From f1e68ffdd07b3844baf83861f644996ecded240c Mon Sep 17 00:00:00 2001 From: Pavel Balazki Date: Thu, 24 Mar 2022 12:33:14 +0100 Subject: [PATCH 1/4] Typos Added spellcheck --- .github/workflows/MarkdownLinksCheck.yml | 26 + .github/workflows/SpellChecker.yml | 17 + .github/workflows/XRefCheck.yml | 23 + .github/workflows/mlc_config.json | 6 + .github/workflows/wordlist.txt | 1281 +++++++++++++++++ .spellcheck.yml | 18 + Evaluation/Input/Content/References.md | 2 +- .../Input/Content/Section1_Introduction.md | 4 +- Evaluation/Input/Content/Section2.2_Data.md | 2 +- Evaluation/Input/Content/glossary.md | 2 +- Evaluation/Workflow.m | 6 +- 11 files changed, 1379 insertions(+), 8 deletions(-) create mode 100644 .github/workflows/MarkdownLinksCheck.yml create mode 100644 .github/workflows/SpellChecker.yml create mode 100644 .github/workflows/XRefCheck.yml create mode 100644 .github/workflows/mlc_config.json create mode 100644 .github/workflows/wordlist.txt create mode 100644 .spellcheck.yml diff --git a/.github/workflows/MarkdownLinksCheck.yml b/.github/workflows/MarkdownLinksCheck.yml new file mode 100644 index 0000000..20350ca --- /dev/null +++ b/.github/workflows/MarkdownLinksCheck.yml @@ -0,0 +1,26 @@ +name: Check Markdown links + +on: + pull_request: + branches: + - review + push: + branches: + - review + +permissions: + contents: read + +jobs: + markdown-link-check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + with: + ref: ${{ github.event.pull_request.head.sha }} + - uses: gaurav-nelson/github-action-markdown-link-check@2a60e0fe41b5361f446ccace6621a1a2a5c324cf + with: + use-quiet-mode: 'yes' + use-verbose-mode: 'yes' + config-file: '.github/workflows/mlc_config.json' + folder-path: 'report' diff --git a/.github/workflows/SpellChecker.yml b/.github/workflows/SpellChecker.yml new file mode 100644 index 0000000..fa03010 --- /dev/null +++ b/.github/workflows/SpellChecker.yml @@ -0,0 +1,17 @@ +name: Spellcheck + +on: + pull_request: + push: + +permissions: + contents: read + +jobs: + Spellcheck: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + with: + ref: ${{ github.event.pull_request.head.sha }} + - uses: rojopolis/spellcheck-github-actions@0.14.0 diff --git a/.github/workflows/XRefCheck.yml b/.github/workflows/XRefCheck.yml new file mode 100644 index 0000000..5b4ed2f --- /dev/null +++ b/.github/workflows/XRefCheck.yml @@ -0,0 +1,23 @@ +name: XRefCheck + +on: + pull_request: + branches: + - review + push: + branches: + - review + +permissions: + contents: read + +jobs: + markdown-link-check2: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + with: + ref: ${{ github.event.pull_request.head.sha }} + - uses: serokell/xrefcheck-action@959c7cecf1b316023bfd204ae88642338f6bb91c + with: + xrefcheck-args: --ignored evaluation --ignored README.md \ No newline at end of file diff --git a/.github/workflows/mlc_config.json b/.github/workflows/mlc_config.json new file mode 100644 index 0000000..00b2784 --- /dev/null +++ b/.github/workflows/mlc_config.json @@ -0,0 +1,6 @@ +{ + "retryOn429": true, + "retryCount": 5, + "fallbackRetryDelay": "30s", + "aliveStatusCodes": [200, 403] +} diff --git a/.github/workflows/wordlist.txt b/.github/workflows/wordlist.txt new file mode 100644 index 0000000..09c6952 --- /dev/null +++ b/.github/workflows/wordlist.txt @@ -0,0 +1,1281 @@ +aap +AAPS +aas +abb +Absorbability +AbsTol +Aburatani +Aciclovir +ACM +ACOS +Acta +actionToExecute +actp +actpo +AddAction +addir +addirg +addirr +addOutputInterval +addOutputs +addParameterPaths +AddPoint +addPoints +adjustbox +ADME +ae +ageMax +ageMin +ageParam +ageUnit +agg +agof +agofg +agofo +Ahonen +Ahr +ai +aintro +al +alfentanil +allAciclovirMolecules +AllOfSameType +allometric +allOutputs +allPKParameterSensitivitiesFor +allPKParametersFor +allPkParams +AllPlots +allPoints +allQuantityPaths +allUnits +anastomoses +antecubital +Anthracycline +anthropo +anthropometry +aod +ap +apkr +apkrg +apkrr +AppData +Appl 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+opentci +OSPy +overprediction +Restrepo +Samii +Schnider +Shafer +SL +Struys +Takizawa +TW +UDP +Uridine +vx +WS +Youngs +pbpk diff --git a/.spellcheck.yml b/.spellcheck.yml new file mode 100644 index 0000000..462c4a8 --- /dev/null +++ b/.spellcheck.yml @@ -0,0 +1,18 @@ +matrix: +- name: Markdown + aspell: + lang: en + dictionary: + wordlists: + - .github/workflows/wordlist.txt + encoding: utf-8 + pipeline: + - pyspelling.filters.markdown: + - pyspelling.filters.html: + comments: false + ignores: + - code + - pre + sources: + - '**/*.md' + default_encoding: utf-8 diff --git a/Evaluation/Input/Content/References.md b/Evaluation/Input/Content/References.md index 45642ae..a830b9c 100644 --- a/Evaluation/Input/Content/References.md +++ b/Evaluation/Input/Content/References.md @@ -36,7 +36,7 @@ **SmPC Namuscla ** SmPC Namuscla 167 mg hard capsules, 2019, website medicines.org.uk/emc/product/9838/smpc -**Stanczyk 1983** Stanczyk FZ, Mroszczak EJ, Ling T, et al. Plasma levels and pharmacokinetics of norethindrone and ethinylestradiol administered in solution and as tablets to women. *Contraception*. 1983;28(3):241-251.. +**Stanczyk 1983** Stanczyk FZ, Mroszczak EJ, Ling T, et al. Plasma levels and pharmacokinetics of norethindrone and ethinylestradiol administered in solution and as tablets to women. *Contraception*. 1983;28(3):241-251. **Stanczyk 2013** Stanczyk FZ, Archer DF, Bhavnani BR. Ethinyl estradiol and 17beta-estradiol in combined oral contraceptives: pharmacokinetics, pharmacodynamics and risk assessment. *Contraception*. 2013;87(6):706-727. diff --git a/Evaluation/Input/Content/Section1_Introduction.md b/Evaluation/Input/Content/Section1_Introduction.md index efe171d..51c1f5c 100644 --- a/Evaluation/Input/Content/Section1_Introduction.md +++ b/Evaluation/Input/Content/Section1_Introduction.md @@ -6,10 +6,10 @@ Ethinylestradiol is an estrogen medication which is used widely as a birth contr **Distribution**: ethinylestradiol is rapidly distributed throughout most body tissues with the largest concentration found in adipose tissue. It distributes into breast milk, with low concentrations. More than 80% of ethinylestradiol in serum is conjugated as sulphate and almost all the conjugated form is bound to albumin. -**Metabolism**: ethinylestradiol is metabolised in the liver. Hydroxylation appears to be the main metabolic pathway. 60% of a dose is excreted in the urine and 40% in the faeces. +**Metabolism**: ethinylestradiol is metabolized in the liver. Hydroxylation appears to be the main metabolic pathway. 60% of a dose is excreted in the urine and 40% in the faeces. **Excretion**: About 30% is excreted in the urine and bile as the glucuronide or sulphate conjugate. The rate of metabolism of ethinylestradiol is affected by several factors, including enzyme-inducing agents, antibiotics, and cigarette smoking. The elimination half-life of ethinylestradiol ranges from 5 to 16 hours. -After i.v administration, ethinylestradiol displays approximately linear dose relationship in the dose range 30-100 µg. A wide variability is present in the terminal part of the dose-normalized concentrations. +After i.v. administration, ethinylestradiol displays approximately linear dose relationship in the dose range 30-100 µg. A wide variability is present in the terminal part of the dose-normalized concentrations. After p.o. single dose, ethinylestradiol shows linear dose relationship in the dose range 30-3000 µg. Secondary peaks can be observed in individual data, compatible with enterohepatic re-circulation. However, mean data do not display such feature as a result of such peak being averaged out. Therefore, enterohepatic re-circulation was not taken into account in the model. diff --git a/Evaluation/Input/Content/Section2.2_Data.md b/Evaluation/Input/Content/Section2.2_Data.md index a265674..20024b7 100644 --- a/Evaluation/Input/Content/Section2.2_Data.md +++ b/Evaluation/Input/Content/Section2.2_Data.md @@ -16,7 +16,7 @@ A literature search was performed to collect available information on physico-ch | Km UGT1A1+ | µmol/l | 19.22 | [Ezuruike 2018](#5-references) | UGT1A1 saturation constant | | Vmax UGT1A1+ | pmol/min/mg prot. | 408.5 | [Ezuruike 2018](#5-references) | Maximal metabolization rate by UGT1A1 | | Renal Elimination+ | l/h | 2.079 | [Stanczyk 2013](#5-references) | Renal clearance | -| Clint HLM+ | µL/min/mg prot. | 118.83 | [Ezuruike 2018](#5-references) | Inttrinsic clearance in Human Liver Microsomes | +| Clint HLM+ | µL/min/mg prot. | 118.83 | [Ezuruike 2018](#5-references) | Intrinsic clearance in Human Liver Microsomes | | Ki CYP1A2 | µmol/l | 10.6 | [Karjalainen 2008](#5-references) | CYP1A2 inhibition constant | **Table 1:** Physico-chemical and *in-vitro* metabolization properties of ethinylestradiol extracted from literature. *+: Value used in final model* diff --git a/Evaluation/Input/Content/glossary.md b/Evaluation/Input/Content/glossary.md index 6b02d33..0428812 100644 --- a/Evaluation/Input/Content/glossary.md +++ b/Evaluation/Input/Content/glossary.md @@ -44,7 +44,7 @@ | q.d. | Once daily (quaque diem) | | SD | Single Dose | | SE | Standard error | -| s.d.SPC | Single doseSummary of Product Characteristics | +| s.d.SPC | Single dose Summary of Product Characteristics | | SD | Standard deviation | | TDI | Time dependent inhibition | | t.i.d | Three times a day (ter in die) | diff --git a/Evaluation/Workflow.m b/Evaluation/Workflow.m index f256db1..3011b1c 100644 --- a/Evaluation/Workflow.m +++ b/Evaluation/Workflow.m @@ -7,9 +7,9 @@ % -------------------------------------------------------------- % replace qualificationRunnerFolder and markdownJoinerFolder with your paths -qualificationRunnerFolder = 'c:\Program Files\Open Systems Pharmacology\QualificationRunner 9.0'; -markdownJoinerFolder = 'c:\Program Files\Open Systems Pharmacology\markdown-joiner'; -PKSimPortableFolder = 'd:\Work\PK-Sim\'; +qualificationRunnerFolder = 'c:\Program Files\Open Systems Pharmacology\QualificationRunner 10'; +markdownJoinerFolder = 'c:\Program Files\Open Systems Pharmacology\markdown-joiner\'; +PKSimPortableFolder = 'd:\Work\OSPS\Repos\PK-Sim10.0\'; % -------------------------------------------------------------- % replace basisDir and qualificationPlanName with your paths From 2d0ff8289c920ab6d4dd46800c3d073c1c871e0e Mon Sep 17 00:00:00 2001 From: Pavel Balazki Date: Thu, 24 Mar 2022 14:20:34 +0100 Subject: [PATCH 2/4] Broken link --- .../Content/Section2.3_Model_Parameters_and_Assumptions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Evaluation/Input/Content/Section2.3_Model_Parameters_and_Assumptions.md b/Evaluation/Input/Content/Section2.3_Model_Parameters_and_Assumptions.md index 3d9da36..c14a83a 100644 --- a/Evaluation/Input/Content/Section2.3_Model_Parameters_and_Assumptions.md +++ b/Evaluation/Input/Content/Section2.3_Model_Parameters_and_Assumptions.md @@ -23,7 +23,7 @@ Renal plasma clearance is modeled with `Plasma clearance` set to 2.079 l/h repor ### 2.3.4 Enzyme Inhibition -Simulations of co-administration of ethinylestradiol with tizanidine (see [CYP1A2 DDI Qualification report](link)) indicate that the reported competitive inhibition of CYP1A2 by ethinylestradiol ([Karjalainen 2008](#5-references)) is not sufficient to describe the increased concentrations of tizanidine after multiple days administration. Therefore, it was decided to fit a time-dependent inhibition (TDI) function to the CYP1A2 enzyme system. The parameters `Kinact` and `K_kinact_half` were estimated by fitting the model to concentration-time profiles of tizanidine ([Granfors 2005](#5-references)). +Simulations of co-administration of ethinylestradiol with tizanidine (see [CYP1A2 DDI Qualification report](https://github.com/Open-Systems-Pharmacology/OSP-Qualification-Reports/releases)) indicate that the reported competitive inhibition of CYP1A2 by ethinylestradiol ([Karjalainen 2008](#5-references)) is not sufficient to describe the increased concentrations of tizanidine after multiple days administration. Therefore, it was decided to fit a time-dependent inhibition (TDI) function to the CYP1A2 enzyme system. The parameters `Kinact` and `K_kinact_half` were estimated by fitting the model to concentration-time profiles of tizanidine ([Granfors 2005](#5-references)). ### 2.3.5 Automated Parameter Identification From a761edc9f896c53bbe36ca640cb30680990a3a08 Mon Sep 17 00:00:00 2001 From: Pavel Balazki Date: Thu, 24 Mar 2022 16:16:50 +0100 Subject: [PATCH 3/4] Fix broken links --- Evaluation/Input/Content/References.md | 8 ++++---- Evaluation/Input/Content/Section2.2_Data.md | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/Evaluation/Input/Content/References.md b/Evaluation/Input/Content/References.md index a830b9c..04a6c07 100644 --- a/Evaluation/Input/Content/References.md +++ b/Evaluation/Input/Content/References.md @@ -12,13 +12,13 @@ **Ezuruike 2018** Ezuruike U, Humphries H, Dickins M, Neuhoff S, Gardner I, Rowland Yeo K. Risk–Benefit Assessment of Ethinylestradiol Using a Physiologically Based Pharmacokinetic Modeling Approach. *Clin Pharmacol Ther*. 2018;104(6):1229-1239 -**FDA. QUARTETTE ** FDA. QUARTETTE (levonorgestrel/ethinyl estradiol and ethinyl estradiol) tablets, for oral use. Website: accessdata.fda.gov/drugsatfda_docs/label/2013/204061s000lbl.pdf.2013. +**FDA. QUARTETTE** FDA. QUARTETTE (levonorgestrel/ethinyl estradiol and ethinyl estradiol) tablets, for oral use. Website: https://www.accessdata.fda.gov/drugsatfda_docs/label/2013/204061s000lbl.pdf **Goebelsmann 1986** Goebelsmann U, Hoffman D, Chiang S, Woutersz T. The relative bioavailability of levonorgestrel and ethinyl estradiol administered as a low-dose combination oral contraceptive. *Contraception*. 1986;34(4):341-351. **Granfors 2005** Granfors MT, Backman JT, Laitila J, Neuvonen PJ. Oral contraceptives containing ethinyl estradiol and gestodene markedly increase plasma concentrations and effects of tizanidine by inhibiting cytochrome P450 1A2. *Clin Pharmacol Ther*. 2005;78(4):400-411. -**Karjalainen 2008** Karjalainen, M. (Thesis, 2008). Inhibition of CYP1A2-mediated drug metabolism in vitro and in humans: With special emphasis on rofecoxib and other NSAIDs. Website: helda.helsinki.fi/bitstream/handle/10138/23039/inhibiti.pdf?sequence=1&origin=publication_detail +**Karjalainen 2008** Karjalainen, M. (Thesis, 2008). Inhibition of CYP1A2-mediated drug metabolism in vitro and in humans: With special emphasis on rofecoxib and other NSAIDs. Website: https://helda.helsinki.fi/bitstream/handle/10138/23039/inhibiti.pdf?sequence=1&origin=publication_detail **Kothare 2012** Kothare PA, Seger ME, Northrup J, Mace K, Mitchell MI, Linnebjerg H. Effect of exenatide on the pharmacokinetics of a combination oral contraceptive in healthy women: an open-label, randomised, crossover trial. *BMC Clin Pharmacol*. 2012;12:8. @@ -34,7 +34,7 @@ **Sidhu 2006** Sidhu J, Job S, Singh S, Philipson R. The pharmacokinetic and pharmacodynamic consequences of the co-administration of lamotrigine and a combined oral contraceptive in healthy female subjects. *Br J Clin Pharmacol*. 2006;61(2):191-199. -**SmPC Namuscla ** SmPC Namuscla 167 mg hard capsules, 2019, website medicines.org.uk/emc/product/9838/smpc +**SmPC Namuscla** SmPC Namuscla 167 mg hard capsules, 2019, website https://www.medicines.org.uk/emc/product/9838/smpc **Stanczyk 1983** Stanczyk FZ, Mroszczak EJ, Ling T, et al. Plasma levels and pharmacokinetics of norethindrone and ethinylestradiol administered in solution and as tablets to women. *Contraception*. 1983;28(3):241-251. @@ -52,6 +52,6 @@ **Willmann 2007** Willmann S, Höhn K, Edginton A, Sevestre M, Solodenko J, Weiss W, Lippert J, Schmitt W. Development of a physiology-based whole-body population model for assessing the influence of individual variability on the pharmacokinetics of drugs. *J Pharmacokinet Pharmacodyn* 2007, 34(3): 401-431. -**Zanaflex prescribing information** Zanaflex prescribing information. Website: accessdata.fda.gov/drugsatfda_docs/label/2006/020397s021,021447s002lbl.pdf, 2006, Acorda Therapeutics Inc +**Zanaflex prescribing information** Zanaflex prescribing information. Website: https://www.accessdata.fda.gov/drugsatfda_docs/label/2006/020397s021,021447s002lbl.pdf , 2006, Acorda Therapeutics Inc **Zhang 2017** Zhang C, Li H, Xiong X, et al. An open-label, two-period comparative study on pharmacokinetics and safety of a combined ethinylestradiol/gestodene transdermal contraceptive patch. *Drug Des Devel Ther*. 2017;11:725-731. \ No newline at end of file diff --git a/Evaluation/Input/Content/Section2.2_Data.md b/Evaluation/Input/Content/Section2.2_Data.md index 20024b7..577e979 100644 --- a/Evaluation/Input/Content/Section2.2_Data.md +++ b/Evaluation/Input/Content/Section2.2_Data.md @@ -1,6 +1,6 @@ ### 2.2.1 In vitro and physico-chemical data -A literature search was performed to collect available information on physico-chemical properties of ethinylestradiol ([Table 1](#Table 1)). +A literature search was performed to collect available information on physico-chemical properties of ethinylestradiol, see [Table 1](#Table 1). | **Parameter** | **Unit** | **Value** | Source | **Description** | | :------------------------------ | ----------------- | ---------------- | --------------------------------- | ---------------------------------------------- | @@ -23,7 +23,7 @@ A literature search was performed to collect available information on physico-ch ### 2.2.2 Clinical data -A literature search was performed to collect available clinical data on ethinylestradiol ([Table 2](#Table 2)). +A literature search was performed to collect available clinical data on ethinylestradiol, see [Table 2](#Table 2). | **Source** | Route | **Dose [mg]/** **Schedule \*** | **Pop.** | **Sex** | **N** | **Form.** | | -------------------- | ------------------------------- | ------------ | ------- | --------------------------------- | --------------------------------- | --------------------------------- | From 6ad67a57078e51ac8b4b3234f5bf6e3a76bf6743 Mon Sep 17 00:00:00 2001 From: Pavel Balazki Date: Fri, 25 Mar 2022 12:47:45 +0100 Subject: [PATCH 4/4] Fix table links --- Evaluation/Input/Content/Section2.2_Data.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Evaluation/Input/Content/Section2.2_Data.md b/Evaluation/Input/Content/Section2.2_Data.md index 577e979..97fea12 100644 --- a/Evaluation/Input/Content/Section2.2_Data.md +++ b/Evaluation/Input/Content/Section2.2_Data.md @@ -1,6 +1,6 @@ ### 2.2.1 In vitro and physico-chemical data -A literature search was performed to collect available information on physico-chemical properties of ethinylestradiol, see [Table 1](#Table 1). +A literature search was performed to collect available information on physico-chemical properties of ethinylestradiol, see [Table 1](#table-1). | **Parameter** | **Unit** | **Value** | Source | **Description** | | :------------------------------ | ----------------- | ---------------- | --------------------------------- | ---------------------------------------------- | @@ -19,11 +19,11 @@ A literature search was performed to collect available information on physico-ch | Clint HLM+ | µL/min/mg prot. | 118.83 | [Ezuruike 2018](#5-references) | Intrinsic clearance in Human Liver Microsomes | | Ki CYP1A2 | µmol/l | 10.6 | [Karjalainen 2008](#5-references) | CYP1A2 inhibition constant | -**Table 1:** Physico-chemical and *in-vitro* metabolization properties of ethinylestradiol extracted from literature. *+: Value used in final model* +**Table 1:** Physico-chemical and *in-vitro* metabolization properties of ethinylestradiol extracted from literature. *+: Value used in final model* ### 2.2.2 Clinical data -A literature search was performed to collect available clinical data on ethinylestradiol, see [Table 2](#Table 2). +A literature search was performed to collect available clinical data on ethinylestradiol, see [Table 2](#table-2). | **Source** | Route | **Dose [mg]/** **Schedule \*** | **Pop.** | **Sex** | **N** | **Form.** | | -------------------- | ------------------------------- | ------------ | ------- | --------------------------------- | --------------------------------- | --------------------------------- | @@ -44,4 +44,4 @@ A literature search was performed to collect available clinical data on ethinyle | [Kothare 2012](#5-references)+ | p.o. | 0.03/0.03 q.d. | HV | F | 20 | tablet | | [Timmer 2000](#5-references)+ | p.o. | 0.03 | HV | F | - | tablet | -**Table 2:** Literature sources of clinical concentration data of ethinylestradiol used for model development and validation. *\*: single dose unless otherwise specified;+: Data used for final parameter identification* \ No newline at end of file +**Table 2:** Literature sources of clinical concentration data of ethinylestradiol used for model development and validation. *\*: single dose unless otherwise specified;+: Data used for final parameter identification* \ No newline at end of file