Nature Polishing

Nature-Style Academic Polishing — Router

This skill is split into two layers:

• A static layer under static/ that holds versioned, reusable content fragments (core principles, paper-type playbooks, per-section guidance, language-specific rules, per-journal style).
• A dynamic layer (this file plus manifest.yaml) that detects the request's axes and loads only the fragments needed for the current job.

Do not try to apply the polishing logic from memory or from this router. Always load fragments from disk as described below.

Routing protocol

Follow these five steps every time the skill is invoked.

1. Load the manifest and the core layer

Read manifest.yaml. It declares the axes (paper_type, section, language, journal), the allowed values, and the file paths each value maps to.

Also read every file listed under always_load. These hold the default stance, failure-mode diagnosis, ethics, and output format that apply to every polish job.

2. Detect the axis values for this request

For each axis in the manifest, decide the value using the manifest's detect: hint and the user's input:

• paper_type — research / methods / hypothesis / algorithmic / review. Default: research.
• section — abstract / intro / results / discussion / conclusion / title / methods. May be multiple. Ask the user if it is ambiguous and matters for the polish.
• language — en or zh-to-en. Detect from the draft itself.
• journal — nature / nat-comms / generic. Default: generic. If the user names a Nature subjournal, treat it as nature.

State the detected axis values in one short line to the user before proceeding, so they can correct you cheaply.

3. Load the matching fragments

For each axis value, Read the file mapped in the manifest. Skip the section axis only if the user has supplied free-floating prose with no section context.

Do not read every fragment in static/. Load only what step 2 selected.

4. Polish using the loaded material

Apply the loaded fragments in this priority order, matching the paper type -> section job -> paragraph logic -> claim/evidence/boundary -> sentence polish rule from core/failure-modes.md:

1. Paper-type playbook (architecture, writing order). 2. Section-specific job and failure modes. 3. Journal-specific framing and constraints. 4. Language-specific sentence and paragraph rules (apply last). 5. Core stance and ethics throughout.

If a paragraph's structural problem cannot be fixed without inventing content, flag it instead of papering over it.

5. Reach for references only when needed

The files under references/ are deep references, not defaults. Open them on demand per the references.on_demand table in the manifest, for example when the user explicitly asks for phrasebank-style alternatives or a stricter style audit.

Layout/typesetting (排版) requests are different. If the user asks to fix placement rather than wording — loose/sparse pages, stranded headings, figures that don't fill the page or split across pages, "Float too large", multi-panel arrangement, sparse Supplementary Information — skip the prose axes (paper_type, section, language, journal) and load references/latex-layout.md directly. That file is self-contained: it carries the diagnosis workflow (render → contact-sheet → read the log), the float-glue and [H]/\clearpage/placeins patterns, and the "regenerate wide figures taller at the source" rule. Always compile and visually inspect rendered pages before and after — never judge layout from the .tex alone.

Why this split

• The static layer is versioned and reviewable. Adding a new journal style or paper type is one new file plus one manifest line.
• The dynamic layer keeps each invocation cheap: only the fragments relevant to this draft enter context, instead of the full 1000-line monolith.
• The router itself is short on purpose. Update fragments, not this file, when adding scope.

nature-polishing skill

An academic-writing skill for polishing, restructuring, and translating manuscript prose into concise Nature-leaning English.

Source hierarchy:

• Main strategy: the course notes in Chapter1-Week1-7 full version.pdf
• Published article patterns: curated Nature and Nature Communications examples
• Reference support: Academic-Phrasebank-Navigable-PDF-2023.pdf

What changed

• The main SKILL.md now follows the first PDF's architecture: paper type, reader workflow, hourglass structure, writing order, section responsibilities, intellectual debt, and AI/ethics boundaries.
• Article-level polishing can now use the published-paper pattern reference for abstracts, introductions, Results, Discussions, conclusions, and titles.
• The reference folder now serves a narrower role: phrase families, move templates, and style checks derived from the second PDF.
• The skill now distinguishes research papers from methods papers.
• The skill treats core argument ownership as a central rule, not a side note.

File structure

nature-polishing/
├── SKILL.md
├── README.md
└── references/
    ├── published-article-patterns.md
    ├── phrasebank-playbook.md
    ├── section-moves.md
    ├── style-guardrails.md
    ├── writing-strategy.md
    └── latex-layout.md

When to use

• polishing an abstract, introduction, results, discussion, conclusion, or title
• polishing a methods section or a methods paper with fair-comparison logic
• translating Chinese academic text into publishable English
• tightening section logic before submission
• softening overclaims and fixing evidence-weighted language
• making prose read more like strong journal English without inventing content
• fixing LaTeX layout/typesetting (排版): loose or sparse pages, stranded section headings, figures that don't fill the page or split across pages, "Float too large", multi-panel arrangement, sparse Supplementary Information

Design intent

The skill should:

• preserve facts, citation intent, and author responsibility
• make the first PDF the governing writing strategy
• improve rhetorical sequencing at paragraph level
• keep sentences short and readable
• use the second PDF only as the phrase and reference layer
• avoid generic AI prose and unsupported claims

Reference map

• section-moves.md: section order and move patterns
• published-article-patterns.md: writing patterns from curated Nature and Nature Communications articles
• phrasebank-playbook.md: hedging, transitions, evidence, limitations, future work
• style-guardrails.md: British style, articles, abbreviations, units, register, overclaim control
• writing-strategy.md: paragraph- and section-level argument logic
• latex-layout.md: LaTeX float/page typesetting — top-aligned float glue, the \clearpage+[H] heading-figure unit, placeins caveats, regenerating wide-and-short figures taller at the source, multi-panel stacking, and a render-and-contact-sheet diagnosis workflow

Notes

• The skill is designed for polishing and restructuring, not for fabricating scientific content.
• The main strategic rules live in SKILL.md; the reference files should not overrule them.
• The reference files are intentionally selective. They are meant to guide choices, not to encourage boilerplate copying.

LaTeX layout & float typesetting for Nature-style manuscripts

Deep reference for typesetting/layout requests (排版): loose pages, stranded headings, figures that don't fill the page, "Float too large", page-splitting figures, Supplementary Information that looks sparse. This is about placement, not prose. Load it when the user asks to fix layout, spacing, figure placement, page breaks, or "make it less empty / more compact / more beautiful".

Golden rule: change → compile → render to image → look → iterate. Never judge layout from the .tex alone. Measure, don't guess.

---

0. Diagnosis workflow (do this first)

1. Compile and read the log for the three signals that matter:

• Float too large for page by Xpt — a float (often figure+caption) exceeds the text height.
• Overfull \vbox — content ran past the bottom margin (often [H] placement).
• Reference ... undefined / Citation ... undefined — re-run needed (and for xr-hyper, compile the SI first, then the main file twice).

2. Render pages to PNG and look. With pymupdf: fitz.open(pdf)[i].get_pixmap(dpi=90).save(...). Build a contact sheet (all pages as a grid) to spot whitespace, stranded headings, and split floats at a glance. 3. Measure figure aspect ratios from the source PDFs (pypdf mediabox, or pymupdf): aspect = width/height. Then displayed_height_pt ≈ textwidth_pt / aspect. For a 1-in-margin article on US Letter, \textwidth ≈ 468 pt, usable \textheight ≈ 620–650 pt. Budget every page against that height.

---

1. The "loose / 松散" float page — top-align the glue

Symptom: a page holding only floats (two tables, or a figure) has a big band of whitespace in the middle / above, content seemingly centered with gaps.

Cause: LaTeX's float-page glue is rubber and spreads floats to fill the page: \@fptop = 0pt plus 1fil, \@fpsep = 8pt plus 2fil, \@fpbot = 0pt plus 1fil.

Fix: top-align floats so they pack from the top and slack collects at the bottom (reads as an intentional page tail, not "loose"):

\makeatletter
\setlength{\@fptop}{0pt}            % no stretch at top → floats start at top
\setlength{\@fpsep}{14pt}           % fixed gap between stacked floats
\setlength{\@fpbot}{0pt plus 1fil}  % all slack to the bottom
\makeatother
% Let a page hold more float and less forced text:
\renewcommand{\topfraction}{0.95}
\renewcommand{\bottomfraction}{0.95}
\renewcommand{\textfraction}{0.06}
\renewcommand{\floatpagefraction}{0.80}
\setlength{\textfloatsep}{16pt plus 3pt minus 3pt}
\setlength{\floatsep}{14pt plus 3pt minus 3pt}

This single change fixed the spread-apart table pages in practice (a two-table page went from a centered gap to a tight top-aligned block). Apply it in the SI preamble.

---

2. Wide-and-short figures can never fill a portrait page — fix at the source

Symptom: a figure (e.g. a 1×N strip of per-dataset bars) sits at full width but is short (aspect 3:1–4:1), leaving ~40–50% of the page empty; it also tends to strand the next heading (see §4).

Why LaTeX can't fix it: the figure is width-bound at \textwidth. A 3.3:1 figure at 468 pt wide is only ~140 pt tall. You cannot make it taller without making it wider than the text, and stretching (height=... without keeping aspect) distorts it.

Correct fix — regenerate the figure with a taller aspect (target ~1.9:1–2.2:1) so two stacked panels + caption fill the portrait page. In matplotlib this is just the figsize height, e.g. figsize=(17, 4.1) → figsize=(17, 6.8). Then:

• Verify faithfulness before trusting regeneration: re-run at the original size

first and pixel-diff against the shipped PDF. Only if identical do you trust that changing the height won't drift fonts/colors/style.

• Only touch the SI branch. Main-text and SI versions are often produced by

different functions (plot_avg_bar vs plot_grouped_bar); change only the one the SI uses, or you'll silently alter approved main-text figures.

• Font-size caveat: the on-page text size is set by the display width (figure

scaled to \textwidth). Making a figure taller does not enlarge tick/label fonts — it only adds vertical extent (taller bars, more breathing room). To enlarge labels you must narrow the figure (more scale-up to \textwidth) or bump the in-plot font, not add height.

• Mind the caption budget. A 5–6 line caption is ~80 pt. Size the figure so

heading + intro + 2 panels + subcaptions + caption ≤ usable height. A long-caption figure (e.g. a timeline) often needs to be ~0.5 in shorter than a short-caption one.

---

3. Do NOT rotate to landscape (Nature house style)

Nature / Nature Communications discourage rotated/landscape figures that force the reader to turn the page. Prefer a taller redraw (§2) over `\rotatebox` / `sidewaysfigure`. Landscape is tolerated in SI for genuinely un-squarable figures, but try the redraw first. If the user defers ("do what Nature does"), choose upright.

---

4. Float backlog → stranded section headings

Symptom (very common in figure-heavy SI): two or more section headings pile at the top of a page above a huge empty gap; their figures appear pages later.

Cause: big floats can't be placed, so they defer; meanwhile body text and the next \section keep flowing and stack up. The headings out-run their figures.

Fix — bind each figure section into a "heading + figure" unit:

1. Make the figure short enough to share a page with its heading + intro (heading + intro + figure ≤ usable height; see §2 caption budget). 2. Start the section on a fresh page: \clearpage immediately before the \section. This guarantees full height is available. 3. Pin the figure with [H] (needs \usepackage{float}) right after the heading/intro so it cannot float away:

\clearpage
\section{Per-dataset context scaling}
Figure~\ref{fig:scaling} shows ...        % short intro
\begin{figure}[H]                         % H = exactly here, no floating
  ...two stacked panels...
  \caption{...}\label{fig:scaling}
\end{figure}

Result: a fresh page with heading + intro + figure + caption that fills the page, with no stranded heading.

*Also pin the preceding section's trailing figure.* A \clearpage before a heading flushes the page early — if the previous section ended with a big floating figure whose intro text is still on the page, you strand that text instead. Give that trailing figure [H] too (and size it to fit with its intro), so the page before the \clearpage is also full. (In practice: a timeline figure had to be shrunk ~10% so its intro paragraph + figure + long caption fit one page.)

---

5. [H] and placeins — sharp edges

• `[H]` (float package) does not float. If the figure doesn't fit in the remaining

space it either page-breaks before itself (stranding preceding text) or overflows (Overfull \vbox). Safe only when you guarantee room — hence pair it with \clearpage and size-to-fit. Great for the heading+figure unit; risky mid-page.

• `\usepackage[section]{placeins}` puts a \FloatBarrier at every \section, keeping

a section's floats inside it. Useful against backlog — but it flushes the previous float and can strand the current heading alone on a page if that section's figure is too tall to share. It fixed a two-heading pile-up yet produced one-heading-per-empty-page until figures were also shortened. Use it with §2/§4 sizing, not as a standalone cure.

• Don't blanket-`\clearpage` every section. Section-boundary clearpages create

near-empty pages when a section is short. Use \clearpage surgically (figure sections, §4), not everywhere. (Removing 8 blanket clearpages once took an SI 23→21 pages with even density.)

---

6. Multi-panel main-text figures — stack, don't cram

• A 2×2 grid shrinks panels; for wide panels prefer a single-column vertical stack

(a over b over c over d), each near full width, on a dedicated float page [p]. Reads larger and matches a 2-panel a/b stacked figure elsewhere.

• Tune inter-panel space with \vspace between subfigures (e.g. 0.3em–0.8em).
• If you see Float too large for page by X pt and X is small (<5 pt), shave the

smallest thing first: reduce inter-panel \vspace, or panel width by ~2%, before touching the figure itself.

\begin{figure}[p]\centering
  \begin{subfigure}{0.66\textwidth}\includegraphics[width=\textwidth]{a}\caption{}\end{subfigure}
  \vspace{0.3em}
  \begin{subfigure}{0.66\textwidth}\includegraphics[width=\textwidth]{b}\caption{}\end{subfigure}
  ...
  \caption{...}\label{...}
\end{figure}

---

7. Page-count is not the metric — fullness is

Tightening loose pages can reduce count; enlarging short figures to fill pages can increase it. Both are correct. A 20-page SI where every page is full beats a 19-page SI with half-empty figure pages. Optimize for even density and no stranded headings, not for the smallest page count.

---

8. Quick checklist

• [ ] Top-aligned float glue in the preamble (§1).
• [ ] Wide-short figures regenerated to ~2:1, SI branch only, faithfulness pixel-checked (§2).
• [ ] Upright, not landscape (§3).
• [ ] Each figure section: \clearpage + [H] heading-figure unit; trailing figure of the

previous section also [H] and sized to fit (§4).

• [ ] No blanket section clearpages; no stranded headings (§5).
• [ ] Compile clean: no "Float too large", no "Overfull \vbox", no undefined refs.
• [ ] Contact-sheet the final PDF and eyeball every page (§0).

Phrasebank Playbook

Use this file after the main argument and section role are already clear. It is a phrasebank layer derived from Academic Phrasebank, not a substitute for deciding what the paragraph is trying to do.

Evidence strength

Choose verbs that match the evidence.

Strong

• show
• demonstrate
• establish
• reveal
• identify

Use only when the design and data justify a strong claim.

Moderate

• suggest
• indicate
• support the view that
• are consistent with
• point to

Use when the interpretation is plausible but not definitive.

Speculative

• may reflect
• could arise from
• appears to
• seems likely
• might be explained by

Use when moving beyond direct observation.

Evidence collocations

Adjectives for evidence:

• weak: limited, scant, insufficient
• developing: growing, emerging, accumulating
• strong: robust, reliable, convincing, considerable

Useful patterns:

• The evidence presented here suggests that ...
• The available evidence supports the view that ...
• Current evidence raises important questions about ...
• The data point to a need for ...

Transition families

Contrast

• however
• by contrast
• nevertheless
• despite this
• whereas

Addition

• furthermore
• in addition
• moreover
• also

Consequence

• therefore
• thus
• consequently
• as a result
• thereby

Qualification

• notably
• importantly
• approximately
• in part
• at least in this cohort

Prefer the smallest connective that does the job. Do not decorate every sentence with a transition word.

Paragraph linking without sounding repetitive

Prefer these patterns over repeated This suggests:

• restate the noun: Such heterogeneity ...
• definite noun phrase: The resulting gradient ...
• participial summary: Taken together, ...
• zero-connective progression when the logic is already obvious

Limit demonstrative-led openings. One per paragraph is usually enough.

Gap language

Use gap statements that are precise rather than dramatic:

• remains poorly understood
• has not been examined in ...
• has received limited attention
• few studies have addressed ...
• evidence remains sparse for ...

Avoid:

• no one has ever studied
• completely unknown
• ignored by all previous work

Comparison with prior work

To align with earlier work:

• These results are consistent with ...
• This finding accords with ...
• Our observations broadly support ...

To mark divergence fairly:

• In contrast to earlier reports, ...
• This finding differs from ...
• One possible reason for this discrepancy is ...

Limitation language

Useful patterns:

• These findings should be interpreted with caution because ...
• A limitation of this study is that ...
• The generalisability of these results is limited by ...
• We cannot exclude the possibility that ...
• Another source of uncertainty is ...

Pair limitation language with the actual source of uncertainty, not with vague modesty.

Implication language

Useful patterns:

• An implication of this is that ...
• These findings may help to explain ...
• These data support further investigation of ...
• This work has implications for ...

Implications should stay within the evidence boundary.

Future-work language

Useful patterns:

• Further work is needed to determine whether ...
• Future studies should examine ...
• A useful next step would be to ...
• Larger studies are required to validate ...

Future work should emerge from an actual limitation, uncertainty, or opportunity.

Published Article Patterns

Use this file when polishing should improve scientific argument, not just English. The patterns below are distilled from curated Nature and Nature Communications research articles across materials, energy systems, construction decarbonization and machine learning. Do not copy their wording. Use the patterns to diagnose and reshape the user's manuscript.

Abstract pattern

Strong abstracts usually move in six steps:

1. name the field-scale problem or opportunity 2. show why existing approaches are incomplete 3. state the specific intervention or method 4. give the decisive result with scale, comparison or constraint 5. explain why the result changes what is possible 6. close with scope, application or boundary

Polishing rule: if an abstract starts with the method, add the problem and gap first. If it ends with enthusiasm, replace it with a bounded implication.

Introduction pattern

High-performing introductions often use scale -> bottleneck -> prior attempts -> missing capability -> present study.

• Scale: quantify why the problem matters, preferably with field-level stakes.
• Bottleneck: name the physical, computational, clinical or practical barrier.
• Prior attempts: acknowledge existing strategies fairly.
• Missing capability: explain what those strategies still cannot do.
• Present study: state what the paper does, not what it hopes to do.

Polishing rule: keep the gap narrow enough that the study can actually fill it. Avoid novelty claims that depend on weakening prior work.

Results pattern

Results sections usually work best as an evidence ladder:

1. overview of the system, workflow or design space 2. validation that the platform works under controlled conditions 3. primary performance result 4. comparison with baselines or current practice 5. mechanism, interpretation or diagnostic analysis 6. scale-up, generalization or real-world application

Each Results paragraph should begin with the question or test, then report the observation, then give the quantitative or comparative support. Interpretation should be brief unless the paragraph is explicitly bridging into Discussion.

Discussion pattern

Effective Discussion writing starts from the central advance and then widens:

• what the study demonstrates
• why the evidence is credible
• how it changes an existing workflow, design rule or conceptual boundary
• what constraints remain
• what future work is enabled, without promising untested outcomes

Do not turn the Discussion into a second Results section. Use it to state what the results mean and where that meaning stops.

Conclusion pattern

Nature-style conclusions are compact. They usually combine:

1. the contribution in one sentence 2. the mechanism, performance or feasibility evidence that supports it 3. the scale or application implied by the work 4. one boundary condition, if the claim could otherwise overreach

Polishing rule: remove new data from conclusions. Preserve confidence, but add scope control.

Title pattern

Strong titles are concrete and searchable. They often combine:

• object or system
• action or capability
• application, scale or consequence

Prefer titles that reveal the central scientific move. Avoid titles that sound like grant aims, slogans or broad fields.

Sentence-level pattern

Published prose often looks simple because each sentence does one job:

• background sentence: field stake or known fact
• gap sentence: unresolved limitation
• method sentence: what was done
• result sentence: observed effect plus condition
• comparison sentence: baseline or previous state
• implication sentence: meaning with scope
• limitation sentence: boundary or dependency

When polishing, label each sentence by job. If two jobs compete in one sentence, split it or subordinate one job.

Overclaim checks from article patterns

Flag and soften claims when:

• a laboratory or simulation result is written as an immediate field-wide solution
• a single material, model or system is described as universally applicable
• correlation is rewritten as mechanism
• a comparison lacks a fair baseline
• a future application is stated as an achieved outcome

Good Nature-leaning prose can be ambitious, but the ambition must be attached to evidence, scale and boundary.

Section Moves

Use this file only after the main section logic has been decided in SKILL.md. This file is for phrase-level and move-level support derived from Academic Phrasebank, not for deciding the paper's overall writing strategy.

Introduction

Questions this section must answer:

1. Why does the topic matter? 2. What is already known? 3. What is still missing or contested? 4. What does the present study ask or do?

Preferred move order:

1. establish importance 2. summarize what is known 3. identify a gap, limitation, or controversy 4. state the study aim 5. indicate value or approach

Useful phrase families:

• Recent years have seen increasing interest in ...
• X is a central issue in ...
• Previous studies have shown that ...
• However, the mechanisms underlying ... remain poorly understood.
• Few studies have examined ...
• Here, we investigate whether ...
• This work provides ...

Avoid:

• long historical throat-clearing
• detailed results
• inflated novelty claims before the gap is defined

Literature Review

Questions this section must answer:

1. What lines of work define the field? 2. What has been established? 3. Where do findings diverge or remain incomplete? 4. Which gap matters for the present paper?

Preferred move order:

1. describe the scope of existing work 2. identify dominant approaches 3. state what has been established 4. note disagreements or contradictions 5. isolate the missing piece

Useful phrase families:

• A substantial body of work has focused on ...
• Most studies have relied on ...
• Previous work has established that ...
• Findings have been mixed regarding ...
• By contrast, little attention has been paid to ...
• No study has yet examined ...

Avoid:

• citation-by-citation summary
• treating all prior work as uniformly weak

Methods

Question this section must answer:

• Could another group reproduce the work from this description, or from this description plus a clearly cited protocol?

Preferred move order:

1. design or cohort 2. materials or data source 3. procedure 4. outcome measures 5. analysis and statistics 6. ethics when relevant

Useful phrase families:

• A cross-sectional study was undertaken to ...
• Samples were collected from ...
• X was quantified using ...
• We used ... to assess ...
• Differences were analysed using ...
• All analyses were performed in ...

Avoid:

• under standard conditions
• using routine methods
• data were analysed statistically

Results

Question this section must answer:

• What was observed, under which condition, and with what evidence?

Preferred move order:

1. orient the reader to the figure, table, or experiment 2. state the main observation 3. add quantitative detail 4. note expected or unexpected patterns 5. compare with prior work only if it clarifies the result

Useful phrase families:

• Figure 1 shows ...
• As shown in Table 1, ...
• The most notable finding was that ...
• Contrary to expectations, ...
• No significant difference was observed in ...
• These results are consistent with ...
• In contrast to earlier reports, ...

Avoid:

• discussion-length mechanism explanations
• repeating every visual detail from the figure

Discussion

Questions this section must answer:

1. What do the main findings mean? 2. How do they relate to earlier work? 3. Which explanations are plausible? 4. What limitations constrain interpretation? 5. What follows from the findings, and what does not?

Preferred move order:

1. restate the main finding 2. explain plausible reasons 3. compare with earlier work 4. note limitations 5. state implications 6. point to future work if needed

Useful phrase families:

• Taken together, these findings suggest that ...
• A possible explanation is that ...
• This discrepancy may reflect ...
• These results should be interpreted with caution because ...
• An implication of this is that ...
• Further work is needed to determine whether ...

Avoid:

• repeating the Results section in new words
• claiming mechanism when only association was shown

Conclusion

Questions this section must answer:

1. What was the central contribution? 2. Which finding matters most? 3. What implication follows, with what boundary?

Preferred move order:

1. return to the aim 2. summarize the decisive finding 3. state contribution or significance 4. give a boundary or forward look

Useful phrase families:

• This study set out to ...
• The present findings indicate that ...
• These results extend our understanding of ...
• Notwithstanding these limitations, ...
• Further studies are required to ...

Avoid:

• introducing new experiments
• ending on vague praise of the work

Abstract

Questions this section must answer:

1. What problem or gap is being addressed? 2. What was done? 3. What was found? 4. Why should the reader care?

Preferred move order:

1. broad context 2. concrete gap 3. approach 4. key result with numbers if available 5. implication

Useful phrase families:

• X remains challenging because ...
• Here, we ...
• Using ... , we found that ...
• We show that ...
• These findings suggest ...

Keep the abstract selective. If a detail does not affect editorial triage, it probably does not belong.

Title

Question this section must answer:

• Which few words make the paper searchable, accurate, and interesting without overclaiming?

Target properties:

• searchable
• specific
• restrained
• defensible

Useful patterns:

• [Core entity] in/through/by [mechanism or context]
• [Process] shapes [outcome] in [system]
• [Signature/pattern/framework] of [phenomenon]

Avoid:

• A study of ...
• vague hooks
• unverified first
• stacked jargon

Style Guardrails

Use this file for mechanical and stylistic checks after the main rewrite. This file should refine prose and correctness, not override the main writing strategy in SKILL.md.

Academic style

• prefer cautious, precise prose over conversational confidence
• avoid contractions
• avoid rhetorical questions in polished manuscript prose
• define abbreviations on first use
• use British spelling by default if the target is Nature-style prose
• keep figure legends concise; if aiming for Nature style, <= 300 words is a good upper bound
• if aiming for Nature style, keep titles at <= 75 characters including spaces

Articles

Common checks:

• first mention of a singular count noun: a or an
• later mention of the same item: the
• generic plural: usually no article
• unique entity: often the
• abstract nouns used generally: often no article

Typical repair:

• bad: The hypoxia induces ...
• better: Hypoxia induces ...

Numbers and units

• use numerals for measurements
• leave a space between the value and the unit: 25 cm, 3.2 s
• keep statistical symbols and mathematical notation consistent
• use en dashes for ranges where appropriate

Do not rewrite numbers into words unless the surrounding house style demands it.

Academic register

• avoid spoken fillers and weak evaluative language
• use we only when it suits the discipline and document type
• keep nominalisation useful, not excessive
• keep the prose impersonal where appropriate, but do not force lifelessness

Sentence and paragraph checks

• each sentence should express one main proposition
• dependent clauses must stay attached to a main clause
• do not join two independent clauses with only a comma
• each paragraph needs a controlling idea and supporting material
• avoid common structure errors such as sentence fragments introduced by although or whereas

Overclaim checklist

Flag and soften:

• prove
• conclusively
• unprecedented
• best
• superior
• first

Safer replacements:

• show
• suggest
• to our knowledge
• among the strongest
• in this cohort

Integrity rules

• do not invent references
• do not alter quantitative values unless correcting an obvious typo requested by the user
• do not upgrade association to causation
• do not imply broader generalisability than the study supports

AI boundary

Use AI for language control, not for scientific fabrication.

Allowed:

• grammar and clarity
• restructuring and hedging
• translation with terminology checking

Not allowed:

• fabricated citations or datasets
• invented mechanisms presented as fact
• unsupported claims of novelty

Writing Strategy

Use this file when the user is not just asking for cleaner English, but for better scientific writing logic. This is the layer that should govern all paragraph- and section-level rewriting.

Core stance

Academic polishing is not only about style. It is also about making the reasoning legible. A polished paragraph that still performs the wrong rhetorical job is a failed edit.

Hourglass structure

Most strong research writing follows a broad -> narrow -> broad pattern:

• Introduction: open the territory, narrow to the gap, then state the study
• Discussion/Conclusion: start from the specific findings, then widen to implications and limits

Use this pattern when deciding paragraph order and section scope. If a draft jumps between background, results, and implications without control, rebuild the progression first.

Writing order is not reading order

The author may draft in one order and the reader may consume in another. A useful planning sequence is:

1. results 2. introduction and conclusion 3. title 4. discussion 5. methods 6. abstract

The practical rule for this skill is simple: organize around evidence and argumentative function, not around the chronology of the raw draft.

Claim, evidence, boundary

Every important scientific statement should have three parts:

1. claim: what is being said 2. evidence: what supports it 3. boundary: where the claim stops, or what uncertainty remains

Typical failures:

• claim without evidence
• data without an explicit point
• implication without a scope condition
• correlation rewritten as mechanism

When polishing, repair these failures before polishing rhythm.

Section responsibilities

Introduction

The Introduction should answer four questions:

1. What is already known? 2. What remains unresolved? 3. What exact question does this study ask? 4. How does the study address it?

Do not summarize results or conclusions here.

Results

Results state what was observed. They should provide:

• object or system
• condition
• quantitative support
• direct result

Do not turn Results into a Discussion section by adding long mechanistic interpretation.

Discussion

Discussion explains what the findings mean. It should address:

• how the work fits the broader field
• what has been added to understanding
• which earlier work is being supported, revised, or complicated
• which explanations are plausible
• which limitations constrain the interpretation

Discussion is the natural home for hedging.

Methods

Methods should pass a reproducibility test: could another group repeat the work from this description, or from this description plus a clearly cited prior protocol?

Reject vague writing such as:

• under standard conditions
• using routine methods
• data were analysed statistically

Conclusion

Conclusion is not a mini-discussion. A strong closing usually does three things:

1. restates the central contribution 2. identifies the decisive evidence 3. states the implication with a boundary

Do not introduce new data here.

Abstract

The abstract is a mini-paper:

1. context or problem 2. gap 3. approach 4. key result 5. implication

It should help the reader decide whether the paper is relevant, credible, and potentially important.

Citation as positioning

Citation is not just a formatting issue. It tells the reader how the current work stands relative to earlier work.

Useful categories:

• support: prior work supports the premise
• borrow: current work adopts a method, framework, or protocol
• contrast: current work differs in result, setting, or interpretation
• reuse/adaptation: material, data, code, or images come from elsewhere

Always cite the source actually read and verified. Do not cite a paper as direct support if you only know it through another paper's summary.

Fairness to earlier work

Do not manufacture novelty by flattening previous studies into a weak baseline. Prefer language like:

• Although previous studies showed ..., their performance in ... remains unclear.
• Earlier work established ..., but did not address ...

This preserves intellectual honesty while still making the gap explicit.

Overclaim control

Watch for:

• prove
• conclusively
• unprecedented
• best
• unqualified first

Replace or qualify them unless the evidence is unusually strong and the scope is tightly defined.

Diagnose failure mode before editing

Before rewriting, identify the main problem:

• wrong paper type logic
• missing gap or poor positioning
• claim without evidence
• evidence without a clear claim
• missing boundary or limitation
• Results and Discussion mixed together
• weak title or abstract signal
• inconsistent terminology, abbreviations, units, or notation across sections
• sentence-level clutter only

Prioritize fixes in this order:

paper type -> section job -> paragraph logic -> claim/evidence/boundary -> sentence polish

Do not sentence-polish a draft whose section job is wrong. Surface the structural problem first, then polish.

Terminology consistency is a cross-cutting check that runs at every level: build the Terminology Ledger on first contact (see ../../../_shared/core/terminology-ledger.md) and enforce its canonical forms throughout the polish.

Output format

Default output:

1. The polished text as plain prose, not in a code block. 2. Revision notes: with 3-5 short bullets on the major structural and stylistic changes. 3. If the rewrite changed section logic, say so explicitly.

If the user asks for side-by-side revision, provide:

• Original
• Polished
• Why changed

If any paragraph's structural problem could not be fixed without inventing content, say so under Revision notes: instead of papering over it.

Default stance

• Language serves argument. Do not polish sentences while leaving the reasoning broken.
• Write with empathy for the reader: relevance first, then novelty, then trust, then reuse, then meaning.
• There should be no mystery for the writer, but there may be one for the reader.
• Do not invent data, references, mechanisms, or novelty claims.
• Do not let AI draft the paper's core scientific argument from scratch.
• If the draft is Chinese or structurally rough, reconstruct the logic first and the prose second.
• On first contact with the draft, build a Terminology Ledger and keep terms, abbreviations, units, and notation consistent across every section. Do not introduce synonyms to vary the prose. See ../../../_shared/core/terminology-ledger.md.
• Avoid em dashes in polished output by default. Prefer commas, parentheses, or full stops. Use colons sparingly unless the user explicitly asks to preserve dash-based punctuation or wants a colon-led style.

Reader workflow

See ../../../_shared/core/reader-workflow.md (loaded via manifest always_load) for the 5-step reader question sequence. Polishing should help the paper answer those questions in order.

Protect the core argument

The paper's core argument includes:

• the scientific question the paper actually answers
• why that question matters
• how the work differs from existing research
• what the results imply
• how the main line of reasoning unfolds

AI may help polish, structure, or compare phrasings. AI should not invent or author the core argument. If the argument is weak or unclear, expose that weakness rather than hiding it under polished language.

Journal: generic

Used when the user has not named a target journal, or the journal is not specifically modeled by another fragment.

Defaults

• Apply Nature-leaning style without enforcing Nature's strictest length or significance-framing demands.
• Keep the em-dash and hedging defaults from core/stance.md.
• If the user later names a journal, ask whether to re-polish under that journal's fragment rather than guess.

Things to ask the user before final polish

• Target journal and section format (structured vs unstructured abstract; word limits; reference style).
• Audience breadth: subfield vs broad readership.
• Whether the draft will go through a separate copy-edit pass (affects how aggressively to rewrite vs flag).

Journal: Nature Communications (polishing)

Read the shared facts first

Open ../../../../_shared/journal-formats/nat-comms.md for the authoritative formatting facts: word limits, abstract rules, figure specs, reference style, mandatory statements, and common desk-rejection patterns.

The notes below are the polishing action layer on top of those facts.

Audience

Open-access, broader than a subfield journal but more specialist-tolerant than Nature. The reader is typically an active researcher in an adjacent area.

Polishing priorities

• Significance framing matters, but a less aggressive opening than Nature is acceptable.
• Word count is more forgiving than Nature, but the ~5,000-word cap includes Methods. If polishing brings the manuscript near the limit, surface a word-budget check rather than just compressing prose.
• Methods can stay more detailed in-line; do not strip reproducibility content just to hit length.
• Same em-dash and hedging defaults as Nature.
• Abstract is unstructured, 150 words, no citations. If the user's abstract has citations or is structured (Background/Methods/Results), restructure before sentence polishing.

Length-aware polishing checks

When polishing a Nature Communications Article, run these word-budget checks before sentence-level work:

1. Estimate total word count including Methods. If over ~5,000, flag the gap and ask the user where to cut before polishing. 2. If display items > 10, flag for redistribution into Supplementary Information before deeper edits. 3. If references > ~60, flag for trimming or consolidation. 4. If the abstract is > 150 words or contains citations, restructure first.

These are diagnostic, not destructive — surface the problem in Revision notes: rather than silently cutting.

Things the shared facts already cover

Do not restate facts that live in _shared/journal-formats/nat-comms.md. Reference them when the user asks. Examples Claude should respond by reading shared facts:

• "What's the reference style?" → cite the format example from shared
• "How many figures can I have?" → cite the 10-item cap from shared
• "What's the abstract limit?" → 150 words, unstructured, no citations

Journal: Nature (and Nature subjournals)

Audience

A broad, multi-disciplinary readership. A reader outside the immediate subfield must be able to grasp the claim, the gap, and the significance from the first paragraph and the abstract.

Polishing priorities

• The opening sentence must signal significance for a non-specialist audience without overclaiming.
• Avoid jargon that does not appear in the headline of a typical Nature News piece. Define or replace.
• Abstract is unstructured prose for many Nature titles; check the target journal's current guideline if the user names one.
• Length discipline: Nature articles are unforgiving on word count. Prefer cuts to compressions.
• No em dashes in body prose. Use commas, parentheses, or shorter sentences.
• Hedging should be calibrated. Avoid both overclaim (proves, definitive) and timidity (might possibly suggest).

Things to flag, not silently fix

• If the manuscript leans on a specialist mechanism the broad audience would not follow, flag it for the author rather than over-translate.
• If significance for a non-specialist is genuinely thin, surface that as a structural problem in Revision notes:.

Language: English source

Sentence rules

• In polished prose, aim for sentences in the 10-30 word range.
• Keep every sentence at <= 30 words.
• Do not produce full sentences under 10 words unless the user explicitly asks for terse style or the item is a heading, label, or fixed technical expression.
• If any sentence exceeds 20 words, check whether it contains more than one main proposition.
• Split overloaded sentences rather than polishing them cosmetically.
• The last sentence of a paragraph often becomes the longest and weakest. Check it explicitly.
• Prefer one core subject-verb proposition per sentence.
• Do not use em dashes as prose punctuation in the polished version unless the user explicitly requests them. Rewrite with commas, parentheses, or shorter sentences instead. Use colons only when they add clear structural value.

Paragraph rules

• Each paragraph should have one controlling idea followed by support.
• Supporting material may include data, comparison, explanation, consequence, literature, or limitation.
• If a new idea appears, start a new paragraph instead of stacking it onto the old one.
• Use thematic linking, not repetitive This suggests ... openings.

Language: Chinese-to-English

When the source is Chinese or strongly Chinese-influenced English, do not translate clause-by-clause.

Workflow

1. Extract the core propositions first. List them in plain English before drafting prose. 2. Reconstruct explicit logical links: contrast, cause, implication, limitation. Chinese academic prose often elides these connectives — restore them. 3. Verify terminology, causality, and hedging strength against the source. 4. Keep technical terms, gene/protein names, model names, dataset names, and statistical terms stable; do not "translate" them into rough paraphrases. 5. Apply the English sentence and paragraph rules from language/en.md only after the logic is rebuilt.

Common Chinese-influenced patterns to fix

• Topic-comment chains rewritten as subject-verb sentences.
• Strings of short clauses joined by commas — split or add connectives.
• Vague generalizations (many studies have shown) — convert to specific citations or remove.
• Hedging asymmetry: Chinese drafts often understate; English Nature-style asks for precise hedging matched to evidence strength, neither over- nor under-claiming.
• Repetition of the topic noun where English would use a pronoun or omit it.

Paper type: algorithmic or device

The argument proposes a procedure, tool, or system and must show that it performs reliably and advantageously.

What the reader expects

• a clear problem formulation and the precise scope being claimed
• the proposed procedure or device, described to a level a peer could re-implement
• a fair comparison against credible baselines under matched conditions
• ablations or controls that isolate why the new approach works
• failure modes, runtime/cost characteristics, and applicability boundaries

Polishing priorities

• Separate "what the system is" from "why it works" from "how well it works"; do not braid them.
• Performance claims must specify the dataset, metric, baseline, and conditions, not stand as bare numbers.
• Avoid marketing verbs (leverages, enables, empowers) unless they carry information.
• The Discussion should name the failure modes the experiments revealed, not only the wins.

Paper type: hypothesis-based

The argument tries to establish or rule out a causal explanation.

What the reader expects

• a clearly stated hypothesis, framed before the evidence
• a falsification path: what observations would refute it
• evidence presented in support, against, or as boundary conditions
• alternative explanations addressed, not ignored

Polishing priorities

• Make the hypothesis statement explicit and locatable; do not bury it in the third paragraph of the Introduction.
• Distinguish supporting evidence from consistent-but-non-discriminating evidence.
• In the Discussion, address rival explanations before generalizing.
• Hedging should match the strength of the causal claim. Avoid overclaiming mechanism from correlational data.

Paper type: methods

The reader of a methods paper asks:

• whether the method works
• whether it is reproducible
• whether it is better under a fair comparison

Results section job

The Results section must show the advantages of the method over existing methods. Typical questions are:

• Is it more reliable?
• Is it faster?
• Does it require fewer resources?
• Is the comparison fair and reproducible?

Methods section detail

The Methods section in a methods paper may need additional detail such as:

• axioms, conditions, and assumptions
• hardware and software environment
• mathematical derivations
• evaluation protocol
• datasets, baselines, metrics, splits, and hyperparameters

Productive writing order

1. Methods 2. Results 3. Introduction 4. Conclusion 5. Discussion 6. Abstract

Paper type: research

The reader of a research paper asks:

• why the phenomenon matters
• what was done
• what was found
• what it means

Hourglass structure

Strong research papers mirror an hourglass:

• Introduction: open broadly, then narrow to the specific gap, question, hypothesis, methods, and study
• Discussion/Conclusion: widen again, connecting the findings back to the literature and explaining how the knowledge gap was filled

If a paragraph or section violates this architecture, rebuild it before polishing wording.

Productive writing order

1. Results 2. Introduction and Conclusion 3. Title 4. Discussion 5. Materials and Methods 6. Authors 7. Abstract

Follow the logic of evidence and argument, not the raw order in which the user drafted sentences.

Paper type: review

The reader asks: what is the state of the field, where is the disagreement, and what is the path forward.

What the reader expects

• a clear scope statement (which sub-area, which time window, which inclusion criteria)
• a synthesis that organizes the literature by argument, not by paper
• explicit positioning of disagreements and gaps
• an outlook that names the most informative open questions

Polishing priorities

• A review is not a survey list. Replace Author A reported X. Author B reported Y. with synthesis that groups claims by mechanism, method, or conclusion.
• Position the reviewer's own stance carefully: a review can take a view, but it must show its reasoning.
• Avoid generic transitions (furthermore, additionally). Use connectives that signal the logical relation (in contrast, building on this, the remaining disagreement is).
• The closing section should leave the reader with a usable map, not a summary of what was just read.

Section: Abstract

The abstract is a mini-paper:

context/problem -> gap/objective -> approach -> key results -> implication

It should answer:

1. What question was addressed? 2. How was it addressed? 3. What was found? 4. Why should anyone care?

Some journals require a strict abstract format. Follow the journal if it conflicts with the generic pattern. (See the loaded journal/*.md fragment for journal-specific constraints.)

Polishing priorities

• Cut sentences that summarize background that the title already implies.
• Make the gap and the contribution one short, locatable sentence each.
• The last sentence should state significance, not repeat the result.

Section: Conclusion

Use the three-part close:

1. restate the central contribution 2. summarize the key evidence or outcome 3. state the implication with a boundary

Do not introduce new data in the conclusion. Always run an overclaim check here.

Overclaim check

• Does each claim trace back to evidence in this paper?
• Are mechanism words (demonstrates, proves, establishes) backed by the right study design?
• Is the scope of the implication narrower than or equal to the scope of the evidence?

Section: Discussion

Discussion should answer:

• how the work fits within the broader field
• what has been added to understanding
• who should be credited for earlier work
• whether the findings support, complicate, or revise earlier results
• how the findings are interpreted
• when that interpretation may fail

Short rule:

• Results = what we observed
• Discussion = how we understand it, and when it may fail

Sentence syntax

Discussion sentences usually interpret:

• may reflect
• suggests that
• could indicate
• is likely due to
• may facilitate

Hedging strength should match evidence strength. Do not promote a "consistent with" finding to "demonstrates" wording.

Common failure modes

• Re-summarizing Results instead of interpreting them.
• Skipping rival explanations.
• Omitting boundaries: when does the interpretation stop holding?

Section: Introduction

The Introduction should:

• tell the reader why the work matters
• explain what gap it fills
• explain why that gap matters
• state what is already known
• state what remains unresolved
• state what question the paper asks
• indicate how the study addresses it

Do not summarize the Results section here. Do not summarize the Conclusion here.

Common failure modes

• Opening paragraph reads as a textbook rather than a positioning move.
• The gap is implied but never explicitly named.
• The transition from "what is known" to "what this paper does" is missing.
• Methods are previewed in detail; keep that for Methods.

Section: Materials and Methods

Methods should be specific, complete, transparent, and reproducible.

Another group should be able to determine:

• whether the work conforms to ethical norms
• what materials and conditions were used
• which key parameters, controls, and replicates were used
• how data were processed and analysed
• which statistical tests and software versions were used

It is acceptable to abbreviate by citing an earlier report only when that report truly contains the necessary detail.

Forbidden vague phrases

Never leave wording such as:

• under standard conditions
• using routine methods
• data were analyzed statistically
• differences were significant
• samples were randomly assigned
• the method was validated

Replace them with the actual reproducible information.

Section: Results

Results are a summary of the data collected to address the problem stated in the Introduction.

Results writing should:

• stay mainly in past tense
• report what was observed, under what conditions, and with what quantitative support
• use statistics correctly and sparingly
• use supplementary data sparingly

Results should answer what happened, not what it ultimately means.

Sentence syntax (Results vs Discussion)

Results sentences usually report:

• was detected
• increased
• showed
• enabled
• achieved

Do not let a Results paragraph drift into Discussion syntax (may reflect, suggests that, is likely due to) unless the transition is intentional.

Common failure modes

• Interpreting findings inline instead of in Discussion.
• Citing supplementary data when the result should stand in the main text.
• Vague comparisons (higher than control) without effect size or test.

Section: Title

A strong title should:

• tell the reader what to expect
• avoid unnecessary technical language
• be easy to search
• be substantiated by data
• create curiosity without sacrificing credibility

Use curiosity with credibility, not empty cleverness. A hook is only acceptable if the claim remains fully defensible.

Polishing approach

• If asked for alternatives, generate 3-5 candidates spanning declarative, question, and finding-led patterns; mark the most defensible.
• Strip jargon that the target journal's general audience would not recognize.
• Verify every quantitative claim in the title against the manuscript.