Synthesis

Synthesis

Integrates all accumulated notes and prior drafts to generate the Discussion and Abstract sections, connecting findings to the broader literature.

Prerequisites

Required files:

• scope.md - Research question and key findings
• notes/papers/*.md - Literature notes
• notes/search/*.md - Web search notes
• notes/references/*.md - Reference-chained paper notes
• notes/literature-synthesis.md - Aggregated themes and findings (key input!)
• notes/code-analysis.md - Methods context
• notes/data-analysis.md - Results context
• drafts/introduction.md - For narrative continuity
• drafts/methods.md - For methodological context
• drafts/results.md - Findings to discuss

Workflow

[Load all notes and drafts]
     │
     ▼
[Map findings to literature] ─── What supports/contradicts
     │
     ▼
[Draft Discussion] ─── Interpret, compare, contextualize
     │
     ▼
[Draft Abstract] ─── Structured summary
     │
     ▼
[Output] ─── drafts/discussion.md, drafts/abstract.md

Step 1: Load and Organize Materials

Read Literature Synthesis (Primary Reference)

Start with notes/literature-synthesis.md - this document already contains:

• Source inventory with relationships to our work
• Key themes identified across all papers
• Findings that support our hypothesis
• Contradictory findings to address
• Methodological patterns
• Gaps our study addresses
• Citation map showing foundational papers
• Implications for Discussion section

This synthesis is the primary guide for drafting the Discussion.

Read All Notes

ls notes/papers/*.md notes/search/*.md notes/references/*.md notes/*.md

Use individual paper notes for specific quotes and statistics.

Mapping from Literature Synthesis

The synthesis document provides:

• Which sources support our findings
• Which sources provide contrasting results
• Which sources explain mechanisms
• Which sources address limitations

Extract Key Results

From drafts/results.md and notes/data-analysis.md:

• Primary finding (statistic and interpretation)
• Secondary findings
• Unexpected results
• Null findings (if any)

Review Scope

From scope.md:

• Research question being answered
• Hypothesis (was it supported?)
• Limitations to address

Step 2: Map Findings to Literature

Use notes/literature-synthesis.md as the starting point - it already contains:

• "Findings That Support Our Hypothesis" table
• "Contradictory or Conflicting Findings" table
• "Implications for Discussion" section

Extend this mapping with our actual results from drafts/results.md:

For each finding, the synthesis document identifies:

1. Agreement: Papers with similar findings
2. Disagreement: Papers with different findings (explain why)
3. Mechanism: Papers that explain why this occurs
4. Clinical relevance: Papers that contextualize importance

Step 3: Draft Discussion

Create drafts/discussion.md following this structure:

Discussion Structure (6-7 paragraphs)

# Discussion

## Principal Findings (Paragraph 1)

[Open with main finding - interpret, don't just restate]

This study demonstrates that [interpretation of primary finding]. 
[Connect to research question from scope.md].
[One sentence on significance].

## Comparison with Literature (Paragraphs 2-3)

[Compare findings to existing work]

Our findings are consistent with [Author et al.], who reported [finding] [citation]. 
Similarly, [Author2 et al.] demonstrated [related finding] [citation].

[Address any discrepancies]

In contrast to [Author3 et al.], who found [different result] [citation], our study suggests [explanation]. 
This difference may be attributed to [methodological differences, population differences, etc.].

## Mechanistic Interpretation (Paragraph 4)

[Explain WHY these results might occur]

These findings may reflect [biological/clinical mechanism]. 
[Author et al.] previously showed that [mechanistic evidence] [citation], 
which supports the hypothesis that [explanation].

[If speculative, use appropriate hedging: "may", "might", "could potentially"]

## Clinical/Practical Implications (Paragraph 5)

[What does this mean for practice?]

These results have several implications for [clinical practice / research / etc.].
First, [implication 1].
Second, [implication 2].
[If applicable: These findings suggest that clinicians should consider...]

## Limitations (Paragraph 6)

[Honest but constructive discussion of limitations]

This study has several limitations that should be considered.
First, [limitation 1 with mitigation if possible].
Second, [limitation 2].
[Frame constructively: "While [limitation], [mitigating factor]..."]

Common limitations to address:
- Sample size
- Single-center
- Retrospective design
- Selection bias
- Technical limitations
- Generalizability

## Future Directions (Paragraph 7)

[What should come next?]

Future studies should [specific actionable suggestion].
Prospective validation in [population] is warranted.
Additionally, [another future direction].

---

## Discussion References

[List all citations used in Discussion with note references]

Writing Guidelines

• Present tense: General truths ("MRI enables...")
• Past tense: Specific studies ("Smith et al. found...")
• Hedging: Match to evidence strength
• No new data: All statistics should be in Results

Literature Integration Phrases

Agreement:

• "Consistent with prior work [X], we found..."
• "Our findings support those of [X], who demonstrated..."
• "In line with [X], our results indicate..."

Disagreement:

• "In contrast to [X], our study suggests..."
• "Unlike [X], who reported..., we found..."
• "Our results differ from [X], possibly due to..."

Extension:

• "Our findings extend those of [X] by demonstrating..."
• "Building on work by [X], we show..."
• "While [X] established..., our study further demonstrates..."

Step 4: Draft Abstract

Create drafts/abstract.md:

# Abstract

## Background/Purpose
[2-3 sentences: Gap in knowledge + study objective]

[Clinical/scientific problem]. [What is unknown]. The purpose of this study was to [objective].

## Methods
[3-4 sentences: Design, population, key methods, statistics]

This [study design] included [n] patients from [setting]. [Key methods]. [Primary outcome measure]. [Statistical approach].

## Results  
[3-4 sentences: Key findings with numbers]

[Primary finding with statistics]. [Secondary finding]. [Additional notable result].

## Conclusion
[1-2 sentences: Main takeaway + implication]

[Main conclusion]. [Clinical/research implication].

---

**Word Count**: [count]
**Keywords**: [keyword1], [keyword2], [keyword3], [keyword4], [keyword5]

Abstract Guidelines

• Standalone: Understandable without reading paper
• Specific: Include key numbers (n, primary statistic, p-value)
• Consistent: Match paper content exactly
• Past tense: Throughout (this study was conducted)
• No citations: Never cite in abstract
• No abbreviations: Or define on first use

Word Count Targets

Adjust based on scope.md target journal requirements.

Step 5: Generate Title Options

Based on synthesis, suggest 2-3 title options:

## Suggested Titles

1. [Descriptive]: "[Method/Approach] for [Application]: [Key Finding]"
   
2. [Question-answer]: "[Research Question]? A [Study Type]"
   
3. [Finding-focused]: "[Key Finding] in [Population] Using [Method]"

Title guidelines:

• 10-15 words maximum
• No abbreviations (usually)
• Informative > clever
• Include key method and finding if possible

Output

Save to:

• drafts/discussion.md - Discussion section
• drafts/abstract.md - Structured abstract with title options

Return to parent skill with summary:

• Discussion word count: [n]
• Abstract word count: [n]
• Literature sources cited in Discussion: [n]
• Title options: [n]