@researai/deepscientist 1.5.16 → 1.6.0

package/src/skills/nature-polishing/references/section-moves.md

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+# 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

package/src/skills/nature-polishing/references/style-guardrails.md

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+# 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

package/src/skills/nature-polishing/references/writing-strategy.md

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+# 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.