medsci-skills 4.1.0

package/skills/meta-analysis/references/LICENSES.md

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+# Checklist Licenses
+
+Attribution for bundled reporting guideline checklists.
+
+| File | Guideline | Reference | License |
+|------|-----------|-----------|---------|
+| STROBE.md | STROBE 2007 | von Elm E et al. PLoS Med 2007 | CC BY |
+| STARD.md | STARD 2015 | Bossuyt PM et al. BMJ 2015 | CC BY 4.0 |
+| TRIPOD_AI.md | TRIPOD+AI 2024 | Collins GS et al. BMJ 2024 | CC BY 4.0 |
+| PRISMA_2020.md | PRISMA 2020 | Page MJ et al. BMJ 2021 | CC BY |
+| ARRIVE_2.md | ARRIVE 2.0 | Percie du Sert N et al. PLoS Biol 2020 | CC0 |
+| PRISMA_DTA.md | PRISMA-DTA 2018 | McInnes MDF et al. JAMA 2018 | CC BY |
+| QUADAS2.md | QUADAS-2 | Whiting PF et al. Ann Intern Med 2011 | CC BY |
+| RoB2.md | RoB 2 | Sterne JAC et al. BMJ 2019 | CC BY |
+| ROBINS_I.md | ROBINS-I | Sterne JAC et al. BMJ 2016 | CC BY |
+| PROBAST.md | PROBAST | Wolff RF et al. Ann Intern Med 2019 | CC BY |
+| NOS.md | Newcastle-Ottawa Scale | Wells GA et al. Ottawa Hospital Research Institute | Public Domain |
+
+These files are educational summaries of published assessment tools. The original
+checklist documents should be cited in any manuscript that uses them. All files are
+compatible with the MIT license of this repository.

package/skills/meta-analysis/references/PROSPERO_template.md

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+# PROSPERO Registration Template
+
+## Overview
+
+PROSPERO (International Prospective Register of Systematic Reviews) requires completion of
+a structured web form. This template provides field-by-field guidance with word limits and
+common pitfalls from real registration experience.
+
+**Key constraint**: Initial registrations are NOT allowed after data extraction is completed.
+Searching and screening may be completed.
+
+---
+
+## Form Fields Reference
+
+### REVIEW TITLE AND BASIC DETAILS
+
+#### 1. Review title (max 50 words)
+Include: study design (systematic review, meta-analysis, pooled analysis), condition,
+intervention, population qualifier if relevant.
+
+#### 2. Review question (max 250 words)
+Structure around PICO/PIRD. State both primary and secondary objectives clearly.
+For pooled analysis designs, distinguish between pooled proportion and comparative questions.
+
+#### 3. Condition/domain being studied (max 200 words)
+Define the condition. Explain why it matters. Note the clinical gap.
+
+#### 4. Keywords
+Semicolon-separated. Include MeSH-equivalent terms.
+
+---
+
+### ELIGIBILITY CRITERIA
+
+#### 5. Population (max 200 words)
+State included and excluded populations. Include age, disease status, anatomical specifics.
+
+#### 6. Intervention/exposure (max 200 words)
+Define all eligible interventions with specifics (technique, device, imaging guidance).
+State minimum reporting requirement ("must report at least one clinical outcome").
+
+#### 7. Comparator/control (max 200 words)
+If both comparative and single-arm studies are included, state this explicitly:
+"For the comparative analysis, [comparator description]. For the pooled proportion analysis,
+single-arm studies without a comparator are also included."
+
+#### 8. Type of study to be included (max 150 words)
+List included and excluded study designs separately. Be specific about minimum sample size
+(e.g., "case reports with fewer than 5 patients excluded").
+
+---
+
+### SEARCHING AND SCREENING
+
+#### 9. Searches (max 300 words)
+Name databases, date range, language restrictions. Reference supplementary search strategies.
+
+#### 10. Search strategy (max 300 words)
+Show actual search blocks with Boolean structure. No need for full line-by-line syntax here
+(reference supplementary materials for that).
+
+#### Sub-fields in the web form:
+- **Search for unpublished studies**: Yes/No (select based on protocol)
+- **Main databases**: Select from checklist (PubMed, Embase.com vs Embase via Ovid — distinguish!)
+- **Language restrictions**: State explicitly
+- **Date restrictions**: State explicitly
+- **Other methods**: Check ONLY what was actually done:
+  - reference list checking (backward citation)
+  - contacting authors
+  - conference proceedings
+  - trial registers
+  - forward citation searching (snowballing)
+  - **WARNING**: Do not check methods you did not perform — reviewers may ask for results
+- **Link to search strategy**: Reference protocol or supplementary materials
+- **Selection process**: "Two reviewers independently..." with disagreement resolution
+- **Other info about screening**: PRISMA flow diagram reference (optional)
+
+---
+
+### DATA COLLECTION PROCESS
+
+#### 11. Data extraction (max 300 words)
+List extracted variables by category: study characteristics, population, intervention,
+outcomes. State unit of analysis policy (patient vs tumor level). If Kaplan-Meier
+reconstruction is used, cite methods (Tierney 2007, Guyot 2012).
+
+#### Sub-fields:
+- **Extraction method**: Select "independently by at least two people"
+- **Author contact**: Yes/No
+- **IPD**: Usually No for standard MA
+
+#### 12. Risk of bias/Quality assessment (max 200 words)
+Name tool(s) per study design. If using tools not in the PROSPERO checklist (e.g., JBI),
+select "Other" and describe in text.
+
+Common tool mapping:
+| Study design | Tool |
+|---|---|
+| RCT | Cochrane RoB 2 |
+| Non-randomized comparative | Newcastle-Ottawa Scale (NOS) or ROBINS-I |
+| Single-arm / case series | JBI Critical Appraisal Checklist (select "Other") |
+| DTA | QUADAS-2 |
+| Prediction model | PROBAST |
+
+State number of assessors and disagreement resolution.
+
+#### 13. Reporting bias assessment
+For pooled proportion (k>=10): funnel plot + Egger's regression test.
+For comparative (k<10): funnel plot visual inspection only.
+Do NOT promise trim-and-fill or contour-enhanced funnel unless actually planned.
+
+#### 14. Certainty assessment
+Select "No" unless GRADE or equivalent is explicitly planned in the protocol.
+If "Yes": requires Summary of Findings table — significant additional work.
+
+---
+
+### OUTCOMES TO BE ANALYSED
+
+#### 15. Primary outcomes (max 300 words)
+Define each outcome precisely: what it measures, how it is defined, at what time points.
+State the effect measure (proportion, OR, HR, etc.).
+
+#### 16. Secondary outcomes (max 300 words)
+List all secondary outcomes. Include exploratory outcomes that will be "extracted if reported."
+
+---
+
+### PLANNED DATA SYNTHESIS
+
+#### 17. Strategy for data synthesis (max 400 words)
+Structure as:
+1. **Primary analysis**: model, estimator, transformation
+2. **Secondary analysis**: model, estimator, CI adjustment
+3. **Heterogeneity**: I-squared, Q test, interpretation thresholds
+4. **Publication bias**: methods (reference field 13)
+5. **Software**: R packages with versions
+
+#### 18. Subgroups/subsets (max 250 words)
+Number and list all pre-specified subgroup analyses.
+Number and list all pre-specified sensitivity analyses.
+State interaction test method.
+Mention leave-one-out if planned.
+
+---
+
+### CURRENT REVIEW STAGE
+
+#### 19. Review stage checklist
+| Stage | Allowed at registration |
+|---|---|
+| Pilot work | Started or Completed OK |
+| Formal searching | Started or Completed OK |
+| Screening | Started or Completed OK |
+| **Data extraction** | **Not started or Started ONLY** |
+| Risk of bias | Not started |
+| Data synthesis | Not started |
+
+**CRITICAL**: If data extraction is "Completed", registration will be REJECTED.
+If protocol restructuring invalidates prior extraction → defensible to mark "Not started."
+
+#### 20. Review status
+Usually: "The review is planned or ongoing"
+
+---
+
+### REVIEW AFFILIATION, FUNDING AND PEER REVIEW
+
+#### 21. Review team members
+All authors with ORCID and affiliation. One must be Guarantor + Named Contact.
+Guarantor = typically first or corresponding author.
+
+#### 22. Funding
+- If no funding: "This review received no specific funding from any agency in the public,
+  commercial, or not-for-profit sectors."
+- Do NOT write "supported by academic institutions" unless there is actual institutional funding.
+
+#### 23. Peer review
+Usually "Not peer reviewed" for initial registration.
+
+---
+
+### ADDITIONAL INFORMATION
+
+#### 24. Additional info (max 250 words)
+Standard text: "Any important protocol amendments will be documented in the PROSPERO record
+and clearly reported in the final publication."
+
+#### 25. MeSH terms
+Auto-generated but editable. Review and add missing terms (e.g., Microwaves for MWA studies).
+
+---
+
+## Common Pitfalls Checklist
+
+Before submitting, verify:
+
+- [ ] **HTML entities**: Preview PDF and check all `>=`, `<`, `&` symbols display correctly
+      (common breakage: `&gt;`, `&lt;`, `&amp;` appearing literally)
+- [ ] **Word limits**: Each field within stated maximum
+- [ ] **Database names**: Embase.com vs Embase via Ovid (different options in form)
+- [ ] **Other methods**: Only checked items actually performed
+- [ ] **RoB tool**: JBI requires "Other" selection (not in standard list)
+- [ ] **Certainty/GRADE**: "No" unless explicitly planned with SoF table
+- [ ] **Funding text**: Matches actual funding status
+- [ ] **Data extraction stage**: Not marked as "Completed"
+- [ ] **Similar records**: All reviewed and confirmed "not similar"
+- [ ] **All authors**: Listed with correct ORCID and affiliation
+- [ ] **End date**: In the future (update if past)
+- [ ] **Comparator field**: Addresses both comparative and single-arm inclusion if applicable
+
+---
+
+## Output Format
+
+When generating PROSPERO content for the user:
+1. Produce a single Markdown file with all fields, word counts per field
+2. Convert to DOCX via pandoc for copy-paste convenience
+3. Flag any fields requiring user decision (e.g., author contact, unpublished search)
+4. Include the Common Pitfalls Checklist at the end

package/skills/meta-analysis/references/ai_pre_screening_template.py

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+"""AI-Assisted Pre-Screening Template for R3 Adjudication.
+
+PURPOSE
+-------
+For systematic review screening, the methodologically sound workflow requires
+TWO independent human reviewers with Cohen's kappa, followed by adjudication
+of disagreements (R3) by the first reviewer. R3 commonly involves 100+ records
+and is the bottleneck.
+
+This template generates AI-assisted *suggestions* (NOT decisions). The first
+reviewer must still confirm or overturn each suggestion. This preserves
+methodological integrity while compressing R3 from 2-3 hours x 2-3 days to
+~30-60 minutes.
+
+NOT a replacement for human reviewer. Methods boilerplate is provided below.
+
+INPUT
+-----
+TSV with at minimum these columns:
+    uid, title, abstract_preview, journal, doi, round2_tag, round2_reason
+
+`round2_tag` values expected:
+    INCLUDE   -> AI default = CONFIRM-INCLUDE; flag review/conf abstract patterns
+    MAYBE     -> AI requires per-uid manual decisions (UNCERTAIN if not pre-coded)
+    EXCLUDE   -> typically not in R3 sheet; if present, AI default = CONFIRM-EXCLUDE
+
+OUTPUT
+------
+Same TSV plus columns:
+    ai_suggestion : INCLUDE / EXCLUDE / UNCERTAIN / CONFIRM-INCLUDE / CONFIRM-EXCLUDE
+    ai_reason     : one-sentence justification
+
+USAGE
+-----
+1. Copy this file to your project's `1_Code/` directory.
+2. Customize:
+   - `PROJECT_PECOS` (eligibility criteria summary)
+   - `MAYBE_DECISIONS` (per-uid manual judgments after reading each abstract)
+   - `EXCLUDE_PATTERNS` (project-specific keyword patterns)
+3. Run; review priority-sorted output (use companion `make_review_priority_view.py`).
+
+METHODS BOILERPLATE
+-------------------
+"Round 3 adjudication of records flagged as 'maybe' by either reviewer was
+performed by the first reviewer (initials) with AI-assisted pre-screening
+(model name and version). The AI model was prompted with the prespecified
+PECOS criteria and produced a suggestion plus brief justification for each
+record; the first reviewer independently confirmed or overturned every
+suggestion against the title, abstract, and (when needed) full text. AI
+suggestions were not used as final inclusion decisions."
+
+CITATION
+--------
+Inspired by emerging AI-assisted screening practice (e.g., Khalil et al.,
+Syst Rev 2022). Document model and version in the manuscript.
+"""
+from __future__ import annotations
+import csv
+from pathlib import Path
+
+# ============================================================================
+# 1. PROJECT CONFIGURATION — customize per project
+# ============================================================================
+
+PROJECT_PECOS = """
+Replace this string with a one-paragraph summary of your PECOS criteria.
+Used as documentation only; the AI logic below must be coded explicitly.
+"""
+
+# Per-uid MAYBE decisions. Fill after reading each MAYBE abstract.
+# Format: uid -> (suggestion, one-sentence reason)
+# Suggestion values: INCLUDE / EXCLUDE / UNCERTAIN
+MAYBE_DECISIONS: dict[str, tuple[str, str]] = {
+    # "study_0042": ("INCLUDE", "Title confirms target population + intervention; design = RCT."),
+    # "study_0099": ("EXCLUDE", "Conference abstract without full publication."),
+    # "study_0123": ("UNCERTAIN", "Abstract truncated; full text needed to confirm intervention arm."),
+}
+
+# ============================================================================
+# 2. INCLUDE-row heuristic classifier — common patterns; tune for your project
+# ============================================================================
+
+# Hard EXCLUDE keyword patterns (title or first 300 chars of abstract)
+REVIEW_KEYWORDS = [
+    "systematic review", "meta-analysis", "narrative review",
+    " review of ", "scoping review", "review article",
+    "editorial", "commentary", "letter to the editor",
+]
+
+# Conference abstract / supplement detection
+CONF_JOURNAL_KEYWORDS = ["abstracts", "supplement"]
+# Common DOI markers for supplements (tune to your field)
+CONF_DOI_PATTERNS = ["suppl_", "/circ.144.suppl", "/circ.146.suppl",
+                     ".abstract.", "-snis.", "-esmint."]
+
+# Single case report markers
+CASE_KEYWORDS = ["case report", "case series"]
+
+
+def classify_include_row(uid: str, title: str, abstract: str, journal: str,
+                         doi: str, reason: str,
+                         topic_keywords: list[str] | None = None) -> tuple[str, str]:
+    """Heuristic AI suggestion for INCLUDE-tagged rows.
+
+    Default = CONFIRM-INCLUDE. Returns EXCLUDE for clear review/conference/
+    case-report patterns, or when no topic keyword appears in title or abstract.
+
+    Args:
+        topic_keywords: list of lowercase keywords; if NONE found in title or
+            abstract, suggest EXCLUDE. Pass project topic terms (e.g., for an
+            aneurysm SR: ["aneurysm", "intracranial", "cerebral", "vasc"]).
+    """
+    t = title.lower()
+    a = abstract.lower()
+    j = journal.lower()
+    d = doi.lower()
+
+    # Review / editorial filter
+    if (any(k in t for k in REVIEW_KEYWORDS) or
+            any(k in a[:300] for k in REVIEW_KEYWORDS)):
+        if "primary" not in a[:500] and "we developed" not in a[:500]:
+            return ("EXCLUDE", "Likely review/editorial based on title/abstract keywords.")
+
+    # Conference abstract filter
+    if (any(k in j for k in CONF_JOURNAL_KEYWORDS) or
+            any(k in d for k in CONF_DOI_PATTERNS)):
+        return ("EXCLUDE",
+                "Conference abstract / supplement; likely no full peer-reviewed publication.")
+
+    # Single case report
+    if any(k in t for k in CASE_KEYWORDS):
+        if "single" in t or "single case" in a[:300]:
+            return ("EXCLUDE", "Single case report -- excluded by study design criterion.")
+
+    # Off-topic check
+    if topic_keywords:
+        if (not any(k in t for k in topic_keywords) and
+                not any(k in a[:500] for k in topic_keywords)):
+            return ("EXCLUDE", "No topic keyword in title or abstract.")
+
+    return ("CONFIRM-INCLUDE",
+            "Title/abstract consistent with PECOS; default include, verify at full-text extraction.")
+
+
+# ============================================================================
+# 3. Main pipeline
+# ============================================================================
+
+def run_pre_screening(src_tsv: Path, dst_tsv: Path,
+                      topic_keywords: list[str] | None = None) -> None:
+    """Read screening TSV, add ai_suggestion/ai_reason columns, write output."""
+    rows = list(csv.DictReader(src_tsv.open(encoding="utf-8"), delimiter="\t"))
+    if not rows:
+        raise SystemExit(f"No rows in {src_tsv}")
+
+    in_fields = list(rows[0].keys())
+    extra = [c for c in ("ai_suggestion", "ai_reason") if c not in in_fields]
+    out_fields = ["uid", "ai_suggestion", "ai_reason"] + [
+        c for c in in_fields if c not in ("uid", "ai_suggestion", "ai_reason")
+    ]
+
+    counts: dict[str, int] = {}
+    with dst_tsv.open("w", encoding="utf-8", newline="") as f:
+        w = csv.DictWriter(f, fieldnames=out_fields, delimiter="\t",
+                           quoting=csv.QUOTE_MINIMAL)
+        w.writeheader()
+
+        for r in rows:
+            uid = r["uid"]
+            tag = r.get("round2_tag", "").upper()
+
+            if tag == "MAYBE":
+                if uid in MAYBE_DECISIONS:
+                    sug, why = MAYBE_DECISIONS[uid]
+                else:
+                    sug, why = ("UNCERTAIN",
+                                "MAYBE row without pre-coded decision; full review needed.")
+            elif tag == "INCLUDE":
+                sug, why = classify_include_row(
+                    uid,
+                    r.get("title", ""),
+                    r.get("abstract_preview", ""),
+                    r.get("journal", ""),
+                    r.get("doi", ""),
+                    r.get("round2_reason", ""),
+                    topic_keywords=topic_keywords,
+                )
+            elif tag == "EXCLUDE":
+                sug, why = ("CONFIRM-EXCLUDE",
+                            "Round 2 EXCLUDE; reviewer to confirm with brief check.")
+            else:
+                sug, why = ("UNCERTAIN", f"Unexpected round2_tag={tag!r}")
+
+            counts[sug] = counts.get(sug, 0) + 1
+            r["ai_suggestion"] = sug
+            r["ai_reason"] = why
+            w.writerow({k: r.get(k, "") for k in out_fields})
+
+    print(f"Wrote {dst_tsv} ({len(rows)} rows)")
+    print("AI suggestion distribution:")
+    for k in sorted(counts):
+        print(f"  {k}: {counts[k]}")
+
+
+# ============================================================================
+# 4. Companion: priority-sorted view
+# ============================================================================
+
+PRIORITY_ORDER = {
+    "UNCERTAIN": 0,
+    "EXCLUDE": 1,
+    "INCLUDE": 2,
+    "CONFIRM-EXCLUDE": 3,
+    "CONFIRM-INCLUDE": 4,
+}
+
+
+def write_priority_view(src_tsv: Path, dst_tsv: Path) -> None:
+    """Sort AI-pre-screened TSV by review priority."""
+    rows = list(csv.DictReader(src_tsv.open(encoding="utf-8"), delimiter="\t"))
+    rows.sort(key=lambda r: (PRIORITY_ORDER.get(r["ai_suggestion"], 9), r["uid"]))
+    fields = list(rows[0].keys())
+    with dst_tsv.open("w", encoding="utf-8", newline="") as f:
+        w = csv.DictWriter(f, fieldnames=fields, delimiter="\t",
+                           quoting=csv.QUOTE_MINIMAL)
+        w.writeheader()
+        w.writerows(rows)
+    print(f"Wrote priority view: {dst_tsv}")
+
+
+# ============================================================================
+# 5. Example invocation
+# ============================================================================
+
+if __name__ == "__main__":
+    # Customize these paths and topic keywords for your project.
+    PROJECT_ROOT = Path(__file__).resolve().parent
+    SRC = PROJECT_ROOT / "round3_adjudication_TEMPLATE.tsv"
+    AI = PROJECT_ROOT / "round3_adjudication_AI_TEMPLATE.tsv"
+    PRIORITY = PROJECT_ROOT / "round3_priority_TEMPLATE.tsv"
+
+    TOPIC_KEYWORDS = ["TOPIC1", "TOPIC2"]  # e.g., ["aneurysm", "intracranial"]
+
+    run_pre_screening(SRC, AI, topic_keywords=TOPIC_KEYWORDS)
+    write_priority_view(AI, PRIORITY)

package/skills/meta-analysis/references/checklists/JBI_Case_Series.md

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+# JBI Critical Appraisal Checklist for Case Series
+
+Reference: Munn Z, Barker TH, Moola S, et al. Methodological quality of case series
+studies: an introduction to the JBI critical appraisal tool. JBI Evid Synth. 2020;18(10):2127-2133.
+
+## 10 Signalling Questions
+
+| # | Question | Y/N/U/NA |
+|---|----------|----------|
+| Q1 | Were there clear criteria for inclusion in the case series? | |
+| Q2 | Was the condition measured in a standard, reliable way for all participants included in the case series? | |
+| Q3 | Were valid methods used for identification of the condition for all participants included in the case series? | |
+| Q4 | Did the case series have consecutive inclusion of participants? | |
+| Q5 | Did the case series have complete inclusion of participants? | |
+| Q6 | Was there clear reporting of the demographics of the participants in the study? | |
+| Q7 | Was there clear reporting of clinical information of the participants? | |
+| Q8 | Were the outcomes or follow-up results of cases clearly reported? | |
+| Q9 | Was there clear reporting of the presenting site(s)/clinic(s) demographic information? | |
+| Q10 | Was statistical analysis appropriate? | |
+
+## Scoring
+
+- **Y** = Yes (criterion met)
+- **N** = No (criterion not met)
+- **U** = Unclear
+- **NA** = Not applicable
+
+## Overall Appraisal
+
+| Rating | Criterion |
+|--------|-----------|
+| **Include** | ≥7 "Yes" responses |
+| **Exclude** | <7 "Yes" responses (or critical methodological concerns) |
+| **Seek further info** | Insufficient information to judge key items |
+
+## Notes
+
+- Q4 and Q5 distinguish consecutive vs complete inclusion:
+  - Q4 (consecutive): Were participants enrolled sequentially without selection bias?
+  - Q5 (complete): Were all eligible participants during the study period included?
+- Q9 applies to multi-site studies; for single-site studies, mark as NA if site demographics
+  are adequately covered by Q6.
+- When used alongside NOS for mixed comparative + single-arm meta-analyses, map NOS to
+  comparative studies and JBI to case series. In PROSPERO, select "Other" for RoB tool
+  and specify both.

package/skills/meta-analysis/references/checklists/NOS.md

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+# Newcastle-Ottawa Scale (NOS) Assessment Guide
+
+Quality assessment tool for non-randomised studies in meta-analyses.
+Reference: Wells GA et al. Ottawa Hospital Research Institute.
+
+## Structure
+
+NOS uses a "star system" (maximum 9 stars) across 3 categories.
+Higher stars = higher quality.
+
+## Cohort Studies (max 9 stars)
+
+### Selection (max 4 stars)
+1. **Representativeness of the exposed cohort** (1 star)
+   - a) Truly representative of the average [describe] in the community *
+   - b) Somewhat representative *
+   - c) Selected group of users
+   - d) No description
+
+2. **Selection of the non-exposed cohort** (1 star)
+   - a) Drawn from the same community as the exposed *
+   - b) Drawn from a different source
+   - c) No description
+
+3. **Ascertainment of exposure** (1 star)
+   - a) Secure record (e.g., surgical records) *
+   - b) Structured interview *
+   - c) Written self-report
+   - d) No description
+
+4. **Demonstration that outcome was not present at start** (1 star)
+   - a) Yes *
+   - b) No
+
+### Comparability (max 2 stars)
+5. **Comparability of cohorts on the basis of design or analysis** (up to 2 stars)
+   - a) Study controls for [most important factor] *
+   - b) Study controls for any additional factor *
+
+### Outcome (max 3 stars)
+6. **Assessment of outcome** (1 star)
+   - a) Independent blind assessment *
+   - b) Record linkage *
+   - c) Self-report
+   - d) No description
+
+7. **Was follow-up long enough for outcomes to occur?** (1 star)
+   - a) Yes (select adequate follow-up period) *
+   - b) No
+
+8. **Adequacy of follow-up of cohorts** (1 star)
+   - a) Complete follow-up (all subjects accounted for) *
+   - b) Subjects lost to follow-up unlikely to introduce bias (<=20% lost, or description provided) *
+   - c) Follow-up rate <80% and no description of those lost
+   - d) No statement
+
+## Case-Control Studies (max 9 stars)
+
+### Selection (max 4 stars)
+1. Is the case definition adequate?
+2. Representativeness of the cases
+3. Selection of controls
+4. Definition of controls
+
+### Comparability (max 2 stars)
+5. Comparability of cases and controls (same 2-star system)
+
+### Exposure (max 3 stars)
+6. Ascertainment of exposure
+7. Same method of ascertainment for cases and controls
+8. Non-response rate
+
+## Interpretation
+
+| Stars | Quality |
+|-------|---------|
+| 7-9 | Good (high quality) |
+| 4-6 | Fair (moderate quality) |
+| 0-3 | Poor (low quality) |
+
+Alternative thresholds may be pre-specified in the protocol.
+
+## When to Use
+
+- Observational cohort studies in intervention or exposure meta-analyses
+- Case-control studies
+- Simpler alternative to ROBINS-I when full domain-level assessment is not needed
+- Note: NOS does not provide domain-level judgments -- only an aggregate score

package/skills/meta-analysis/references/checklists/PRISMA_DTA.md

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+# PRISMA-DTA Checklist
+
+Preferred Reporting Items for Systematic Reviews and Meta-Analyses of Diagnostic Test Accuracy Studies.
+Reference: McInnes MDF et al. JAMA 2018;319(4):388-396.
+
+## Checklist Items
+
+| # | Section | Item |
+|---|---------|------|
+| 1 | Title | Identify the report as a systematic review (+/- meta-analysis) of diagnostic test accuracy studies |
+| 2 | Abstract - Structured | Provide structured summary including objectives, data sources, study eligibility, participants, interventions, study appraisal and synthesis methods, results, limitations, conclusions, registration number |
+| 3 | Introduction - Rationale | Describe the rationale for the review in the context of what is already known |
+| 4 | Introduction - Objectives | State precise objectives, including PIRD elements |
+| 5 | Methods - Protocol | Indicate if a review protocol exists, where it can be accessed, and registration information |
+| 6 | Methods - Eligibility | Specify study characteristics and reporting characteristics used as criteria for eligibility |
+| 7 | Methods - Information sources | Describe all information sources in the search and date last searched |
+| 8 | Methods - Search | Present full electronic search strategy for at least one database |
+| 9 | Methods - Study selection | State the process for selecting studies |
+| 10 | Methods - Data collection | Describe method of data extraction from primary DTA studies and any processes for obtaining and confirming data from investigators |
+| 11 | Methods - Data items | List and define all variables for which data were sought and any assumptions/simplifications made |
+| 12 | Methods - Risk of bias | Describe methods used for assessing risk of bias of individual studies and how this information is used in data synthesis |
+| 13 | Methods - Diagnostic accuracy measures | State the principal diagnostic accuracy measures and how they were calculated |
+| 14 | Methods - Synthesis | Describe methods of handling data and combining results of studies including measures of statistical consistency |
+| 15 | Methods - Risk of bias across studies | Specify any assessment of risk of bias that may affect the cumulative evidence |
+| 16 | Methods - Additional analyses | Describe methods of additional analyses if done (e.g., sensitivity or subgroup analyses, meta-regression) |
+| 17 | Results - Study selection | Give numbers of studies screened, assessed for eligibility, and included with reasons for exclusions at each stage; consider a flow diagram |
+| 18 | Results - Study characteristics | For each study, present characteristics for which data were extracted and provide the citations |
+| 19 | Results - Risk of bias within studies | Present risk of bias assessments for each included study |
+| 20 | Results - Individual study results | For each analysis in each study, report 2x2 data with confidence intervals |
+| 21 | Results - Synthesis of results | Describe test performance and present key results including confidence intervals for the meta-analysis |
+| 22 | Results - Risk of bias across studies | Present results of any assessment of risk of bias across studies |
+| 23 | Results - Additional analyses | Give results of additional analyses (subgroup, sensitivity, meta-regression) |
+| 24 | Discussion - Summary | Summarize the main findings including strength of evidence |
+| 25 | Discussion - Limitations | Discuss limitations at study and outcome level and at review level |
+| 26 | Discussion - Conclusions | Provide a general interpretation of the results in the context of other evidence and implications for future research |
+| 27 | Funding | Describe sources of funding for the systematic review and other support; role of funders |