psyclaw 0.28.1 → 0.28.3

package/vendor/nature-skills/skills/nature-shared/core/research-compliance.md

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+# Nature Portfolio research-compliance routing
+
+Use this conditional reference when a manuscript involves regulated research,
+specialist reporting forms, sensitive images, structures, samples or materials.
+It is a readiness screen, not legal, clinical or ethics-board advice.
+
+## Contents
+
+1. Applicability gate
+2. Reporting summaries
+3. Human-participant research
+4. Animal research
+5. Clinical research
+6. Image integrity
+7. Structures, chemistry and materials
+8. Taxonomy and provenance-sensitive samples
+9. Audit output
+10. Official sources
+
+## 1. Applicability gate
+
+Classify every item as `required`, `not applicable`, or
+`AUTHOR_INPUT_NEEDED`. Never infer an approval, consent, registration, permit,
+protocol, accession, validation report or exemption.
+
+Open only the relevant blocks below. Do not burden a computational or
+theoretical manuscript with unrelated biomedical requirements.
+
+## 2. Reporting summaries
+
+Require the relevant current Nature Portfolio form when the study is:
+
+- life sciences
+- behavioural or social sciences
+- ecology, evolution or environmental science
+- a physical-science Article in a specifically covered area, including solar
+  cells or claims of lasing
+
+The form is supplied to editors and reviewers and published with accepted
+manuscripts. Advanced form features require Adobe Reader. Treat the form as a
+substantive cross-check against Methods, statistics and figure legends, not as
+a checkbox exercise.
+
+## 3. Human-participant research
+
+Check that the submitted manuscript states:
+
+- compliance with the Declaration of Helsinki where applicable
+- the approving ethics committee's name and reference number
+- details of any formally granted exemption and the committee granting it
+- that informed consent was obtained from all participants
+- consent for publication of identifiable information or images when relevant
+- how population categories such as race, ethnicity, sex and gender were
+  defined, justified and handled analytically when they are used
+- safeguards for vulnerable groups, privacy and sensitive data
+
+Route controlled-access data wording to `nature-data`.
+
+## 4. Animal research
+
+For experiments involving live vertebrates or higher invertebrates, check:
+
+- the corresponding author's confirmation of compliance with relevant rules
+- the institutional or licensing committee and relevant approval details
+- sex and other animal characteristics that may affect results
+- housing and husbandry details where they may influence results
+- reporting against ARRIVE 2.0 where applicable
+- accepted anaesthesia and euthanasia practice
+
+Flag methods that appear inconsistent with accepted welfare norms rather than
+trying to repair the wording.
+
+## 5. Clinical research
+
+### Registration
+
+- register every qualifying prospective clinical trial in an acceptable WHO
+  primary registry or ClinicalTrials.gov before enrolment of the first
+  participant
+- state the trial number clearly in both the abstract and Methods
+- treat primary results from an unregistered qualifying trial as a blocking
+  issue
+
+### Submission files
+
+Clinical trial reports should include:
+
+- the latest English protocol, signed and dated
+- all amendments plus a summary and rationale for changes
+- the latest English statistical analysis plan when separate
+- machine-readable versions of original documents not written in English
+- visible design, analysis and outcome-reporting content even when sensitive
+  material is redacted
+
+Confirm that the primary analysis matches the prespecified protocol and SAP.
+Explain deviations in Methods. Label unplanned post-hoc or exploratory analyses
+in the abstract and manuscript.
+
+### Study-type reporting
+
+Use the current guideline that matches the design, including:
+
+- CONSORT 2025 and relevant extensions for randomized trials
+- CONSORT-AI for clinical trials involving AI interventions
+- STROBE for observational studies
+- PRISMA for systematic reviews and meta-analyses
+- STARD or REMARK for diagnostic/prognostic biomarker studies
+- TRIPOD or TRIPOD-AI for prediction models
+- TARGET for observational target-trial emulation
+- CARE or the applicable N-of-1 CONSORT extension for case reports/series
+- BRISQ Tier 1 characteristics for human biospecimens when relevant
+
+Do not provide clinical-statistical advice beyond manuscript reporting checks
+without the protocol and SAP.
+
+## 6. Image integrity
+
+At review and revision, verify that:
+
+- submitted images are minimally processed and faithfully represent originals
+- unprocessed data and metadata are retained and can be supplied on request
+- acquisition tools, software, settings and processing are described in Methods
+- images gathered at different times or locations are not combined without
+  disclosure and clear boundaries
+- cloning, healing or tools that obscure manipulation are not used
+- brightness and contrast changes are global, applied equally to controls and
+  do not remove data
+- pseudocolour, nonlinear/gamma changes and channel-specific adjustments are
+  disclosed
+
+For gels and blots, record lane rearrangement, loading controls, crop boundaries,
+parallel processing and duplication checks. Accepted life-science papers require
+unprocessed original gel and western-blot images for Supplementary Information.
+
+## 7. Structures, chemistry and materials
+
+### Small-molecule crystallography
+
+Require at submission when applicable:
+
+- a standard `.cif` file
+- a structural figure with probability ellipsoids for Supplementary Information
+- structure factors for every structure
+- IUCr CheckCIF validation output as a PDF
+- explanations for all A- or B-level alerts
+
+### Other structures and materials
+
+- obtain official wwPDB validation reports for macromolecular structures when
+  required for peer review
+- deposit electron-microscopy density maps and coordinate data in the required
+  repositories
+- identify individual organic and inorganic compounds in order of first
+  appearance with logical bold numerals; do not number standard buffers,
+  reagents or solvents
+- for new compounds central to the conclusions, provide structure, synthesis
+  and characterization in enough detail for reproduction
+- use RRIDs or other persistent identifiers for key biological resources where
+  available
+- report cell-line source, authentication and distribution restrictions
+
+## 8. Taxonomy and provenance-sensitive samples
+
+- new or revised formal animal taxonomy may require registration and LSIDs from
+  ZooBank
+- geological, archaeological and palaeontological samples need transparent
+  provenance, permits and compliance with local laws
+- palaeontological and type specimens should be deposited in a recognized
+  museum or collection with accession codes where applicable
+- flag protected-site materials without documented permission
+
+## 9. Audit output
+
+Return a compact table:
+
+| Requirement | Applies? | Evidence in manuscript/files | Status | Required action |
+|---|---|---|---|---|
+
+Use `blocked` for missing registration, approval, consent, essential protocol,
+mandatory repository deposit, validation report or unavailable original data.
+Use `AUTHOR_INPUT_NEEDED` when applicability or administrative facts are not
+known.
+
+## 10. Official sources
+
+Verified 2026-08-08:
+
+- Research ethics: <https://www.nature.com/nature-portfolio/editorial-policies/ethics-and-biosecurity>
+- Clinical research: <https://www.nature.com/nature-portfolio/editorial-policies/clinical-research>
+- Reporting and availability: <https://www.nature.com/nature-portfolio/editorial-policies/reporting-standards>
+- Image integrity: <https://www.nature.com/nature-portfolio/editorial-policies/image-integrity>
+- Nature initial submission: <https://www.nature.com/nature/for-authors/initial-submission>

package/vendor/nature-skills/skills/nature-shared/core/terminology-ledger.md

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+# Terminology Ledger
+
+A manuscript must use one name for one thing. The same method, model, dataset,
+gene, metric, or concept must not drift across shifting names, spellings, or
+capitalisation. Reviewers read inconsistent terminology as careless work, and a
+term that changes between sections forces the reader to re-learn it.
+
+Build the ledger **before** drafting or polishing prose, and treat it as the
+single source of truth for the rest of the job. Consistency against a standard
+is impossible if the standard was never written down.
+
+## 1. Build the ledger on first contact
+
+When you first receive a manuscript, draft, or set of notes, extract every
+recurring domain term into a ledger before editing any prose:
+
+- methods, models, systems, algorithms, modules, frameworks
+- datasets, benchmarks, cohorts, materials, reagents
+- genes, proteins, species, cell lines (respect established field nomenclature)
+- metrics, units, statistical symbols, mathematical notation
+- abbreviations and acronyms, each with its full form
+- key concepts the paper defines or repeatedly relies on
+
+For each term, record its canonical form, its first-use expansion (for
+abbreviations), and any variants already present in the source.
+
+## 2. Present the ledger to the user
+
+Show a compact table before or alongside the first output:
+
+| Canonical term | First-use definition | Variants seen in source | Decision |
+|---|---|---|---|
+| scRNA-seq | single-cell RNA sequencing (scRNA-seq) | "single cell RNA-seq", "scRNAseq" | spell out once, then use "scRNA-seq" |
+
+Flag every collision explicitly: the same concept under different names, or one
+name reused for two different concepts. Ask the user to confirm the canonical
+choice only when the decision is genuinely ambiguous or domain-sensitive.
+Otherwise adopt the form the source uses most often and state that choice.
+
+## 3. Lock and enforce
+
+Once set, the ledger is fixed for the whole job:
+
+- Use only canonical forms in every output. Do not introduce synonyms to vary
+  the prose. Terminology consistency outranks lexical variety in scientific
+  writing.
+- Define each abbreviation once, at first use, then use the short form.
+- Keep units, symbols, and notation identical across every section.
+- When drafting or polishing a later section, reference the ledger built from
+  the earlier sections instead of re-deciding term by term.
+- If the user later renames a term, change every occurrence in the manuscript,
+  not just the current passage, and update the ledger.
+
+## 4. Do not invent terms
+
+Do not coin new names for the author's methods, modules, or concepts. If a term
+is missing, undefined, or used inconsistently in ways you cannot resolve from
+the source, ask the user or flag it. Never fill the gap with a guessed name.

package/vendor/nature-skills/skills/nature-shared/journal-formats/nat-comms.md

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+# Nature Communications — formatting facts
+
+Authoritative facts about Nature Communications formatting requirements. Used by both `nature-polishing` and `nature-writing` when `journal=nat-comms`. This file holds the **facts**; each skill's `static/fragments/journal/nat-comms.md` adds the **action layer**.
+
+> Always verify against the journal's current guidelines before final submission. Limits change. The numbers below are accurate as of early 2026.
+
+## Article types and limits
+
+| Article type | Body words | Abstract | References | Display items | Methods placement |
+|---|---|---|---|---|---|
+| **Article** | ~5,000 (incl. Methods) | 150 words | ~60 | up to 10 (figures + tables combined) | within main text |
+| **Brief Communication** | ~2,000 (incl. Methods) | 100 words | ~20 | up to 4 | within main text |
+| **Review** | ~6,000 | 200 words | ~100 | flexible | N/A |
+| **Perspective** | ~4,000 | 150 words | ~50 | flexible | N/A |
+| **Correspondence** | ~500 | none | ~10 | 1 | within main text |
+
+### Critical word-count quirk (Articles)
+
+The ~5,000-word limit **includes Methods**. This is the single biggest practical difference from *Nature* (where Methods sits after references with its own ~3,000-word allowance).
+
+Budget upfront, e.g.:
+- ~3,500 words for Introduction + Results + Discussion
+- ~1,500 words for Methods
+
+A paper with 4,800 words of Intro/Results/Discussion plus 1,500 words of Methods is **30% over the limit**.
+
+## Abstract
+
+- 150 words maximum
+- Unstructured single paragraph
+- No citations
+- Spell out abbreviations at first use
+- Keywords are assigned by editorial staff, not submitted
+- Include quantitative results where possible (`94% conversion with 99% selectivity`, not `significant improvement`)
+- Lead with the finding, not the background — editors triage on the abstract
+
+## Figures and display items
+
+- **Up to 10 display items** in the main article (figures + tables combined)
+- **No Extended Data tier** (unlike *Nature*). Items beyond 10 go into Supplementary Information (downloadable, but still peer-reviewed)
+
+### Resolution and format
+
+| Parameter | Requirement |
+|---|---|
+| Line art resolution | 1,200 dpi minimum |
+| Halftone / photo resolution | 300 dpi minimum |
+| Combination (line + halftone) | 600 dpi minimum |
+| File formats | TIFF, EPS, PDF, or JPEG |
+| Color mode | RGB (online-only journal) |
+| Single-column width | 89 mm |
+| Double-column width | 183 mm |
+| In-figure font | Arial / Helvetica / sans-serif, 5–7 pt |
+| Panel labels | Lowercase bold letters (`a`, `b`, `c`, …) |
+
+Online-only publication means: color is free, no CMYK requirement, design for screen reading (sufficient contrast, colorblind-friendly palettes, clear labels).
+
+### Multi-panel figures
+
+Common and accepted. A single figure with panels `a`–`l` is normal. No formal panel cap, but readability is enforced informally — if panel labels need magnification, the figure has too many panels.
+
+## References
+
+- **Style**: standard Nature reference style
+- **In-text**: superscript numbers, sequential by first appearance. Multiple: `^1,2`. Ranges: `^3–7`.
+- **Cap**: ~60 for Articles (more generous than *Nature*'s ~30)
+- **Format example**:
+  ```
+  1. Smith, A. B., Johnson, C. D. & Williams, E. F. Title of article. Nat. Commun. 16, 1234 (2025).
+  ```
+- Author names: `Last, Initials` (no periods on initials)
+- `&` before the last author
+- Journal names abbreviated per ISO 4
+- Volume in **bold**
+- **Article number** (e.g., `1234`), not page range — Nature Communications is online-only
+- Year in parentheses
+- DOIs encouraged
+- Reference list appears **before** the Methods section in the published article, even though Methods is part of the main text in the manuscript
+
+## Supplementary Information
+
+- Single PDF or multiple files; peer-reviewed
+- Organize with a table of contents if it exceeds 10 pages
+- Labels: `Supplementary Fig. 1`, `Supplementary Table 1`, `Supplementary Note 1`, `Supplementary Methods`
+- Large tables → separate Excel files
+
+## Mandatory statements
+
+- **Data Availability statement** — required. Must specify repositories, accession numbers, DOIs. Enforced at production stage; **invalid or pre-publication accession numbers block publication**.
+- **Code Availability statement** — required if custom code was used. Must include repository URL and DOI (e.g., via Zenodo).
+- **Author contributions** — in the manuscript after the main text
+- **Competing interests** — in the manuscript
+- **Reporting Summary** — Nature Portfolio Reporting Summary required (Life Sciences Reporting Summary for life sciences). Sent to reviewers; not a checkbox exercise.
+
+## Cover page elements
+
+- **Title**: concise, informative, no abbreviations; recommended ≤ 15 words
+- Author names with superscript affiliation numbers
+- Affiliations with full institutional addresses
+- Corresponding author(s) with email
+- ORCID iDs required for corresponding author, encouraged for all
+
+## Cover letter (separate upload)
+
+Editors use the cover letter for triage. Do not waste it on generic statements like "broad interest." State explicitly:
+
+1. What the finding is (one sentence)
+2. What makes it new (one sentence)
+3. Why it matters across multiple scientific disciplines (one sentence)
+
+## Open access and licensing
+
+- Fully open access — APC applies (verify current rate; substantial)
+- Default license: **CC BY 4.0**
+- Some funders (e.g., UKRI) require CC BY; others allow CC BY-NC — check funder requirements
+
+## Transparent peer review
+
+- **Default since November 2022**: reviewer reports and author responses published alongside accepted articles
+- Authors may opt out during submission — opt-out must be deliberate
+- Consider opt-out if reviewer exchanges contain content not suitable for public record
+
+## Manuscript formats
+
+- Initial submission: single PDF preferred (Word- or LaTeX-generated), figures embedded
+- Revision: Springer Nature Word template **or** LaTeX `sn-jnl` class with `nature` option
+- BibTeX: `sn-nature.bst`
+- Both formats equally acceptable; no editorial preference
+
+## Common desk-rejection / production-hold patterns
+
+1. **Methods word count not budgeted** — most common formatting error, especially for authors transferring from *Nature*
+2. **Reporting Summary completed as checkbox** — vague `N/A` responses, no explanation for outlier exclusions, missing blinding info, weak power calculations → generates specific revision requests
+3. **Data availability statement with unresolved accession numbers** — production verifies all accessions before publication; invalid IDs block release
+4. **Generic cover letter** — fails to establish cross-disciplinary significance; signals authors haven't considered scope fit
+
+## Transfer from Nature
+
+Manuscripts rejected from *Nature* can transfer with reviews intact. Editors may decide on existing reviews or send for additional review. **Formatting differences (Methods placement, word limit including Methods, no Extended Data tier) are handled at revision, not at transfer**.