Which part of the Anti-MDA5-positive dermatomyositis ILD descriptive-study proposal should I draft in detail first?

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anti-MDA5 positive dermatomyositis interstitial lung disease descriptive cohort study Philippines

"Dermatomyositis"[MeSH Terms] AND "MDA5"

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"Dermatomyositis"[MeSH Terms] AND "Lung Diseases, Interstitial"[MeSH Terms]

"Dermatomyositis"[MeSH Terms] AND "Lung Diseases, Interstitial"[MeSH Terms]

https://jtd.amegroups.org/article/view/124232/html

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"Dermatomyositis"[MeSH Terms] AND "Interferon-Induced Helicase, IFIH1"

"Dermatomyositis"[MeSH Terms] AND "Lung Diseases, Interstitial"[MeSH Terms]

anti-MDA5 dermatomyositis associated interstitial lung disease retrospective descriptive cohort clinical characteristics outcomes

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PMID: 40746563

PMID: 42039189

PMID: 34200737

https://pmc.ncbi.nlm.nih.gov/articles/PMC12359913

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mkdir -p "/tmp/workspace/anti-mda5-dm-ild-proposal/src" "/tmp/workspace/anti-mda5-dm-ild-proposal/output" && printf '%s' 'ready'

python3 - <<'PY' from pathlib import Path p=Path('/tmp/workspace/anti-mda5-dm-ild-proposal/src/create_proposal.py') p.write_text(r'''from docx import Document from docx.shared import Inches, Pt, RGBColor from docx.enum.text import WD_ALIGN_PARAGRAPH from docx.enum.table import WD_TABLE_ALIGNMENT, WD_CELL_VERTICAL_ALIGNMENT from docx.oxml import OxmlElement from docx.oxml.ns import qn from docx.enum.section import WD_SECTION OUT='/tmp/workspace/anti-mda5-dm-ild-proposal/output/Anti-MDA5_DM-ILD_Clinical_Research_Proposal_Draft.docx' def shade(cell, fill): tcPr=cell._tc.get_or_add_tcPr(); shd=OxmlElement('w:shd'); shd.set(qn('w:fill'),fill); tcPr.append(shd) def set_cell_text(cell,text,bold=False): cell.text=''; p=cell.paragraphs[0]; r=p.add_run(text); r.bold=bold; r.font.size=Pt(9); cell.vertical_alignment=WD_CELL_VERTICAL_ALIGNMENT.CENTER def add_table(doc, headers, rows, widths=None): t=doc.add_table(rows=1, cols=len(headers)); t.style='Table Grid'; t.alignment=WD_TABLE_ALIGNMENT.CENTER for i,h in enumerate(headers): set_cell_text(t.rows[0].cells[i],h,True); shade(t.rows[0].cells[i],'D9EAF7') for row in rows: cells=t.add_row().cells for i,x in enumerate(row): set_cell_text(cells[i],str(x)) if widths: for row in t.rows: for i,w in enumerate(widths): row.cells[i].width=Inches(w) doc.add_paragraph('') return t def bullet(doc,text,level=0): p=doc.add_paragraph(style='List Bullet' if level==0 else 'List Bullet 2'); p.add_run(text); return p def heading(doc,text,level=1): doc.add_heading(text,level=level) doc=Document(); sec=doc.sections[0] sec.top_margin=Inches(.65); sec.bottom_margin=Inches(.65); sec.left_margin=Inches(.75); sec.right_margin=Inches(.75) normal=doc.styles['Normal']; normal.font.name='Arial'; normal._element.rPr.rFonts.set(qn('w:eastAsia'),'Arial'); normal.font.size=Pt(10); normal.paragraph_format.space_after=Pt(5) for s in ['Title','Heading 1','Heading 2','Heading 3']: st=doc.styles[s]; st.font.name='Arial'; st._element.rPr.rFonts.set(qn('w:eastAsia'),'Arial'); st.font.color.rgb=RGBColor(31,78,121) doc.styles['Heading 1'].font.size=Pt(14); doc.styles['Heading 2'].font.size=Pt(12) # footer footer=sec.footer.paragraphs[0]; footer.alignment=WD_ALIGN_PARAGRAPH.CENTER footer.add_run('Draft for institutional review only | Anti-MDA5 DM-ILD descriptive study | Page ') fld=OxmlElement('w:fldSimple'); fld.set(qn('w:instr'),'PAGE'); footer._p.append(fld) p=doc.add_paragraph(); p.alignment=WD_ALIGN_PARAGRAPH.CENTER; r=p.add_run('CLINICAL RESEARCH PROPOSAL - DRAFT'); r.bold=True; r.font.size=Pt(15); r.font.color.rgb=RGBColor(31,78,121) p=doc.add_paragraph(); p.alignment=WD_ALIGN_PARAGRAPH.CENTER; r=p.add_run('Clinical Characteristics, Radiologic Patterns, Treatment, and Outcomes of Patients With Anti-MDA5 Antibody-Positive Dermatomyositis-Associated Interstitial Lung Disease at [Hospital Name], Philippines: A Retrospective Descriptive Study'); r.bold=True; r.font.size=Pt(14) doc.add_paragraph('') add_table(doc,['Proposal field','Draft entry'],[ ('Principal investigator','[Name, MD] - Pulmonary Fellow, [Department / Institution]'),('Co-investigators','[Pulmonology consultant]; [Rheumatology consultant]; [Radiologist]; [Statistician]'),('Study site','[Hospital Name], [City], Philippines'),('Protocol version/date','Version 1.0 | 24 September 2026'),('Funding','None anticipated / [state source]'),('Study duration','Record review: [Month Year] to [Month Year]; study period: [Month Year] to [Month Year]'),('Design','Single-center retrospective descriptive chart review / case series'),('Data source','Electronic and paper medical records, laboratory database, imaging archive, and pharmacy records'),('Target population','Adults with anti-MDA5 antibody positivity, dermatomyositis or clinically amyopathic dermatomyositis, and ILD')],[1.65,5.8]) heading(doc,'I. Executive Summary') doc.add_paragraph('Anti-melanoma differentiation-associated gene 5 (anti-MDA5) antibody-positive dermatomyositis (DM) is an uncommon inflammatory myopathy phenotype with frequent and potentially rapidly progressive interstitial lung disease (ILD). Philippine data describing presentation, computed tomography (CT) patterns, treatment choices, and clinical outcomes are limited. This study will retrospectively identify all eligible patients managed at [Hospital Name] during a predefined period and describe their baseline characteristics, disease course, and outcomes. No intervention, recruitment, or alteration of care will occur.') doc.add_paragraph('The study is intentionally descriptive. Its purpose is to establish a local case series, characterize feasibility of diagnostic and therapeutic pathways, and generate data for future multicenter studies. It is not designed or powered to establish prognostic or treatment effects.') heading(doc,'II. Background and Rationale') doc.add_paragraph('Dermatomyositis may involve characteristic skin disease, skeletal muscle disease, or both. Typical cutaneous manifestations include heliotrope rash, Gottron papules or sign, periungual changes, and poikiloderma. Skin features can precede muscle findings, and clinically amyopathic forms occur. Rheumatology, 2-Volume Set (2022), section “Dermatomyositis,” lines 8078-8089.') doc.add_paragraph('Myositis-related ILD requires coordinated clinical assessment, antibody testing, imaging, and evaluation of severity. Anti-MDA5 positivity is particularly associated with a potentially rapidly progressive phenotype, for which early recognition is important (Waseda, 2021, PMID: 34200737). In a recent retrospective series, ILD occurred in 73.1% and rapidly progressive ILD (RP-ILD) in 34.6% of anti-MDA5 DM patients; organizing pneumonia and nonspecific interstitial pneumonia patterns were described on CT (PMID: 40826379).') doc.add_paragraph('Contemporary syntheses identify RP-ILD, older age, fever, smoking, inflammation, ferritin elevation, and lymphopenia as variables associated with mortality, and anti-Ro52 positivity, elevated LDH, and short disease duration as variables associated with RP-ILD. These are reasons to capture, not presume, these variables in the local cohort (Yang et al., 2025, PMID: 40746563; Li et al., 2026, PMID: 42039189). The applicability of those associations to Filipino patients and a small single-center sample is uncertain.') heading(doc,'III. Research Question, Objectives, and Outcomes') heading(doc,'Research question',2) doc.add_paragraph('Among patients with anti-MDA5 antibody-positive DM-associated ILD managed at [Hospital Name], what are the demographic, clinical, laboratory, radiologic, treatment, and outcome characteristics?') heading(doc,'General objective',2) doc.add_paragraph('To describe the clinical characteristics, radiologic patterns, treatment regimens, and outcomes of anti-MDA5 antibody-positive DM-associated ILD at [Hospital Name].') heading(doc,'Specific objectives',2) for x in ['Describe demographic characteristics, clinical manifestations, and comorbidities at first hospital assessment.','Describe pulmonary presentation, oxygen requirement, HRCT findings, and available pulmonary function tests.','Describe serologic and laboratory findings, including anti-MDA5 assay method and result, anti-Ro52 status if tested, CK, LDH, ferritin, CRP, complete blood count, and arterial blood gas results where available.','Describe initial and subsequent immunomodulatory treatment, supportive pulmonary care, adverse events, and treatment escalation.','Describe RP-ILD, ICU admission, ventilatory support, infection, pneumomediastinum, lung transplantation referral or transplantation, discharge status, and all-cause mortality during available follow-up.']: bullet(doc,x) heading(doc,'Primary descriptive outcomes',2) add_table(doc,['Outcome','Operational measure'],[ ('ILD phenotype','HRCT pattern and distribution, documented by thoracic radiologist review or formal report.'),('RP-ILD','New or worsening hypoxemia and radiologic progression of ILD within 3 months of respiratory symptom onset, after reasonable exclusion of infection, fluid overload, pulmonary embolism, and other causes.'),('Vital status','Alive, dead, or unknown at last documented contact; date and attributed cause if recorded.'),('Pulmonary support','Highest level: room air, low-flow oxygen, HFNC/NIV, invasive ventilation, ECMO.'),('Clinical course','Stable/improved, progressive, relapsed, or indeterminate at last follow-up based on chart documentation, oxygen need, PFT and/or imaging.')],[1.5,5.95]) heading(doc,'IV. Methods') heading(doc,'Study design and setting',2) doc.add_paragraph('This is a single-center retrospective descriptive study of consecutive eligible cases. The study will be undertaken at [Hospital Name], a [tertiary/referral] hospital in [City], Philippines. Records dated from [1 January 2016] through [31 December 2026] will be screened. The final dates should be matched to the local availability of anti-MDA5 testing and ethics approval.') heading(doc,'Study population and case identification',2) doc.add_paragraph('Potential cases will be identified through laboratory/myositis-panel records, rheumatology and pulmonology clinic lists, discharge diagnosis databases, radiology reports, and pharmacy records. Duplicates will be removed using medical record number. A screening log containing only study codes and eligibility status will be maintained separately from the analytic dataset.') heading(doc,'Eligibility criteria',2) add_table(doc,['Include if all apply','Exclude if any apply'],[ ('Age ≥18 years at index presentation.','Anti-MDA5 result is borderline/indeterminate and cannot be confirmed as positive.'),('Documented anti-MDA5 antibody positivity by a laboratory assay, with test method, laboratory, date, and qualitative/quantitative result recorded.','No imaging evidence of ILD or insufficient documentation to confirm ILD.'),('Diagnosis of DM or clinically amyopathic DM by treating rheumatologist/dermatologist, or fulfillment of 2017 EULAR/ACR IIM classification criteria when sufficient data are available.','An alternative dominant cause of diffuse lung disease, such as drug toxicity, infection, environmental exposure, or another connective-tissue disease, is judged more likely by the treating team.'),('ILD demonstrated by HRCT or chest CT report compatible with ILD and adjudicated by study radiology review where images are available.','Record contains only a laboratory result with no usable clinical record.'),('At least one clinical encounter after index assessment, unless death occurs during index admission.','Pediatric patient.')],[3.65,3.8]) heading(doc,'Index date and follow-up',2) doc.add_paragraph('The index date is the earliest date on which anti-MDA5 positivity and ILD are both documented. Baseline variables will be abstracted from the period from 30 days before to 14 days after the index date. Patients will be followed from index date to death, last documented clinical contact, lung transplantation, or end of study observation, whichever occurs first.') heading(doc,'Operational definitions',2) add_table(doc,['Term','Definition for this protocol'],[ ('Anti-MDA5 positive','Positive result reported by the performing laboratory. Assay platform, cutoff, titer/value, and test date will be captured. The study will not combine borderline and positive results.'),('DM / CADM','Treating specialist diagnosis. CADM: characteristic cutaneous DM features with no clinically significant muscle weakness for at least 6 months, or as documented by rheumatology; classification status will be recorded rather than retrospectively forced.'),('ILD','Interstitial abnormalities on HRCT/CT interpreted as compatible with ILD by a thoracic radiologist or two designated readers, plus compatible clinical context.'),('RP-ILD','Deterioration in respiratory symptoms/oxygenation plus radiologic ILD progression within 3 months of respiratory symptom onset. Competing causes must be considered from chart data. If uncertainty remains, classify as indeterminate rather than RP-ILD.'),('HRCT pattern','Predominant pattern categorized as OP, NSIP, OP/NSIP overlap, UIP-like, diffuse alveolar damage/acute lung injury features, unclassifiable, or no HRCT available.'),('Infection','Microbiologically confirmed infection or treating team diagnosis requiring antimicrobial therapy. This will be reported separately from ILD progression.'),('Treatment exposure','Medication actually administered, route, dose where available, start and stop dates, and sequence. No causal effectiveness comparison is planned.')],[1.55,5.9]) heading(doc,'Variables and data collection',2) doc.add_paragraph('A standardized electronic case report form will be pilot-tested on 2 records and refined before final abstraction. Two investigators will independently review a random 10% of records and reconcile discrepancies. The principal investigator will adjudicate unresolved abstraction issues with a rheumatologist and thoracic radiologist, documenting the decision.') add_table(doc,['Domain','Variables'],[ ('Demographics','Study code; age; sex; residence region; smoking/vaping status and pack-years; occupation/exposures; BMI; dates of symptom onset, diagnosis, and index date.'),('Clinical phenotype','Dyspnea, cough, fever; Gottron papules/sign, heliotrope rash, ulceration, mechanic’s hands, alopecia, arthritis/arthralgia, Raynaud phenomenon, dysphagia; proximal weakness; CADM/DM classification; malignancy evaluation if documented.'),('Laboratory/serology','Assay platform and anti-MDA5 result; ANA; anti-Ro52 and other myositis antibodies; CK, aldolase if available, AST/ALT, LDH, ferritin, CRP/ESR, CBC with differential, albumin, creatinine; PaO2/FiO2 if available.'),('Pulmonary and imaging','Resting oxygen support; ABG; PFT FVC, FEV1, TLC, DLCO and % predicted; 6MWT if available; HRCT date, pattern, distribution, ground-glass opacity, consolidation, reticulation/fibrosis, traction bronchiectasis, honeycombing, pneumomediastinum/pneumothorax.'),('Treatment','Glucocorticoids; calcineurin inhibitor; cyclophosphamide; mycophenolate; rituximab; JAK inhibitor; IVIG; plasma exchange; antimicrobial prophylaxis; oxygen, NIV, invasive ventilation, ECMO; transplant referral.'),('Outcomes','RP-ILD; hospital/ICU admission; infections; adverse drug events; change in oxygen need; PFT/imaging change if available; relapse; vital status; cause/date of death; duration of follow-up.')],[1.55,5.9]) heading(doc,'Data analysis plan',2) doc.add_paragraph('Analysis will be descriptive. The number screened, eligible, included, excluded, and reasons for exclusion will be presented in a flow diagram. Categorical variables will be summarized as frequency and percentage. Continuous variables will be summarized as mean (standard deviation) if plausibly symmetric, or median (interquartile range) if skewed. Missing data will be explicitly reported using available-case denominators; no imputation will be performed.') doc.add_paragraph('The cohort may be descriptively stratified by RP-ILD status and by survival status. Any between-group comparisons, if performed, will be clearly labeled exploratory and limited to Fisher exact tests and nonparametric comparisons as appropriate. Regression modeling, propensity methods, and claims of treatment efficacy will not be undertaken unless an adequate sample size and a prespecified amended analysis plan are approved. Statistical analysis will use [R/Stata/SPSS] version [x]; two-sided p-values, if reported, will be interpreted cautiously without causal claims.') heading(doc,'Sample size',2) doc.add_paragraph('No formal sample-size calculation is proposed because this is a rare-disease, census-based retrospective descriptive study. All consecutive eligible patients within the defined period will be included. The final sample size will be reported with the screening denominator and will determine the precision of estimates.') heading(doc,'V. Ethical Considerations') doc.add_paragraph('This study is a minimal-risk retrospective review. No participant contact, additional diagnostic testing, treatment change, or biological specimen collection is planned. The investigators will seek approval from the [Institutional Scientific Review Committee / Institutional Review Board] before accessing records for research. A waiver of informed consent will be requested only if permitted by local policy because the study is retrospective, poses no more than minimal risk, could not practicably be conducted with individual consent, and includes safeguards for privacy and confidentiality.') doc.add_paragraph('Only the minimum necessary data will be extracted. Each participant will receive a unique study code. Names, medical record numbers, addresses, and contact details will not appear in the analytic dataset, presentation, manuscript, or shared files. The linkage file will be encrypted, stored separately on a password-protected institutional drive, and accessible only to authorized study staff. Data will be retained for [5 years or institutional requirement] after study completion and then securely destroyed. Aggregate results will be reported; cells with very small counts will be suppressed if re-identification is plausible.') heading(doc,'VI. Risks, Benefits, and Dissemination') heading(doc,'Risks',2); doc.add_paragraph('The principal risk is inadvertent disclosure of confidential health information. This will be mitigated through coded datasets, role-based access, encrypted storage, secure transfer, and reporting only aggregate data.') heading(doc,'Benefits',2); doc.add_paragraph('There is no direct participant benefit. The study may improve local recognition of anti-MDA5 DM-ILD, identify gaps in diagnostic access and follow-up, and support future collaborative research.') heading(doc,'Dissemination',2); doc.add_paragraph('Findings may be presented at departmental meetings, scientific conferences, and submitted to a peer-reviewed journal. Any dissemination will occur only after institutional approvals and will contain no identifiable information.') heading(doc,'VII. Work Plan and Budget') add_table(doc,['Activity','Months after approval'],[ ('Finalize protocol, CRF, data dictionary, and IRB materials','1'),('Case-finding and eligibility screening','2-3'),('Data abstraction and imaging review','3-5'),('Data cleaning, analysis, and internal review','6'),('Manuscript/abstract preparation and dissemination','7-8')],[4.5,3.0]) add_table(doc,['Item','Estimated cost'],[ ('Personnel time','Covered by investigators / departmental support'),('Chart access and secure storage','Institutional resources'),('Statistical software','[Specify if paid]'),('Printing/administrative costs','PHP [amount]'),('Total','PHP [amount] / no external funding')],[4.5,3.0]) heading(doc,'VIII. Limitations') for x in ['Retrospective records may contain missing, nonuniform, or time-misaligned clinical, laboratory, and imaging data.','Anti-MDA5 assay platforms, cutoffs, and availability may vary over time.','Small sample size and single-center referral bias will limit generalizability and preclude reliable inference on prognostic factors or comparative treatment effectiveness.','Clinical decisions and treatment exposures are confounded by illness severity; treatment descriptions must not be interpreted as efficacy estimates.','RP-ILD can overlap with infection and other acute pulmonary complications; an indeterminate category will be retained where adjudication is not possible.']: bullet(doc,x) heading(doc,'IX. References') refs=[ 'Waseda Y. Myositis-Related Interstitial Lung Disease: A Respiratory Physician’s Point of View. Medicina (Kaunas). 2021;57(6):599. doi:10.3390/medicina57060599. PMID: 34200737.', 'Yang Y, Li Y, Yuan W, et al. Risk factors for mortality in anti-MDA5 antibody-positive dermatomyositis with interstitial lung disease: a systematic review and meta-analysis. Front Immunol. 2025. doi:10.3389/fimmu.2025.1628748. PMID: 40746563.', 'Li H, Yi M, Da G, et al. Influencing factors for rapidly progressive interstitial lung disease in patients with anti-MDA5 antibody-positive dermatomyositis: a systematic review and meta-analysis. Front Immunol. 2026. doi:10.3389/fimmu.2026.1796496. PMID: 42039189.', 'Clinical characteristics and outcomes of anti-MDA5 dermatomyositis: a retrospective study. 2025. PMID: 40826379. PMCID: PMC12359913.', 'Palmucci S, Di Mari A, Cancemi G, et al. Clinical and Radiological Features of Interstitial Lung Diseases Associated with Polymyositis and Dermatomyositis. Medicina (Kaunas). 2022;58(12):1757. PMID: 36556960.', 'Rheumatology, 2-Volume Set. 2022. Section: Dermatomyositis, lines 8078-8089.' ] for r in refs: doc.add_paragraph(r,style='List Number') heading(doc,'Appendix A. Data Collection Form (abbreviated)',1) for title,items in [ ('A. Identification and eligibility',['Study code','Medical record number - linkage file only','Screening source','Eligibility checklist and exclusion reason','Index date and last follow-up date']), ('B. Baseline phenotype',['Age, sex, smoking, comorbidities','Dates: first symptom, DM diagnosis, anti-MDA5 test, ILD confirmation','Cutaneous, joint, muscle, swallowing, and constitutional manifestations','DM/CADM classification and criteria source']), ('C. Investigations',['Anti-MDA5 assay/laboratory/value/cutoff; ANA, anti-Ro52, other antibodies','CBC, LDH, ferritin, CRP/ESR, CK, AST/ALT, albumin, creatinine','ABG; PFTs; 6MWT','CT date and pattern; extent and complications']), ('D. Treatment and outcomes',['Drug name, dose, start/stop dates, treatment sequence','Oxygen, ICU, NIV/IMV/ECMO, infections, adverse events','RP-ILD status and adjudication notes','Vital status, cause/date of death if applicable, last clinical status'])]: heading(doc,title,2) for i in items: bullet(doc,i) heading(doc,'Appendix B. Pre-submission completion checklist',1) for x in ['Replace all bracketed fields with institution-specific information.','Confirm whether local policy requires a full waiver-of-consent application, data privacy impact assessment, or department permissions.','Confirm the exact anti-MDA5 testing platform, cutoff, and earliest test availability at the hospital.','Set study dates based on actual records and ensure a complete capture pathway for laboratory, imaging, and clinical records.','Have the statistician and radiologist review the operational definitions before IRB submission.','Adapt the formatting to the institution’s current Annex A Form 1A after the original template is available.']: bullet(doc,x) doc.save(OUT) print(OUT) ''') PY python3 "/tmp/workspace/anti-mda5-dm-ild-proposal/src/create_proposal.py" python3 - <<'PY' from docx import Document p='/tmp/workspace/anti-mda5-dm-ild-proposal/output/Anti-MDA5_DM-ILD_Clinical_Research_Proposal_Draft.docx' d=Document(p) print('paragraphs',len(d.paragraphs),'tables',len(d.tables)) print('title',d.paragraphs[1].text[:120]) print('last',d.paragraphs[-1].text) PY

python3 - <<'PY' from docx import Document p='/tmp/workspace/anti-mda5-dm-ild-proposal/output/Anti-MDA5_DM-ILD_Clinical_Research_Proposal_Draft.docx' d=Document(p) headings=[x.text for x in d.paragraphs if x.style and x.style.name.startswith('Heading')] print('Headings:', len(headings)) for x in headings: print('-',x) print('Tables:',len(d.tables)) for i,t in enumerate(d.tables,1): print(i, len(t.rows), len(t.columns), ' | '.join(c.text[:35] for c in t.rows[0].cells)) PY ls -lh "/tmp/workspace/anti-mda5-dm-ild-proposal/output/Anti-MDA5_DM-ILD_Clinical_Research_Proposal_Draft.docx"

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anti-MDA5 dermatomyositis ILD retrospective descriptive study clinical characteristics Philippines

"Dermatomyositis"[MeSH Terms] AND "Interferon-Induced Helicase, IFIH1"

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python3 - <<'PY' from pathlib import Path from pypdf import PdfReader p=Path('/tmp/workspace/attachments/d09e6704-b302-44d6-a5bd-f7565dc767eb/ISRC Annex A Form 1A Clinical Research Proposal_Ong (April 2026 Final) with stamps.pdf') print('exists:',p.exists(),'size:',p.stat().st_size) r=PdfReader(str(p)) print('pages:',len(r.pages),'encrypted:',r.is_encrypted) fields=r.get_fields() print('form_fields:',len(fields) if fields else 0) if fields: for k,v in fields.items(): print('FIELD',repr(k),'=',repr(v.get('/V'))) for i,page in enumerate(r.pages): t=(page.extract_text() or '') print('\n--- PAGE',i+1,'chars',len(t),'---\n',t[:5000]) PY

~/anti-mda5-dm-ild-proposal/

cat > "/tmp/workspace/anti-mda5-dm-ild-proposal/src/create_annex_a_format.py" <<'PY' from docx import Document from docx.shared import Inches, Pt, RGBColor from docx.enum.text import WD_ALIGN_PARAGRAPH from docx.enum.table import WD_TABLE_ALIGNMENT, WD_CELL_VERTICAL_ALIGNMENT from docx.oxml import OxmlElement from docx.oxml.ns import qn OUT='/tmp/workspace/anti-mda5-dm-ild-proposal/output/Annex_A_Form_1A_Anti-MDA5_DM-ILD_Proposal_Draft.docx' BLUE=RGBColor(31,78,121) def set_repeat_table_header(row): trPr=row._tr.get_or_add_trPr(); el=OxmlElement('w:tblHeader'); el.set(qn('w:val'),'true'); trPr.append(el) def shade(c,fill='D9EAF7'): x=c._tc.get_or_add_tcPr(); s=OxmlElement('w:shd'); s.set(qn('w:fill'),fill); x.append(s) def cell(c,text,bold=False,size=9): c.text=''; p=c.paragraphs[0]; p.paragraph_format.space_after=Pt(0); r=p.add_run(str(text)); r.bold=bold; r.font.size=Pt(size); c.vertical_alignment=WD_CELL_VERTICAL_ALIGNMENT.CENTER def table(doc,heads,rows,widths=None): t=doc.add_table(rows=1,cols=len(heads)); t.style='Table Grid'; t.alignment=WD_TABLE_ALIGNMENT.CENTER set_repeat_table_header(t.rows[0]) for i,h in enumerate(heads): cell(t.rows[0].cells[i],h,True); shade(t.rows[0].cells[i]) for rr in rows: cs=t.add_row().cells for i,v in enumerate(rr): cell(cs[i],v) if widths: for row in t.rows: for i,w in enumerate(widths): row.cells[i].width=Inches(w) doc.add_paragraph('') def bullet(doc,text): p=doc.add_paragraph(style='List Bullet'); p.add_run(text) def h(doc,text,lvl=1): doc.add_heading(text,lvl) def para(doc,text,boldstart=None): p=doc.add_paragraph() if boldstart and text.startswith(boldstart): r=p.add_run(boldstart);r.bold=True;p.add_run(text[len(boldstart):]) else:p.add_run(text) return p d=Document(); sec=d.sections[0] sec.top_margin=Inches(.62);sec.bottom_margin=Inches(.58);sec.left_margin=Inches(.75);sec.right_margin=Inches(.75) st=d.styles['Normal'];st.font.name='Arial';st._element.rPr.rFonts.set(qn('w:eastAsia'),'Arial');st.font.size=Pt(10);st.paragraph_format.space_after=Pt(4) for n in ['Title','Heading 1','Heading 2','Heading 3']: s=d.styles[n];s.font.name='Arial';s._element.rPr.rFonts.set(qn('w:eastAsia'),'Arial');s.font.color.rgb=BLUE # header footer head=sec.header.paragraphs[0];head.alignment=WD_ALIGN_PARAGRAPH.RIGHT;rr=head.add_run('Protocol Version 01 dated 24 September 2026');rr.font.size=Pt(8) foot=sec.footer.paragraphs[0];foot.alignment=WD_ALIGN_PARAGRAPH.CENTER;rr=foot.add_run('Draft for institutional review only | Page ');rr.font.size=Pt(8);fld=OxmlElement('w:fldSimple');fld.set(qn('w:instr'),'PAGE');foot._p.append(fld) p=d.add_paragraph();p.alignment=WD_ALIGN_PARAGRAPH.CENTER;r=p.add_run('R&B Form No. 1A');r.bold=True;r.font.size=Pt(13);r.font.color.rgb=BLUE p=d.add_paragraph();p.alignment=WD_ALIGN_PARAGRAPH.CENTER;r=p.add_run('[INSTITUTION NAME]\nRESEARCH AND BIOTECHNOLOGY');r.bold=True;r.font.size=Pt(12) p=d.add_paragraph();p.alignment=WD_ALIGN_PARAGRAPH.CENTER;r=p.add_run('1.1. CLINICAL RESEARCH PROPOSAL');r.bold=True;r.font.size=Pt(14);r.font.color.rgb=BLUE h(d,'1. Research Title',2) para(d,'Clinical Characteristics, Radiologic Patterns, Treatment, and Outcomes of Patients With Anti-MDA5 Antibody-Positive Dermatomyositis-Associated Interstitial Lung Disease at a Tertiary Hospital in the Philippines: A Retrospective Descriptive Study') h(d,'Investigators',2) table(d,['Role','Name and Signature','Unit/Position'],[ ['Project Leader/s:\n(Consultant/Manager/Faculty)','[Name, MD, FPCP, FPCCP]\nSignature: ____________________','Consultant, Institute of Pulmonary Medicine'], ['Co-Project Leader/s:\n(Resident/Fellow/Student)','[Name, MD]\nSignature: ____________________','Pulmonary Fellow'], ['Co-Investigator/s','[Name, MD]\n[Name, MD]\n[Name, MD]','Rheumatology\nThoracic Radiology\nBiostatistics'], ['Research Fellow','N/A',''], ['Inst./Dept./Center/Group','Institute of Pulmonary Medicine, [Hospital Name]','']],[1.7,2.9,2.25]) h(d,'2. Brief Description / Summary',1) para(d,'Anti-melanoma differentiation-associated gene 5 (anti-MDA5) antibody-positive dermatomyositis (DM) is a rare inflammatory myopathy phenotype that is frequently complicated by interstitial lung disease (ILD), including a potentially rapidly progressive form associated with substantial morbidity and mortality. Data on this phenotype from the Philippines are sparse. This proposed study will describe the local clinical presentation, imaging patterns, laboratory and serologic findings, treatment regimens, and outcomes of adults with anti-MDA5-positive DM-associated ILD managed at [Hospital Name].') para(d,'This will be a single-center retrospective descriptive chart review of all consecutive eligible adults from [January 2016] to [December 2026]. Data will be extracted from electronic and physical medical records, myositis-panel results, pulmonary function testing records, CT imaging archives, and pharmacy records. No intervention, participant contact, new laboratory testing, or alteration of clinical care will occur. The study will identify local patterns of disease and care, document the frequency of rapidly progressive ILD (RP-ILD), and provide a foundation for future multicenter research.') para(d,'DATABANK INFO NEEDED: ☐ No ☒ Yes\nIf yes, specify: Retrospective medical-record and diagnostic database review. No biological samples will be stored or collected for this study.') h(d,'3. Introduction',1) h(d,'3.1. Significance of the Project',2) para(d,'Anti-MDA5-positive DM-associated ILD is clinically important because pulmonary disease may develop with little or no overt myositis and can deteriorate rapidly. A respiratory presentation may therefore precede a complete rheumatologic diagnosis. In a tertiary Philippine setting, clinicians may encounter delayed antibody testing, variable access to HRCT and pulmonary function testing, and differences in immunomodulatory treatment availability. Describing local cases can help clarify these care pathways and inform earlier pulmonary-rheumatology collaboration.') para(d,'The study aims to:') for x in ['Describe the demographic, clinical, serologic, radiologic, and pulmonary characteristics of local anti-MDA5-positive DM-ILD cases.','Describe treatments and short- and longer-term outcomes, including RP-ILD, ICU admission, respiratory support, and death.','Identify practical gaps in availability and timing of diagnostic tests and follow-up data to support future protocol development.'] : bullet(d,x) h(d,'3.2. Rationale for doing the study',2) para(d,'Anti-MDA5-positive DM-ILD has marked phenotypic variability across populations and is uncommon in any one institution. International studies may not translate directly to Filipino patients because referral patterns, diagnostic access, concomitant infection burden, and treatment availability differ. The intended study is therefore descriptive rather than analytic: it will report all eligible local cases, preserve the clinical context of treatment decisions, and avoid causal claims regarding prognostic markers or therapy in a small sample.') para(d,'Recent systematic reviews associate RP-ILD and mortality with clinical and laboratory variables such as age, fever, inflammatory markers, ferritin, lymphopenia, and anti-Ro52 positivity. These observations support collecting these variables when available, but they do not justify using them as deterministic predictors in a local small cohort. The proposed chart review fills a local data gap and is feasible because it relies on existing records.') h(d,'3.3. Background Information and Brief Literature Review',2) para(d,'Dermatomyositis is an idiopathic inflammatory myopathy with characteristic cutaneous findings, including heliotrope rash, Gottron papules or sign, periungual changes, and poikiloderma. Skin manifestations may precede muscle symptoms, and amyopathic disease can occur. Rheumatology, 2-Volume Set (2022), section “Dermatomyositis,” lines 8078-8089.') para(d,'Myositis-related ILD should be evaluated through history, physical examination, imaging, myositis-associated serology, and assessment of disease severity. Anti-MDA5 positivity is associated with a phenotype in which rapidly progressing ILD may occur and prompt recognition is required (Waseda, 2021). A recent retrospective study reported ILD in 19 of 26 patients with anti-MDA5 DM, with RP-ILD in 9 patients; organizing pneumonia and nonspecific interstitial pneumonia patterns were common CT descriptions (PMID: 40826379).') para(d,'A 2025 systematic review and meta-analysis of 1,153 patients found that RP-ILD, older age, smoking, fever, higher inflammatory markers, ferritin ≥800 ng/mL, and lymphopenia were associated with mortality in anti-MDA5 DM-ILD (Yang et al., 2025, PMID: 40746563). A 2026 systematic review/meta-analysis reported associations of RP-ILD with male sex, older age, disease duration below three months, fever, anti-Ro52 positivity, elevated CRP, LDH and ferritin, and lymphopenia (Li et al., 2026, PMID: 42039189). These data guide the protocol’s data fields, not a risk-prediction model.') h(d,'4. Objectives',1) h(d,'4.1. General Objective',2) para(d,'To describe the clinical characteristics, radiologic patterns, treatment regimens, and outcomes of adult patients with anti-MDA5 antibody-positive dermatomyositis-associated interstitial lung disease managed at [Hospital Name].') h(d,'4.2. Specific Objectives',2) for x in ['To describe baseline demographics, comorbidities, cutaneous, musculoskeletal, and respiratory manifestations.','To describe anti-MDA5 assay characteristics, accompanying serologies, and available inflammatory, muscle, and pulmonary laboratory results.','To describe HRCT patterns and extent of ILD, pulmonary function results, and oxygen or ventilatory support requirements.','To describe immunomodulatory and supportive pulmonary therapies actually administered.','To describe the occurrence of RP-ILD, ICU admission, respiratory support, infection, pneumomediastinum, discharge status, and all-cause mortality during available follow-up.'] : bullet(d,x) h(d,'5. Methods',1) h(d,'5.1. Type of Study, Time Period and Target Population',2) para(d,'This is a retrospective descriptive observational case series at [Hospital Name], a tertiary hospital in [City], Philippines. The target population comprises adult patients with anti-MDA5-positive DM or clinically amyopathic DM and radiologically confirmed ILD. The record-review period will be [January 2016 to December 2026], subject to confirmation of laboratory test availability.') para(d,'Time Period\n• Data Collection Period: [Month Year] to [Month Year].\n• Patient Follow-up: From the index date, defined as the first date when anti-MDA5 positivity and ILD are both documented, through death, last documented clinical encounter, lung transplantation, or end of the observation period, whichever occurs first.') h(d,'5.2. Criteria for Subject Selection',2) h(d,'5.2.1. Inclusion Criteria',3) for x in ['Age ≥18 years at the index date.','Positive anti-MDA5 antibody test reported by the performing laboratory.','Diagnosis of DM or clinically amyopathic DM documented by the treating rheumatologist/dermatologist, or sufficient data to meet 2017 EULAR/ACR idiopathic inflammatory myopathy classification criteria.','ILD on HRCT or chest CT compatible with ILD, supported by radiology report and clinical context.','At least one clinical encounter after index assessment, unless death occurred during the index admission.'] : bullet(d,x) h(d,'5.2.2. Exclusion Criteria',3) for x in ['Borderline, indeterminate, or unconfirmed anti-MDA5 result.','No imaging evidence of ILD or insufficient imaging documentation to assess ILD.','Alternative dominant explanation for diffuse lung disease, including drug-induced lung disease, infection, environmental exposure, or another connective-tissue disease, as determined from treating-team documentation.','Record that contains only a laboratory test with no usable clinical chart.','Patient aged <18 years.'] : bullet(d,x) h(d,'5.3. Operational definitions, if applicable',2) table(d,['Variable','Definition'],[ ['Anti-MDA5 positivity','A positive anti-MDA5 antibody result as reported by the laboratory. Assay method, cutoff, value/titer, test date, and laboratory will be recorded. Borderline results will not be classified as positive.'], ['Dermatomyositis / clinically amyopathic DM','Treating specialist diagnosis. CADM will be recorded where characteristic cutaneous DM features are present with absent or minimal clinical muscle disease, according to treating-team documentation.'], ['Interstitial lung disease','Interstitial abnormalities on HRCT/chest CT compatible with ILD, documented by a radiologist or formal report and interpreted in the clinical context.'], ['Rapidly progressive ILD (RP-ILD)','Deterioration in respiratory symptoms or oxygenation plus radiologic progression of ILD within 3 months of respiratory symptom onset. Infection, fluid overload, pulmonary embolism, and other causes must be considered. Uncertain cases will be categorized as indeterminate.'], ['HRCT pattern','Predominant pattern classified as organizing pneumonia (OP), nonspecific interstitial pneumonia (NSIP), OP/NSIP overlap, UIP-like, diffuse alveolar damage/acute lung injury features, unclassifiable, or no HRCT available.'], ['Index date','Earliest date when anti-MDA5 positivity and ILD are both documented.'], ['All-cause mortality','Death from any cause during documented follow-up, with date and chart-attributed cause recorded when available.']],[1.7,5.2]) h(d,'5.4. Description of Study Procedure',2) h(d,'5.4.1. For observational studies:',3) h(d,'5.4.1.1. Method of subject selection',3) para(d,'Potential subjects will be identified retrospectively from laboratory/myositis-panel databases, rheumatology and pulmonology clinic lists, hospital discharge databases, radiology reports, and pharmacy records. Charts will be screened against the eligibility criteria. Duplicate records will be removed using medical record number. A screening log will contain study code, eligibility status, and reason for exclusion only.') h(d,'5.4.1.2. Data to be gathered',3) for x in ['Demographics: age, sex, smoking status/pack-years, BMI if available, occupation/exposure history, comorbidities.','Clinical phenotype: symptom onset, dyspnea, cough, fever, skin manifestations, arthritis/arthralgia, Raynaud phenomenon, dysphagia, muscle weakness, and DM/CADM classification.','Serology and laboratory data: anti-MDA5 assay platform/result, ANA, anti-Ro52 and other myositis antibodies if tested; CBC, LDH, ferritin, CRP/ESR, CK, AST/ALT, albumin, creatinine, and ABG where available.','Pulmonary data: oxygen requirement, pulmonary function tests, 6-minute walk test where available, HRCT date/pattern/distribution/extent, and pneumomediastinum or pneumothorax.','Treatment and outcome data: corticosteroids, immunomodulators, IVIG, plasma exchange, oxygen, NIV/IMV/ECMO, ICU admission, infection, treatment adverse events, transplant referral, vital status, and last follow-up status.'] : bullet(d,x) h(d,'5.4.1.3. Description of procedures to be done to subjects',3) para(d,'No procedure will be performed on participants. This is a retrospective chart review using data obtained during routine clinical care.') h(d,'5.4.1.4. If applicable, instrument/s used for measuring exposure &/or outcome',3) para(d,'The standardized case report form in Appendix 8.1 will be the data collection instrument. Laboratory values will be abstracted from official reports, and clinical outcomes from physician notes, medication administration records, pulmonary function reports, radiology reports, discharge summaries, and mortality documentation. A random 10% sample of charts will undergo independent second review and discrepancy reconciliation.') h(d,'5.4.1.5. Method of validating measuring instruments',3) para(d,'No new measuring instrument will be validated. Data abstraction reliability will be supported by a pilot review of two records, a written data dictionary, independent checking of a random 10% sample, and adjudication by the principal investigator with rheumatology/radiology input when needed.') h(d,'5.4.1.6. Laboratory procedures to be performed, if any',3) para(d,'No new laboratory procedures will be performed. Only results already generated in routine clinical care will be reviewed.') h(d,'5.4.1.7. Follow-up procedures, if any',3) para(d,'No direct follow-up procedure will occur. Available clinical follow-up in the medical record will be abstracted until last documented contact, death, transplantation, or end of study observation.') h(d,'5.5. Description of Outcome Measures',2) para(d,'The primary descriptive outcome is the proportion of included patients who develop RP-ILD. Secondary outcomes are all-cause mortality during available follow-up, ICU admission, highest respiratory support, hospital length of stay for the index admission, infection, pneumomediastinum/pneumothorax, change in oxygen requirement, and documented clinical, pulmonary function, or radiologic status at last follow-up. Outcomes will be summarized descriptively, not used to make causal inferences about treatment.') h(d,'5.6. Sample Size Estimation',2) para(d,'No formal sample-size calculation is proposed. This is a rare-disease, census-based retrospective descriptive study that will include all consecutive eligible patients within the defined study period. The final sample size, number screened, reasons for exclusion, and precision of descriptive estimates will be reported. The study is not powered for multivariable modeling or comparative treatment-effect analysis.') h(d,'5.7. Data Analysis',2) para(d,'Data will be analyzed using [R/Stata/SPSS] version [x]. Categorical variables will be summarized as frequency and percentage. Continuous variables will be summarized as mean (standard deviation) if plausibly symmetric or median (interquartile range) if skewed. Missingness will be reported using available-case denominators, and no imputation will be performed. RP-ILD and survival strata may be displayed descriptively. If exploratory comparisons are undertaken, they will be clearly labeled exploratory, use appropriate small-sample tests such as Fisher exact or Mann-Whitney U tests, and will not be used to claim prognostic or treatment effects.') h(d,'5.8. Ethical Consideration',2) para(d,'This is a minimal-risk retrospective chart review. It may include vulnerable populations such as elderly patients, pregnant patients, or persons living with HIV. There will be no direct contact, change in clinical care, or additional test. The protocol will be submitted to the [Institutional Ethics Review Committee] before research access. A waiver of informed consent will be requested if allowable under institutional policy, because the study is retrospective, presents no more than minimal risk, is impracticable to conduct with individual consent, and includes confidentiality safeguards.') h(d,'5.8.1. Method/s of dealing with adverse events, serious adverse events, and indemnification policy, if any',3) para(d,'Not applicable. The study cannot cause an adverse event because it involves no intervention or participant contact. If a chart-review process identifies a clinically significant unresolved issue that could affect current care, the principal investigator will notify the appropriate treating team through institutional channels.') h(d,'5.8.2. Anticipated risks and discomforts to subjects',3) para(d,'The only anticipated risk is inadvertent breach of confidentiality. Risk will be minimized through immediate coding of extracted data, restricted access, password protection, encryption, separation of the linkage file from analytic data, and aggregate-only reporting.') h(d,'5.8.3. Expected benefits to the subject and to others',3) para(d,'There is no direct participant benefit. The study may improve local recognition and documentation of anti-MDA5 DM-ILD, identify diagnostic and follow-up gaps, and guide future collaborative research and quality-improvement work.') h(d,'5.8.4. Protection of confidentiality (i.e. where records will be stored, who can inspect the records)',3) for x in ['The study will adhere to the Declaration of Helsinki, applicable ICH-GCP principles, the Philippine Data Privacy Act of 2012, and institutional policies.','The protocol and relevant documents will be reviewed and approved by the [Institutional Ethics Review Committee] before research access.','Each participant will be assigned a study code. Names, hospital numbers, addresses, and contact information will not appear in the analytic dataset, presentations, or publications.','The coded dataset will be held in a password-protected encrypted institutional folder accessible only to the named investigators. The re-identification key will be stored separately.','Study documents will be retained securely for at least 5 years after completion, or according to institutional policy, then securely destroyed.','Authorized institutional ethics monitors and auditors may inspect study documentation for compliance. Results will be reported only in aggregate.'] : bullet(d,x) h(d,'6. Schedule of Activities',1) table(d,['RESEARCH PHASE','SPECIFIC ACTIVITIES','EXPECTED OUTPUT','DURATION BY MONTH\n1 2 3 4 5 6 7 8'],[ ['Research Proposal','Finalize proposal and present to department','Approved revised proposal','● ●'], ['Protocol Development','Finalize CRF, data dictionary, and screening log','Research protocol and CRF',' ● ●'], ['IRB Review','Submit protocol and respond to committee queries','Approved research protocol',' ● ●'], ['Data Collection','Case-finding, screening, abstraction, and imaging review','Clean coded dataset',' ● ● ●'], ['Statistical Analysis','Descriptive analysis and internal review','Analysis tables and figures',' ●'], ['Final Paper','Write manuscript, revisions, presentation/submission','Final research paper',' ●']],[1.25,2.2,1.65,2.0]) h(d,'7. References',1) for x in [ 'Waseda Y. Myositis-Related Interstitial Lung Disease: A Respiratory Physician’s Point of View. Medicina (Kaunas). 2021;57(6):599. doi:10.3390/medicina57060599. PMID: 34200737.', 'Yang Y, Li Y, Yuan W, Zhang S, He X, Ji J. Risk factors for mortality in anti-MDA5 antibody-positive dermatomyositis with interstitial lung disease: a systematic review and meta-analysis. Front Immunol. 2025. doi:10.3389/fimmu.2025.1628748. PMID: 40746563.', 'Li H, Yi M, Da G, Li M, Wang Z. Influencing factors for rapidly progressive interstitial lung disease in patients with anti-MDA5 antibody-positive dermatomyositis: a systematic review and meta-analysis. Front Immunol. 2026. doi:10.3389/fimmu.2026.1796496. PMID: 42039189.', 'Clinical characteristics and outcomes of anti-MDA5 dermatomyositis: a retrospective study. 2025. PMCID: PMC12359913. PMID: 40826379.', 'Palmucci S, Di Mari A, Cancemi G, et al. Clinical and Radiological Features of Interstitial Lung Diseases Associated with Polymyositis and Dermatomyositis. Medicina (Kaunas). 2022;58(12):1757. PMID: 36556960.', 'Rheumatology, 2-Volume Set. 2022. Section: Dermatomyositis, lines 8078-8089.' ]: d.add_paragraph(x,style='List Number') h(d,'8. Appendix',1) h(d,'8.1. Data Collection Forms',2) para(d,'Study Title: Clinical Characteristics, Radiologic Patterns, Treatment, and Outcomes of Patients With Anti-MDA5 Antibody-Positive Dermatomyositis-Associated Interstitial Lung Disease at a Tertiary Hospital in the Philippines: A Retrospective Descriptive Study') for title,lines in [ ('SECTION A. SUBJECT IDENTIFICATION (CODED)',['Study Code: ____________________','Hospital Record Number (linkage file only): ____________________','Date of first respiratory symptom: ____ / ____ / ______','Index Date: ____ / ____ / ______','Last documented follow-up / Death: ____ / ____ / ______']), ('SECTION B. DEMOGRAPHIC DATA',['Age at index date: ______ years','Sex: ☐ Male ☐ Female ☐ Other / not recorded','Height: ______ cm Weight: ______ kg BMI: ______ kg/m²','Smoking: ☐ Never ☐ Former ☐ Current ☐ Not recorded Pack-years: ______','Occupation/exposure history: ______________________________']), ('SECTION C. CLINICAL PHENOTYPE',['Presenting features: ☐ Dyspnea ☐ Cough ☐ Fever ☐ Arthritis/arthralgia ☐ Dysphagia ☐ Proximal weakness','Cutaneous features: ☐ Heliotrope rash ☐ Gottron papules/sign ☐ Ulceration ☐ Mechanic’s hands ☐ Periungual changes ☐ Other: ______','DM phenotype: ☐ DM ☐ CADM ☐ Uncertain','Comorbidities: ☐ Hypertension ☐ Diabetes ☐ CKD ☐ Malignancy ☐ Other: ______']), ('SECTION D. SEROLOGY AND LABORATORY DATA',['Anti-MDA5: assay/laboratory: __________ value/titer: ______ cutoff: ______ date: ______','ANA: ______ Anti-Ro52: ______ Other myositis antibodies: ____________________','CBC: WBC ______ Neutrophils ______ Lymphocytes ______ Hb ______ Platelets ______','CK ______ LDH ______ Ferritin ______ CRP ______ ESR ______ Albumin ______ Creatinine ______']), ('SECTION E. PULMONARY AND RADIOLOGIC FINDINGS',['Respiratory support at baseline: ☐ Room air ☐ Low-flow O₂ ☐ HFNC/NIV ☐ IMV ☐ ECMO','PFT: FVC ______ % predicted ______; DLCO ______ % predicted ______','CT date: ______ Predominant pattern: ☐ OP ☐ NSIP ☐ OP/NSIP ☐ UIP-like ☐ DAD/acute injury ☐ Other','Findings: ☐ GGO ☐ Consolidation ☐ Reticulation/fibrosis ☐ Traction bronchiectasis ☐ Honeycombing ☐ Pneumomediastinum ☐ Pneumothorax']), ('SECTION F. TREATMENT',['Corticosteroids: ____________________','Immunomodulators: ☐ Tacrolimus/cyclosporine ☐ Cyclophosphamide ☐ MMF ☐ Rituximab ☐ JAK inhibitor ☐ IVIG ☐ Plasma exchange','Antimicrobial prophylaxis / treatment: ____________________','Transplant referral: ☐ Yes ☐ No']), ('SECTION G. OUTCOMES',['RP-ILD: ☐ Yes ☐ No ☐ Indeterminate','ICU admission: ☐ Yes ☐ No Highest support: ____________________','Infection: ☐ Yes ☐ No; organism/site: ____________________','Vital status at last contact: ☐ Alive ☐ Dead ☐ Unknown; date/cause if applicable: ____________________','Last clinical status: ☐ Improved/stable ☐ Progressive ☐ Relapse ☐ Indeterminate']), ('SECTION H. ELIGIBILITY AND DATA QUALITY',['Inclusion criteria met: ☐ Yes ☐ No','Exclusion criterion present: ☐ Yes ☐ No; specify: ____________________','☐ Required fields checked against source record','Abstractor: ____________________ Date: ____________'])]: h(d,title,2) for ll in lines: para(d,ll) d.save(OUT) print(OUT) PY python3 "/tmp/workspace/anti-mda5-dm-ild-proposal/src/create_annex_a_format.py" python3 - <<'PY' from docx import Document p='/tmp/workspace/anti-mda5-dm-ild-proposal/output/Annex_A_Form_1A_Anti-MDA5_DM-ILD_Proposal_Draft.docx' d=Document(p) print('paragraphs',len(d.paragraphs),'tables',len(d.tables)) print('first',d.paragraphs[0].text) print('last',d.paragraphs[-1].text) PY ls -lh "/tmp/workspace/anti-mda5-dm-ild-proposal/output/Annex_A_Form_1A_Anti-MDA5_DM-ILD_Proposal_Draft.docx"

python3 - <<'PY' from docx import Document p='/tmp/workspace/anti-mda5-dm-ild-proposal/output/Annex_A_Form_1A_Anti-MDA5_DM-ILD_Proposal_Draft.docx' d=Document(p) required=['1. Research Title','2. Brief Description / Summary','3. Introduction','3.1. Significance of the Project','3.2. Rationale for doing the study','3.3. Background Information and Brief Literature Review','4. Objectives','5. Methods','5.1. Type of Study, Time Period and Target Population','5.2. Criteria for Subject Selection','5.3. Operational definitions, if applicable','5.4. Description of Study Procedure','5.5. Description of Outcome Measures','5.6. Sample Size Estimation','5.7. Data Analysis','5.8. Ethical Consideration','6. Schedule of Activities','7. References','8. Appendix'] texts=[x.text for x in d.paragraphs] missing=[x for x in required if x not in texts] print('Missing template headings:',missing) print('Tables:',len(d.tables), 'all tables have rows:',all(len(t.rows)>1 for t in d.tables)) print('File verified') PY