385 lines
12 KiB
Markdown
385 lines
12 KiB
Markdown
---
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name: research-medical
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description: Use when researching medical/scientific topics and encountering paywalled journals, access failures, or needing primary sources - provides strategies for PubMed Central, DOI resolution, preprint servers, and fallback approaches for medical literature access
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---
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# Medical Research Access
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Strategies for accessing medical and scientific literature when direct web access fails or sources are paywalled.
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## When to Use This Skill
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**Use when:**
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- Webfetch fails on medical journal sites (NIH, Nature, JAMA, NEJM, etc.)
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- Research requires primary sources (studies, trials, systematic reviews)
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- Need to access paywalled medical literature
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- Looking for recent research not yet peer-reviewed
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- Extracting citations when full text unavailable
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**When NOT to use:**
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- General web research (use standard webfetch)
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- Medical journalism is sufficient (STAT News, MedPage Today)
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- Topic well-covered in open-access sources
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## Quick Reference: Access Strategies
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| Source Type | Primary Method | Fallback | Notes |
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|-------------|---------------|----------|-------|
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| Peer-reviewed studies | PubMed Central | DOI resolution, preprints | Always check PMC first |
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| Recent research | Preprint servers | Author websites | May not be peer-reviewed yet |
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| Clinical trials | ClinicalTrials.gov | Trial registries | Protocol vs results |
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| Meta-analyses | Cochrane Library | PubMed search | Often open access |
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| Medical journalism | STAT News, Medscape | Press releases | Secondary sources |
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| Guidelines | Professional societies | NIH, CDC | Usually open access |
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## Access Strategies
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### 1. PubMed Central (PMC) - First Stop
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**Why PMC:** Free full-text archive of biomedical literature, subset of PubMed with actual paper content.
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**Search approaches:**
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```markdown
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# Direct PMC search
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https://www.ncbi.nlm.nih.gov/pmc/?term=ivermectin+COVID-19+randomized+controlled+trial
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# Filters to add:
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- Free full text
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- Article type (Clinical Trial, Meta-Analysis, Systematic Review)
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- Publication date range
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```
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**When webfetch fails on PMC:**
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- Try PubMed instead (has abstracts even without full text)
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- Search by PMID if you have it: `https://pubmed.ncbi.nlm.nih.gov/[PMID]/`
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- Look for "Free PMC article" badge in PubMed results
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### 2. DOI Resolution Services
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**What is DOI:** Digital Object Identifier - permanent link to research papers.
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**Primary resolver:**
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```markdown
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https://doi.org/[DOI-HERE]
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Example: https://doi.org/10.1056/NEJMoa2115869
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```
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**When DOI resolution hits paywall:**
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- Try adding DOI to Google Scholar: `https://scholar.google.com/scholar?q=[DOI]`
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- Check for "All versions" link in Scholar (may include preprint or author PDF)
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- Look for institutional repository versions
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**Extracting DOI from citations:**
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- Usually in format: `10.XXXX/journal.year.number`
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- Found at end of citation or in URL
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- Can search PubMed by DOI to get PMID
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### 3. Preprint Servers - Recent Research
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**Primary servers:**
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| Server | Focus | URL Pattern |
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|--------|-------|-------------|
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| medRxiv | Medicine | `https://www.medrxiv.org/content/[ID]` |
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| bioRxiv | Biology | `https://www.biorxiv.org/content/[ID]` |
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| SSRN | Social science, econ | `https://papers.ssrn.com/sol3/papers.cfm?abstract_id=[ID]` |
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**Important notes:**
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- Preprints are NOT peer-reviewed
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- Always note preprint status in citations
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- Check if preprint later published in journal (search by title)
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- Good for very recent research (last 6-12 months)
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**Search strategy:**
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```markdown
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# Search medRxiv directly
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https://www.medrxiv.org/search/ivermectin%20COVID-19
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# Or use Google Scholar with "preprint" filter
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site:medrxiv.org OR site:biorxiv.org [search terms]
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```
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### 4. Medical Journalism Without Paywalls
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**Freely accessible sources:**
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- **STAT News** (`statnews.com`) - High-quality medical journalism, no paywall
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- **Medscape** (`medscape.com`) - Free with registration, clinical news
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- **The Conversation** (`theconversation.com`) - Academic experts, open access
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- **Science Daily** (`sciencedaily.com`) - Press releases and summaries
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- **NIH News** (`nih.gov/news-events`) - Government research announcements
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**When to use journalism vs primary sources:**
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- Journalism: Background, context, expert opinions, controversy overview
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- Primary sources: Specific claims, data, methodology, for fact-checking
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**Citation approach:**
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- Use journalism to identify key studies
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- Track down primary sources for verification
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- Cite primary source when making factual claims
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- Cite journalism when discussing expert opinions or controversy
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### 5. Clinical Trial Registries
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**ClinicalTrials.gov** - Official US registry:
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```markdown
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https://clinicaltrials.gov/search?term=[drug/intervention]
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Filter by:
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- Study Status (Completed, Published)
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- Study Type (Interventional)
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- Study Results (Studies with Results)
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```
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**What you get:**
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- Trial protocol and design
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- Primary/secondary outcomes
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- Results summary (if published)
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- Links to published papers
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**Other registries:**
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- WHO ICTRP (international): `https://trialsearch.who.int/`
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- EU Clinical Trials Register: `https://www.clinicaltrialsregister.eu/`
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### 6. Professional Society Guidelines
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**Often open access:**
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- CDC guidelines: `cdc.gov`
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- WHO guidelines: `who.int`
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- NIH treatment guidelines: `covid19treatmentguidelines.nih.gov`
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- Professional societies (AMA, ACP, IDSA) - check guidelines sections
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**Good for:**
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- Official recommendations
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- Evidence summaries
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- Standard of care
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- Consensus positions
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### 7. Google Scholar Strategies
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**When direct access fails:**
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```markdown
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# Search with specific terms
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"ivermectin" "COVID-19" "randomized controlled trial"
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# Use "All versions" link to find:
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- Preprint versions
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- Author PDFs
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- Institutional repository copies
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# Filter by date range for recent research
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```
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**Citation extraction when full text unavailable:**
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- Scholar provides formatted citations
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- Shows "Cited by" count (impact indicator)
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- Links to related articles
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- May show abstract even without full text
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### 8. Author Websites and ResearchGate
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**When other methods fail:**
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- Search author name + paper title
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- Check university faculty pages (often have PDFs)
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- ResearchGate (`researchgate.net`) - researchers share papers
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- Academia.edu - similar to ResearchGate
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**Caution:**
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- Verify version matches published paper
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- Note if it's a preprint or draft
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- Check publication date
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## Webfetch vs Direct Access Decision Tree
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**Use webfetch when:**
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- Source is known to be open access
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- Medical journalism sites (STAT, Medscape)
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- Government sites (NIH, CDC, FDA)
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- Preprint servers
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- Professional society guidelines
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**Skip webfetch, use search strategies when:**
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- Major journal sites (Nature, JAMA, NEJM, Lancet) - usually paywalled
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- You have DOI - use DOI resolver or Scholar
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- Need recent research - go to preprint servers
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- Previous webfetch attempts failed on similar sources
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**General agent with web search when:**
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- Exploratory research (don't know specific sources yet)
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- Need to identify key studies first
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- Looking for expert commentary or summaries
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- Building initial source list
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## Citation Extraction Techniques
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### When Full Text Unavailable
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**From abstracts (PubMed):**
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- Study design and methods
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- Primary outcomes
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- Sample size
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- Key findings (usually in abstract)
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- Limitations (sometimes mentioned)
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**From press releases:**
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- High-level findings
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- Author quotes
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- Institution and funding
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- Link to actual paper (follow this)
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**From systematic reviews/meta-analyses:**
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- Summary of multiple studies
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- Effect sizes across studies
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- Quality assessments
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- Usually cite all included studies (mine these)
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### Citation Format Best Practices
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**Minimum required:**
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```markdown
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Author(s). Title. Journal Year;Volume(Issue):Pages. DOI: [DOI]
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```
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**Enhanced format:**
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```markdown
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Author(s). Title. Journal Year;Volume(Issue):Pages. DOI: [DOI]. PMID: [PMID]. [Access status]
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Example:
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Lopez-Medina E, et al. Effect of Ivermectin on Time to Resolution of Symptoms Among Adults With Mild COVID-19. JAMA 2021;325(14):1426-1435. DOI: 10.1001/jama.2021.3071. PMID: 33662102. [Free full text via PMC]
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```
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**Always include:**
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- DOI (for verification and access)
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- PMID if available (PubMed tracking)
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- Access status (open access, PMC free, paywalled)
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- Preprint status if applicable
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## Common Mistakes
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### ❌ Giving up after first webfetch failure
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**Problem:** Many medical sites block automated access or require authentication.
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**Fix:** Use systematic fallback strategy:
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1. Try PubMed Central search
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2. Use DOI resolver if you have DOI
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3. Check preprint servers
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4. Search Google Scholar for alternative versions
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5. Use medical journalism to identify sources, then track down primary
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### ❌ Citing journalism when primary source is accessible
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**Problem:** Secondary source citation when primary is available weakens credibility.
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**Fix:**
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- Use journalism to find studies
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- Always attempt to access primary source
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- Cite primary source for factual claims
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- Cite journalism only for expert opinions or controversy framing
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### ❌ Not noting preprint vs peer-reviewed status
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**Problem:** Preprints lack peer review and may contain errors or later be contradicted.
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**Fix:**
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- Always check publication status
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- Note in citation: "[Preprint, not peer-reviewed]"
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- Search by title to see if later published in journal
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- Weight peer-reviewed sources more heavily
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### ❌ Ignoring "Cited by" counts and publication dates
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**Problem:** May miss that study was retracted, contradicted, or superseded.
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**Fix:**
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- Check "Cited by" in Google Scholar
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- Look for retractions or corrections
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- Check for more recent systematic reviews
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- Note if study is outlier vs consensus
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### ❌ Using only abstracts for detailed claims
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**Problem:** Abstracts omit important limitations, methods details, and context.
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**Fix:**
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- Use abstract for high-level findings only
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- For specific claims, need full text
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- If full text unavailable, note limitation: "[Based on abstract only]"
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- Look for systematic reviews that analyzed full text
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### ❌ Not tracking access failures for optimization
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**Problem:** Repeated failures on same source types waste time.
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**Fix:**
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- Note which sources consistently fail webfetch
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- Build project-specific access strategy
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- Document successful access patterns
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- Update AGENTS.md with project-specific guidance
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## Real-World Impact
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**Session context:** Pierre Kory/ivermectin research encountered 4 failed web access attempts (NIH, FDA, Nature, JAMA, MedPage Today), limiting source diversity to 2 primary sources.
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**With this skill:**
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- PubMed Central search would provide free full-text access to key trials
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- DOI resolution would access Nature and JAMA papers via alternative routes
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- Preprint servers would surface early ivermectin research
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- Medical journalism (STAT News) would provide controversy context without paywall
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- Clinical trial registries would provide TOGETHER trial and other RCT data
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**Expected improvement:** 5-8 accessible sources instead of 2, with mix of primary sources and expert commentary.
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## Workflow Integration
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### Research Session Startup
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1. **Identify topic and key terms**
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2. **Start with PubMed Central search** (free full text)
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3. **Check for systematic reviews** (summarize evidence)
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4. **Search preprint servers** (recent research)
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5. **Use medical journalism** (context and expert opinions)
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6. **Track citations** (DOI, PMID, access status)
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### When Webfetch Fails
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1. **Don't retry same URL** - move to fallback strategy
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2. **Extract DOI from citation** - use DOI resolver
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3. **Search PubMed by title** - may find PMC version
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4. **Check Google Scholar** - look for "All versions"
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5. **Note failure** - document for future optimization
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### Citation Verification
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1. **Have DOI or PMID** - verify via PubMed lookup
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2. **Check publication status** - preprint vs peer-reviewed
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3. **Look for retractions** - search "[title] retraction"
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4. **Note access method** - for reproducibility
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5. **Capture full citation** - author, title, journal, DOI, PMID
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## Additional Resources
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**PubMed search tips:**
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- Use MeSH terms (Medical Subject Headings) for precise searches
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- Combine with Boolean operators (AND, OR, NOT)
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- Use filters: Free full text, Article type, Publication date
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- Save searches for repeated use
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**Understanding study types:**
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- RCT (Randomized Controlled Trial) - gold standard
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- Systematic Review/Meta-Analysis - synthesis of multiple studies
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- Cohort Study - observational, follows groups over time
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- Case-Control Study - compares cases to controls
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- Case Series/Report - descriptive, lowest evidence level
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**Red flags in research:**
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- Preprint only (not peer-reviewed)
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- Retracted or corrected
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- Conflicts of interest not disclosed
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- Small sample size with strong claims
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- Outlier findings not replicated
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