psyclaw 0.28.1 → 0.28.2

package/vendor/nature-skills/skills/nature-polishing/references/phrasebank-playbook.md

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+# Phrasebank Playbook
+
+## Contents
+
+- [Evidence strength](#evidence-strength)
+- [Evidence collocations](#evidence-collocations)
+- [Transition families](#transition-families)
+- [Paragraph linking without sounding repetitive](#paragraph-linking-without-sounding-repetitive)
+- [Gap language](#gap-language)
+- [Comparison with prior work](#comparison-with-prior-work)
+- [Limitation language](#limitation-language)
+- [Implication language](#implication-language)
+- [Future-work language](#future-work-language)
+
+
+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.

package/vendor/nature-skills/skills/nature-polishing/references/published-article-patterns.md

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+# Published Article Patterns
+
+## Contents
+
+- [Abstract pattern](#abstract-pattern)
+- [Introduction pattern](#introduction-pattern)
+- [Results pattern](#results-pattern)
+- [Discussion pattern](#discussion-pattern)
+- [Conclusion pattern](#conclusion-pattern)
+- [Title pattern](#title-pattern)
+- [Sentence-level pattern](#sentence-level-pattern)
+- [Overclaim checks from article patterns](#overclaim-checks-from-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.

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

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+# Section Moves
+
+## Contents
+
+- [Introduction](#introduction)
+- [Literature Review](#literature-review)
+- [Methods](#methods)
+- [Results](#results)
+- [Discussion](#discussion)
+- [Conclusion](#conclusion)
+- [Abstract](#abstract)
+- [Title](#title)
+
+
+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/vendor/nature-skills/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