Enhance citation management and literature review guidelines

- Updated SKILL.md in citation management to include best practices for identifying seminal and high-impact papers, emphasizing citation count thresholds, venue quality tiers, and author reputation indicators. - Expanded literature review SKILL.md to prioritize high-impact papers, detailing citation metrics, journal tiers, and author reputation assessment. - Added comprehensive evaluation strategies for paper impact and quality in literature_search_strategies.md, including citation count significance and journal impact factor guidance. - Improved research lookup scripts to prioritize results based on citation count, venue prestige, and author reputation, enhancing the quality of research outputs.
2026-03-27 07:09:27 +08:00 · 2026-01-05 13:01:10 -08:00
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+# Medical Journal Writing Style Guide
+
+Comprehensive writing guide for NEJM, Lancet, JAMA, BMJ, Annals of Internal Medicine, and other major medical journals.
+
+**Last Updated**: 2024
+
+---
+
+## Overview
+
+Medical journals prioritize **clinical relevance**, **patient outcomes**, and **evidence-based practice**. Writing must be precise, evidence-focused, and directly applicable to clinical decision-making.
+
+### Key Philosophy
+
+> "Every sentence should help a clinician make better decisions for their patients."
+
+**Primary Goal**: Communicate research findings that can improve patient care and clinical practice.
+
+---
+
+## Audience and Tone
+
+### Target Reader
+
+- Practicing physicians and clinicians
+- Clinical researchers
+- Healthcare policymakers
+- Medical educators
+- Some public health and patient advocacy readers
+
+### Tone Characteristics
+
+| Characteristic | Description |
+|---------------|-------------|
+| **Evidence-focused** | Appropriate hedging based on study design |
+| **Patient-centered** | Focus on patient outcomes, not just biomarkers |
+| **Clinical** | Emphasize practical applicability |
+| **Precise** | Exact numbers, confidence intervals, NNT |
+| **Measured** | Claims match evidence strength |
+
+### Voice
+
+- **Passive voice common**: "Patients were randomized to..."
+- **First person acceptable**: "We conducted a trial..."
+- **Third person for patients**: "Patients" not "subjects"
+
+---
+
+## Abstract: Structured Format
+
+### Overview
+
+Most major medical journals require **structured abstracts** with labeled sections. This is one of the few venues where structured abstracts are expected.
+
+### Standard Structure (IMRAD-based)
+
+```
+Background: [Why this study was needed - 1-2 sentences]
+
+Methods: [Study design, setting, participants, intervention, 
+main outcomes - 2-4 sentences]
+
+Results: [Primary and key secondary outcomes with statistics - 
+3-5 sentences]
+
+Conclusions: [Clinical implications, with appropriate hedging - 
+1-2 sentences]
+```
+
+### Word Limits by Journal
+
+| Journal | Abstract Limit |
+|---------|---------------|
+| NEJM | 250 words |
+| Lancet | 300 words |
+| JAMA | 350 words |
+| BMJ | 300 words |
+| Annals | 325 words |
+
+### Example Structured Abstract (NEJM Style)
+
+```
+BACKGROUND
+Type 2 diabetes is associated with increased cardiovascular risk, but 
+the effects of intensive glucose control on cardiovascular outcomes 
+remain uncertain.
+
+METHODS
+We randomly assigned 10,251 patients with type 2 diabetes and established 
+cardiovascular disease to receive intensive glucose-lowering therapy 
+(target HbA1c <6.0%) or standard therapy (target HbA1c 7.0-7.9%). The 
+primary outcome was a composite of nonfatal myocardial infarction, 
+nonfatal stroke, or death from cardiovascular causes.
+
+RESULTS
+After a median follow-up of 3.5 years, the primary outcome occurred in 
+352 patients (6.9%) in the intensive-therapy group and in 371 patients 
+(7.2%) in the standard-therapy group (hazard ratio, 0.90; 95% CI, 0.78 
+to 1.04; P=0.16). Severe hypoglycemia was more common with intensive 
+therapy (3.1% vs. 1.0%; P<0.001). All-cause mortality was similar 
+between groups (5.0% vs. 4.8%; hazard ratio, 1.04; 95% CI, 0.87 to 1.24).
+
+CONCLUSIONS
+In patients with type 2 diabetes and established cardiovascular disease, 
+intensive glucose lowering did not significantly reduce major 
+cardiovascular events compared with standard therapy and was associated 
+with increased severe hypoglycemia.
+```
+
+---
+
+## Evidence Language
+
+### The Cardinal Rule
+
+**Match your language to your evidence strength.**
+
+### Language by Study Design
+
+| Study Design | Appropriate Language |
+|-------------|---------------------|
+| **Meta-analysis of RCTs** | "Treatment X reduces mortality..." |
+| **Large RCT** | "Treatment X reduced mortality in this trial..." |
+| **Small RCT** | "Treatment X was associated with reduced mortality..." |
+| **Cohort study** | "Treatment X was associated with lower mortality..." |
+| **Case-control** | "Treatment X was associated with reduced odds of death..." |
+| **Cross-sectional** | "Treatment X use was associated with lower mortality..." |
+| **Case series** | "These cases suggest that treatment X may..." |
+| **Case report** | "This case illustrates that treatment X can..." |
+
+### Causal Language Rules
+
+❌ **Never say** (unless RCT): "Treatment X prevents..." / "Treatment X causes..."
+
+✅ **Use for observational**: "Treatment X was associated with..." / "Treatment X was linked to..."
+
+✅ **Use for RCTs**: "Treatment X resulted in..." / "Treatment X reduced..."
+
+### Hedging Phrases
+
+| Certainty Level | Phrases |
+|----------------|---------|
+| **High** | "demonstrates," "shows," "confirms" |
+| **Moderate** | "suggests," "indicates," "supports" |
+| **Low** | "may," "might," "could potentially" |
+| **Speculative** | "it is possible that," "one interpretation is" |
+
+---
+
+## Reporting Numbers
+
+### Absolute vs. Relative Risk
+
+**Always report both absolute and relative measures.**
+
+❌ **Incomplete**: "Treatment reduced mortality by 50%"
+
+✅ **Complete**: "Treatment reduced relative mortality by 50% (absolute risk reduction, 2.5 percentage points; number needed to treat, 40)"
+
+### Confidence Intervals
+
+**Always include 95% confidence intervals.**
+
+❌ "The hazard ratio was 0.75"
+
+✅ "The hazard ratio was 0.75 (95% CI, 0.62 to 0.91)"
+
+### P-values
+
+- Report exact P-values when possible: P=0.003
+- Use P<0.001 for very small values
+- Consider clinical significance alongside statistical significance
+
+### Number Needed to Treat (NNT)
+
+Include NNT for clinically important outcomes:
+
+```
+"The intervention prevented one additional death for every 40 patients 
+treated (NNT=40; 95% CI, 28 to 67)."
+```
+
+---
+
+## Introduction
+
+### Length and Structure
+
+- **3-4 paragraphs** (500-700 words)
+- Focus on clinical problem and rationale
+
+### Paragraph Structure
+
+**Paragraph 1: Clinical Problem**
+- Burden of disease (incidence, prevalence, mortality)
+- Impact on patients and healthcare system
+- Why this matters clinically
+
+```
+"Type 2 diabetes affects more than 450 million adults worldwide and is 
+a leading cause of cardiovascular disease, renal failure, and premature 
+death. Despite advances in glucose-lowering therapies, patients with 
+diabetes continue to face a two- to four-fold increased risk of 
+cardiovascular events compared with the general population."
+```
+
+**Paragraph 2: Current Knowledge and Limitations**
+- What treatments/approaches exist
+- What evidence gaps remain
+- Why more research was needed
+
+**Paragraph 3: Rationale and Objectives**
+- Why this study was conducted
+- Clear statement of objectives/hypothesis
+- Primary outcome stated
+
+```
+"We therefore conducted a randomized, controlled trial to evaluate 
+whether intensive glucose-lowering therapy, compared with standard 
+therapy, would reduce major cardiovascular events in patients with 
+type 2 diabetes and established cardiovascular disease."
+```
+
+---
+
+## Methods
+
+### Structure (CONSORT/STROBE Aligned)
+
+Medical methods sections follow reporting guidelines:
+
+```
+METHODS
+├── Study Design
+├── Setting and Participants
+│   ├── Eligibility Criteria
+│   └── Recruitment
+├── Randomization and Blinding (for RCTs)
+├── Interventions
+├── Outcomes
+│   ├── Primary Outcome
+│   └── Secondary Outcomes
+├── Sample Size Calculation
+├── Statistical Analysis
+├── Ethics Approval
+└── Registration
+```
+
+### Key Elements
+
+**Eligibility Criteria**
+- List inclusion and exclusion criteria explicitly
+- Be specific (age ranges, disease definitions, lab values)
+
+**Primary Outcome**
+- Define precisely, including timing of assessment
+- State how it was measured
+
+**Statistical Analysis**
+- Pre-specified analysis plan
+- Handling of missing data
+- Subgroup analyses (pre-specified vs. exploratory)
+
+### Example Methods Paragraph
+
+```
+We enrolled adults aged 40 years or older with type 2 diabetes (defined 
+as HbA1c ≥6.5% or use of glucose-lowering medication) and established 
+cardiovascular disease (previous myocardial infarction, stroke, or 
+revascularization procedure). Patients were excluded if they had an 
+HbA1c level below 7.5% or above 11.0%, estimated glomerular filtration 
+rate below 30 ml per minute per 1.73 m² of body-surface area, or a 
+cardiovascular event within the past 30 days.
+```
+
+---
+
+## Results
+
+### Structure
+
+**Opening: Participant Flow**
+- Screening, enrollment, randomization, follow-up, analysis
+- Reference CONSORT flow diagram
+
+**Baseline Characteristics**
+- Table 1: Baseline demographics and clinical characteristics
+- Note any imbalances
+
+**Primary Outcome**
+- Report first and prominently
+- Include point estimate, CI, P-value
+- State clinical significance
+
+**Secondary Outcomes**
+- Report all pre-specified secondary outcomes
+- Be cautious about multiple comparisons
+
+**Adverse Events**
+- Report serious adverse events systematically
+- Include deaths, hospitalizations, SAEs by category
+
+### Example Results Paragraph
+
+```
+Of 12,537 patients assessed for eligibility, 10,251 underwent 
+randomization: 5,128 were assigned to intensive therapy and 5,123 to 
+standard therapy (Figure 1). Baseline characteristics were similar 
+between groups (Table 1). Median follow-up was 3.5 years (interquartile 
+range, 2.8 to 4.2), with vital status available for 99.2% of patients.
+
+The primary outcome occurred in 352 patients (6.9%) in the intensive-
+therapy group and 371 patients (7.2%) in the standard-therapy group 
+(hazard ratio, 0.90; 95% confidence interval [CI], 0.78 to 1.04; 
+P=0.16). The absolute difference was 0.3 percentage points (95% CI, 
+-0.7 to 1.4). Results were consistent across pre-specified subgroups 
+(Figure 3).
+```
+
+---
+
+## Discussion
+
+### Structure
+
+**Paragraph 1: Summary of Main Findings**
+- Restate primary outcome result
+- State whether hypothesis was supported
+
+**Paragraphs 2-3: Interpretation and Context**
+- How do findings compare with prior evidence?
+- What mechanisms might explain findings?
+- Clinical interpretation
+
+**Paragraph 4: Strengths**
+- Study design features
+- Generalizability
+- Completeness of follow-up
+
+**Paragraph 5: Limitations**
+- Be specific and thoughtful
+- Discuss how limitations might affect interpretation
+- Avoid generic statements
+
+**Final Paragraph: Conclusions and Implications**
+- Clinical implications
+- Policy implications
+- Future research needs
+
+### Example Limitations Paragraph
+
+```
+Our study has several limitations. First, despite randomization, we 
+cannot exclude residual confounding from unmeasured factors. Second, 
+the open-label design may have introduced bias in outcome assessment 
+for subjective endpoints, though the primary outcome of death was 
+objective. Third, our findings may not generalize to patients without 
+established cardiovascular disease or to healthcare settings with 
+different resources. Fourth, the 3.5-year follow-up may have been 
+insufficient to detect cardiovascular benefits that emerge over 
+longer periods.
+```
+
+---
+
+## Journal-Specific Requirements
+
+### NEJM (New England Journal of Medicine)
+
+- **Word limit**: 2,700 words (excluding abstract, references)
+- **Abstract**: 250 words, structured
+- **References**: ~40-50 typical
+- **Figures/Tables**: 4-5 combined
+- **Style**: Definitive, authoritative
+- **Emphasis**: Major clinical trials, transformative research
+
+### Lancet
+
+- **Word limit**: 3,500 words for research articles
+- **Abstract**: 300 words, structured
+- **Summary box (Panel)**: Key messages highlighted
+- **Research in Context**: Required section explaining contribution
+- **Style**: Global health perspective valued
+
+### JAMA (Journal of the American Medical Association)
+
+- **Word limit**: 3,000 words for original investigations
+- **Abstract**: 350 words, structured
+- **Key Points box**: Required summary
+- **Visual abstract**: Encouraged
+- **Style**: Policy-relevant, public health focus
+
+### BMJ (British Medical Journal)
+
+- **Word limit**: 3,000 words for research
+- **Abstract**: 300 words, structured
+- **What this paper adds**: Required box
+- **Strengths and limitations box**: Explicit section
+- **Style**: Practical, evidence-based
+
+### Annals of Internal Medicine
+
+- **Word limit**: 3,000 words
+- **Abstract**: 325 words, structured
+- **Style**: Focused on internal medicine practice
+- **Clinical Trials and Meta-analyses**: Specialty
+
+---
+
+## Reporting Guidelines Compliance
+
+### CONSORT (RCTs)
+
+**25-item checklist** including:
+- Trial design, randomization, blinding
+- Participant flow (diagram required)
+- All outcomes with effect sizes and CIs
+- Harms and adverse events
+
+### STROBE (Observational)
+
+**22-item checklist** for:
+- Cohort, case-control, cross-sectional studies
+- Setting, participants, variables, data sources
+- Bias assessment, sensitivity analyses
+
+### PRISMA (Systematic Reviews)
+
+**27-item checklist** including:
+- Search strategy
+- Study selection process (diagram)
+- Risk of bias assessment
+- Synthesis methods
+
+### STARD (Diagnostic Studies)
+
+**30 items** for diagnostic accuracy studies
+
+---
+
+## Tables and Figures
+
+### Table 1: Baseline Characteristics
+
+Standard format:
+```
+                              Intensive Therapy  Standard Therapy
+                                  (N=5128)          (N=5123)
+Age — yr                        63.4 ± 8.7        63.6 ± 8.5
+Male sex — no. (%)              3389 (66.1)       3401 (66.4)
+Body-mass index                 32.1 ± 5.4        32.0 ± 5.3
+HbA1c — %                        8.3 ± 1.1         8.3 ± 1.0
+Duration of diabetes — yr       10.2 ± 7.8        10.1 ± 7.6
+Prior MI — no. (%)              2435 (47.5)       2411 (47.1)
+```
+
+### CONSORT Flow Diagram
+
+Required for RCTs:
+```
+Assessed for eligibility (n=12,537)
+    │
+    ├─► Excluded (n=2,286)
+    │     ├─ Not meeting criteria (n=1,854)
+    │     ├─ Declined to participate (n=389)
+    │     └─ Other reasons (n=43)
+    │
+Randomized (n=10,251)
+    │
+    ├─► Intensive therapy (n=5,128)
+    │     ├─ Lost to follow-up (n=52)
+    │     └─ Analyzed (n=5,076)
+    │
+    └─► Standard therapy (n=5,123)
+          ├─ Lost to follow-up (n=48)
+          └─ Analyzed (n=5,075)
+```
+
+### Kaplan-Meier Curves
+
+Standard presentation:
+- Survival curves with shaded confidence bands
+- Number at risk table below
+- Hazard ratio with 95% CI
+- Log-rank P-value
+
+---
+
+## Common Mistakes in Medical Writing
+
+1. **Overclaiming causation**: Using "caused" for observational data
+2. **Relative risk only**: Not reporting absolute measures
+3. **Missing CIs**: Reporting point estimates without uncertainty
+4. **Vague limitations**: "Our study has limitations" without specifics
+5. **Ignoring negative results**: Selective reporting of outcomes
+6. **Clinical significance confusion**: Statistically significant ≠ clinically meaningful
+7. **Subgroup fishing**: Post-hoc subgroup analyses presented as confirmatory
+8. **Missing CONSORT/STROBE items**: Incomplete reporting
+
+---
+
+## Pre-Submission Checklist
+
+### Required Elements
+- [ ] Structured abstract (journal-specific format)
+- [ ] Trial registration number (for RCTs)
+- [ ] Ethics committee approval statement
+- [ ] Conflict of interest disclosures
+- [ ] CONSORT/STROBE checklist completed
+
+### Statistical Reporting
+- [ ] Primary outcome reported with CI and P-value
+- [ ] Absolute and relative measures included
+- [ ] All pre-specified outcomes reported
+- [ ] NNT calculated for significant clinical outcomes
+
+### Evidence Language
+- [ ] Claims match study design
+- [ ] Appropriate hedging used
+- [ ] Causal language only for RCTs
+
+### Clinical Relevance
+- [ ] Clinical implications stated
+- [ ] Patient-centered outcomes emphasized
+- [ ] Generalizability discussed
+
+---
+
+## See Also
+
+- `venue_writing_styles.md` - Master style overview
+- `journals_formatting.md` - Technical formatting requirements
+- `reviewer_expectations.md` - What medical reviewers seek
+- Reporting guideline resources: consort-statement.org, strobe-statement.org
+