@research-copilot/plugin 1.1.17 → 1.1.19

package/dist/skills/medical-imaging-review/references/MCP_SETUP.md

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+# MCP Server Configuration for Literature Collection
+
+Set up arxiv-mcp / pubmedmcp / zotero-mcp for use in Phase 2 (Literature Collection + Verification). For each server, this file documents installation, tools available, and the searches that match the workflow.
+
+---
+
+## ArXiv MCP (Preprints & Latest Research)
+
+**Repository:** https://github.com/blazickjp/arxiv-mcp-server
+
+### Configuration
+
+Add to `~/.claude/mcp.json` (or your MCP config file):
+
+```json
+{
+  "mcpServers": {
+    "arxiv": {
+      "command": "uvx",
+      "args": ["arxiv-mcp-server"],
+      "env": {
+        "ARXIV_STORAGE_PATH": "~/.arxiv-mcp-server/papers"
+      }
+    }
+  }
+}
+```
+
+### Available tools
+
+| Tool | Purpose |
+|---|---|
+| `mcp__arxiv-mcp-server__search_papers` | Search by keywords with date range and category filters |
+| `mcp__arxiv-mcp-server__download_paper` | Download paper PDF by arXiv ID |
+| `mcp__arxiv-mcp-server__list_papers` | List all downloaded papers |
+| `mcp__arxiv-mcp-server__read_paper` | Read downloaded paper content (Markdown) |
+
+### Search strategy
+
+```
+Query: "[topic] AND (segmentation OR detection OR classification)"
+Categories: cs.CV, eess.IV, cs.LG
+Date: Last 3 years for current state of the art
+Max results: 50-80 per query (discriminate aggressively — quality over breadth)
+```
+
+### Example queries
+
+- `"medical image segmentation transformer"` (cs.CV, eess.IV)
+- `"coronary artery deep learning"` (cs.CV)
+- `"CT scan neural network"` (eess.IV)
+- `"foundation model medical segmentation"` (cs.CV, cs.LG)
+
+### Workflow integration
+
+Per CITATION_INTEGRITY.md Rule 2, when adding an arXiv paper to bibliography:
+
+1. `search_papers` to find candidates
+2. `download_paper(paper_id)` for promising ones
+3. `read_paper(paper_id)` to read full text (or at least abstract + methods + results)
+4. Note actual first author, full author list, exact module names, headline numbers
+5. Cross-check: arxiv abstract page = `https://arxiv.org/abs/<id>` for author list verification
+
+---
+
+## PubMed MCP (Biomedical Literature)
+
+**Repository:** https://github.com/grll/pubmedmcp
+
+Access 35+ million biomedical literature citations.
+
+### Configuration
+
+```json
+{
+  "mcpServers": {
+    "pubmedmcp": {
+      "command": "uvx",
+      "args": ["pubmedmcp@latest"],
+      "env": {
+        "UV_PRERELEASE": "allow",
+        "UV_PYTHON": "3.12"
+      }
+    }
+  }
+}
+```
+
+### Available tools
+
+| Tool | Purpose |
+|---|---|
+| `mcp__pubmed-mcp-server__pubmed_search_articles` | Search PubMed with MeSH and free-text queries |
+
+### Search tips
+
+- Use MeSH terms for precise medical searches
+- Combine with publication type filters (Review, Clinical Trial)
+- Filter by date for recent literature
+
+### Example MeSH queries
+
+- `"Deep Learning"[MeSH] AND "Coronary Vessels"[MeSH]`
+- `"Image Processing, Computer-Assisted"[MeSH] AND "Tomography, X-Ray Computed"[MeSH]`
+- `"Cardiac Imaging Techniques"[MeSH] AND "Artificial Intelligence"[MeSH]`
+
+### Direct WebFetch for verification
+
+`pubmed_search_articles` returns PMIDs. For metadata verification (CITATION_INTEGRITY.md Rules 1-2):
+
+```
+WebFetch on https://pubmed.ncbi.nlm.nih.gov/<PMID>/
+  → Extract: full author list, journal, year, vol, issue, pages, DOI, finding direction
+```
+
+This is the canonical first-source verification step for medical clinical papers.
+
+---
+
+## Zotero Integration
+
+Access user's local Zotero database via Zotero-MCP.
+
+### Direct API Access (fallback)
+
+```bash
+# List collections
+curl -s "http://localhost:23119/api/users/[USER_ID]/collections"
+
+# Get items from a collection
+curl -s "http://localhost:23119/api/users/[USER_ID]/collections/[KEY]/items"
+```
+
+### Zotero-MCP (recommended)
+
+**Repository:** https://github.com/54yyyu/zotero-mcp
+
+Provides structured access:
+
+| Tool | Purpose |
+|---|---|
+| `mcp__zotero__zotero_search_collections` | Find collections by name / keyword |
+| `mcp__zotero__zotero_get_collection_items` | List items in a collection |
+| `mcp__zotero__zotero_search_items` | Search items by keyword |
+| `mcp__zotero__zotero_get_item_metadata` | Get full metadata for an item |
+| `mcp__zotero__zotero_get_item_fulltext` | Get full paper text from attached PDF |
+| `mcp__zotero__zotero_get_annotations` | Get user highlights / notes |
+| `mcp__zotero__zotero_semantic_search` | Semantic search across library |
+
+### Workflow integration
+
+For closed-access journals (Med Image Anal, Eur Radiol, JACC family, Lancet family, Nature family), the user often has PDFs in Zotero that aren't accessible via WebFetch. Workflow:
+
+```
+1. mcp__zotero__zotero_search_items(query: "<author> <method>", limit: 5)
+2. mcp__zotero__zotero_get_item_metadata(item_key: "<key>")
+3. mcp__zotero__zotero_get_item_fulltext(item_key: "<key>") for body content
+```
+
+### Extractable fields
+
+- title
+- abstractNote
+- date
+- creators (author list — verify against first-source per Rule 2)
+- publicationTitle
+- DOI
+- tags
+- collections
+
+---
+
+## Source Selection Guide
+
+| Source | Best for | Strengths | Workflow phase |
+|---|---|---|---|
+| **ArXiv** | Methodological preprints, ML/AI advances | Fast access, CS/AI focus, full text | Phase 2.1 |
+| **PubMed** | Peer-reviewed clinical / validation, MeSH-indexed | Authoritative for medical, free metadata access | Phase 2.2 |
+| **Zotero** | Closed-access journals where user has PDFs | Local, supports fulltext extraction | Phase 2.3 |
+| **Crossref** | DOI verification | API gives canonical metadata | All phases (verification) |
+
+---
+
+## Verification helper commands
+
+For Phase 4 (per-claim verification) and Phase 5 (peer review):
+
+```
+# Crossref by DOI
+WebFetch on https://api.crossref.org/works/<DOI>
+  → Returns JSON: title, full author list, container-title (journal), volume, issue, page, DOI, published year
+
+# Crossref by topic search
+WebFetch on https://api.crossref.org/works?query.bibliographic=<keywords>&rows=5
+  → Returns top 5 matching entries
+
+# PubMed by PMID
+WebFetch on https://pubmed.ncbi.nlm.nih.gov/<PMID>/
+  → Returns parsed page: title, authors, journal info, DOI, abstract
+
+# arXiv abstract page (for author list verification)
+WebFetch on https://arxiv.org/abs/<id>
+  → Returns abstract + full author list
+```
+
+---
+
+## When MCP servers fail
+
+If an MCP server is not configured or fails:
+
+- **ArXiv fallback**: WebFetch on `https://arxiv.org/abs/<id>` directly
+- **PubMed fallback**: WebFetch on `https://pubmed.ncbi.nlm.nih.gov/<PMID>/` directly
+- **Zotero fallback**: ask the user to share PDFs directly, or use direct API access via curl
+
+The skill is designed to work even without MCP — WebFetch on the underlying APIs is always available.

package/dist/skills/medical-imaging-review/references/PARADIGM.md

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+# Phase 0: Paradigm Capture
+
+Before writing the manuscript, extract a style spec from 2-3 exemplar reviews in the target journal tier. This anchors the draft to flagship-review style and prevents drift toward the generic "survey paper" register that LLMs default to.
+
+---
+
+## Why this phase exists
+
+LLMs trained on the entire web have absorbed every register of medical writing — vendor white papers, methodological surveys, textbook chapters, narrative reviews, systematic reviews, flagship reviews — and have no built-in preference among them. By default, the register they generate is somewhere between "good survey paper" and "Wikipedia article": numbered chapters, hedging language, neutral catalogue, dense subsections.
+
+Flagship-tier reviews (Nature Reviews / Nat Med / Lancet family / JACC) write differently:
+
+- 2 heading levels, no number prefixes
+- 1-2 sentence "verdict" closers per axis section
+- Equations and dataset details in Boxes, not body
+- Vendor names confined to a single Table
+- Authorial position taken explicitly when evidence supports it
+- 1.5-2.5 references per paragraph, well-targeted
+- Often a 4-5 bullet "Key Points" box after the title
+
+Without an exemplar anchor, even careful writing drifts toward the generic register. With one, every paragraph has a benchmark.
+
+---
+
+## Action 1: Select 2-3 exemplar reviews
+
+### Selection criteria
+
+- **Same modality or same problem family** as your topic. (For coronary AI, look at recent coronary or cardiovascular AI reviews. For brain tumor segmentation, look at neuroradiology AI reviews.)
+- **Same journal tier** as your target. If aiming for Nat Med, read a recent Nat Med review. If aiming for Eur Radiol, read a recent Eur Radiol review.
+- **Last 3 years**. Older exemplars may have outdated stylistic conventions.
+- **Recognized authors**. Reviews authored by senior figures in the field carry the conventions of their target journals more reliably.
+
+### Suggested exemplars by tier
+
+**Top tier (Nature Reviews / Nat Med / Lancet family):**
+
+- Nature Reviews Cardiology — for cardiovascular AI
+- Nat Med — for AI-in-medicine narrative reviews
+- Lancet Digital Health — for AI clinical translation
+
+**Second tier (specialty journals):**
+
+- JACC: Cardiovascular Imaging — for cardiac imaging AI
+- Radiology / Eur Radiol — for general imaging AI
+- IEEE TMI — for methodological reviews with clinical context
+
+**Methodological tier:**
+
+- Medical Image Analysis — for purely methodological reviews
+- IEEE JBHI — for AI-in-healthcare methods
+
+### Acquiring the PDFs
+
+Most flagship reviews are accessible via:
+
+- The user's Zotero library (check first — they likely already have them)
+- PubMed Central (for open-access)
+- The journal's website (subscription / institutional access)
+- arXiv preprint version (sometimes available)
+
+---
+
+## Action 2: Read carefully — not skim
+
+Spend 60-90 minutes per exemplar. Read the full text, including Boxes, Figure captions, and Table footnotes.
+
+Pay attention to:
+
+### Heading structure
+
+- How many levels deep? (Almost always 2 for top tier.)
+- Are headings numbered or unnumbered? (Almost always unnumbered for top tier.)
+- How long are H2 sections? (Typically 800-1500 words.)
+- How long are H3 sections? (Typically 300-800 words.)
+- How are deeper subsections handled? (Bold lead-in `**Topic.**`, not H4.)
+
+### Paragraph rhythm
+
+- How does a paragraph open? (Topic claim — almost never "In recent years," or "It is worth noting.")
+- How does evidence flow? (1-3 sentences of specifics with citations, not loose generalities.)
+- How does a paragraph close? (Either with a transition or with a verdict — not with hedging.)
+- How many sentences per paragraph? (Usually 4-7.)
+
+### Citation density
+
+- Count references per paragraph in 5 random paragraphs.
+- Top tier: usually 1.5-2.5 refs per paragraph.
+- Lower density suggests overclaiming; higher suggests stacking refs uncritically.
+
+### Equation handling
+
+- Are display equations in body or Boxes?
+- If in body, is there a Box at all?
+- How are metric definitions handled — formula or prose?
+
+### Vendor handling
+
+- Search for any commercial product name. Does it appear in body text or only in Tables?
+- How are FDA / regulatory facts cited?
+
+### Authorial voice
+
+- Find the 3-5 strongest claims in the review. How are they phrased?
+- Does the author take positions like "X is currently the best approach for Y" or stay neutral throughout?
+- Where does hedging appear? (Usually only when evidence genuinely supports caution.)
+
+### Boxes and Figures
+
+- How many Boxes? (1-3 typical.)
+- What goes in a Box? (Definitions, key trials, controversies.)
+- How many Figures? (3-5 typical.)
+- What kinds of Figures? (Overview / taxonomy / workflow / data-driven plot.)
+
+### Tables
+
+- How many Tables? (2-4 typical — rarely 5+.)
+- What goes in a Table? (Datasets, methods comparison, commercial products.)
+- How dense? (10-20 rows is common; 30+ is unusual.)
+
+### Key Points box
+
+- Is there one? (Yes for most top tier.)
+- How many bullets? (4-5 typical.)
+- How long is each bullet? (1-3 sentences.)
+
+---
+
+## Action 3: Write `PARADIGM.md` in the project root
+
+Use this template:
+
+```markdown
+# Paradigm Spec for [Project Name]
+
+## Target journal: [name and tier]
+
+## Exemplars studied
+1. [Author Year]. [Title]. [Journal]. [PMID/DOI]. (PDF: <path>)
+2. [Author Year]. [Title]. [Journal]. [PMID/DOI]. (PDF: <path>)
+
+## Extracted style spec
+
+### Heading structure
+- Max depth: [N] levels
+- Numbering: [yes / no]
+- Typical H2 length: [N-N] words
+- Deeper subsections: [H4 / bold lead-in / other]
+
+### Paragraph rhythm
+- Opening: [observed pattern, e.g., "Topic claim sentence, no temporal preamble"]
+- Body: [observed pattern, e.g., "2-4 sentences of specifics with citations"]
+- Closing: [observed pattern, e.g., "Transition or verdict"]
+- Typical length: [N-N] sentences
+
+### Citation density
+- Average refs per paragraph: [N]
+- Multi-citation cap (max refs in one bracket): [N]
+
+### Equations
+- Location: [body / Box / both / none]
+- Display style: [LaTeX / inline / prose]
+
+### Vendor handling
+- Body: [allowed / disallowed]
+- Table: [yes / no]
+- Total Tables containing vendor names: [N]
+
+### Authorial voice
+- Hedging frequency: [observed examples]
+- Strong claims: [N observed across 3 reviews]
+- Verdict closers per section: [observed pattern]
+
+### Boxes and Figures
+- Box count: [N]
+- Box purposes: [list]
+- Figure count: [N]
+- Figure types: [list]
+
+### Tables
+- Count: [N]
+- Density: [N-N rows]
+
+### Key Points
+- Present: [yes / no]
+- Bullet count: [N]
+- Bullet length: [N-N sentences]
+
+## Manuscript style targets (binding for Phase 4 writing)
+
+Phase 4 writing should conform to this spec. Specifically:
+- Max heading depth: ...
+- No numbered headings.
+- Box 1 for metrics / formulas.
+- Vendor names only in Table N.
+- ≥ 3 verdict sentences across the manuscript.
+- Citation density 1.5-2.5 refs/paragraph.
+- Key Points: 4-5 bullets after title.
+
+## Anti-patterns observed in v2 drafting (to specifically avoid)
+
+(Copy / adapt from this skill's HALLUCINATION_PATTERNS.md to the extent the patterns are domain-relevant.)
+```
+
+---
+
+## Action 4: Re-read PARADIGM.md before each Phase 4 writing session
+
+Phase 4 is multi-day. Drift is the main risk. At the start of each writing session, re-read `PARADIGM.md` to re-anchor.
+
+---
+
+## Time budget
+
+- Exemplar selection: 30 min
+- Reading 2 exemplars: 2-3 hours
+- Writing the spec: 30-45 min
+
+Total: 3-4 hours.
+
+This is the highest-ROI 3-4 hours in the entire project. Skipping it almost guarantees survey-paper-register drift, which is then extremely expensive to fix in revision.

package/dist/skills/medical-imaging-review/references/QUALITY_CHECKLIST.md

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+# Quality Checklist for Medical Imaging AI Reviews
+
+This checklist runs at multiple checkpoints — end of each section, end of each writing day, before peer-review phase, before submission.
+
+**v3 changes from v2:** Dropped "hedging language used", "80-120 references", and format-only metric checks. Replaced with substance checks (citation integrity, conclusion direction, verdict presence, structural discipline).
+
+---
+
+## Citation Integrity (Hard Gate)
+
+These are non-negotiable. Any failure must be fixed before continuing.
+
+- [ ] No placeholder DOIs (grep `xxx`, `[TBD]`, `x):xxx`)
+- [ ] Every reference's first and last author verified against first-source
+- [ ] Body↔bibliography `[N]` reconciliation — spot-check 10 random citations per section
+- [ ] Every directional claim (higher/lower, increased/decreased) verified against source
+- [ ] No vendor white papers cited as if peer-reviewed
+- [ ] No duplicate references (same paper listed under two numbers)
+
+See [CITATION_INTEGRITY.md](CITATION_INTEGRITY.md) for the full 5-rule protocol.
+
+---
+
+## Structural Discipline
+
+- [ ] Heading depth ≤ 2 levels (H2 + H3 only in body)
+- [ ] No numbered headings (no `## 1.`, `### 1.1`)
+- [ ] H4 (`####`) absent from body — deeper grouping via bold lead-in `**Topic.**`
+- [ ] §Methods uses 3-axis grouping (Architectural / Inductive / Data regime), not flat 10-subsection list
+- [ ] Verdict sentences present in 3-5 places (not on every paragraph, not absent entirely)
+- [ ] Key Points box has 4-5 bullets, 1-3 sentences each
+- [ ] Standard sections present: Introduction / Methods / Applications / Translation / Discussion (names may vary, structure fixed)
+
+---
+
+## Voice and Register
+
+- [ ] No "has shown promising results" / "may suggest" / "interestingly" / "in recent years," / "it is worth noting" anywhere
+- [ ] Hedging used only when evidence genuinely supports caution, not as default register
+- [ ] Strong findings (≥2 independent groups confirming) stated strongly
+- [ ] Each major method axis (3 axes in §Methods) closes with a verdict sentence
+- [ ] No "neutral catalogue" stretches longer than 3 paragraphs without a verdict / position
+
+---
+
+## Equations and Boxes
+
+- [ ] Display equations (`$$...$$`) appear only in Boxes, not in body paragraphs
+- [ ] Textbook formulas (DSC, IoU, FedAvg) handled in prose if not in Box 1, not displayed inline
+- [ ] Box 1 (metrics) present and complete
+- [ ] Total Box count appropriate for target journal (typically 1-3)
+
+---
+
+## Vendor Names
+
+- [ ] No vendor name (HeartFlow, Cleerly, Caristo, Keya, Shukun, etc.) appears in body paragraph
+- [ ] All vendor names appear in Table 3 (Commercial Products) only
+- [ ] Body uses category descriptors with table cross-reference
+
+```bash
+# Quick check
+for name in HeartFlow Cleerly Caristo "Keya Medical" "Shukun Technology"; do
+  grep -n "$name" manuscript_draft.md | grep -v "| $name |"
+done
+# Expected: 0 hits per name
+```
+
+---
+
+## Tables
+
+- [ ] Table 1: Public datasets (year, cases, annotation type, access)
+- [ ] Table 2: Method comparison (modality / family / dataset / metric — pick 12-20 papers)
+- [ ] Table 3: Commercial products with regulatory evidence
+- [ ] Total tables ≤ 4 (typical flagship reviews stay at 2-3)
+- [ ] Each table has a title, body, and footnote explaining abbreviations / caveats
+
+---
+
+## Figures
+
+- [ ] Figure 1: Review overview / taxonomy
+- [ ] Figure 2: Representative architectures or method evolution
+- [ ] Figure 3: Clinical workflow or downstream applications
+- [ ] (Optional) Figure 4: Data-driven plot (e.g., performance landscape, trial effect sizes)
+- [ ] All figures have ≤ 100-word captions following Nature style: bold lead-in title sentence + body sentences
+- [ ] No `[Figure placeholder]` strings before submission
+
+---
+
+## Content Coverage
+
+- [ ] All major method axes covered (Architectural / Inductive / Data regime)
+- [ ] Negative trials included where they exist (LLM bias: only positive)
+- [ ] Inter-vendor reproducibility / cross-site validation discussed where relevant
+- [ ] Demographic bias / fairness considerations addressed where relevant
+- [ ] Controversies and unresolved questions engaged, not glossed
+- [ ] Future directions specific and actionable (not "more research is needed" platitudes)
+
+---
+
+## Self-check Commands
+
+```bash
+# Numbered headings
+grep -cE "^#{2,4} [0-9]" manuscript_draft.md
+# Expected: 0
+
+# Heading depth violation
+grep -c "^#### " manuscript_draft.md
+# Expected: 0
+
+# Placeholder DOIs
+grep -c "xxx\|x):xxx\|\[TBD\]" manuscript_draft.md
+# Expected: 0
+
+# LLM tell phrases
+for tell in "has shown promising" "may suggest" "interestingly," "in recent years," "it is worth noting"; do
+  echo "=== $tell ==="
+  grep -nF "$tell" manuscript_draft.md
+done
+# Expected: 0 per tell
+
+# Vendor names in body
+for vendor in HeartFlow Cleerly Caristo; do
+  count=$(grep -c "$vendor" manuscript_draft.md)
+  in_table=$(grep "| $vendor " manuscript_draft.md | wc -l)
+  echo "$vendor: total $count, in table $in_table, in body $((count - in_table))"
+done
+# Expected: in body == 0 for each
+
+# Inline equations
+grep -n '\$\$' manuscript_draft.md
+# All hits should be inside Box context (check 2 lines before)
+
+# Verdict-sentence presence
+grep -nE "currently the most|has yet to demonstrate|best understood as|next [0-9]+ years will" manuscript_draft.md
+# Expected: ≥ 3 hits
+
+# Citation count (no quantity target — but useful for sanity)
+grep -cE "^[0-9]+\." manuscript_draft.md
+# Use as input for body↔bib reconciliation
+```
+
+---
+
+## What's NOT on this checklist (intentional removals from v2)
+
+- ❌ "Hedging language used" — was actively harmful; hedging-by-default is the LLM tell, not the flagship-review voice
+- ❌ "80-120 references" — was driving Claude to pad the bibliography, which encouraged fabrication
+- ❌ "Performance metrics consistent (Dice: 0.XXX format)" — checking format ≠ checking correctness
+- ❌ "All major methods covered" — was driving exhaustive enumeration over selective synthesis
+- ❌ "Recent literature included (>50% from last 3 years)" — date-based filter has no relationship to quality
+
+These were structural illusions of quality. They've been replaced with substantive checks above.
+
+---
+
+## Severity Levels for Failures
+
+When a checklist item fails during writing:
+
+| Severity | Examples | Action |
+|---|---|---|
+| **CRITICAL** | Placeholder DOI, wrong-author list on real paper, citation direction flipped | **STOP and fix immediately**. These are reviewer-facing trust-killers. |
+| **HIGH** | Body↔bib drift, vendor name in body, verdict absent in axis section | Fix before completing the current section. |
+| **MEDIUM** | Heading numbered, equation inline | Fix at section end. |
+| **LOW** | Multi-citation bracket > 4 refs, table > 20 rows | Note and address during peer-review phase. |