apraga/org - Change EOZSQ7457A6ZEBQTDNBPHVILS36HZYTU2OOOXWRXFHZMI4RZAOJQC

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Created by Alexis Praga on June 9, 2024

EOZSQ7457A6ZEBQTDNBPHVILS36HZYTU2OOOXWRXFHZMI4RZAOJQC

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Replacement in projects.org at line 36 [5.179]

B:BD[4.476] → [4.476:525]

**** TODO Algorithme rapide intersection VCF-BED

[4.476]

[4.525]

**** DONE Algorithme rapide intersection VCF-BED
CLOSED: [2024-06-09 Sun 23:27] SCHEDULED: <2024-06-08 Sat>

Insertion in projects.org at line 44 [5.179]

[2.231]

[4.565]

**** DONE Comparaison algo naïf avec bedtools intersect: on reste sur bedtools
CLOSED: [2024-06-09 Sun 23:27] SCHEDULED: <2024-06-09 Sun>
/Entered on/ [2024-06-09 Sun 13:49]

Replacement in projects.org at line 76 [5.179]

B:BD[5.514] → [5.514:539]

B:BD[5.539] → [4.956:989]

** Intermediate Japanese
SCHEDULED: <2024-06-06 Thu .+1d>

[5.514]

[5.572]

** TODO Intermediate Japanese
SCHEDULED: <2024-06-09 Sun .+1d>

Replacement in projects.org at line 82 [5.179]

B:BD[5.645] → [4.990:1176]

∅:D[4.1176] → [6.296:358]

B:BD[5.645] → [6.296:358]

∅:D[6.358] → [7.936:1060]

B:BD[5.645] → [7.936:1060]

∅:D[7.1060] → [8.1307:1431]

B:BD[5.645] → [8.1307:1431]

∅:D[8.1431] → [9.307:369]

B:BD[5.645] → [9.307:369]

∅:D[9.369] → [10.37:99]

B:BD[5.645] → [10.37:99]

∅:D[10.99] → [11.37:99]

B:BD[5.645] → [11.37:99]

∅:D[11.99] → [12.176:362]

B:BD[5.645] → [12.176:362]

∅:D[12.362] → [13.477:539]

B:BD[5.645] → [13.477:539]

∅:D[13.539] → [14.634:696]

B:BD[5.645] → [14.634:696]

∅:D[14.696] → [5.645:831]

B:BD[5.645] → [5.645:831]

- State "DONE"       from ""           [2024-06-05 Wed 10:01]
- State "DONE"       from ""           [2024-06-04 Tue 10:01]
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- State "DONE"       from ""           [2024-05-22 Wed 14:47]
- State "DONE"       from ""           [2024-05-21 Tue 14:47]
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- State "DONE"       from ""           [2024-05-18 Sat 14:47]
- State "DONE"       from ""           [2024-05-17 Fri 14:47]
- State "DONE"       from ""           [2024-05-16 Thu 14:47]
- State "DONE"       from ""           [2024-05-15 Wed 14:47]

[5.645]

[15.409]

- State "DONE"       from "TODO"           [2024-06-08 Sat 10:01]
- State "DONE"       from "TODO"           [2024-06-07 Fri 10:01]
- State "DONE"       from "TODO"           [2024-06-06 Thu 10:01]
- State "DONE"       from "TODO"           [2024-06-05 Wed 10:01]
- State "DONE"       from "TODO"           [2024-06-04 Tue 10:01]
- State "DONE"       from "TODO"           [2024-06-02 Sun 10:01]
- State "DONE"       from "TODO"           [2024-06-01 Sat 10:01]
- State "DONE"       from "TODO"           [2024-05-31 Fri 10:01]
- State "DONE"       from "TODO"           [2024-05-30 Thu 10:01]
- State "DONE"       from "TODO"           [2024-05-29 Wed 10:01]
- State "DONE"       from "TODO"           [2024-05-28 Tue 10:01]
- State "DONE"       from "TODO"           [2024-05-26 Sun 10:01]
- State "DONE"       from "TODO"           [2024-05-25 Sat 14:47]
- State "DONE"       from "TODO"           [2024-05-24 Fri 14:47]
- State "DONE"       from "TODO"           [2024-05-22 Wed 14:47]
- State "DONE"       from "TODO"           [2024-05-21 Tue 14:47]
- State "DONE"       from "TODO"           [2024-05-20 Mon 14:47]
- State "DONE"       from "TODO"           [2024-05-19 Sun 14:47]
- State "DONE"       from "TODO"           [2024-05-18 Sat 14:47]
- State "DONE"       from "TODO"           [2024-05-17 Fri 14:47]
- State "DONE"       from "TODO"           [2024-05-16 Thu 14:47]
- State "DONE"       from "TODO"           [2024-05-15 Wed 14:47]

Replacement in projects.org at line 117 [5.179]

B:BD[8.1584] → [4.1177:1210]

** WAIT Suspendre assurance moto

[8.1584]

[4.1210]

** DONE Suspendre assurance moto
CLOSED: [2024-06-08 Sat 18:39]

Replacement in projects.org at line 178 [5.179]

B:BD[8.1894] → [4.1604:1631]

B:BD[4.1631] → [3.3:30]

** TODO Utiliser token RED
DEADLINE: <2024-06-09 Sun>

[8.1894]

[4.1686]

** TODO Utiliser token RED: à télécharge
SCHEDULED: <2024-06-10 Mon> DEADLINE: <2024-06-09 Sun>

Replacement in projects.org at line 181 [5.179]

B:BD[4.1722] → [2.521:593]

** TODO Finir télécharger aerial spincity
SCHEDULED: <2024-06-08 Sat>

[4.1722]

[2.593]

** DONE Finir télécharger aerial spincity
CLOSED: [2024-06-09 Sun 15:38] SCHEDULED: <2024-06-08 Sat>

Insertion in projects.org at line 184 [5.179]

[2.629]

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** WAIT Nettoyer bookmarks buku
/Entered on/ [2024-06-08 Sat 18:39]
** DONE Relire rapport Ben
CLOSED: [2024-06-09 Sun 23:28] SCHEDULED: <2024-06-08 Sat>
/Entered on/ [2024-06-08 Sat 18:42]

Deletion in notes/maladies_infectieuses.org at line 6 [7.2783]
B:BD[7.2903] → [6.460:461]

Replacement in notes/maladies_infectieuses.org at line 7 [7.2783]

B:BD[7.2904] → [6.462:795]

∅:D[6.795] → [7.2904:2961]

B:BD[7.2904] → [7.2904:2961]

B:BD[16.4852] → [16.4852:4909]

B:BD[16.4909] → [3.3538:3665]


[[id:9c228cdd-e721-4dd4-8546-d69a5aa02442][Angines]]
[[id:e4807368-00e0-4e3b-81e5-8231002de347][Gastro-entérites]]
[[id:4fa9f349-d2df-46fe-8132-697c20d65328][Infections cutanées]]
[[id:e6fc90b1-6aa5-4397-9d9a-82e72a96ef07][Infections sexuellement transmissibles]]
[[id:c085bebe-fe0c-4a2d-958e-64a8b0aec5eb][Infections urinaires]]
[[id:6c33ba0a-0794-49ed-949a-9e056c185eb0][Légionelle]]
[[id:7972bb4d-9a13-40ac-a1c2-015fee9d0d02][Méningites]]
[[id:d19455f2-4d40-4d55-a5a5-e6143a37d0ed][Diarrhées]]
[[id:2929b4d1-d0a3-475c-8a15-2e427c0bbfef][Endocardites infectieuses]]

[7.2904]

- [[id:9c228cdd-e721-4dd4-8546-d69a5aa02442][Angines]]
- [[id:d19455f2-4d40-4d55-a5a5-e6143a37d0ed][Diarrhées]]
- [[id:2929b4d1-d0a3-475c-8a15-2e427c0bbfef][Endocardites infectieuses]]
- [[id:e4807368-00e0-4e3b-81e5-8231002de347][Gastro-entérites]]
- [[id:4fa9f349-d2df-46fe-8132-697c20d65328][Infections cutanées]]
- [[id:e6fc90b1-6aa5-4397-9d9a-82e72a96ef07][Infections sexuellement transmissibles]]
- [[id:c085bebe-fe0c-4a2d-958e-64a8b0aec5eb][Infections urinaires]]
- [[id:6c33ba0a-0794-49ed-949a-9e056c185eb0][Légionelle]]
- [[id:7972bb4d-9a13-40ac-a1c2-015fee9d0d02][Méningites]]

Replacement in notes/bacteriologie.org at line 7 [17.1259]

B:BD[7.6380] → [7.6380:6448]

[[id:a54652d5-68c8-4668-aed9-50c9d719c207][Maladies infectieuses]]

[7.6380]

[7.6448]

- [[id:a54652d5-68c8-4668-aed9-50c9d719c207][Maladies infectieuses]]
- [[id:86fb6c69-d3dc-4ec1-a40f-9031d8ba5faf][Antibiotiques]]

Deletion in notes/bacteriologie.org at line 11 [17.1259]
B:BD[7.6455] → [7.6455:6474]
```
[[Antibiotiques]]
```
File move: Antibiotiques.org → antibiotiques.org
BF:BFD[18.3988] → [18.7284:7325]
BF:BF[18.7325] → [19.424434:424434]
[18.188]
[19.424434]

Replacement in notes/antibiotiques.org at line 1 [19.424434]

B:BD[19.424434] → [19.424435:424458]

#bacterio ## Cibles

[19.424434]

[19.424458]

:PROPERTIES:
:ID:       86fb6c69-d3dc-4ec1-a40f-9031d8ba5faf
:END:
#+title: Antibiotiques
#+filetags: bacterio

Replacement in notes/antibiotiques.org at line 7 [19.424434]

B:BD[19.424459] → [19.424459:424552]

- inhibition synthèse de la paroi bactérienne = β-lactamine,
  glycopeptides, fosfomycine

[19.424459]

[19.424552]

* Cibles
- inhibition synthèse de la paroi bactérienne = β-lactamine, glycopeptides, fosfomycine

Replacement in notes/antibiotiques.org at line 13 [19.424434]
B:BD[19.424703] → [19.424703:424748]
```
[[/images/microbiologie/antibio-action.png]]
```
[19.424703]
[19.424748]
```
[[./images/microbiologie/antibio-action.png]]
```
Replacement in notes/antibiotiques.org at line 15 [19.424434]
B:BD[19.424749] → [19.424749:424835]
```
** Mécanisme de résistance
:PROPERTIES:
:CUSTOM_ID: mécanisme-de-résistance
:END:
```
[19.424749]
[19.424835]
```
* Mécanisme de résistance
```

Replacement in notes/antibiotiques.org at line 21 [19.424434]

B:BD[19.424904] → [19.424904:424981]

[[../../images/microbiologie/antibio-resistance.png]] Résistance
naturelle

[19.424904]

[19.424981]

[[./images/microbiologie/antibio-resistance.png]]
Résistance naturelle

Replacement in notes/antibiotiques.org at line 27 [19.424434]
B:BD[19.425068] → [19.425068:425135]
```
*** Synthèse paroi
:PROPERTIES:
:CUSTOM_ID: synthèse-paroi
:END:
```
[19.425068]
[19.425135]
```
** Synthèse paroi
```

Replacement in notes/antibiotiques.org at line 29 [19.424434]

B:BD[19.425151] → [19.425151:425243]


   - Les β-lactamine inhibent la synthèse de la paroi bactérienne
     (peptidoglycane)

[19.425151]

[19.425243]

   - Les β-lactamine inhibent la synthèse de la paroi bactérienne (peptidoglycane)

Replacement in notes/antibiotiques.org at line 43 [19.424434]

B:BD[19.425737] → [19.425737:425890]

*** Synthèse protéine bactérienne
:PROPERTIES:
:CUSTOM_ID: synthèse-protéine-bactérienne
:END:
[[../../images/microbiologie/antibio-ribosome.png]]

[19.425737]

[19.425890]

** Synthèse protéine bactérienne
[[./images/microbiologie/antibio-ribosome.png]]

Replacement in notes/antibiotiques.org at line 52 [19.424434]
B:BD[19.426143] → [19.426143:426232]
```
*** Synthèse acide nucléique
:PROPERTIES:
:CUSTOM_ID: synthèse-acide-nucléique
:END:
```
[19.426143]
[19.426232]
```
** Synthèse acide nucléique
```
Deletion in notes/antibiotiques.org at line 58 [19.424434]
B:BD[19.426394] → [19.426394:426431]
```
:PROPERTIES:
:CUSTOM_ID: notes
:END:
```

Replacement in notes/antibiotiques.org at line 59 [19.424434]

B:BD[19.426496] → [19.426496:426988]

- glycopeptides inefficaces sur bactérie Gram négatif car elles ont une
  membrane externe qui ne laisse pas passer les grosses molécules
- synergie β-lactamine - aminoside sur strepto et entérocoque :
  destruction de la paroi par les β-lactamine pour que l'aminoside
  accède au ribosome
- seules les antibio pénétrant dans les cellules (macrolides,
  fluoroquinolones, rifampicine, cycline ) sont actives contre les
  bactéries "intracellulaires " (Chlamydia, Coxiella burnetti,

[19.426496]

[19.426988]

- glycopeptides inefficaces sur bactérie Gram négatif car elles ont une membrane externe qui ne laisse pas passer les grosses molécules
- synergie β-lactamine - aminoside sur strepto et entérocoque : destruction de la paroi par les β-lactamine pour que l'aminoside accède au ribosome
- seules les antibio pénétrant dans les cellules (macrolides, fluoroquinolones, rifampicine, cycline ) sont actives contre les bactéries "intracellulaires " (Chlamydia, Coxiella burnetti,

Deletion in notes/antibiotiques.org at line 65 [19.424434]
B:BD[19.427073] → [19.427073:427113]
```
:PROPERTIES:
:CUSTOM_ID: résumé
:END:
```

Insertion in notes/antibiotiques.org at line 71 [19.424434]

[19.428041]

|--------------------+----------------------------+--------------------------------------------+---------------------------------+---------------------|

Insertion in notes/antibiotiques.org at line 73 [19.424434]

[19.428197]

|--------------------+----------------------------+--------------------------------------------+---------------------------------+---------------------|

Insertion in notes/antibiotiques.org at line 85 [19.424434]

[19.429238]

|------------+----------------------------------+--------------------+---------------------------------|

Insertion in notes/antibiotiques.org at line 98 [19.424434]

[19.430405]

|----------------------+------------------------------------------+---------------------------+------------------------------------|

Insertion in notes/antibiotiques.org at line 101 [19.424434]

[19.430679]

|----------------------+------------------------------------------+---------------------------+------------------------------------|

Replacement in notes/antibiotiques.org at line 104 [19.424434]

B:BD[19.430816] → [19.430816:430928]

(1) Pas de monothérpaie pour P. aeruginosa et Staphylocoque aureus
(risque mutants) (2) amikacine, gentamicine

[19.430816]

[19.430928]

(1) Pas de monothérpaie pour P. aeruginosa et Staphylocoque aureus (risque mutants)
(2) amikacine, gentamicine

Insertion in notes/antibiotiques.org at line 113 [19.424434]

[19.431808]

|---------------------+-------------------------------+------------------+-----------------------------------------+----------------------------|

Insertion in notes/antibiotiques.org at line 115 [19.424434]

[19.431957]

|---------------------+-------------------------------+------------------+-----------------------------------------+----------------------------|

Replacement in notes/antibiotiques.org at line 118 [19.424434]

B:BD[19.432105] → [19.432105:432182]

(1) erythro, azithromycine, clarithromycine (2) clindamycine (3)
vancomycine

[19.432105]

[19.432182]

(1) erythro, azithromycine, clarithromycine
(2) clindamycine
(3) vancomycine

Deletion in notes/antibiotiques.org at line 123 [19.424434]
B:BD[19.432202] → [19.432202:432249]
```
:PROPERTIES:
:CUSTOM_ID: interprétation
:END:
```
Deletion in notes/antibiotiques.org at line 157 [19.424434]
B:BD[19.434609] → [19.434609:434645]
```
:PROPERTIES:
:CUSTOM_ID: mslb
:END:
```

Replacement in notes/antibiotiques.org at line 158 [19.424434]

B:BD[19.434677] → [19.434677:434807]


- sensible pristinamycine : regarder si induction ("interaction"), si
  oui, MSLB inductible donc possible sélection de mutant.

[19.434677]

[19.434807]

- sensible pristinamycine : regarder si induction ("interaction"), si oui, MSLB inductible donc possible sélection de mutant.

Replacement in notes/antibiotiques.org at line 162 [19.424434]

B:BD[19.434865] → [19.434865:435009]

:PROPERTIES:
:CUSTOM_ID: piège
:END:
- SAUR sensible oxa mais résistance peni G => pénicillinase ->
  résistance à toute les pénicillines

[19.434865]

[19.435009]

- SAUR sensible oxa mais résistance peni G => pénicillinase -> résistance à toute les pénicillines

Replacement in notes/antibiotiques.org at line 165 [19.424434]

B:BD[19.435086] → [19.435086:435178]

  - résistance gentamicine => forcément résistant tobramycine,
    amikacine, kanamycine

[19.435086]

[19.435178]

  - résistance gentamicine => forcément résistant tobramycine, amikacine, kanamycine

Replacement in notes/antibiotiques.org at line 170 [19.424434]

B:BD[19.435324] → [19.435324:435505]

:PROPERTIES:
:CUSTOM_ID: aminosides
:END:
Action = bactéricide, concentration dépendant. Perturbe la synthèse des
protéine (fixation sous unité 30s des ribosomes) Résistances

[19.435324]

[19.435505]

Action = bactéricide, concentration dépendant.
Perturbe la synthèse des protéine (fixation sous unité 30s des ribosomes)

Insertion in notes/antibiotiques.org at line 173 [19.424434]
[19.435506]
[19.435506]
```
*** Résistances
```
Deletion in notes/antibiotiques.org at line 180 [19.424434]
B:BD[19.435809] → [19.435809:435850]
```
:PROPERTIES:
:CUSTOM_ID: sulfamide
:END:
```

Replacement in notes/antibiotiques.org at line 186 [19.424434]

B:BD[19.436054] → [19.436054:436239]

:PROPERTIES:
:CUSTOM_ID: fluoroquinolone
:END:
- 4 générations: initialement répartition extra-cellulaire -> large et
  homogène (intracellulaire) avec les dernières générations

[19.436054]

[19.436239]

- 4 générations: initialement répartition extra-cellulaire -> large et homogène (intracellulaire) avec les dernières générations

Replacement in notes/antibiotiques.org at line 188 [19.424434]

B:BD[19.436270] → [19.436270:436432]

- Effets indésriable nombreux : digestif, phototoxique, trouble nerveur,
  inhibe cytochrme P450 (! interactions)
- Contre-indication : déficit G6PI, grossesse

[19.436270]

[19.436432]

- Effets indésriable nombreux : digestif, phototoxique, trouble nerveux, inhibe cytochrme P450 (! interactions)
- Contre-indication : déficit G6PD, grossesse

Replacement in notes/antibiotiques.org at line 193 [19.424434]

B:BD[19.436542] → [19.436542:436630]

  - quinolones = cystite aigùe simple non compliquée, récidivantes chez
    l'adulte

[19.436542]

[19.436630]

  - quinolones = cystite aigùe simple non compliquée, récidivantes chez l'adulte
  - 2e génération : infections sévères à bacille Gram négatif
  - 3e et 4e génération : sinusite aigüe bactériennes, exacerbation pneumopathie communutaire, infection compliquée peau + tissus mous

Replacement in notes/antibiotiques.org at line 197 [19.424434]

B:BD[19.436631] → [19.436631:436698]

  - 2e génération : infetions sévères à bacille Gram négatif

[19.436631]

[19.436698]

    Résistante : en augmentation chez entérobactéries (E. coli, Klebsiella)

Deletion in notes/antibiotiques.org at line 199 [19.424434]

B:BD[19.436699] → [19.436699:436929]

  - 3e et 4e génération : sinusite aigüe bactériennes, exacerpbation
    pneumopathie communutaire, infection compliquée peau + tissus mous
    Résistante : en augmentatino chez entérobactéries (E. coli,
    Klebsiella)

Deletion in notes/antibiotiques.org at line 200 [19.424434]
B:BD[19.436947] → [19.436947:436993]
```
:PROPERTIES:
:CUSTOM_ID: métronidazole
:END:
```
Deletion in notes/antibiotiques.org at line 203 [19.424434]
B:BD[19.437052] → [19.437052:437113]
```
:PROPERTIES:
:CUSTOM_ID: infection-ostéo-articulaires
:END:
```

File addition: 20240609 (----------)

[20.636]

* 2024-06-09
** 14:01 Bisonex : algo naïf vs bedtools intersect
 bedtools intersect -a clinvar_ref.vcf.gz -b Twist_Exome_Core_Covered_Targets_hg38_sorted.bed -wa | save lol_ref.vcf -f
❯ zgrep -c -v '^#' lol_ref.vcf
189038
❯ zgrep -c -v '^#' lol.vcf
6257
❯  awk -F '\t' '{print $1" "$2}' intersect.vcf | save pos.txt
❯ awk -F '\t' '{print $1" "$2}' intersect_ref.vcf | save pos_ref.txt
❯ diff lol_pos.txt lol_ref_pos.txt | head -n 100
Par exemple, la borne inf du chr1 1789052
Le problème est que la position des indel est -1 du changement !
Après correction, mieux mais pas encore ça
 zgrep -c -v '^#' intersect*
intersect.vcf:13425
intersect_ref.vcf:189038

Insertion in inbox.org at line 2 [5.3292]

[5.3311]

* TODO Répétition Ben
DEADLINE: <2024-06-09 Sun 16:00>
/Entered on/ [2024-06-08 Sat 18:42]