apraga/org - Change EQXX5KDJMDEDXPJ7QQWDXHEFFE4K4UWEZ5ZCJNOPK57D26SB7H6AC

Diabète

Created by Alexis Praga on July 7, 2024

EQXX5KDJMDEDXPJ7QQWDXHEFFE4K4UWEZ5ZCJNOPK57D26SB7H6AC

Dependencies

In channels

main

Change contents

Insertion in projects.org at line 56 [6.179]

[5.240]

**** DONE Compiler sur mésocentre Patch tensorflow distutils
CLOSED: [2024-07-07 Sun 12:21] SCHEDULED: <2024-07-07 Sun>
/Entered on/ [2024-07-07 Sun 10:55]
**** WAIT PR Patch tensorflow distutils
/Entered on/ [2024-07-07 Sun 10:55]

Insertion in projects.org at line 81 [6.179]

[5.717]

[7.353]

*** TODO Inscription jcadd 2024
SCHEDULED: <2024-09-02 Mon>
/Entered on/ [2024-07-06 Sat 14:51]
*** TODO Présentation JCADD 2024
SCHEDULED: <2024-09-25 Wed> DEADLINE: <2024-10-30 Wed>
/Entered on/ [2024-07-06 Sat 14:52]

Replacement in projects.org at line 284 [6.179]
B:BD[8.656] → [8.656:692]
B:BD[8.692] → [9.405:433]
```
** TODO Review PR  gitftless 154351
SCHEDULED: <2024-07-07 Sun>
```
[8.656]
[8.692]
```
** WAIT Review PR  gitftless 154351
```

Replacement in projects.org at line 286 [6.179]

B:BD[8.728] → [10.240:318]

** TODO tester rapidement gradle2nix v2 pour gatk
SCHEDULED: <2024-07-07 Sun>

[8.728]

[10.318]

** HOLD tester rapidement gradle2nix v2 pour gatk

Replacement in projects.org at line 320 [6.179]
B:BD[11.161] → [11.161:189]
```
SCHEDULED: <2024-07-02 Tue>
```
[11.161]
[11.189]
```
SCHEDULED: <2024-07-08 Mon>
```
Replacement in notes/biblio/Aganezov2022.org at line 7 [12.104769]
B:BD[12.104896] → [12.104896:104912]
```
**** Résultats
```
[12.104896]
[12.104912]
```
* Résultats
```

File addition: 20240707142811-proteinurie.org (----------)

[13.188]

:PROPERTIES:
:ID:       a151d21a-b016-4de8-a269-29673c636355
:END:
#+title: Protéinurie
#+filetags: biochimie
Diagonstic + surveillance IRC, risque cardiovasculaire
Microalbuminurie : 30-300 sur 24h (mg/j) ou rapport albumine/créatinine 30-300/mg/
Protéinurie > 300mg/j sur 24h ou > 300mg/g pour le rapport
Microabl = faible quantité l'ablumine dans les urine -> atteinte endothéolique
Facteur de risque de néphropathie diabétique + surmortalité cardiovasculaire chez les diabétique

File addition: 20240707135547-debit_de_filtration_glomerulaire_dfg.org (----------)

[13.188]

:PROPERTIES:
:ID:       f9caff5e-5572-4e86-81e2-c7897fdd9248
:END:
#+title: Débit de filtration glomérulaire (DFG)
#+filetags: biochimie
Inconvénient : valable seulement si fonction rénale stable
fastidieux (recueil sur 24h)
La clairance de la créatine > DFG (car créatine sécrétée par les tubules rénaux)
Formules :
- cockroft et gault
- MDRD
- CKD/Epi : plus précise que MDRD pour DFG not. si clairance > 60

File addition: 20240707134057-fructosamine.org (----------)

[13.188]

:PROPERTIES:
:ID:       dd35f673-81f0-4d95-b4b2-99ca2090689f
:END:
#+title: Fructosamine
#+filetags: biochimie
Pré-analytique: sérum/plasma EDTA/héparine
Interférence : ictère, hémolyse, turbidité
Physiopath: reflète protéine plasmatiques glyquée. Fructorasime = glycémie moyenne 2-3 semaine avant prélèvement
Indication:
- surveillance court terme du diabète
- anémie, hémoglobinopathie
- *IR stade terminal*, *Grossesse*
  Peu utilisé en tournie (HbA1c suffit)

File addition: 20240707133407-anomalie_lipidique.org (----------)

[13.188]

:PROPERTIES:
:ID:       1ab5aa3c-f88a-45f9-a551-2507fc6642ff
:END:
#+title: Anomalie lipidique
#+filetags: biochimie endocrino
Exploration: après 12h de jeune
1ere intention
- cholestérole totale, triglycérides, HDL-c
- LDL-c : dosage direct si TG > 0.4gL ou diabète ou maladie vasculaire connue. Sinon la formule de Friedewald
  #+begin_src latex
  cholestérol total - HDLc - TG/5 (pour un résultat en g/L)
  #+end_src
  NB: estime le cholestérol lié au VLDL mais incorrect si hypertriglycéridémie
Confirmaton par 2e dosage si anormal
Si HDL < 0.35g/L ou > 0.8g/L contrôle possible de l'apoA1 par le biologiste

Replacement in notes/20240706234445-diabete.org at line 10 [4.373]

B:BD[4.596] → [4.596:925]

Définition:
- glycémie à jeun normale < 1.1g/L (6.06mmol/L)
- hyperglycémie modélure à jeun entre 1.1 et 1.26 g/L (inclus) soit 6.93mmol/L)
  - si 2H après 75g de gulose >= 2g/L (11mmol/L) -> diabète
- diabète : >= 1.26g/L à 2 reprise *ou* >= 2g/L
*Seule la glycémie veineuse au labo donne le diag*
* Préanalytique

[4.596]

[4.925]

* Diagnostic
** Préanalytique

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```
** Variants
```
[4.1120]
[4.1132]
```
*** Variants
```
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```
* Analytique
```
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[4.1239]
```
** Analytique
```
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```
* Dosages
** Lecteurs de glycémie
```
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```
** Dosages
*** Lecteurs de glycémie
```
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B:BD[4.1437] → [4.1437:1451]
```
** Glycosurie
```
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```
*** Glycosurie
```
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```
** Corps cétonique
```
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```
*** Corps cétonique
```
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```
** Bandelette urinaire
```
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[4.1856]
```
*** Bandelette urinaire
```
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```
** Hémglobine glyquée
```
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```
*** Hémglobine glyquée
```
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B:BD[4.2441] → [4.2441:2464]
```
** Diabète auto-immun
```
[4.2441]
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```
*** Diabète auto-immun
```

Replacement in notes/20240706234445-diabete.org at line 60 [4.373]

B:BD[4.2925] → [4.2925:3176]

* Prédisposition génétique
- type 1: CMH2 = facteur de risque, facteurs de prédisposition (haplotype DR3, DR4) ou prodection (DR15)
  - autres : VNTR (insuline), CTLA-4 (immunomodulation LT), PTP-N22
- type 2 : nb gènes mais utilité incertaines

[4.2925]

[4.3176]

** Définition:
- glycémie à jeun normale < 1.1g/L (6.06mmol/L)
- hyperglycémie modélure à jeun entre 1.1 et 1.26 g/L (inclus) soit 6.93mmol/L)
  - si 2H après 75g de gulose >= 2g/L (11mmol/L) -> diabète
- diabète : >= 1.26g/L à 2 reprise *ou* >= 2g/L
*Seule la glycémie veineuse au labo donne le diag*

Replacement in notes/20240706234445-diabete.org at line 77 [4.373]

B:BD[4.3808] → [4.3808:3878]

| Génétique: rares ATCD famailiaux | ATCD familiaux fréquence    |

[4.3808]

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| Génétique: rares ATCD familiaux  | ATCD familiaux fréquence    |

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** Prédisposition génétique
- type 1: CMH2 = facteur de risque, facteurs de prédisposition (haplotype DR3, DR4) ou prodection (DR15)
  - autres : VNTR (insuline), CTLA-4 (immunomodulation LT), PTP-N22
- type 2 : nb gènes mais utilité incertaines

Insertion in notes/20240706234445-diabete.org at line 88 [4.373]

[4.4214]


* Complications
Exploration des complications micro-vasculaires
- rétinopathie: rénitographie/fond d'oeil
- néphropathie : BU + albuminurie, créatininémie, DFG
- neuropathie : ROT, test monofilament (anormal = 50% de risque de trouble dans l'année, normal n'écarte pas ...)
Et macrovasculaire : AVC maladie coronarienne donc
- pression artérielle, ECG, [[id:1ab5aa3c-f88a-45f9-a551-2507fc6642ff][Anomalie lipidique]]
- doppelr MI et TSA, IPS (pression systolique cheville/brachial -> anormal si < 0.9)
 [[id:dd35f673-81f0-4d95-b4b2-99ca2090689f][Fructosamine]] : peu utilisé
[[id:97cfbabe-78e8-49e8-8b00-01e47a6f2da9][Créatinine]]
[[id:f9caff5e-5572-4e86-81e2-c7897fdd9248][Débit de filtration glomérulaire (DFG)]]
[[id:a151d21a-b016-4de8-a269-29673c636355][Protéinurie]]
** IR
À cherche une fois par an :
- BU (protéuinurie, hématire, leucocyturie)
- créatininémie + estimation DFG
- albuminurie (rapport albu/créat)
Attente rénale si protéinurie/albumuniraire ou DFG < 60 pendant > 3

Insertion in notes/20240702225354-creatinine.org at line 7 [11.6629]

[11.6741]

Si maladie rénale établie, inutile de mesure la clairance. Il suffit de surveiller par la créatinine plasmatique
Influencé par : ivande, exercice et masse musculaire

Insertion in notes/20240702225354-creatinine.org at line 10 [11.6629]

[11.6754]


Attention, le DFG doit diminuer de 50% avant que la concentration de créatinine plasmatique > normale !

Insertion in notes/20240515225840-nixpkgs.org at line 22 [14.163095]

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  Vérifier avec
  #+begin_src
nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD"
  #+end_src

Insertion in notes/20240515225840-nixpkgs.org at line 49 [14.163095]

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** Copier une dérivation en ssh
nix copy --from ssh://meso /nix/store/f3ak3jvb9kxv6jd6r7kjbjr1a59hzyrb-tensorflow-2.13.0-python

Replacement in notes/20240504165801-debugger_un_paquet_nix.org at line 62 [14.862858]

B:BD[14.864122] → [14.864122:864269]

- [[https://nixos.wiki/wiki/Nixpkgs/Create_and_debug_packages][Source]]
- [[https://nixos.wiki/wiki/Packaging/Tutorial]]
- [[[#nixpkgs][nixpkgs]]]

[6.2910]

- https://nixos.wiki/wiki/Create_and_debug_nix_packages
- [[id:0edbf593-2192-479a-8cc4-aefd3e991f2a][Nixpgs]]

File move: 20220327225315-cooking.org → 20220327225315-recettes.org
BF:BFD[13.188] → [2.5776:5826]
BF:BF[2.5826] → [14.659896:659896]
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[14.659896]
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B:BD[14.659896] → [14.659897:659908]
```
* Desserts
```
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B:BD[14.659921] → [14.659921:659942]
```
:CUSTOM_ID: desserts
```
[14.659921]
[14.659942]
```
:ID:       dfd5ff3e-57a3-4578-b90e-24ccde5d4a93
```
Insertion in notes/20220327225315-recettes.org at line 4 [14.659896]
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[14.659948]
```
#+title: Recettes
* Desserts
```
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B:BD[14.659972] → [14.659972:660024]
```
:PROPERTIES:
:CUSTOM_ID: done-biscuit-cuiller
:END:
```

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B:BD[14.660150] → [14.660150:660361]

:PROPERTIES:
:CUSTOM_ID: retry-biscuit-de-savoie
:END:
[[https://www.meilleurduchef.com/cgi/mdc/l/fr/recette/biscuit-savoie.html][meilleur
du chef]]) : cuire vraiment plus longtemps en bas du four. Bien beurrer

[14.660150]

[14.660361]

[[https://www.meilleurduchef.com/cgi/mdc/l/fr/recette/biscuit-savoie.html][meilleur du chef]] : cuire vraiment plus longtemps en bas du four. Bien beurrer

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B:BD[14.660449] → [14.660449:660499]
```
:PROPERTIES:
:CUSTOM_ID: done-blackout-cake
:END:
```

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B:BD[14.665464] → [14.665464:665581]

:PROPERTIES:
:CUSTOM_ID: retry-bounty
:END:
[[http://www.750g.com/bounty-maison-r97803.htm][750g]]) : prendre du bon

[14.665464]

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[[http://www.750g.com/bounty-maison-r97803.htm][750g]] : prendre du bon

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```
:PROPERTIES:
:CUSTOM_ID: retry-brioche
:END:
```
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B:BD[14.726592] → [14.726592:726629]
```
:PROPERTIES:
:CUSTOM_ID: pains
:END:
```

Deletion in inbox.org at line 2 [6.3292]

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* TODO Inscription jcadd 2024
SCHEDULED: <2024-09-02 Mon>
/Entered on/ [2024-07-06 Sat 14:51]
* TODO Présentation JCADD 2024
SCHEDULED: <2024-09-25 Wed> DEADLINE: <2024-10-30 Wed>
/Entered on/ [2024-07-06 Sat 14:52]

File addition: filterOrgRoam.hs (----------)

[15.2]

{-# LANGUAGE TemplateHaskell            #-}
{-# LANGUAGE QuasiQuotes                #-}
{-# LANGUAGE TypeFamilies               #-}
{-# LANGUAGE MultiParamTypeClasses      #-}
{-# LANGUAGE GADTs                      #-}
{-# LANGUAGE GeneralizedNewtypeDeriving #-}
{-# LANGUAGE RecordWildCards            #-}
{-# LANGUAGE FlexibleInstances          #-}
{-# LANGUAGE OverloadedStrings          #-}
{-# LANGUAGE DerivingStrategies         #-}
{-# LANGUAGE StandaloneDeriving         #-}
{-# LANGUAGE UndecidableInstances       #-}
{-# LANGUAGE DataKinds #-}
import qualified Database.Persist.TH as PTH
import Database.Persist (Entity(..))
import Database.Persist.Sql (toSqlKey)
import qualified Data.Text as T
import Database.Persist.Sqlite
import Control.Monad.IO.Class
import Control.Monad.Logger
import Text.Pandoc.JSON
import System.FilePath (addExtension, dropExtension, makeRelative)
import System.Directory (getCurrentDirectory)
PTH.share [PTH.mkPersist PTH.sqlSettings, PTH.mkMigrate "migrateAll"] [PTH.persistLowerCase|
  Node sql=nodes
    Id T.Text sql=id
    file T.Text
    title T.Text
    deriving Show
|]
path =  "/home/alex/.emacs.d/.local/cache/org-roam.db"
unescape :: T.Text -> T.Text
unescape = T.replace "\"" ""
-- From "id:XXXX" search in org-roam database for path to file
-- If there is no id, just return the string unchanged
pathFromID :: T.Text -> IO (T.Text)
pathFromID id = runSqlite path $ do
    -- Get id and add (escaped) quote
    let s = T.concat ["\"", last (T.splitOn "id:" id), "\""]
    test <- get (NodeKey s)
    let res = case test of
                Just x -> unescape . nodeFile $ x
                Nothing -> id
    return res
-- Change link to HTML version for publishing it
-- Link is transformed from absolute to relative
htmlLink :: FilePath -> FilePath -> FilePath
htmlLink f pwd = makeRelative pwd (addExtension (dropExtension f) ".html")
-- Replace org-mode internal link to link to the full path of the file
replaceLink :: Inline -> IO (Inline)
replaceLink (Link attr xs t) = do
  p <- pathFromID (fst t)
  pwd <- getCurrentDirectory
  let p' = htmlLink (T.unpack p) pwd
  return $ Link attr xs (T.pack p', snd t)
replaceLink x = return x
main :: IO ()
main = toJSONFilter replaceLink

File addition: Shakefile.hs (----------)

[15.2]

import Development.Shake
import Development.Shake.Command
import Development.Shake.FilePath
import Development.Shake.Util
siteExe :: String
siteExe = "_build/hakyll-site"
-- This only works in Gentoo with packages installed globally
-- TODO: add a switch to use cabal (cabal build and cabal run) outside gentoo
-- Note: nix-build fails with some encoding issues (hGetConts).
-- Nix flakes builds several GHC version...
main :: IO ()
main = shakeArgs shakeOptions{shakeFiles="_build"} $ do
    want ["_build/notes/index.html"]
    "_build/notes/index.html" %> \out -> do
        let src = "notes/index.org"
        org <- getDirectoryFiles "" ["notes/medecine/*.org"]
        let html = ["_build" </> n -<.> "html" | n <- org]
        need html
        cmd "pandoc" src "--filter ./filterOrgRoam -o" [out]
    "_build/notes/medecine/*.html" %> \out -> do
        let org = dropDirectory1 $ out -<.> "org"
        putInfo org
        putInfo out
        cmd "pandoc" [org] "--filter ./filterOrgRoam -o" [out]
  --   want ["build", "hut"]
  --   siteExe  %> \out -> do
  --     let src = "src/Main.hs"
  --     need [src, "notes/20230511180745-microbiologie.org"]
  --     cmd_ "ghc --make -o" [out] [src]
  --   -- Shake cannot use directories
  --   phony "build" $ do
  --       need [siteExe]
  --       cmd_ siteExe "build"
    phony "clean" $ do
        -- putInfo "Cleaning site "
  --       cmd_ siteExe "clean"
        putInfo "Cleaning files in _build"
        removeFilesAfter "_build" ["//*"]
  --   phony "hut" $ do
  --       putInfo "Upload to blog hosted by sourcehut"
  --       need ["archive"]
  --       cmd_ "hut pages publish _build/site.tar.gz -d scut.srht.site"
  --   phony "archive" $ do
  --       need ["build"]
  --       cmd_ "tar cvzf " ["_build/site.tar.gz"] "-C _site ."
  -- -- z option is important to avoid re-uploading everything
  --   phony "free" $ do
  --       putInfo "Upload to blog hosted by Free"
  --       cmd_ "ncftpput -z -f login.cfg -R . _site/*"
  --       cmd_ "ncftpput -z -f login.cfg -R . files/*"
  --   phony "watch" $ do
  --       putInfo "Generate site locally"
  --       cmd_ "_build/hakyll-site watch"

Diabète

Dependencies

In channels

Change contents

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File addition: 20240707142811-proteinurie.org (----------)

File addition: 20240707135547-debit_de_filtration_glomerulaire_dfg.org (----------)

File addition: 20240707134057-fructosamine.org (----------)

File addition: 20240707133407-anomalie_lipidique.org (----------)

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File move: 20220327225315-cooking.org → 20220327225315-recettes.org

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File addition: filterOrgRoam.hs (----------)

File addition: Shakefile.hs (----------)