majiayu000 Scientific Manuscript Skill
Craft and refine manuscripts for high-impact journals through structured feedback, comparative analysis with exemplar papers, and sentence-level prose craft.
Core Focus Areas
This skill emphasizes four dimensions of high-impact writing:
- Narrative arc — how the story builds across sections and paragraphs
- Paragraph architecture — how individual paragraphs create momentum and impact
- Sentence-level craft — concise, punchy prose with word economy
- Strategic rhetoric — calculated use of adjectives and flourishes
Reference Files
Section-Specific Guides
| Section | Reference File |
|---|---|
| Abstract | references/abstract.md |
| Introduction | references/introduction.md |
| Results | references/results.md |
| Discussion | references/discussion.md |
| Methods | references/methods.md |
| Figures | references/figures.md |
Craft-Level Guides (Load for any section)
| Focus | Reference File | When to Load |
|---|---|---|
| Narrative structure | references/narrative-structure.md |
Story arc, section flow, momentum |
| Prose craft | references/prose-craft.md |
Sentence-level style, word economy, rhetoric |
| Evaluation | references/rubrics.md |
Systematic scoring |
Annotated Examples
| Paper | File | Best for |
|---|---|---|
| Musser 2021 Science | references/examples/musser_2021_science.md |
Paradox hooks, cell type papers |
| Ruperti 2024 Curr Biol | references/examples/ruperti_2024_curbio.md |
Challenging paradigms, quantitative prose |
| Tarashansky 2021 eLife | references/examples/tarashansky_2021_elife.md |
Methods papers, comparative analysis |
| Vergara 2021 Cell | references/examples/vergara_2021_cell.md |
Resource papers, multimodal data |
Feedback Modes
Mode 1: Narrative Analysis
Analyze story arc and momentum. Use when:
- Draft feels flat or disjointed
- User asks about "flow" or "structure"
- Sections don't build toward a conclusion
Load: references/narrative-structure.md
Format:
**Arc diagnosis**: [Where tension is established, where it resolves, what's missing]
**Momentum check**: [Which paragraphs build vs. stall]
**Pivot analysis**: [How you transition from known → unknown → your contribution]
**Suggested restructuring**: [Concrete reordering or additions]
Mode 2: Prose Craft Review
Sentence-level style analysis. Use when:
- User asks about "style" or "writing quality"
- Prose feels bloated or academic
- User wants text to be "punchier" or "more concise"
Load: references/prose-craft.md
Format:
**Bloat patterns**: [Specific phrases to cut with rewrites]
**Verb weakness**: [Weak verbs → strong verb suggestions]
**Sentence rhythm**: [Where variation is needed]
**Adjective audit**: [Which add meaning vs. clutter]
**Power positions**: [Sentences where key info is buried]
Mode 3: Comparative Critique
Compare to exemplar papers. Use when:
- User wants to see "how good papers do it"
- Draft has rhetorical issues best shown by contrast
Load: Relevant example file from references/examples/
Format:
**Your draft**: [quote passage]
**Exemplar**: [quote from example paper]
**Key difference**: [What the exemplar does that yours doesn't]
**Principle**: [The generalizable technique]
**Suggested revision**: [Concrete rewrite applying the principle]
Mode 4: Rubric Evaluation
Systematic scoring. Use when:
- User asks "Is this ready for submission?"
- Comprehensive assessment needed
Load: references/rubrics.md
Mode 5: Iterative Dialogue
Socratic questioning. Use when:
- Logic or argument needs development
- User refining specific claims
Quick Diagnostics
The Arc Check
For any section, ask:
- Where is the tension established?
- Where does it resolve?
- Does each paragraph advance toward resolution?
The First/Last Test
- First sentence of each paragraph: Does it state the main point?
- Last sentence of the paper: Is it memorable and quotable?
- Last sentence of each section: Does it transition or conclude powerfully?
The Economy Test
Flag these bloat patterns:
- "It is important to note that" → [delete]
- "plays a role in" → "regulates" / "drives"
- "is involved in" → [specific verb]
- "in order to" → "to"
- Stacked adjectives → choose one
The Flourish Audit
Flourishes should appear at:
- Paper opening (hook)
- Key conceptual pivot
- Paper closing (take-home)
NOT in: routine findings, methods, figure descriptions
Handling Requests
"Review my introduction"
→ Load introduction.md + narrative-structure.md, analyze arc and pivot, check prose craft
"Make this punchier"
→ Load prose-craft.md, do sentence-level audit, provide rewrites
"How does this compare to good examples?" → Load relevant example file, do comparative critique
"Is the narrative working?"
→ Load narrative-structure.md, analyze tension-resolution arc, check paragraph momentum
"Help me cut this down"
→ Load prose-craft.md, identify bloat patterns, suggest cuts with preserved meaning
"Is this ready for submission?"
→ Load rubrics.md + all relevant references, comprehensive evaluation
Output Principles
- Quote exactly: Reference specific passages from the draft
- Rewrite concretely: Don't just diagnose—show the fix
- Be honest: User wants critical feedback, not encouragement
- Prioritize: Identify 2-3 highest-impact changes
- Model excellence: Pull from exemplar papers to show what good looks like