kératose / parage et drainage + ATB si
infection ± revascularisation si nécrose
- risque d\'ostéite
Autres :
- infections `\thus`{=latex} examen cutané++, stomato, uro-génital,
respi
- dentiste tous 6 mois
Complications métabolique :
- coma cétoacidosique
- diag= cétonémie, cétonurie
- ttt insuline rapide IV, recharge volumique, K+ ± glucose, cause
- coma hyperosmolaire :
- diag = glycosurie, cétonurie (BU) et hyperglycémie (dextro)
- ttt : réhydratation lente, insuline IV, héparine, cause
- hypoglycémie : inévitable, non mortelle. Cf [*item
238*]{.spurious-link target="238 Hypoglycémie"}
## 246 Prévention par la nutrition
## 247 Modifications thérapeutiques du mode de vie
## 248 Dénutrition (à compléter)
## 249 Amaigrissement (à compléter)
Vérifier l\'amaigrissement !
Causes endocrino : insuf. surrénale (primaire/secondaire)diabète,
hyperthyroïdie, hypercalcémie
## 250 Troubles nutritionnels chez sujet âgé (à compléter)
## 251 Obésité (à compléter)
IMC ≥ 30 kg/m^2^ (grade 1 si \< 35, grade 3 si ≥ 40)
Étiologie : génétique, communes++ (déséquilibre apport-dépense).
Complications : `\inc`{=latex} RR mortablité, métabolique, CV, respi,
ostéoarticulaire, digestive, rénale, gynéco, cutanée, néoplasique,
psychosociale
Interrogatoire. Ttt = diététique, activité physique, psychologique +
orlistat si IMC ≥ 30 (ou 27 et comobridité). Chir bariatrique en 2eme
intention.
### Enfant/ado
IMC \> 25 kg/m^2^
Étiologie : commune++ (facteur env., prédisposition génétiuqe),
génétique, secondaire
Complication : HTA, insulinorésistance, stéatose hépatique non
alcoolique, articulaire, psycho
Interrogatoire + EC. Ttt = prévention
## 252 Diabète gestationnel + nutrition et grossesse (à compléter)
Pré-gestationnel
- risque fœtus : fausses couches, malformations congénitales, mort
fœtales,
- risque mère : HTA ++, rétinopathie, néphropathie
- avant grossesse : HbA1c \< 7%, glycémie ∈ \[0.7,1.20\] préprandial
et \[1, 1.14\] en post (`\inc`{=latex} insuline si DT1, +insuline si
DT2
- pendant : 6 glycémie/jour pour équilibre
Dépister diabète gestationnel ssi FR : { ≥ 35 ans, IMC ≥ 25 kg/m^2^,
ATCD DG, DT parents 1er degr}
- PEC si glycémie jeun ≥ 0.92g/L (début), sinon teste 24-28SA avec HGO
- ttt : diét., **pas** d\'antidiabétique, surveillance
## 253 Nutrition chez le sportif
Examen d\'aptitude : ATCD familiaux (CV), EC complet, ECG d\'effort
Bénéficices du sport : 150min/semaine (ou 75min si intense) chez
l\'adulte. 60min/jour chez l\'enfant + renforcement
- adulte :
- prévention = K (colon, sein), CV, métabolique, ostéoporose ♀,
- maintien = `\dec`{=latex} mortalité prématuré, `\inc`{=latex}
autonomie
- traite = cardiomyopathie, ischém, BPCO, obésité, diabète 2
neuro, rhumatismal, dégénératif
- enfant : dev psychosocial, dev psychomotoeur, prévient sd
métabolique, surpoids, CV, `\inc`{=latex} masse maigre et densité
osseuse
Bseoins :
- glucides (50%) : IG faible à distance, élevé juste avant.
reconstituer stocks après
- lipides (30%) à limiter si compétition
- protéines (20%)
- calcium 1g/j, Fer 10-15mg/j, vit D 5 μg/j `\thus`{=latex} surveiller
chez l\'enfant
## 265 Hypocalcémie, dyskaliémie, hyponatrémie
Hypocalcémie :
- clinique : troubles du rythme, parésthésie, tétanie
- causes hypoparathyroïdie, anomalie vitamine D (carence,
malabsorption...)
- ttt : aigü calcium IV lente. Chronique : vitamine D et calcium
Hyperkaliémie (risque cardiaque )
- étiologies : hypoaldostéronisme (IS) , acidose métabolique [^50]
Hypokaliémie (risque cardiaque )
- étiologie : excès d\'insuline, hyperaldostéronisme, dénutrition
sévère
Hyponatrémie endocrinienne (hospitalisé++)
- étiologie selon osmolalité : si `\inc`{=latex}, hyperglycémie, si N,
hyperTG, hyperprotidémie. Si `\dec`{=latex}, \"vraie\" hyponatrémie
: table [tab:hyponatremie](tab:hyponatremie)
------------------------ ------------------------------------------------------- ------------------------
volémie `\inc`{=latex} IC, cirrhose, sd néphrotique Sérum isotonique
volémie R hypothyroïdie, insuf corticotrope, SIADH Sérum hypertonique
volémie `\dec`{=latex} perte digestive, rénale, insuf corticosurrénale aigüe Restriction hydrosodée
------------------------ ------------------------------------------------------- ------------------------
: hyponatrémie \"vraie\"
## 266 Hypercalcémie
Étiologie :
- PTH `\inc`{=latex} ou N
- hyperparathyroïdie primaire (55%) : ttt = chir conventionnelle
- hypercalcémie-hypocalciurie familiale bénigne
- PTH `\dec`{=latex}
- maligne (30%)
- iatrogène, granulomatose
Ttt (hors hyperparathyroïdie primaire) : bsiphosphonates, calcimimétique
## 303 Tumeurs de l\'ovaire (hormono-sécrétante)
Sécrète des œstrogènes : tumeurs de la granulosa++ :
- sympto : pseudo-puberté précoce ou aménorrhée/ménométrorragie ou
saignement vaginal
- ttt = ovariectomie unilatérale
Sécrète des androgènes : tumeurs à c. de sertoli-Leydig (Hirsutisme, ttt
conservateur), à c. de Leydig (virilisante, ttt = ovariectomie bilat),
germinales sécrétantes [^51]
## 305 Tumeurs du pancréas (endocrine)
Clinique selon sécrétion (insuline, gastrine, ACTH, glucagon, VIP, GHRH)
## 310 Tumeurs du testicule (aspects endocriniens)
Clinique : pseudo-puberté précoce/gynécomastie
Sécrète testostérone/œstradiol ou gonadotrophine chorionique/hCGA
(tumeurs germinales)
Diag = palpation testiculaire + écho
Ttt = chir (glucocorticoïdes si inclusions surrénaliennes)
# Ophtalmo
## 1 Sémiologie oculaire
Anatomie
- Membrane externe (cornée, conjonctive, sclère), uvée (iris, corps
ciliaire, choroïde), rétine
- Contenu : humeur aqueuse (chambre antérieure), cristallin, corps
vitré (postérieur)
- Voie optique : nerf optique - chiasma - bandelettes - corps
genouillés externes - radiations optiques - cortex occipital
- Nerfs oculomoteurs : IV = oblique sup, VI = droit externe et les
autres = III
Examens :
- AV (Parinaud = près, Monoyer = loin)
- lampe à fente (segment antérieur), gonioscopie (angle iridocornéen)
- pression intraoculaire par tonomètre à pair pulsé (hypertonie si ≥
22mHg)
- FO
Complémentaires
- CV (périmétrie statique = dépistage glaucome), couleurs
- angiographie (DMLA)
- électrorétinogramme, potentiels évoqués visuels (SEP),
électro-oculogramme
- écho (mode A = longeur, mode B = décollement rétine)
- OCT (glaucome chronique, macula : DLMA)
## 2 Réfraction
Œil = 60 dioptries (42 cornée, 20 cristallin).
Myope = trop convergent `\thus`{=latex} verre concave/chir. Hypermétrope
= pas assez convergent `\thus`{=latex} verre convexe/chir. Astigmate
`\thus`{=latex} verres cylindriques/chir
## 3 Suivi d\'un nourisson
Dépister enter 9 et 12 mois : réfraction, strabisme + réfraction après
cycloplégie (amblyopie).
## 4 Strabisme de l\'enfant
= symptôme !
Examen motilité (paralytique vs motilité normale) Ttt : correction
optique ± occlusion œil si amblyopie (chir si persistance)
## 5 Diplopie (binoculaire)
Clinique : dédoublement même direction, disparaît à l\'occlusion d\'un
œil
Exament : motilité, cover-test, verre rouge, Lancaster
Étiologie :
- anévrisme intracrânien++ (jeune, céphalée, 0 FR vasc),
- tumeur (25%), SEP (10%) révélee, myasthénie
- autres : accidents vasculaires ischémique/hémorragiques
## 6 Œil rouge/douloureux
BAV, douloureux : cf [tab:oeil_bav_douloureux](tab:oeil_bav_douloureux).
Sans BAV, douloureux :
- épisclérite (ttt = corticoïdes)
- sclérite (étio = polyarthrite rhumatoïde)
- conjonctivite : allergique (collyre), virale++ (ttt =0)
- sd sec oculaire++ (ttt = substituts lacrymaux)
Sans BAV, sans douleur :
- conjonctivite (bactérienne : collyre antiseptiqu)
- hémorragie sous-conjonctivale (HTA, trouble coag ?)
::: table
```{=latex}
\caption{Avec BAV, douloureux: étiologies}
```
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
Type Symptômes Étiologie Ttt
------------------------- ------------------------------------------------------------------------------------- ---------------------------- ------------------------------------------------------
Glaucome aigu par FA Douleur++, \"bille de verre\" inhib. anhydrase carbonique, solutés hyperosmolaires
hypotoniques, myotique (collyre)
Uvéite antérieure aigǜe Synéchies iridocristaliniennes inconnue (50%)
Tyndall`\tablefootnote{Protéines, c. inflammatoires dans l'humeur aqueuse}`{=latex} Spondylarthrie ankylosante
précipités rétro-cornéens herpès, sarcoïdose mydriatiques, corticoïdes (collyre)
Kératite aigüe Ulcération (à la fluorescine) Herpès, bactéries
Glaucome NV Néovaisseaux sur l\'iris Hypotonisants, photocoag/anti-VEGF
Endophtalmie post-op œdème palpébral, hyalite`\tablefootnote{Inflammation du corps vitré}`{=latex}
```{=latex}
}
```
:::
## 7 Altération de la fonction visuelle
BAV progressive
- transparence anormale : cataracte (ttt = chir), cornée, vitré
- sinon :
- atteinte nerf optique : glaucome chronique à AO (ttt =
hypotonisants, chir), neuropathies toxiques
- atteinte rétine = rétinopathies pigmentaires, ou macula = DMLA,
maculopathies héréditaires, œdème maculaire, antipaludéens,
séparation vitré/macula
Altération CV
- ateinte rétine (scotomes centrau, déficits périph)
- atteinte nerf optique : SEP, NOIA, toxique
- atteinte chiasma optique : adénome hypophysaire
- atteinte rétrochiasmatique : vasc, tumoral, trauma
## 8 Anomalies de la vision d\'apparition brutale
BAV, œil rouge douloureux : cf [*chap 6*]{.spurious-link
target="6 \\OE{}il rouge/douloureux"}
BAV, œil blanc indolore :
-------------------------------- ------------------------------------------- -----------------------------------
FO non visible hémorragie intra-vitréenne Écho B
uvéite du vitré
FO visible anormale occlusion artère centrale rétine mydriase aréflexique
macula rouge cerise
(urgence si Horton)
occlusion veine centrale rétine œdème papillaire
hémorragie rétiniennes dissémines
nodules cotonneux
DMLA métamorphopsies brutale
décollement rétine rhegmatogène myodésopsies, phosphène
(semi-urgence)
neuropathie optique ischémique antérieure `\dec`{=latex} RPM direct
œdème papillaire
FO visible normale névrite optique rétrobulbaire scotome central
Cécité monoculaire transitoire
-------------------------------- ------------------------------------------- -----------------------------------
## 9 Prélèvement de cornée
Faire sérologies HIV, HTLV, VHB, VHC, syphilis
CI : locale, infectieuses (sida, rage, Creutzfeld-Jakob, hépatite),
neuro inexpliqué, démence
## 10 Greffe de cornée
Transfixiantes ou juste endothelium.
Indications : trauma, kératocône, kératite herpétiques/infectieuse
## 11 Traumatismes oculaires
Globe ouvert, corps étranger : si doute TDM (☡ pas d\'IRM si corps
étranger)
Chir en urgence : recherche/suture plaie du globe, extraction CE
intraoculaire, plaie du cristallin
## 12 Brûlures oculaires
Brûlures basiques = grave ☡
Ttt urgence = lavage 20min au sérum phys puis collyre corticoïdes
## 13 Cataracte
Opacification du cristallin.
Diag clinique : BAV progressive en vision de loin, lampe à fente
Étiologies : âge, diabète, crorticoïdes, traumatique
Ttt = chir (extraction par phacoémulsification puis implant en chambre
postérieure)
Complications : endophtalmie (ATB !), décollement rétine, œdème
maculaire
## 14 Glaucome chronique
Glaucome primitif à pression élevée (≈ occidentaux), ou pression
[normale]{.underline} (≈ asiatique)
FR: âge, hypertonie oculaire. Physio : perte accélée des fibres
optiques.
Caractéristiques : `\inc`{=latex} excavation papille, altération CV
Ttt à vie : prostaglandine ou β-bloquants[^52] (collyre), laser
(trabéculoplastie) ou chir (trabéculectomie) possible
## 15 Dégénérescence maculaire liée à l\'âge
1ere cause de malvoyance après 50 ans.
Diag = AV, FO, OCT (cf tab [tab:dmla](tab:dmla))
::: table
```{=latex}
\caption{Formes de DMLA}
```
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
Forme Clinique FO Ttt
------------------------- ------------------------------- -------------------------------------------------------------------- -------------------------------------
Débutante /drusen/`\tablefootnote{Petites lésions profondes jaunes}`{=latex} vit E, C, zinc, lutéine, zéaxantine
Atrophique BAV sévère, scotome central atrophie épith. pigment. ∅
Exsudative BAV, métamorphopsies brutales œdème intrarétienne anti-VEGF
(néovaisseux ss rétine) décollement maculaire exsudatif
```{=latex}
}
```
:::
## 16 Occlusions artérielles rétiniennes
Artère centrale de la rétine
- Diag =
- BAV brutale, œil blanc indolore, mydriase aréflective
- FO : macula \"rouge cerise\"
- Étiologie : embolies (athémore carotidien), maladie de horton =
urgence
- CAT = urgence . Très mauvais pronostic fonctionnel
- ttt de l\'étio (antiagrégant/anti vit-K)
Branche de l\'ACR : pronostic visuel bon (amputation), pas d\'Horton
## 17 Occlusions veineuses rétiniennes
Veine centrale de la rétine
- Diag (facile) : BAV brutale, FO = dilatation veineuse, nodules
cotonneux, hémorragies disséminées, œdème papillaire
- FR : \> 50 ans avec FR vasc, hypertonie oculaire
- 2 formes (angiographie fluorescine)
::: table
```{=latex}
\caption{Formes d'OVR}
```
```{=latex}
\centering
```
```{=latex}
\adjustbox{max width=\linewidth}{
```
Forme Évolution TTT
---------------- ---------------------------- -------------------------------------------------------------
non ischémique normalisation anti-VEGF, surveillance mensuelle
ou ischémique
ischémiques pas de récupération fonct. PPR`\tablefootnote{Photocoagulation panrétinienne}`{=latex}
glaucome NV ☡ PPR en urgence
```{=latex}
}
```
:::
Branche veineuse rétinienne : évolution favorable / hémorragie du vitré
(pas de GNV !)
## 18 Pathologies des paupières
Cf Table [tab:paupieres](tab:paupieres)
Autres : entropion (sénile/paralysie VII), ectropion, ptosis (penser
anévrisme IC ), lagophtalmie
----------- ------------------ ----------------------- ------------
Orgelet follicule du cil infection bactérienne ATB 8 j
Chalazion glande Meibomius inflammation corticoïde
----------- ------------------ ----------------------- ------------
: Pathologies des paupières
Tumeurs malignes : carcinome basocellulaire/épidermoide, mélanique,
carcinomes sébacés
## 19 SEP
20% inaugurant SEP. 50% de SEP à 15 ans. Formes :
- neuropathie optique :
- BAV variable, douleurs rétro-oculaire, pupille Marcus-gunn
- scotome (caeco) central, dyschromatopsie d\'aexe rouge-vert
- IRM
- Ttt = corticoïdes + (SEP) interféron
- paralysie du VI, nystagmus, périphlébite rétinienne
## 20 Neuropathie optique ischémique antérieure
Diag = BAV brutale indolore
- FO : œdème papillaire. Examen CV ++ (déficit altidudinal)
Étiologies
- artériosclérose (freq) : FR. Pas de ttt efficaces
- maladie de Horton = urgence . Bio = VS `\inc`{=latex}, CRP
`\inc`{=latex} `\thus`{=latex} corticothérapie générale forte dose
## 21 Rétinopathie diabétique
[]{#sec:retinopathie_diabetique} 1ère cause de cécité chez \< 50 ans.
30% des diabétique
- maculopathie diabétique
- rétinopathie diabétique : non proliférante (hémorragies rétiniennes
dans 4 quadrans/dilatations veineuses 2 quadrants/AMIR 1 quadrant)
puis proliférante (néovaisseaux)
- dépistage annuel FO, OCT
- ttt : équilibre glycémie et TA++. Photocoagulation panrétinienne,
anti-VEGF
## 22 Orbitopathie dysthyroïdienne
Maladie de Basedow++, thyroïdite d\'Hashimoto
Manif = exophtalmie (bilatérale, axile, non pulsatile, indolore),
rétraction paupière, diplopie
TSH effondrée, scanner, IRM, {CV, couleurs, PEV} Ttt
- médical : hyperthyroïdes, anti-inflammatoire si score CAS ≥ 3
- si grave : corticothérapie générale, chir
## 23 Rétinopathie et choroïdopathie hypertensive
Rétinopathie hypertensive : si HTA sévère.
- hémorragie en flammèches superficielles, œdème maculaire
- hémorragies profondes, rondes, nodules cotonneuxs
- pas BAV
Choroïdopathie hypertensive : nécrose de l\'épithelium pigmentaire,
cicatrices (décollement de rétine exsudatif si sévère)
Artériosclérose : asymptomatique, irréversibles. Signe du croisement,
`\inc`{=latex} reflet artériolaire
# Footnotes
[^1]: Arrêt \< 3 ans
[^2]: \> 50 ans ♂, \> 60 ans ♀
[^3]: Père \< 55 ans, mère \< 65 ans
[^4]: Si asymptomatique, chir si dilatation VG/fraction d\'éjection \<
60%
[^5]: Même critère que précédemment : ≥ 55*m**m*
[^6]: Prothèse mécaniques
[^7]: Bioprothèses
[^8]: Asymptomatique, systolique (!), proto/mésosystoliques,
éjectionnels, faible intensité, doux
[^9]: Rétrécissement aortique, EP, cardiomyopathies obstructives,
tamponnades, thromboses de valves
[^10]: TV, bradycardies par bloc AV/dysfonction sinusale
[^11]: Orthostatiques iatrogène/sujet âgé ou hypotension réflexe
[^12]: Retour sinal \> 7j/cardioversion
[^13]: Échec cardioversion
[^14]: Turgescence jugulaire, reflux hépatojugulaire, HMG, œdème périph,
ascite
[^15]: Calmé par froid, surélévation, marche
[^16]: sus-ST concave, T plates, T négatives, normales
[^17]: Ou enregistrement polygraphie ventilation
[^18]: Pas d\'effort respi, contrairement au SAOS
[^19]: Systémique en cas d\'urgence.
[^20]: Obstruction des voies aérienne variable
[^21]: Jusqu\'au contrôle
[^22]: Ou ARA II, β-bloquants
[^23]: Toux sèche, invalidande
[^24]: Risque = asphyxie
[^25]: Silence auscult, matité, 0 transmission cordes vocales, souffle
pleurétique
[^26]: spiculés, polylobé, irrégulier
[^27]: Ou macrolides, pristinamycine
[^28]: I = ADP médiastin brchoniques hilaires bilat, symétriques non
compressives. II = idem + parenchyme. III = parenchyme seulement. IV
= fibrose
[^29]: Fièvre, arthalgie, érythmèe noueux MI, ADP médiastinale
[^30]: Hypoxie-hypocapnie
[^31]: Hypothalamo-hypophysaire
[^32]: Ou si testostérone ∈ \[2.3,3.2\] et SHBG et index T libre bas
[^33]: Nodule de la cortico-surrénale
[^34]: Tumeur de la médullo-surrénale
[^35]: Hirsutisme, acné
[^36]: Faim brutale, trouble concentration, moteurs, sensitifs, visuels,
convulsion, confusion
[^37]: Coma hypoglycémique possible
[^38]: Phéochromocytome, hyperparathyroïdie
[^39]: Arrêt si neutrophiles \< 1G/L
[^40]: Faciès \"lunaire\", voix rauque, macroglossie, hypoacousie
[^41]: Asthénie, somnolence, hypothermie
[^42]: Obj: TSH ∈ \[0.5,2.5\]mUI/L.
[^43]: Élargissement extrémité, visage (prognathisme)
[^44]: Aldostérone : réabsorption Na+ et sécrétion K+
[^45]: Glucocorticoïdes et minéralocorticoïdes respectivement.
[^46]: Doser Ac anti-21 hydroxylase
[^47]: Calcifications aux scanner
[^48]: IMC \> 28 kg/m^2^, HTA, HDL \< 0.35g/L ou TG \> 2g/L ou
dyslipidémie, ATCD diabète (familiale, gestationnel)
[^49]: Sauf insuf. coronarien, rétinopathie proliférante non stabilisée
[^50]: par `\dec`{=latex} élimination rénale, par sortie du K+ de la
cellule respectivement.
[^51]: Si sécrète hCG : ttt = conservateur/chimie, si sd Turner : ttt =
gonadectomie préventive
[^52]: `\inc`{=latex} élimination humeur aqueuse et `\dec`{=latex}
sécrétion respectivement.
% Created 2021-04-22 Thu 11:27
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\author{Alexis Praga}
\date{\today}
\title{Superfiches}
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\begin{document}
\maketitle
\tableofcontents
\section{Cardiologie}
\label{sec:org13b2d0c}
\subsection{218 Athérome}
\label{sec:org5a6b9bb}
1ere cause mortalité dans monde.
Prévention : aspirine, statines, antihypertenseurs
Si rupture de plaque : aspirine, clopidogrel, héparine
Localisations : coronaires, aorte, carotides, artères MI
Prévention secondaire : aspirine/clopidogrel, statines, IEC/ARA II
\subsection{219 Facteur de risques cardio-vasculaires}
\label{sec:orgda2c634}
FR : LDL > 1.6G/L, HDL < 0.4g/L, tabac\footnote{Arrêt < 3 ans}, âge\footnote{> 50 ans \male{}, > 60 ans \female{}}, tension \(\ge\) 140/90, diabète, ATCD
coronaires familiaux\footnote{Père < 55 ans, mère < 65 ans}
Objectifs : tension < 140/90, LDL < 1g/L
\subsection{220 Dyslipidémies}
\label{sec:orgb72c816}
Haut risque : maladie vasculaire/coronaire, diabète 2 et atteinte rénale,
\(p(\text{evt coronaire à 10 ans}) > 0.2\)
Ttt : hypercholestorémie, hyperlipidémies mixtes : statines. Hypertriglycéridémie : fibrate si TG > 4g/L
\subsection{334 Syndromes coronariens aigüs}
\label{sec:org3472b26}
\begin{table}
\caption{SCA}
\centering
\adjustbox{max width=\linewidth}{
\begin{tabular}{llll}
Type & douleur & PEC & Ttt\\
\hline
Angor stable & angineuse & ECG d'effort & Dérivés nitrés (crise)\\
& à l'effort & & Aspirine, \(\beta\)-bloquants\\
& trinitro-sensible & & \\
SCA sans ST & angineuse & \faHospital{} urgente & Aspirine, inhib P2Y12\\
& spontanée > 20min & ECG, troponine & , héparine, \(\beta\)-bloquants, statines\\
& & & Angioplastie percut.\\
SCA ST+ & angineuse & ECG & Angioplastie si < 120min\\
& repos > 30min/jour & & Sinon FIV\\
& trinitro-résistante & & Morphine, \(O_2\), aspirine\\
& & & , inhib P2Y12, héparine (crise)\\
\end{tabular}
}
\end{table}
ST- : sous-ST pendant la douleur \(\ge\) 1 mm dans 2 dérivations contigües
ST+ : sus-ST \(\ge\) 2mm (\(V_1\) à \(V_6\)) ou \(\ge\) 1mm (autres) dans 2 dérivations contigües
\subsection{228 Douleur thoracique aigüe}
\label{sec:org2ccf7fd}
Examens sytématiques : ECG 12 dérivation, RX pulmonaire, troponines
\begin{table}[htbp]
\caption{4 urgences = PIED}
\centering
\begin{tabular}{lll}
Urgence & Caractéristiques & Examens\\
\hline
Péricardite (tamponnade) & signes droits\tablefootnote{Turgescence jugulaire, reflux hépatojugulaire}, choc avec tachy, PAs < 90mmHg & échocardio\\
IDM & douleur spontanée de repos > 20min & ECG, troponine x2\\
Embolie pulmonaire & terrain, douleur basithoracique + dyspnée & D-dimère \thus angioscan/scinti\\
Dissection aortique & douleur déchirement, irradie dans dos & echo cardio et ETO\\
& & \\
\end{tabular}
\end{table}
Non CV : 4P = pneumonie, pleurésie, pneumothorax, pancréatite
\subsection{223 Artériopathie oblitérante (aorte, MI)}
\label{sec:org31627a2}
AOMI : pronostic grave !
\begin{itemize}
\item asymptom. - claudication intermittente - douleur ischémique de repos -
ulcération/gangrène
\item diag: IPS < 0.70 ( + écho-doppler MI en pratique)
\item ttt : FR, antiagrégant, statines, IEC + arrêt tabac, marche \textpm{}
revascularisation (stent/chir)
\end{itemize}
Anévrisme aorte abdominale : âge, tabac, ATCD familiaux
\begin{itemize}
\item scanner abdopelvien/IRM = référence
\item asymptomatique : chir si \diameter \(\ge\) 50-55mm
\item symptomatique : urgence
\end{itemize}
Ischémie aigüe des membres inférieurs = urgence (embolie/thrombose)
\begin{itemize}
\item diag : douleur brutale, intense, broiement avec impotence fonctionnelle et membre froid, livide, douleur palpation musc
\item ttt : anticoagulant, antalgique niv. 3, \(O_2\) et revasc. chir
\end{itemize}
\subsection{231 Rétrécissement aortique}
\label{sec:org3fcf757}
Pronostic vital mis en jeu si symptômes !
Auscult : souffle systolique éjectionnel au foyer aortique
Diag : ETT = \(V_{max} > 4m/s\), gradient moyen > 40mmHg, surface aortique <
1\(cm^2\)
Ttt : chir si symptomatique = valve mécanique ou bio
\subsection{231 Insuffisance mitrale}
\label{sec:org0a43992}
Classif. de Carpentier (I à III)
Auscult : souffle apexo-axillaire holosytolique de régurgitation dès B1
Examen : ETT \textpm{} ETO
Ttt : chir = reconstruction valve ou prothèse (bio/méca)\footnote{Si asymptomatique, chir si dilatation VG/fraction d'éjection < 60\%}
\subsection{231 Insuffisance aortique}
\label{sec:org8850875}
Formes : dystrophiques (valves normales mais non jointive), bicuspidie aortique
Auscult : souffle diastolique. ETT = diagnostic
Opérer :
\begin{itemize}
\item urgence si chronique volumineuse symptomatique ou aigüe volumineuse
\item si dystrophie et aorte dilatée\footnote{Même critère que précédemment : \(\ge\) 55mm}, si chronique volumineuse asymptomatique et (aorte
dilatée, FEVG < 50\%\ldots{})
\end{itemize}
\subsection{150 Surveillance des porteurs de valves, prothèses vasculaires}
\label{sec:org81695d4}
Complications : embolie, thromboses\footnote{Prothèse mécaniques}, désinsertion, EI ,
dégénérescence\footnote{Bioprothèses}, ttt anticoagulant
INR \(\in\) [2.5, 4] à vie pour prothèse mécanique
\subsection{149 Endocardite infectieuse}
\label{sec:org59b0c2e}
Diag = ETO. Critères de Duke : 2 majeur/1 majeur et 3 mineurs/5mineurs
\begin{itemize}
\item majeurs :
\begin{itemize}
\item hémoc = typique sur 2HC ou positive > 12h ou \emph{C. burnetii}
\item végétation/abcès/désinsertion (écho) ou nv souffle régurgitation valvulaire
\end{itemize}
\item mineurs : cardiopathie à risque, > 38\(^\circ\), complication vasc,
immunologique
\end{itemize}
Complications : insuf cardiaque , embolie septiques, neuro , rénale
Ttt :
\begin{itemize}
\item streptocoques (oraux/groupe D) : amoxicilline + gentamicine
\item staphylocoques : cloxacilline si sensible (sinon vancomycine)
\end{itemize}
\subsection{236 Souffle cardiaque chez l'enfant}
\label{sec:org8582cd5}
Néonatale : coarctation aortique préductale (chir urgente ), transposition des gros vaissaux,
malformations complexes
Nourisson (2M - marche) : shunt gauche-droite (communication intraventricul), tétralogie de Fallot
2A-16A : souffles fonctionnels\footnote{Asymptomatique, systolique (!), proto/mésosystoliques, éjectionnels,
faible intensité, doux}
\subsection{337 Malaise, perte de connaissance}
\label{sec:org1e40ef4}
\begin{itemize}
\item Éliminer épilepsie
\item Éliminer urgence (SCA, EP\ldots{}.)
\item ECG, clinique : cause évidente = mécanique\footnote{Rétrécissement aortique, EP, cardiomyopathies obstructives, tamponnades, thromboses de valves}, électrique\footnote{TV, bradycardies par bloc AV/dysfonction sinusale}, hypotensive\footnote{Orthostatiques iatrogène/sujet âgé ou hypotension réflexe} ?
\item Sinon chercher cardiopathie (échocardio)
\end{itemize}
\subsection{230 Fibrillation atriale}
\label{sec:org588e7d7}
ECG indispensable : pas de P, QRS irréguliers
Risques = insuf cardiaque, thromboembolique artériel systémique
Étiologie : HTA, valvulopathies
Ttt
\begin{itemize}
\item 1er épisode : HNF seule
\item FA persistante\footnote{Retour sinal > 7j/cardioversion} : 3 semaines HNF IV puis choc électrique puis 4 semaine anticoagulants oraux
\item FA permanente\footnote{Échec cardioversion} : bradycardisants (\(\beta\)-bloquants)
\item FA paroxystique : anti-arythmique et bradycardisants
\end{itemize}
\subsection{234 Troubles de la conduction intracardiaque}
\label{sec:org7893052}
Bradychardie grave = urgence
Ttt : tachycardisants (atropine, catécholamine)
\begin{table}[htbp]
\caption{EEP = étude électrophysiologique endocavitaire}
\centering
\begin{tabular}{llll}
Type & Causes & Diagnostic & Pacemaker\\
\hline
Dysfonction & dégénérative & ECG + Holter & Si symptomes\\
sinusale & médicaments, vagal & & \\
BAV & hyperkaliémie & ECG \textpm{} Holter/EEP & BAV II symptom.\\
& & si paroxystique & BAV III non curable\\
BdB & dégénérative & ECG + EEP & Si symptômes\\
\end{tabular}
\end{table}
\subsection{229 ECG}
\label{sec:org7826340}
\begin{center}
\begin{tabular}{lll}
Hypertrophie atriale & gauche : P > 0.12s (largeur) & droite : P > 2.5mm (hauteur)\\
Hypertrophie ventriculaire & gauche : \(SV_1 + rV_5 > 35\) mm & droite +110\(^\circ\)\\
\hline
BdB & gauche: QRS > 0.12s ) & droite : QRS > 0.12s\\
& et (rS ou QS en V\textsubscript{1}) & et RsR' en V\textsubscript{1}\\
Hémibloc & antérieur : \(S_3 > S_2\) & postérieur : \(S_1Q_3\)\\
BAV & I : PR > 0.2s , II : \inc PR & III : aucun P\\
Angor & sous-ST & \\
IDM & sus-ST convexe (vers le haut) & \\
Péricardite aigüe & sus-ST concave & \\
\end{tabular}
\end{center}
Troubles supraventriculaire : FA (100-200/min), flutter atrial (300/min), tachy. atriale,
tachy. jonctionnelle, extrasystole
Troubles ventriculaires : tachy. ventricale, fibrillation ventricalure (
absolue), torsade de pointe
\subsection{235 Palpitations}
\label{sec:orgae01964}
Éliminer urgences immédiates (tachy à QRS large !!)
Fréquents : fibrillation/flutters atriaux, tachy jonctionnelle
Tachy sinusale (grossesse, hyperthyroïde, SAS, alcoolisme)
\subsection{232 Insuffisance cardiaque}
\label{sec:org09d0a0a}
Grave : 50\% de DC à 5 ans
EC : dyspnée d'effort, signes d'IC droite\footnote{Turgescence jugulaire, reflux hépatojugulaire, HMG, \oe{}dème périph, ascite}
Examens : ECG, RX thorax, dosage BNP, \emph{ETT}
Cause : ischémie, HTA, cardiomypathie
IC aigüe \(\approx\) OAP : polypnée, sueurs, cyanose, expectorations "mousseuses
saumon", crépitants \thus PEC immédiate
\begin{table}[htbp]
\caption{Ttt insuffisance cardiaque}
\centering
\begin{tabular}{ll}
IC à FE < 40\% & diurétiques + IEC + \(\beta\)-bloquants\footnotemark.\\
& Si échec : ivabradine puis défibrillateur auto\\
IC à FE conservée & mal définie (idem ?)\\
OAP & assis, furosémide, dérivés nitrés, HBPM\\
\end{tabular}
\end{table}
\footnotetext{Pas si crise aigüe ! \danger}
\subsection{221 Hypertension artérielle}
\label{sec:orgd64fbff}
3 catégories. Étiologies :
\begin{itemize}
\item Essentielles (90\%)
\item Secondaire : néphropathie parenchym., HTA rénovasculaire, phéochromocytome, sd Conn,
coarctation aortiques, SAS, médicaments, HTA gravidique
\end{itemize}
Examens : glycémie, cholestérol, kaliémie, créat, BU, ECG
Complications : rein, neuro, CV
Ttt : objectif < 140/90 \thus hygiéno-diét et \{IEC, diurétiques thiazidiques, \(\beta\)-bloquants, ARA II
\subsection{225 Insuffisance veineuse chronique}
\label{sec:orgad66ae8}
FR : varices = âge, ATC, obésité, grossesse; MTEV = immobilisation, K, anomalies hémostase
Clinique : jambes lourdes\footnote{Calmé par froid, surélévation, marche}, dermite ocre, varices
Examen : echo-doppler veineux des MI
Ttt (non curatif) : contention, hygiène de vie, invasif
\subsection{233 Péricardite aigüe}
\label{sec:orgd0cd9f6}
Douleur : thoracique, trinitro-résistant, \inc inspiration, \dec assis en avant
Examens : ECG (4 phases\footnote{sus-ST concave, T plates, T négatives, normales}), marqueurs de nécrose cardio, sd inflammatoire, \emph{échocardio}
Étiologie : péricardite aigüe virale, néoplasiques, tuberculeuse surtout
Ttt : AINS, colchicine
Complications : tamponnade = urgence (drainage/ponction)
\subsection{327 Arrêt cardiocirculatoire}
\label{sec:org6e7212a}
ABCD : maintien voies Aéoriennes, assistance respi (B), massage Cardiaque,
Défibrillation et Drogues
Ttt : adrénaline 1mg/4min et après 2eme choc amiodarone (300mg dans 30mL)
Ventilation, hypothermie
Étio : FA, bradyc, asystolie
\subsection{264 Diurétiques}
\label{sec:orge340436}
\begin{table}[htbp]
\caption{Diurétiques}
\centering
\begin{tabular}{llll}
Type & Molécule & Indication & ES\\
\hline
de l'anse & furosémide & insuf cardiaque, IR & hypoK, déshydratation\\
& & \oe{}dème/ascite cirrhose & \\
thiazidique & hydrochlorothiazidique & HTA & hypoK\\
épargnant le potassium & spironolactone & Insuf cardiaque, HTA & hyperK, IR\\
\end{tabular}
\end{table}
\subsection{326 Antithrombotiques}
\label{sec:org1a7af3e}
\begin{table}
\caption{Antithrombotiques}
\centering
\adjustbox{max width=\linewidth}{
\begin{tabular}{llll}
Type & Action & Indication & Dangers\\
\hline
Antiagrégants & aspirine & AVC, coronaropathie & \\
& \emph{clopidogrel, prasugrel, ticagrelor}\tablefootnote{Inhibiteurs P2Y12} & SCA, post-angio coronaires & hémorr. cérébrale (prasugrel)\\
Héparines & HNF, HBPM, \emph{fondaparinux} & urgence : TVP, EP, SCA & \danger hémorragie, thrompopénie\\
Anti-vit. K & Oral, relais héparine & FA, TVP, EP & \danger hémorragie\\
& & valve cardiaque & \\
Nv anticoag oraux & \emph{dabigatran, rivaroxaban, apixaban} & & Surv. rein\\
& rapide, & & 0 antidote\\
Thrombolytique & \emph{-kinase}, \emph{-téplase} & EP grave, AVC < 6h30 & \\
& & IDM < 6-12h & \\
\end{tabular}
}
\end{table}
\section{Pneumologie}
\label{sec:org60a8ad8}
\subsection{73 Addiction au tabac}
\label{sec:org987c7a2}
16 millions de fumeurs en France. 1 fumeur sur 2 décède d'une malaide liée au
tabac.
Cause 90\% K bronchopulomaire (25\% si passif)
Sevrage : TCC, éducation thérapeutique, substituts nicotiniques.
\subsection{108 Troubles du sommeil de l'adulte}
\label{sec:org9bfdbee}
Sd d'apnée obstructive du sommeil :
\begin{itemize}
\item diagnostic : \{ronflement, pause respi, nycturie et somnolence diurne\} et
polysomnographie\footnote{Ou enregistrement polygraphie ventilation}
\item ttt : pression positive continue
\end{itemize}
Autres : sd d'apnée centrale\footnote{Pas d'effort respi, contrairement au SAOS} (IC cardiaque sévère !), insuf respi chronique avec
hypoventilation alvéolaire, sd obésite hypoventilation (ttt = VNI)
\subsection{151 Infections broncho-pulmonaires communautaires}
\label{sec:org100754b}
Bronchite aigüe : virale++, diag clinique (épidémie, toux, expectoration, pas de
crépitants), ttt symptomatique
Exacerbation BPCO (cf item 205)
Pneumonie aigüe communautaires : grave. Cf table \ref{tab:orgb6d9cd9}
\begin{itemize}
\item Clinique : signes auscult en foyer, crépitants. RX thorax !
\item Ttt : ATB urgence (pneumocoque !), réévaluation 48-72h
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:orgb6d9cd9}PAC}
\centering
\begin{tabular}{lll}
Pneumocoque\tablefootnote{Pas de transmission interhumaine} & Légionellose\tablefootnote{Pas d'isolement} & Atypiques\\
\hline
fréquent++ & progressif & virale \thus inhib neuramidases\\
début brutal, fièvre & myalgies & \emph{Mycoplasmia pneumoniae}\\
RX: condensation systématisée & macrolides & \emph{Chlamydia pneumoniae}, \emph{psitacci}\\
amoxicilline & & \thus macrolides\\
& & RX: opacités multifocales\\
\end{tabular}
\end{table}
\subsection{151 Tuberculose}
\label{sec:orgfffce74}
Diag = IDR/IFN \(\gamma\) si primo infection. Sinon bacille de Koch sur prélèvement
Cf table \ref{tab:org5dc68ce}.
Diag = ED ou culture Löwenstein \thus granulome épithélioïde gigantocellulaire
avec nécrose caséeuse
\begin{table}[htbp]
\caption{\label{tab:org5dc68ce}Formes pulmonaires}
\centering
\begin{tabular}{lll}
Forme & pulmonaire & miliaire\\
\hline
Clinique & AEG, fièvre, sueurs nocturnes & idem, VIH !\\
RX & nodules, infiltrats, cavernes & sd interstitiel\\
Prélèvement & crachat/tubage/fibro & biopsie\\
Diag & sécrétions/tubages & LCS, hémoc, biopsie\\
\end{tabular}
\end{table}
Ttt (PERI) : isoniazide (6M), rifampicine (6M), ethambutol (2M), pyranizamide (2M).
Vaccination !
\subsection{180 Accidents du travail}
\label{sec:org3948441}
Asthme (10-15\%), BPCO (10-20\%), K (mésothéliome ou bronchique primitif), PID
(hypersensibilité, silicose, bérylliose, sidérose, asbestose)
Amiante : K ou pleural
Idemnité : assurance maladie ou FIVA
\subsection{182 Hypersensibilités et allergies respiratoires}
\label{sec:orga61bcb6}
Allergie : le plus souvent médiée par IgE. Asthme et rhinite (cf item 184)
Diag = prick test (\diameter \(\ge\) 3 mm/témoin)
Ttt : éviction, \{antihistaminique (rhinite seulement), corticoïdes\footnote{Systémique en cas d'urgence.},
(adrénaline si choc)\}, immunothérapie spécifique
\subsection{184 Asthme, rhinite}
\label{sec:org98b5459}
Asthme :
\begin{itemize}
\item suspicion sur clinique : dyspnée, gêne, respi, siflement \emph{variable et réversible}
\item diag\footnote{Obstruction des voies aérienne variable} : TVO (VEMS/CVF < 0.7) réversible aux BDCA (\(\ge\) +200mL et \(\ge\) +12\%)
\item ttt de fond \footnote{Jusqu'au contrôle}= corticostéroïdes inhalés (voire anti-leucotriènes, voire cortico
oraux) et symptomatique = \(\beta\)2-mimétique courte durée
\item \{\} exacerbation grave : SAMU + \(\beta\)\textsubscript{2}-mimétique \(\rightarrow\) \faHospital : \(\beta\)\textsubscript{2}-mimétique nébulisé, corticoïdes
oraux, \(O_2\)
\end{itemize}
Rhinite :
\begin{itemize}
\item PAREO : Prurit, Anosmie, Rhinorrhée, Éternuement, Obstruction nasale
\item ttt : antihistaminiques/corticoïdes nasaux
\end{itemize}
\subsection{188, 189 : Pathologies auto-immunes}
\label{sec:org19b2346}
Si ttt pour connectivite, vascularite,
penser 1. infenction 2. médicament 3. manifestation maladie 4. manifestation
indépendante
Cf Table \ref{tab:org541a558}
\begin{table}[htbp]
\caption{\label{tab:org541a558}Manifestations respiratoires}
\centering
\begin{tabular}{ll}
Sclérodermie systémique & PID, HTAP\\
Lupus érythémateux & Pleurésie lupique, sd hémorragie alvéolaire\\
Polymyosite & PID chronique/aigùe\\
Sd Gougerot-Sjögren & Toux chronique , PID\\
Granulomatose avec polyangéite & Nodules\tablefootnote{Évoluant vers excavation, infiltrats diffus bilatéraux}\\
Granulomatose éosinophile avec polyangéite & Asthme, pneumopathie à éosinophiles\\
Polyangéite microscopique & Sd hémorragique alvéolaire\\
\end{tabular}
\end{table}
\subsection{199 Dyspnée aigüe et chronique}
\label{sec:org38ecaf7}
Examens : ECG, RX thorax, gaz du sang, D-dimère, BNP, NFS a minima
Étiologies : cf Tab \ref{tab:org902aa45}, \ref{tab:org89d059b}
\begin{table}[htbp]
\caption{\label{tab:org902aa45}Étiologies de dyspnée aigüe (E = enfant)}
\centering
\begin{tabular}{lll}
Inspiratoire & Expiratoire & Sinon\\
\hline
corps étranger (E) & asthme (sibilants) & EP (ascult normale)\\
épiglottite (E) & BPCO (ATCD, sibilants) & pneumothorax, épanchement pleural\\
laryngite (E) & OAP (crépitants, expector mousseuse) & pneumopathie infectieuse\\
\oe{}dème de Quincke & & OAP (crépitants, expector mousseuse)\\
& & \\
\end{tabular}
\end{table}
\begin{table}[htbp]
\caption{\label{tab:org89d059b}Étiologies de dyspnée chroniques}
\centering
\begin{tabular}{lll}
Sibilants & Crépitants & Auscult normale\\
\hline
BPCO & PID & EP\\
asthme & Insuf cardiaque gauche) & Neuromusc\\
Insuf cardiaque gauche & & Pariétale, hyperventilation\\
\end{tabular}
\end{table}
\subsection{200 Toux chronique}
\label{sec:orga69aa40}
Diagnostic principaux : rhinorrée chronique, RGO, asthme, tabac, médicaments (IEC)\footnote{Ou ARA II, \(\beta\)-bloquants}, coqueluche
Pas d'orientation (dans l'odre) : test rhinorrée post chronique, EFR (asthme),
RGO, sinon antitussif\footnote{Toux sèche, invalidande}/kiné respi
Penser bronchectasies si toux productive quotidienne, hémoptysies RX normale
\thus diag = TDM , ttt = drainage \(\pm\) ATB si exacerbation
\subsection{201 Hémoptysie}
\label{sec:orgf26ec33}
Étiologies : tumeurs bronchopulomaires, bronchectasies, tuberculose,
idiopathique, (EP, ICG)
PEC : confirmer hémoptysie, angio-scanner (ou RX thorax)
Ttt 1ere intention : \faHospital : \(O_2\), terlipressine, protection voie aériennes\footnote{Risque = asphyxie}
\subsection{202 Épanchement pleural}
\label{sec:org2de3370}
Clinique : douleur thoracique, toux sèche + sd pleural\footnote{Silence auscult, matité, 0 transmission cordes vocales, souffle pleurétique}
RX (opacité dense, homogène, concave) et ponction (sauf ICG) !
Selon liquide, voir Tab. \ref{tab:orge05b891}
\begin{table}[htbp]
\caption{\label{tab:orge05b891}Types d'épanchement pleural}
\centering
\begin{tabular}{ll}
Transsudat & Exsudat\\
(prot < 25g/L, liquide clair: mécanique) & (prot > 35g/L, aspect variable : inflammatoire, )\\
\hline
\emph{ICG} & \emph{Tumorale} : K bronchique, mésothéliome pleural\\
cirrhose & \emph{Tuberculose}\\
sd néphrotique & bactérienne, virale\\
& EP\\
\end{tabular}
\end{table}
Si abondant/purulent/à germe : ttt anti-infectieux + évacuation du liquide
pleural
\subsection{203 Opacités et masses thoraciques : tab. \ref{tab:org2a34048}}
\label{sec:org7fd193d}
\begin{table}[htbp]
\caption{\label{tab:org2a34048}Masses thoraciques}
\centering
\begin{tabularx}{\textwidth}{XX}
Nodules (\diameter < 3 cm) & Masses (\diameter > 3cm) médiastinales\\
\hline
- malin si terrain, > 1cm, morphologie\footnotemark, fixe TEP, \inc récente taille & - antérieur : goître, K thyroïdes, thymome, lymphome\\
- chez 1 gros fumeur sur 2 et cancéreux 1 sur 10 & - moyen : lymphome\\
- scanner, TEP-FDG. Diag = ponction transpariétale & - postérieur : neurogène\\
- malignes : métastates (pulmon), primitif (bronchopulmon) & \\
\end{tabularx}
\end{table}\footnotetext[26]{\label{orgc2000f4}spiculés, polylobé, irrégulier}
\subsection{204 Insuffisance respiratoire chronique}
\label{sec:orgbbfb660}
Clinique : dyspnée, hypoxémie (PaO\textsubscript{2} < 70mmHg)
Examens : EFR, RX thorax, écho cardiaque.
Étiologies : table \ref{tab:org499d095}
\begin{table}[htbp]
\caption{\label{tab:org499d095}Étiologies IRC selon TV}
\centering
\begin{tabular}{llll}
Obstructive & Restrictive & Mixte & Pas de TV\\
\hline
BPCO & PID & DDB & HTP\\
asthme & Obésité & Mucoviscidose & \\
\end{tabular}
\end{table}
TTT : arrêt tabac, \(O_2\) longue durée (si \emph{obstructif et PaO\textsubscript{2} < 55 mmHG ou
restrictif et < 60mmHg}) ou ventilation long cours (restrictif)
\subsection{205 BPCO}
\label{sec:orgda128b0}
Clinique : tabac++, dyspnée, toux, expectoration \textpm{} distension thoracique
Diag = VEMS/CV < 0.70 \emph{non réversible}
Ttt :
\begin{itemize}
\item broncho-dilatateur courte durée/longue durée si exacerbation. + corticoïdes
inhalés si besoin.
\item Arrêt tabac, kiné respi, vaccins grippe, pneumocoque
\end{itemize}
Exacerbation BPCO : déclenché par infection
\begin{itemize}
\item diag : BPCO connu, \inc dyspnée, toux ou expectoration
\item ttt : bronchodilatateur courte durée (nébulisé) + amox-acide clav \footnote{Ou macrolides, pristinamycine}si
aggravation/\inc purulence
\end{itemize}
\subsection{206 Pneumopathies infiltrantes diffuses}
\label{sec:orgf083101}
Clinique : dyspnée d'effort (apparition progressive)
Orientation = scanner thoracique++
PID aigüe : éliminer \oe{}dème cardiogénique puis LBA. Si fièvre, ATB
probabilist (sur pneumocoque \textpm{} pneumocystose, tuberculose)
PID subaigüe/chronique :
\begin{itemize}
\item interrogatoire, LBA (fibro), scanner thoracique 1ere intention
\item sarcoïdose , insuf cardiaque gauche , médicaments , fibrose pulmonaire idiopathique lymphangite carcinomateuse
\end{itemize}
\subsection{207 Sarcoïdose}
\label{sec:org4ff6054}
Manifestations:
\begin{itemize}
\item respi : RX thorax 4 stades\footnote{I = ADP médiastin brchoniques hilaires bilat, symétriques non
compressives. II = idem + parenchyme. III = parenchyme seulement. IV = fibrose}
\item oculaire (uvéite), peau (sarcoïdes), ADNP (superficielles), foie (cholestase non ictérique)
\end{itemize}
Diag : clinique + histologie (granulomes sans nécrose caséuse) + élimination
autres granulomatose (ou sd Löfgren typique\footnote{Fièvre, arthalgie, érythmèe noueux MI, ADP médiastinale})
Pronostic favorable 80\%
Ttt : corticoïdes > 1 an
\subsection{222 HTA pulmonaire artérielle}
\label{sec:org47e8d8f}
Classification : HTAP, HTP cardiopathies gauches (\emph{post-capillaire}), HTP respiratoires chroniques, HTP
post-embolique chroniques, HTP multi-factorielle
HTAP = PAP moyenne \(\ge\) 25mmHg (=HTP) et PAPO \(\le\) 15mmHg
(pré-capillaire). Pronostic sombre
Clinique : dyspnée à l'effort
Complémentaire : ECG, RX thorax, EFR, gaz du sang normaux
Diagnostic : ETT et cathétérisme cardiaque droit
\subsection{224 Thrombose veineuse profonde et embolie pulmonaire}
\label{sec:org9f948f0}
\subsubsection{TVP}
\label{sec:org3d931eb}
Probabilité : score de Wells (unilatéral : OMI, douleur trajet veineux\ldots{})
Diagnostic : (D-dimère si proba faible puis) Écho-doppler veineux MI
Étiologies : congénitale ("thrombophilie") ou acquise (K, alitement,
contraception, chir\ldots{})
Prévention : HBPM, contention, lever
\subsubsection{EP}
\label{sec:org8b39091}
Suspicion : proba clinique, RX thorax, ECG, gaz du sang \footnote{Hypoxie-hypocapnie}
Diagnostic : (D-dimère si proba faible puis) scanner (ETT en attendant). Si
scanner toujours non disponible et patient à haut risque, traiter !
\subsubsection{Ttt (TVP + EP)}
\label{sec:org27334e7}
Ttt :
\begin{itemize}
\item HBPM/fondaparinux + relais AVK ou nv anticoag 3 mois (1ere EP, TVP
proximale provoquée) ou 6 mois
\item thrombolyse si EP grave
\item contention si TVP ou EP + TVP
\end{itemize}
\subsection{228 Douleur thoracique aigüe et chronique}
\label{sec:orgc4080b2}
Examens : ECG, \(SpO_2\), RX thorax
\begin{enumerate}
\item Urgences vitales : SCA++, EP, tamponnade, dissection aortique, pneumothorax oppressif
\item Sinon :
\begin{itemize}
\item rythmée par la respiration : pneumothorax, infectieuses, péricardite,
pariétales, EP, trachéobronchites
\item non rythmée par la respiration : SCA, dissection aortique, RGO++, psychogène
\end{itemize}
\end{enumerate}
Chronique : paroi thoracique, plèvre
\subsection{306 Tumeurs du poumon}
\label{sec:orgc09ec78}
K bronchique : 1ere cause de DC par K en France (17\% survie 5 ans). Cause = tabac !
Y penser si SF respi chez tabagique > 40 ans, AEG chez tabagique. Toux souvent révélatrice
2 types :
\begin{itemize}
\item non à petites cellules (80\%) : chir/radio/chimio
\item à petite cellule (15\%) : mauvais pronostic, chimio \textpm{} radio (pas de chir)
\end{itemize}
Diagnostique = histologique (fibroscopie). Extension = TDM
\subsection{333 Oedème de Quincke et anaphylaxie}
\label{sec:org979560c}
Réaction anaphylactique médiée par IgE ou non
Diag = clinique + contexte. Toujours doser tryptase sérique
\begin{itemize}
\item fortement probable : gêne respi "haute" ou asthme aigü ou choc impliquant PV,
\{rash, urticaire, angioedème\}, début brutal et progression rapide
Urgence (atteinte multiviscérale menaçant la vie) : adrénaline \uline{IM}
\end{itemize}
0.01mg/kg toutes 5min, arrêt agent, allongé/PLS
Sinon : antihistaminique + corticoïdes
\subsection{354 Corps étranger des voies aériennes}
\label{sec:org82448b3}
Pics : enfant, âgé
Y penser si symptôme respiratoire chronique/récidivant dans même territoire
Clinique : mobile (sd pénétration, suffocation), expulsé (pétéchies), enclavement
CAT : Toux/Heimlich/réa. Extraction bronchoscopie/centré spé (enfant)
\subsection{354 Détresse respiratoire aigüe}
\label{sec:org6724cf6}
PEC : \(O_2\), VNI/VI et investigation
Diagnostic
\begin{itemize}
\item RX thorax anormale : urgence = pneumonie infectieuse, \oe{}dème pulmonaire
aigu, pneumothorax. Puis SDR, exacerbation path. infiltrative
\item Sinon clinique + gaz du sang : asthme aigü grave, EP, BPCO, anomalie paroi,
neuromusc, pneumothorax
\end{itemize}
SDRA : détresse respi < 7j + anomalie RX (opacités alvéolaire bilat diffuse)
sans défaillance cardiaque
\subsection{356 Pneumothorax}
\label{sec:org4be9689}
Primaire (jeune, longiligne, 0 patho, fumeur) VS secondaire (âgé, patho connue)
Clinique : douleur pleurale (\inc inspiration et otux)
Diag = RX face.
Ttt : sevrage tabac
\begin{itemize}
\item urgence si compressif (aiguille simple).
\item Sinon (mal toléré/grande taille) : exsufflation ou drain.
\end{itemize}
Prévention récidive : pleurodèse
\section{Endocrinologie - Nutrition}
\label{sec:org90fea6e}
\subsection{32 Allaitement maternel}
\label{sec:org38a3110}
\subsection{35 Contraception (gynéco)}
\label{sec:org2f54e3e}
\begin{center}
\begin{tabular}{lll}
& \oe{}stroprogestatif & Micro/macroprogestatifs\\
\hline
& 1ère intention (Minidril), le plus efficace & 2eme intention\\
CI & K sein, HTA non contrôlée, thrombose & K sein, accident TEV récent\\
& hépatopathie sévère, diabète & \\
Surveiller & chostérole, TG, glycémie & spotting\\
\end{tabular}
\end{center}
Urgence : lévonorgestrel < 72h
\subsection{37 Stérilité du couple (gynéco)}
\label{sec:orga8a0b33}
Infertilité : 0 conception à 1 an. Stérilité = définitif
\begin{itemize}
\item \female : anovulation (courbe de température), bilan hormonal, écho ovarienne, hystérographie.
\item \male : volume testiculaire, testostérone, spermogramme. Hormonal si oligo/azoospermie
\end{itemize}
\subsection{40 Aménorrhée (gynéco)}
\label{sec:org75b10ed}
Primaire
\begin{itemize}
\item pas dév. pubertaire :
\begin{itemize}
\item FSH, LH \dec : tumeur H-H\footnote{Hypothalamo-hypophysaire}, sd de Kallmann
\item FSH, LH \inc : sd de Turner (45X)
\item retard pubertaire simple (diag élimination)
\end{itemize}
\item examen gynéco + écho : hyperplasie congénitale des surrénales, anomalie
utéro-vaginale, anomalie sensibilité androne
\end{itemize}
Secondaire :
\begin{enumerate}
\item hCG pour éliminer grossesse
\item prolactine \inc : médicaments, IRM H-H (adénome prolactine, tumeur/infiltration)
\item LH \inc : écho ovaires (sd ovaires polykystiques)
\item estradiol, LH, FSH \dec (déficit gonadotrope) : tumeur/infiltration H-H(IRM) ou nutrition
\item \inc testostérone (insuffisance ovarienne) : scanner surrénales, écho ovarienne
\end{enumerate}
\subsection{47 Puberté (pédia)}
\label{sec:orgb2a28fe}
Retard : pas de seins > 13 ans ou pas de règle > 15 (\female), volume testicule
< 4mL après 14 ans(\male)
\begin{itemize}
\item hormonal (hypogonadotrope)
\begin{itemize}
\item FSH, LH \dec \footnote{"Cassure" courbe croissance} : IRM H-H (infiltratif, tumoral), nutrition, sport, sd Kallmann
\item FSH, LH \inc : caryotype (sd Turner si \female, Klinefelter \male)
\end{itemize}
\item retard pubertaire simple
\end{itemize}
Précoce < 8 ans \female{}, < 9.5 ans \male. Table \ref{tab:orge08904b}
\begin{table}[htbp]
\caption{\label{tab:orge08904b}Puberté précoce}
\centering
\begin{tabularx}{\textwidth}{ccXX}
Type & Diagnostic & Étiologie & Examens\\
\hline
centrale & FSH, LH \inc & ovaire/testicule, surrénale & écho pelvien/testic., test stimulation GnRH\\
périphérique & FSH, LH \dec & idiopathique, tumeurs SNC & imagerie cérébrale\\
\end{tabularx}
\end{table}
\subsection{48 Cryptorchidie (pédia)}
\label{sec:org46489bd}
Exploration : c. de Leydig, c. de Sertoli, FSH, LH + 17-hydroxyprogestérone si
bilatérale
Ttt chir (sinon = infertilité, hypogonadisme, K testiculaire)
\subsection{51 Retard de croissance (pédia)}
\label{sec:orgf337e29}
Définition : taille < -2DS ou ralentissement croissance ou \(<<\) parents
Cf table \ref{tab:org3117b18} + bilainVS, NFS, foie, rein.
\begin{table}[htbp]
\caption{\label{tab:org3117b18}Retards de croissance}
\centering
\begin{tabular}{ll}
Cause & Exploration\\
\hline
Constitutionnelle++ & \\
RCIU & \\
Déficit en GH, hypothyroïdie & GH, \{TSH, T4L\}\\
Maladie coeliaque, mucoviscidose & \{IgA, IgA anti-transglutamase\},test sueur\\
Os & radio\\
Retard pubertaire simple & \\
\end{tabular}
\end{table}
\subsection{69 Troubles des conduites alimentaires (à compléter)}
\label{sec:org15eb36f}
\subsection{78 Dopage}
\label{sec:orgb619925}
\emph{Stéroïdes anabolisant}, testostérone (\inc masse musculaire, puissance)
Autres : GH (\inc masse musculaire), IGF-1. Glucocorticoïdes, ACTH (antalgique, psychostimulant)
\subsection{120 Ménopause et andropause (gynéco, uro)}
\label{sec:org1e3ca70}
Ménopause :
\begin{itemize}
\item diag clinique : sd climatérique, aménorrhée \(\ge\) 1 an (bio si doute FSH \inc, oestradiol \inc)
\item ttt hormonale = \oe{}strogène et progestatif. Surveiller et réévaluation annuelle
\begin{itemize}
\item bénéfice : ttt sd climatérique, prévention ostéoporose
\item risque : \inc incidence K sein, \inc accidents TE veineux \thus \uline{CI}
\end{itemize}
\end{itemize}
Andropause : si testostérone < 2.3ng/mL\footnote{Ou si testostérone \(\in\) [2.3, 3.2] et SHBG et index T libre bas} :
\begin{itemize}
\item FSH, LH \inc = insuf testiculaire primitive (sd Klinefelter)
\item sinon hypogonadisme hypogonadotrope \thus IRM H-H pour adénome hypophysaire
\end{itemize}
\subsection{122 Troubles de l'érection (uro)}
\label{sec:org3416c89}
Étiologies factorielles !
\begin{itemize}
\item psychogène (érections nocturnes) : rassurer, psychothérapie
\item diabète++, hypogonadisme++, hyperprolactinémie
\item vasculaire (HTA), chir pelvienne, anti-hypertenseur, neuro dégénératif, trauma médullaire
\end{itemize}
Bilan bio : glycémie jeun, testostéronémie \textpm{} prolactine, hormones thyroïdiennes
Ttt
\begin{itemize}
\item hypogonadisme confirmé : androgènes (CI nodule prostatique, PSA > 3ng/mL)
\item 1ere intention : inhibiteurs phosphodiéstérase type 5 (Viagra) + stimulation
\end{itemize}
\subsection{124 Ostéopathies}
\label{sec:org0328191}
Ostéoporose secondaires de \female{} : endocrino++ (Table
\ref{tab:orgdbf215f}). \male{} : y penser si hypogonadisem, hypercortisolisme
\begin{table}[htbp]
\caption{\label{tab:orgdbf215f}Causes endocriniennes d'ostéoporose chez \female}
\centering
\begin{tabular}{lll}
Cause & Sous-cause & Ttt\\
\hline
Hypogonadisme & Anorexie mentale & Pilule \oe{}stroprogestative\\
& Activité physique intense & Si aménorrhée, \dec activité ou \oe{}stroprogestatif\\
& Patho. hypophysaire & \OE{}strogènes\\
& Iatrogène & Bisphosphonates\\
& Sd Turner & \OE{}Strogène + GH ou (adulte) \oe{}stroprogestatif\\
Hyperthyroïdie & & Surveillance (ttt supressif) \textpm{} bisphosphonate\\
Hypercortisolisme/corticoïdes & & Vitaminocalcique, bisphosphonates\\
\end{tabular}
\end{table}
\subsection{207 Sarcoidose}
\label{sec:org06474ca}
Penser à sarcoïdose hypothalamo-hypophysaire si diabète insipide.
Diag = défici endocrinien + infiltration HH à l'imagerie si sarcoïdose
connue. Sinon arguments de sarcoïdose (cf \hyperref[sec:org4ff6054]{item de pneumo})
\subsection{215 Hémochromatose}
\label{sec:orgd63eed5}
Suspicion clinique : Asthénie, Arthalgie, \inc ALAT (3 A)
Atteinte : foie (cirrhose++), diabète sucré++, hypogonadisme, chondrocalcilnose
articulaire, c\oe{}ur
Diag : CST \inc et ferritine \inc : chercher mutation C282Y sur HFE
Ttt dès CST \inc : saignées jusque ferritine < 50g/L. Dépistage parents 1er degré
\subsection{221 HTA : hyperaldostorénonisme primaire, sd de Cushing}
\label{sec:org06f889b}
\label{org4c5b3d3}
Iatrogène : \oe{}stroprogestatifs, corticoïdes, réglisse
Hyperminéralocorticisme primaire :
\begin{itemize}
\item suspicion : HTA (\textpm{} résistante) + hypokaliémie
\item diag : aldostérone \inc et rénine \dec \footnote{Si aldostérone \inc et rérine \inc, hyperaldostéronisme secondaire
(sténose des artères rénale++)}
\item TDM ou IRM :
\begin{itemize}
\item adénome de Conn\footnote{Nodule de la cortico-surrénale} \thus chir
\item idiopathique \thus spironolactone, antihypertenseurs
\end{itemize}
\end{itemize}
Phéochromocytomes\footnote{Tumeur de la médullo-surrénale}
\begin{itemize}
\item dépistage : HTA paroxystique, "triade de Ménard" = céphalées + sueurs +
palpitations, NEM2, NF1
\item diag : métanéphrine \inc
\item Imagerie puis chir
\end{itemize}
Sd de Cushing
\begin{itemize}
\item clinique : obésité androïde et graisses facio-tronculaire + vergétures,
ostéoporose + hyperandrogénie\footnote{Hirsutisme, acné}
\item diag = cortisolurie 24h \inc, test freinage minute négatif à DXM
\item étiologie :
\begin{itemize}
\item ACTH \dec \thus adénome surrénalien, cortico-surrénalome malin
\item sinon : test de freinage fort à DXM, test de stimulation ACTH \thus maladie
de Cushing (positif) ou sd paranéoplasique (négatif)
\end{itemize}
\end{itemize}
\subsection{238 Hypoglycémie}
\label{sec:org4f1453b}
Diag : neuroglucopénie\footnote{Faim brutale, trouble concentration, moteurs, sensitifs, visuels,
convulsion, confusion} et glycémie < 0.50g/L et correction à normalisation\footnote{Coma hypoglycémique possible}
Cause :
\begin{itemize}
\item surdosag insuline++ chez diabétique \thus sucre si CS, sinon glucagon IM/SC
(ou perf glucose)
\item insulinome : diag par épreuve de jeune \thus chir
\end{itemize}
\subsection{239 Goitre, nodules thyroïdiens, cancers thyroïdiens}
\label{sec:org5653899}
Goître (hypertrophie thyroïdie) : évolue en multinodulaire (complications ?)
\begin{itemize}
\item étiologie : tabac, déficience iode
\item diag : TSH et T4 (si TSH \inc: Ac anti-TPO et anti-TG (auto-immunité))
\item ttt : ado = correction par levothyroxine , adulte = surveillance. Chir chez l'adulte si symptomatique, hyperfonctionnel,
morphologie suspecte (ou iode 131 si âgé)
\end{itemize}
Nodules (hypertrophie localisée thyroïdie) : doser TSH
\begin{itemize}
\item si signes : hématocèle (brutal + douleur), thyroïdite subaigüe (douleur +
fièvre), cancer (compressif + ADP), toxique (hyperthyroïdie), thyroïdite
lymphocytaire (hypothyroïdie)
\item nodule isolé cf \ref{tab:org3318f03}. Selon cytologie : surveillance si bénin, chir
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:org3318f03}Orientation pour nodule isolé}
\centering
\begin{tabular}{lll}
TSH \dec & TSH N & TSH \inc\\
\hline
nodule hyperfonct ? & tumeurs & thyroiidite ?\\
scinti & écho, cytologie & Ac anti-TPO\\
\end{tabular}
\end{table}
Cancers thyroïdiens :
\begin{itemize}
\item types :
\begin{itemize}
\item différencié d'origine vésiculaire = Papillaire (85\%, excellent
pronostic), Vésiculaire (5\%, très/moins bon pronostic), Anaplasique (1\%, 15\%
survie 1 an)
\item Medullaire (5\%, 80\% survie 5 an)
\end{itemize}
\item ttt = thyroïdectomie totale \textpm{} curage ganglionnaire
\item si origine vésiculaire : iode 131 (après thyroïdectomie totale si haut risque),
L-T4 (si récidive)
\item si médullaire : chercher autres lésions NEM2\footnote{Phéochromocytome, hyperparathyroïdie}
\end{itemize}
\subsection{240 Hyperthyroïdie}
\label{sec:org0d62149}
Clinique : sd thyrotoxicose = asthénie, amaigrissement, sueurs, CV (tachycardie)
Diagnosic : TSH \dec puis T4L \inc
\begin{table}[htbp]
\caption{Étiologies}
\centering
\begin{tabular}{lll}
Étiologie & Clinique & Diagnostic\\
\hline
\emph{maladie de Basedow} & goitre, oculaire (exophtalmie) & oculaire\\
& & ou écho + Ac anti récepteur TSH \tablefootnote{Scinti: fixation homogène diffuse}\\
\emph{goître multinodulaire toxique} & & Scinti: en damier\\
\emph{adénome toxique} & & Scinti: hyperfixation (reste = "froid")\\
De quervain & virale, goitre dur, douloureux & clinique\\
\end{tabular}
\end{table}
Ttt :
\begin{itemize}
\item \(\beta\)-bloquants, contraception, \emph{anti-thyroidiens de synthèse} [Neomercazole] (\danger
agranulocytose\footnote{Arrêt si neutrophiles < 1G/L})
\item spécifique :
\begin{itemize}
\item cardiothyréose = propranolol, anticoag, ATS, chir/radio-iode
\item Crise aigüe thyrotoxique ATS, pronanolol, corticoïdes puis iode
\item Orbitopathie : pas d'ATS, ni d'iode !
\item enceinte : surveillance/ATS/thyroïdectomie selon
\end{itemize}
\end{itemize}
\subsection{241 Hypothyroïdie}
\label{sec:org2125b9e}
Clinique : sd myxoedemateux\footnote{Faciès "lunaire", voix rauque, macroglossie, hypoacousie}, hypométabolisme\footnote{Asthénie, somnolence, hypothermie}
Diag = TSH \inc. Puis doser T4. Étio : Ac anti-TPO, échographie
Étiologies :
\begin{itemize}
\item atteinte thyroïde
\begin{itemize}
\item thyroïdite d'Hashimoto : Ac anti-TPO. Écho = hypoéchogène, hétérogène
\item thyroïdite atrophique (pas de goitre), du post-partum
\item carence iode (endémie), iatrogène (interféron)
\end{itemize}
\item atteinte hypothalamo-hypophysaire \thus IRM
\end{itemize}
Complications : insuf cardiaque, coma myxoedemateux
Ttt : lévothyroxine \footnote{Obj: TSH \(\in\) [0.5, 2.5]mUI/L.}. Surveiller TSH (primaire) ou T4L (atteinte H-H) !
\subsection{242 Adénome hypophysaire}
\label{sec:org673e880}
Découverte : sd tumoral = céphalée, hémianopsie bi-temporale, apoplexie
hypophysaire (rare mais urgence !)
IRM (référence) : microadénome (hypointense, non rehaussé à l'injection) ou
macroadénome (> 10mm, rehaussé injection)
Hypersécrétion par l'hypophyse :
\begin{itemize}
\item prolactine : galactorrhée, spanioménorrhée. Diagnostic =
\begin{itemize}
\item vérifier hyperprolactinémie, éliminer grossesse, médicaments, hypothyroïdie
périph, insuf rénale
\item microadénome : positif. Sinon, test agoniste dopaminergique
\end{itemize}
\item GH (acromégalie) : sd dysmorphique\footnote{Élargissement extrémité, visage (prognathisme)}, HTA
\begin{itemize}
\item complication : insuf cardiaque !, diabète
\item diagnostic : pas de freinage de GH à l'HGO et \inc{} IGF-1
\end{itemize}
\item glucocorticoïdes (indirectement) : cf \hyperref[org4c5b3d3]{HTA et Cushing}
\end{itemize}
Insuffisance hypophysaire : table \ref{tab:orgd0747bc}
\begin{table}[htbp]
\caption{\label{tab:orgd0747bc}Insuffisance hypophysaire}
\centering
\begin{tabular}{ll}
gonadotrope & oestradiol/testostérone \dec ou FSH, LH \dec\\
corticotrope & cortisolémie \dec, synacthène (aldostérone normale !)\\
thyréotrope & T4l \dec mais TSH normale\ldots{}\\
somatotrope & (GH) stimulation GH négative\\
\end{tabular}
\end{table}
\subsection{243 Insuffisance surrénale}
\label{sec:org8824ecc}
Chronique :
\begin{itemize}
\item clinique = asthénie, anorexie, hypotension. Hyperk, hypoNa\footnote{Aldostérone : réabsorption Na+ et sécrétion K+} mélanodermie
(surrénale), pâleur (hypophyse)
\item ttt sans attendre diag : hydrocortisone, fludrocortisone \footnote{Glucocorticoïdes et minéralocorticoïdes respectivement.} + cause
\item diag : cortisol \dec, ACTH \inc si primaire
\item étiologies :
\begin{itemize}
\item primaire (surrénale) = \emph{autoimmune} 80\%\footnote{Doser Ac anti-21 hydroxylase}, \emph{tuberculose} des surrénale
10\%\footnote{Calcifications aux scanner}), VIH, iatrogène, métastases bilatérales
\item secondaire (hypophyse) = interruption corticothérapie prolongé
\end{itemize}
\end{itemize}
IS aigüe = urgence
\begin{itemize}
\item déshydratation extracellulaire, confusion, fièvre. Bio : hémoconcentration,
hypoNa, hyperK, hypoglycémie
\item hydrocortisone 100mg puis \faHospital : NaCL et facteur déclenchant (IS chronique++)
\end{itemize}
\subsection{}
\label{sec:org1660814}
\subsection{244 Gynécomastie}
\label{sec:org507a917}
Palpation : ferme, mobile, centré mamelon. Si doute, mammographie pour élimiter
K et adipomastie
Physiologique : NN, ado (< 20 ans), > 65A (palper testicules !)
Étiologies : médicaments, idiopathique (25\%), cirrhose, insuf
testiculaire/gonadotrope (8\%), tumoral (rare).
\begin{itemize}
\item bilan hormonal si non évident
\end{itemize}
Ttt : cause. Androgène si idiopathique voire chir plastique
\subsection{245 Diabète sucré}
\label{sec:org7f87069}
Glycémie jeun \(\ge\) 1.26 g/L \time 2 ou (\(\ge\) 2g/L + signes d'hyperglycémie)
\subsubsection{Diabète 1}
\label{sec:org666b67d}
insulinopénie (destruction c. \(\beta\) pancréas) auto-immun++ ou idiopathique
Début brutal, sujet jeune, sd cardinal (polyuro-polydipsie, amaigrissement,
polyphagie\}, acidocétose (cétonurie)
Diagnostic : hyperglycémie + triade \{cétonurie, < 35 ans\} ou auto-Ac
PEC :
\begin{itemize}
\item insuline à vie : lent et rapide (3-4)
\item objectif HbA1c < 7\%
\item surveillance : glycémie 4/jour
\item CS : ophtalmo 1/an, dentiste 1/an, diabétologique 3/an \textpm{} cardio 1/an
si sympto/âgé/compliqué
\end{itemize}
Dépistage pendant grossesse !
\subsubsection{Diabète 2 (90 \%)}
\label{sec:orga9ed0bf}
Insulinorésistance \uline{et} déficit insulinosécrétoire
Découverte fortuite (asymptomatique longtemps).
Dépistage : clinique d'hyperglycémie, sd métabolique\footnote{IMC > 28 kg/m\textsuperscript{2}, HTA, HDL < 0.35g/L ou TG > 2g/L ou dyslipidémie, ATCD
diabète (familiale, gestationnel)}
PEC :
\begin{itemize}
\item objectif HbA1c < 7\%
\item activité physique \footnote{Sauf insuf. coronarien, rétinopathie proliférante non stabilisée}, alimentation équilibrée sans sucres rapides
\item metformine (sinon sulfamide, inhibiteurs DPP-4, inhibiteurs
\(\alpha\)-glucosidase)
\item + insuline et HGO si insulinorequérance
\end{itemize}
\subsubsection{Complications}
\label{sec:orgfe90cd1}
\OE{}il : voir \hyperref[orgc28cb24]{partie ophtalmo}
Rein : diabète = 1ere cause d'IR terminale.
\begin{itemize}
\item dépistage 1/an chez D2 : BU (protéinure), albuminure/créatinurie
\item ttt : prévention : diabète, HTA. Puis cf tab \ref{tab:org940e1d4}
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:org940e1d4}2 premiers stade de néphro diabètes = asymptomatique}
\centering
\begin{tabular}{rll}
Stade & type & Ttt\\
\hline
3 & microalbuminurie & Obj: HBA1c < 7\%, PA < 140/85 mmHg\\
4 & macroalbuminurie & IEC/sart + diurétique thiazidique\\
5 & IR avec DFG < 30/mL/min/1.73m\textsuperscript{2} & insuline, répaglinide, inhib. \(\alpha\)-glucosidase\\
\end{tabular}
\end{table}
Neuropathies
\begin{itemize}
\item sensorimotrice : polynévrite symétrique distale++ (hypoesthéie, 0 ROT achilléen, bilat , douleur
neurogène)
\item autonome : digestiv (gastroparésie), dysfonction érectile, parésie vésicale
\item dépistage : examen neuro (pied !!), ECG annuel
\item ttt : préventif++ (glycémie, alcool, tabac\ldots{})
\end{itemize}
Macroangiopathie : 2/3 DC pour cause CV
\begin{itemize}
\item ischémie myocardite silencieuse !!, AOMI
\item prévention : glycémie (metformine), activité physique, LDL (statines),
aspirine, anti-hypertenseurs, poids, 0 tabac
\end{itemize}
Mal perforant plantaire : creux autour d'hyperkératose
\begin{itemize}
\item examen réguliers des pieds et chaussures quotidien
\item ttt : décharge, excision kératose / parage et drainage + ATB si infection \textpm{}
revascularisation si nécrose
\item risque d'ostéite
\end{itemize}
Autres :
\begin{itemize}
\item infections \thus examen cutané++, stomato, uro-génital, respi
\item dentiste tous 6 mois
\end{itemize}
Complications métabolique :
\begin{itemize}
\item coma cétoacidosique
\begin{itemize}
\item diag= cétonémie, cétonurie
\item ttt insuline rapide IV, recharge volumique, K+ \textpm{} glucose, cause
\end{itemize}
\item coma hyperosmolaire :
\begin{itemize}
\item diag = glycosurie, cétonurie (BU) et hyperglycémie (dextro)
\item ttt : réhydratation lente, insuline IV, héparine, cause
\end{itemize}
\item hypoglycémie : inévitable, non mortelle. Cf \hyperref[sec:org4f1453b]{item 238}
\end{itemize}
\subsection{246 Prévention par la nutrition}
\label{sec:orga976228}
\subsection{247 Modifications thérapeutiques du mode de vie}
\label{sec:org5a76e5d}
\subsection{248 Dénutrition (à compléter)}
\label{sec:org0f59f67}
\subsection{249 Amaigrissement (à compléter)}
\label{sec:org07c46a4}
Vérifier l'amaigrissement !
Causes endocrino : insuf. surrénale (primaire/secondaire)diabète, hyperthyroïdie, hypercalcémie
\subsection{250 Troubles nutritionnels chez sujet âgé (à compléter)}
\label{sec:orgb39cad6}
\subsection{251 Obésité (à compléter)}
\label{sec:org55955ff}
IMC \(\ge\) 30 kg/m\textsuperscript{2} (grade 1 si < 35, grade 3 si \(\ge\) 40)
Étiologie : génétique, communes++ (déséquilibre apport-dépense).
Complications : \inc RR mortablité, métabolique, CV, respi, ostéoarticulaire, digestive, rénale,
gynéco, cutanée, néoplasique, psychosociale
Interrogatoire. Ttt = diététique, activité physique, psychologique + orlistat si
IMC \(\ge\) 30 (ou 27 et comobridité). Chir bariatrique en 2eme intention.
\subsubsection{Enfant/ado}
\label{sec:org57c5557}
IMC > 25 kg/m\textsuperscript{2}
Étiologie : commune++ (facteur env., prédisposition génétiuqe), génétique,
secondaire
Complication : HTA, insulinorésistance, stéatose hépatique non alcoolique,
articulaire, psycho
Interrogatoire + EC. Ttt = prévention
\subsection{252 Diabète gestationnel + nutrition et grossesse (à compléter)}
\label{sec:org0365044}
Pré-gestationnel
\begin{itemize}
\item risque f\oe{}tus : fausses couches, malformations congénitales, mort f\oe{}tales,
\item risque mère : HTA ++, rétinopathie, néphropathie
\item avant grossesse : HbA1c < 7\%, glycémie \(\in\) [0.7, 1.20] préprandial et [1,
1.14] en post (\inc insuline si DT1, +insuline si DT2
\item pendant : 6 glycémie/jour pour équilibre
\end{itemize}
Dépister diabète gestationnel ssi FR : \{\(\ge\) 35 ans, IMC \(\ge\) 25 kg/m\textsuperscript{2}, ATCD DG,
DT parents 1er degr\}
\begin{itemize}
\item PEC si glycémie jeun \(\ge\) 0.92g/L (début), sinon teste 24-28SA avec HGO
\item ttt : diét., \textbf{pas} d'antidiabétique, surveillance
\end{itemize}
\subsection{253 Nutrition chez le sportif}
\label{sec:org5629b1b}
Examen d'aptitude : ATCD familiaux (CV), EC complet, ECG d'effort
Bénéficices du sport : 150min/semaine (ou 75min si intense) chez
l'adulte. 60min/jour chez l'enfant + renforcement
\begin{itemize}
\item adulte :
\begin{itemize}
\item prévention = K (colon, sein), CV, métabolique, ostéoporose \female,
\item maintien = \dec mortalité prématuré, \inc autonomie
\item traite = cardiomyopathie, ischém, BPCO, obésité, diabète 2 neuro,
rhumatismal, dégénératif
\end{itemize}
\item enfant : dev psychosocial, dev psychomotoeur, prévient sd métabolique,
surpoids, CV, \inc masse maigre et densité osseuse
\end{itemize}
Bseoins :
\begin{itemize}
\item glucides (50\%) : IG faible à distance, élevé juste avant. reconstituer stocks après
\item lipides (30\%) à limiter si compétition
\item protéines (20\%)
\item calcium 1g/j, Fer 10-15mg/j, vit D 5 \(\mu\)g/j \thus surveiller chez l'enfant
\end{itemize}
\subsection{265 Hypocalcémie, dyskaliémie, hyponatrémie}
\label{sec:orgaa220ce}
Hypocalcémie :
\begin{itemize}
\item clinique : troubles du rythme, parésthésie, tétanie
\item causes hypoparathyroïdie, anomalie vitamine D (carence, malabsorption\ldots{})
\item ttt : aigü calcium IV lente. Chronique : vitamine D et calcium
\end{itemize}
Hyperkaliémie (risque cardiaque )
\begin{itemize}
\item étiologies : hypoaldostéronisme (IS) , acidose métabolique \footnote{par \dec élimination rénale, par sortie du K+ de la cellule respectivement.}
\end{itemize}
Hypokaliémie (risque cardiaque )
\begin{itemize}
\item étiologie : excès d'insuline, hyperaldostéronisme, dénutrition sévère
\end{itemize}
Hyponatrémie endocrinienne (hospitalisé++)
\begin{itemize}
\item étiologie selon osmolalité : si \inc, hyperglycémie, si N, hyperTG,
hyperprotidémie. Si \dec, "vraie" hyponatrémie : table \ref{tab:orga8ac5b0}
\end{itemize}
\begin{table}[htbp]
\caption{\label{tab:orga8ac5b0}hyponatrémie "vraie"}
\centering
\begin{tabular}{lll}
volémie \inc & IC, cirrhose, sd néphrotique & Sérum isotonique\\
volémie R & hypothyroïdie, insuf corticotrope, SIADH & Sérum hypertonique\\
volémie \dec & perte digestive, rénale, insuf corticosurrénale aigüe & Restriction hydrosodée\\
\end{tabular}
\end{table}
\subsection{266 Hypercalcémie}
\label{sec:org2935cf0}
Étiologie :
\begin{itemize}
\item PTH \inc ou N
\begin{itemize}
\item hyperparathyroïdie primaire (55\%) : ttt = chir conventionnelle
\item hypercalcémie-hypocalciurie familiale bénigne
\end{itemize}
\item PTH \dec
\begin{itemize}
\item maligne (30\%)
\item iatrogène, granulomatose
\end{itemize}
\end{itemize}
Ttt (hors hyperparathyroïdie primaire) : bsiphosphonates, calcimimétique
\subsection{303 Tumeurs de l'ovaire (hormono-sécrétante)}
\label{sec:org797547a}
Sécrète des \oe{}strogènes : tumeurs de la granulosa++ :
\begin{itemize}
\item sympto : pseudo-puberté précoce ou aménorrhée/ménométrorragie ou saignement vaginal
\item ttt = ovariectomie unilatérale
\end{itemize}
Sécrète des androgènes : tumeurs à c. de sertoli-Leydig (Hirsutisme, ttt
conservateur), à c. de Leydig (virilisante, ttt = ovariectomie bilat),
germinales sécrétantes \footnote{Si sécrète hCG : ttt = conservateur/chimie, si sd
Turner : ttt = gonadectomie préventive}
\subsection{305 Tumeurs du pancréas (endocrine)}
\label{sec:org3942bb4}
Clinique selon sécrétion (insuline, gastrine, ACTH, glucagon, VIP, GHRH)
\subsection{310 Tumeurs du testicule (aspects endocriniens)}
\label{sec:org3511abe}
Clinique : pseudo-puberté précoce/gynécomastie
Sécrète testostérone/\oe{}stradiol ou gonadotrophine chorionique/hCGA (tumeurs
germinales)
Diag = palpation testiculaire + écho
Ttt = chir (glucocorticoïdes si inclusions surrénaliennes)
\section{Ophtalmo}
\label{sec:org4c0f288}
\subsection{1 Sémiologie oculaire}
\label{sec:orgfb47abe}
Anatomie
\begin{itemize}
\item Membrane externe (cornée, conjonctive, sclère), uvée (iris, corps ciliaire,
choroïde), rétine
\item Contenu : humeur aqueuse (chambre antérieure), cristallin, corps vitré
(postérieur)
\item Voie optique : nerf optique - chiasma - bandelettes - corps genouillés
externes - radiations optiques - cortex occipital
\item Nerfs oculomoteurs : IV = oblique sup, VI = droit externe et les autres = III
\end{itemize}
Examens :
\begin{itemize}
\item AV (Parinaud = près, Monoyer = loin)
\item lampe à fente (segment antérieur), gonioscopie (angle iridocornéen)
\item pression intraoculaire par tonomètre à pair pulsé (hypertonie si \(\ge\) 22mHg)
\item FO
\end{itemize}
Complémentaires
\begin{itemize}
\item CV (périmétrie statique = dépistage glaucome), couleurs
\item angiographie (DMLA)
\item électrorétinogramme, potentiels évoqués visuels (SEP), électro-oculogramme
\item écho (mode A = longeur, mode B = décollement rétine)
\item OCT (glaucome chronique, macula : DLMA)
\end{itemize}
\subsection{2 Réfraction}
\label{sec:org517a374}
\OE{}il = 60 dioptries (42 cornée, 20 cristallin).
Myope = trop convergent \thus verre concave/chir. Hypermétrope = pas assez convergent
\thus verre convexe/chir. Astigmate \thus verres cylindriques/chir
\subsection{3 Suivi d'un nourisson}
\label{sec:org377e670}
Dépister enter 9 et 12 mois : réfraction, strabisme + réfraction après
cycloplégie (amblyopie).
\subsection{4 Strabisme de l'enfant}
\label{sec:org9cad7ec}
= symptôme !
Examen motilité (paralytique vs motilité normale)
Ttt : correction optique \textpm{} occlusion \oe{}il si amblyopie (chir si persistance)
\subsection{5 Diplopie (binoculaire)}
\label{sec:org9c72580}
Clinique : dédoublement même direction, disparaît à l'occlusion d'un \oe{}il
Exament : motilité, cover-test, verre rouge, Lancaster
Étiologie :
\begin{itemize}
\item anévrisme intracrânien++ (jeune, céphalée, 0 FR vasc),
\item tumeur (25\%), SEP (10\%) révélee, myasthénie
\item autres : accidents vasculaires ischémique/hémorragiques
\end{itemize}
\subsection{6 \OE{}il rouge/douloureux}
\label{sec:orga00098a}
BAV, douloureux : cf \ref{org3776bac}.
Sans BAV, douloureux :
\begin{itemize}
\item épisclérite (ttt = corticoïdes)
\item sclérite (étio = polyarthrite rhumatoïde)
\item conjonctivite : allergique (collyre), virale++ (ttt =0)
\item sd sec oculaire++ (ttt = substituts lacrymaux)
\end{itemize}
Sans BAV, sans douleur :
\begin{itemize}
\item conjonctivite (bactérienne : collyre antiseptiqu)
\item hémorragie sous-conjonctivale (HTA, trouble coag ?)
\end{itemize}
\begin{table}
\caption{Avec BAV, douloureux: étiologies}
\centering
\adjustbox{max width=\linewidth}{
\begin{tabular}{llll}
Type & Symptômes & Étiologie & Ttt\\
\hline
Glaucome aigu par FA & Douleur++, "bille de verre" & & inhib. anhydrase carbonique, solutés hyperosmolaires\\
& & & hypotoniques, myotique (collyre)\\
Uvéite antérieure aigǜe & Synéchies iridocristaliniennes & inconnue (50\%) & \\
& Tyndall\tablefootnote{Protéines, c. inflammatoires dans l'humeur aqueuse} & Spondylarthrie ankylosante & \\
& précipités rétro-cornéens & herpès, sarcoïdose & mydriatiques, corticoïdes (collyre)\\
Kératite aigüe & Ulcération (à la fluorescine) & Herpès, bactéries & \\
Glaucome NV & Néovaisseaux sur l'iris & & Hypotonisants, photocoag/anti-VEGF\\
Endophtalmie post-op & \oe{}dème palpébral, hyalite\tablefootnote{Inflammation du corps vitré} & & \\
\end{tabular}
}
\label{org3776bac}
\end{table}
\subsection{7 Altération de la fonction visuelle}
\label{sec:org21384b8}
BAV progressive
\begin{itemize}
\item transparence anormale : cataracte (ttt = chir), cornée, vitré
\item sinon :
\begin{itemize}
\item atteinte nerf optique : glaucome chronique à AO (ttt = hypotonisants,
chir), neuropathies toxiques
\item atteinte rétine = rétinopathies pigmentaires, ou macula = DMLA,
maculopathies héréditaires, \oe{}dème maculaire, antipaludéens, séparation vitré/macula
\end{itemize}
\end{itemize}
Altération CV
\begin{itemize}
\item ateinte rétine (scotomes centrau, déficits périph)
\item atteinte nerf optique : SEP, NOIA, toxique
\item atteinte chiasma optique : adénome hypophysaire
\item atteinte rétrochiasmatique : vasc, tumoral, trauma
\end{itemize}
\subsection{8 Anomalies de la vision d'apparition brutale}
\label{sec:orgdf221ea}
BAV, \oe{}il rouge douloureux : cf \hyperref[sec:orga00098a]{chap 6}
BAV, \oe{}il blanc indolore :
\begin{center}
\begin{tabular}{lll}
FO non visible & hémorragie intra-vitréenne & Écho B\\
& uvéite du vitré & \\
FO visible anormale & occlusion artère centrale rétine & mydriase aréflexique\\
& & macula rouge cerise\\
& & (urgence si Horton)\\
& occlusion veine centrale rétine & \oe{}dème papillaire\\
& & hémorragie rétiniennes dissémines\\
& & nodules cotonneux\\
& DMLA & métamorphopsies brutale\\
& décollement rétine rhegmatogène & myodésopsies, phosphène\\
& & (semi-urgence)\\
& neuropathie optique ischémique antérieure & \dec RPM direct\\
& & \oe{}dème papillaire\\
FO visible normale & névrite optique rétrobulbaire & scotome central\\
Cécité monoculaire transitoire & & \\
\end{tabular}
\end{center}
\subsection{9 Prélèvement de cornée}
\label{sec:orgea39042}
Faire sérologies HIV, HTLV, VHB, VHC, syphilis
CI : locale, infectieuses (sida, rage, Creutzfeld-Jakob, hépatite), neuro
inexpliqué, démence
\subsection{10 Greffe de cornée}
\label{sec:org291d0d2}
Transfixiantes ou juste endothelium.
Indications : trauma, kératocône, kératite herpétiques/infectieuse
\subsection{11 Traumatismes oculaires}
\label{sec:org77febaf}
Globe ouvert, corps étranger : si doute TDM (\danger pas d'IRM si corps
étranger)
Chir en urgence : recherche/suture plaie du globe, extraction CE intraoculaire,
plaie du cristallin
\subsection{12 Brûlures oculaires}
\label{sec:org9c538b5}
Brûlures basiques = grave \danger
Ttt urgence = lavage 20min au sérum phys puis collyre corticoïdes
\subsection{13 Cataracte}
\label{sec:org28d6cf2}
Opacification du cristallin.
Diag clinique : BAV progressive en vision de loin, lampe à fente
Étiologies : âge, diabète, crorticoïdes, traumatique
Ttt = chir (extraction par phacoémulsification puis implant en chambre
postérieure)
Complications : endophtalmie (ATB !), décollement rétine, \oe{}dème maculaire
\subsection{14 Glaucome chronique}
\label{sec:org4aa2b2b}
Glaucome primitif à pression élevée (\(\approx\) occidentaux), ou pression \uline{normale}
(\(\approx\) asiatique)
FR: âge, hypertonie oculaire. Physio : perte accélée des fibres optiques.
Caractéristiques : \inc excavation papille, altération CV
Ttt à vie : prostaglandine ou \(\beta\)-bloquants\footnote{\inc élimination humeur aqueuse et \dec sécrétion respectivement.} (collyre), laser
(trabéculoplastie) ou chir (trabéculectomie) possible
\subsection{15 Dégénérescence maculaire liée à l'âge}
\label{sec:orga35d626}
1ere cause de malvoyance après 50 ans.
Diag = AV, FO, OCT (cf tab \ref{org6dea95e})
\begin{table}
\caption{Formes de DMLA}
\centering
\adjustbox{max width=\linewidth}{
\begin{tabular}{llll}
Forme & Clinique & FO & Ttt\\
\hline
Débutante & & \emph{drusen}\tablefootnote{Petites lésions profondes jaunes} & vit E, C, zinc, lutéine, zéaxantine\\
Atrophique & BAV sévère, scotome central & atrophie épith. pigment. & \(\emptyset\)\\
Exsudative & BAV, métamorphopsies brutales & \oe{}dème intrarétienne & anti-VEGF\\
(néovaisseux ss rétine) & & décollement maculaire exsudatif & \\
\end{tabular}
}
\label{org6dea95e}
\end{table}
\subsection{16 Occlusions artérielles rétiniennes}
\label{sec:org9b429b0}
Artère centrale de la rétine
\begin{itemize}
\item Diag =
\begin{itemize}
\item BAV brutale, \oe{}il blanc indolore, mydriase aréflective
\item FO : macula "rouge cerise"
\end{itemize}
\item Étiologie : embolies (athémore carotidien), maladie de horton = urgence
\item CAT = urgence . Très mauvais pronostic fonctionnel
\begin{itemize}
\item ttt de l'étio (antiagrégant/anti vit-K)
\end{itemize}
\end{itemize}
Branche de l'ACR : pronostic visuel bon (amputation), pas d'Horton
\subsection{17 Occlusions veineuses rétiniennes}
\label{sec:org7474813}
Veine centrale de la rétine
\begin{itemize}
\item Diag (facile) : BAV brutale, FO = dilatation veineuse, nodules cotonneux,
hémorragies disséminées, \oe{}dème papillaire
\item FR : > 50 ans avec FR vasc, hypertonie oculaire
\item 2 formes (angiographie fluorescine)
\end{itemize}
\begin{table}
\caption{Formes d'OVR}
\centering
\adjustbox{max width=\linewidth}{
\begin{tabular}{lll}
Forme & Évolution & TTT\\
\hline
non ischémique & normalisation & anti-VEGF, surveillance mensuelle\\
& ou ischémique & \\
ischémiques & pas de récupération fonct. & PPR\tablefootnote{Photocoagulation panrétinienne}\\
& glaucome NV \danger & PPR en urgence\\
& & \\
\end{tabular}
}
\label{org48cfef9}
\end{table}
Branche veineuse rétinienne : évolution favorable / hémorragie du vitré (pas
de GNV !)
\subsection{18 Pathologies des paupières}
\label{sec:org17e0b53}
Cf Table \ref{tab:org4452f44}
Autres : entropion (sénile/paralysie VII), ectropion, ptosis (penser anévrisme
IC ), lagophtalmie
\begin{table}[htbp]
\caption{\label{tab:org4452f44}Pathologies des paupières}
\centering
\begin{tabular}{llll}
Orgelet & follicule du cil & infection bactérienne & ATB 8 j\\
Chalazion & glande Meibomius & inflammation & corticoïde\\
\end{tabular}
\end{table}
Tumeurs malignes : carcinome basocellulaire/épidermoide, mélanique, carcinomes sébacés
\subsection{19 SEP}
\label{sec:orgc9fffe7}
20\% inaugurant SEP. 50\% de SEP à 15 ans. Formes :
\begin{itemize}
\item neuropathie optique :
\begin{itemize}
\item BAV variable, douleurs rétro-oculaire, pupille Marcus-gunn
\item scotome (caeco) central, dyschromatopsie d'aexe rouge-vert
\item IRM
\item Ttt = corticoïdes + (SEP) interféron
\end{itemize}
\item paralysie du VI, nystagmus, périphlébite rétinienne
\end{itemize}
\subsection{20 Neuropathie optique ischémique antérieure}
\label{sec:orgdfcb5dd}
Diag = BAV brutale indolore
\begin{itemize}
\item FO : \oe{}dème papillaire. Examen CV ++ (déficit altidudinal)
\end{itemize}
Étiologies
\begin{itemize}
\item artériosclérose (freq) : FR. Pas de ttt efficaces
\item maladie de Horton = urgence . Bio = VS \inc, CRP \inc \thus
corticothérapie générale forte dose
\end{itemize}
\subsection{21 Rétinopathie diabétique}
\label{sec:org67bc131}
\label{orgc28cb24}
1ère cause de cécité chez < 50 ans. 30\% des diabétique
\begin{itemize}
\item maculopathie diabétique
\item rétinopathie diabétique : non proliférante (hémorragies rétiniennes dans 4
quadrans/dilatations veineuses 2 quadrants/AMIR 1 quadrant) puis proliférante (néovaisseaux)
\item dépistage annuel FO, OCT
\item ttt : équilibre glycémie et TA++. Photocoagulation panrétinienne, anti-VEGF
\end{itemize}
\subsection{22 Orbitopathie dysthyroïdienne}
\label{sec:orgf52d2b2}
Maladie de Basedow++, thyroïdite d'Hashimoto
Manif = exophtalmie (bilatérale, axile, non pulsatile, indolore), rétraction
paupière, diplopie
TSH effondrée, scanner, IRM, \{CV, couleurs, PEV\}
Ttt
\begin{itemize}
\item médical : hyperthyroïdes, anti-inflammatoire si score CAS \(\ge\) 3
\item si grave : corticothérapie générale, chir
\end{itemize}
\subsection{23 Rétinopathie et choroïdopathie hypertensive}
\label{sec:org136b1b2}
Rétinopathie hypertensive : si HTA sévère.
\begin{itemize}
\item hémorragie en flammèches superficielles, \oe{}dème maculaire
\item hémorragies profondes, rondes, nodules cotonneuxs
\item pas BAV
\end{itemize}
Choroïdopathie hypertensive : nécrose de l'épithelium pigmentaire, cicatrices
(décollement de rétine exsudatif si sévère)
Artériosclérose : asymptomatique, irréversibles. Signe du croisement, \inc reflet artériolaire
\end{document}