psyclaw 0.28.0 → 0.28.2

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Files changed (167) hide show
  1. package/README.md +5 -5
  2. package/agents/recommended/catalog.json +99 -0
  3. package/dist/apps/panel/index.html +5 -5
  4. package/dist/src/adapters/pi/extension.js +164 -18
  5. package/dist/src/adapters/pi/extension.js.map +1 -1
  6. package/dist/src/adapters/pi/rpc.d.ts +2 -0
  7. package/dist/src/adapters/pi/rpc.js +9 -2
  8. package/dist/src/adapters/pi/rpc.js.map +1 -1
  9. package/dist/src/agents/recommended-personas.d.ts +42 -0
  10. package/dist/src/agents/recommended-personas.js +135 -0
  11. package/dist/src/agents/recommended-personas.js.map +1 -0
  12. package/dist/src/ars/mode-editor.d.ts +20 -0
  13. package/dist/src/ars/mode-editor.js +57 -0
  14. package/dist/src/ars/mode-editor.js.map +1 -0
  15. package/dist/src/ars/profile.d.ts +4 -1
  16. package/dist/src/ars/profile.js +23 -6
  17. package/dist/src/ars/profile.js.map +1 -1
  18. package/dist/src/cli.js +6 -3
  19. package/dist/src/cli.js.map +1 -1
  20. package/dist/src/creation/contracts.d.ts +3 -0
  21. package/dist/src/creation/service.js +17 -5
  22. package/dist/src/creation/service.js.map +1 -1
  23. package/dist/src/index.d.ts +1 -0
  24. package/dist/src/index.js +1 -0
  25. package/dist/src/index.js.map +1 -1
  26. package/dist/src/orchestration/bundled-personas.d.ts +16 -0
  27. package/dist/src/orchestration/bundled-personas.js +101 -0
  28. package/dist/src/orchestration/bundled-personas.js.map +1 -0
  29. package/dist/src/orchestration/effects.d.ts +8 -0
  30. package/dist/src/orchestration/effects.js +39 -0
  31. package/dist/src/orchestration/effects.js.map +1 -0
  32. package/dist/src/orchestration/personas.d.ts +2 -1
  33. package/dist/src/orchestration/personas.js +20 -7
  34. package/dist/src/orchestration/personas.js.map +1 -1
  35. package/dist/src/orchestration/pi-executor.d.ts +9 -5
  36. package/dist/src/orchestration/pi-executor.js +55 -22
  37. package/dist/src/orchestration/pi-executor.js.map +1 -1
  38. package/dist/src/orchestration/research-agents.d.ts +3 -7
  39. package/dist/src/orchestration/research-agents.js +5 -69
  40. package/dist/src/orchestration/research-agents.js.map +1 -1
  41. package/dist/src/panel/server.js +6 -0
  42. package/dist/src/panel/server.js.map +1 -1
  43. package/dist/src/style/cli-ui.d.ts +14 -0
  44. package/dist/src/style/cli-ui.js +45 -0
  45. package/dist/src/style/cli-ui.js.map +1 -1
  46. package/dist/src/tui/skill-manager.js +1 -1
  47. package/dist/src/tui/skill-manager.js.map +1 -1
  48. package/dist/src/updates/update.js +9 -3
  49. package/dist/src/updates/update.js.map +1 -1
  50. package/package.json +11 -3
  51. package/vendor/academic-paper-skills/LICENSE +21 -0
  52. package/vendor/academic-paper-skills/NOTICE.md +7 -0
  53. package/vendor/academic-paper-skills/PSYCLAW_SOURCE.json +14 -0
  54. package/vendor/academic-paper-skills/academic-paper-composer/SKILL.md +840 -0
  55. package/vendor/academic-paper-skills/academic-paper-composer/references/section_guides.md +675 -0
  56. package/vendor/academic-paper-skills/academic-paper-composer/references/writing_standards.md +629 -0
  57. package/vendor/academic-paper-skills/academic-paper-composer/scripts/chapter_quality_check.py +470 -0
  58. package/vendor/academic-paper-skills/academic-paper-composer/scripts/final_evaluation.py +550 -0
  59. package/vendor/academic-paper-skills/academic-paper-strategist/SKILL.md +670 -0
  60. package/vendor/academic-paper-skills/academic-paper-strategist/references/quality_standards.md +336 -0
  61. package/vendor/academic-paper-skills/academic-paper-strategist/references/search_strategy.md +459 -0
  62. package/vendor/academic-paper-skills/academic-paper-strategist/scripts/evaluate_samples.py +300 -0
  63. package/vendor/academic-paper-skills/academic-paper-strategist/scripts/gap_analysis.py +399 -0
  64. package/vendor/ars/pi/wrapper.js +9 -0
  65. package/vendor/nature-skills/LICENSE +201 -0
  66. package/vendor/nature-skills/NOTICE.md +7 -0
  67. package/vendor/nature-skills/PSYCLAW_SOURCE.json +19 -0
  68. package/vendor/nature-skills/skills/nature-figure/README.md +107 -0
  69. package/vendor/nature-skills/skills/nature-figure/README_EN.md +107 -0
  70. package/vendor/nature-skills/skills/nature-figure/SKILL.md +154 -0
  71. package/vendor/nature-skills/skills/nature-figure/agents/openai.yaml +4 -0
  72. package/vendor/nature-skills/skills/nature-figure/evals/evals.json +325 -0
  73. package/vendor/nature-skills/skills/nature-figure/manifest.yaml +103 -0
  74. package/vendor/nature-skills/skills/nature-figure/references/ai-graphical-abstract-workflow.md +129 -0
  75. package/vendor/nature-skills/skills/nature-figure/references/api.md +576 -0
  76. package/vendor/nature-skills/skills/nature-figure/references/asset-adaptation.md +72 -0
  77. package/vendor/nature-skills/skills/nature-figure/references/backend-selection.md +118 -0
  78. package/vendor/nature-skills/skills/nature-figure/references/chart-types.md +348 -0
  79. package/vendor/nature-skills/skills/nature-figure/references/common-patterns.md +371 -0
  80. package/vendor/nature-skills/skills/nature-figure/references/demos.md +58 -0
  81. package/vendor/nature-skills/skills/nature-figure/references/design-theory.md +467 -0
  82. package/vendor/nature-skills/skills/nature-figure/references/figure-contract.md +122 -0
  83. package/vendor/nature-skills/skills/nature-figure/references/figure-legend-conventions.md +90 -0
  84. package/vendor/nature-skills/skills/nature-figure/references/multipanel-evidence-architecture.md +268 -0
  85. package/vendor/nature-skills/skills/nature-figure/references/nature-2026-observations.md +124 -0
  86. package/vendor/nature-skills/skills/nature-figure/references/nature-article-requirements.md +149 -0
  87. package/vendor/nature-skills/skills/nature-figure/references/openrouter-image-generation.md +141 -0
  88. package/vendor/nature-skills/skills/nature-figure/references/qa-contract.md +344 -0
  89. package/vendor/nature-skills/skills/nature-figure/references/r-template-index.md +66 -0
  90. package/vendor/nature-skills/skills/nature-figure/references/r-workflow.md +234 -0
  91. package/vendor/nature-skills/skills/nature-figure/references/template-catalog.md +33 -0
  92. package/vendor/nature-skills/skills/nature-figure/references/tutorials.md +260 -0
  93. package/vendor/nature-skills/skills/nature-figure/requirements.txt +1 -0
  94. package/vendor/nature-skills/skills/nature-figure/scripts/audit_figure_collisions.py +742 -0
  95. package/vendor/nature-skills/skills/nature-figure/scripts/audit_panel_alignment.py +933 -0
  96. package/vendor/nature-skills/skills/nature-figure/scripts/audit_pdf_text.py +152 -0
  97. package/vendor/nature-skills/skills/nature-figure/scripts/figure_safety.py +50 -0
  98. package/vendor/nature-skills/skills/nature-figure/scripts/generate_openrouter_schematic.py +260 -0
  99. package/vendor/nature-skills/skills/nature-figure/scripts/nature_figure_backend.py +93 -0
  100. package/vendor/nature-skills/skills/nature-figure/scripts/panel_alignment.R +188 -0
  101. package/vendor/nature-skills/skills/nature-figure/scripts/plot_templates.py +604 -0
  102. package/vendor/nature-skills/skills/nature-figure/scripts/validate_figure.py +835 -0
  103. package/vendor/nature-skills/skills/nature-figure/static/core/contract.md +55 -0
  104. package/vendor/nature-skills/skills/nature-figure/static/core/stance.md +41 -0
  105. package/vendor/nature-skills/skills/nature-figure/static/fragments/backend/python.md +56 -0
  106. package/vendor/nature-skills/skills/nature-figure/static/fragments/backend/r.md +63 -0
  107. package/vendor/nature-skills/skills/nature-figure/tests/test_figure_safety.py +209 -0
  108. package/vendor/nature-skills/skills/nature-polishing/README.md +58 -0
  109. package/vendor/nature-skills/skills/nature-polishing/README_EN.md +58 -0
  110. package/vendor/nature-skills/skills/nature-polishing/SKILL.md +111 -0
  111. package/vendor/nature-skills/skills/nature-polishing/agents/openai.yaml +4 -0
  112. package/vendor/nature-skills/skills/nature-polishing/manifest.yaml +101 -0
  113. package/vendor/nature-skills/skills/nature-polishing/references/latex-layout.md +211 -0
  114. package/vendor/nature-skills/skills/nature-polishing/references/nat-comms-2025-diction.md +73 -0
  115. package/vendor/nature-skills/skills/nature-polishing/references/phrasebank-playbook.md +175 -0
  116. package/vendor/nature-skills/skills/nature-polishing/references/published-article-patterns.md +126 -0
  117. package/vendor/nature-skills/skills/nature-polishing/references/section-moves.md +252 -0
  118. package/vendor/nature-skills/skills/nature-polishing/references/style-guardrails.md +94 -0
  119. package/vendor/nature-skills/skills/nature-polishing/references/writing-strategy.md +160 -0
  120. package/vendor/nature-skills/skills/nature-polishing/static/core/failure-modes.md +29 -0
  121. package/vendor/nature-skills/skills/nature-polishing/static/core/output-format.md +21 -0
  122. package/vendor/nature-skills/skills/nature-polishing/static/core/stance.md +26 -0
  123. package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/generic.md +17 -0
  124. package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/nat-comms.md +38 -0
  125. package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/nat-mach-intell.md +102 -0
  126. package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/nature.md +19 -0
  127. package/vendor/nature-skills/skills/nature-polishing/static/fragments/language/en.md +19 -0
  128. package/vendor/nature-skills/skills/nature-polishing/static/fragments/language/zh-to-en.md +19 -0
  129. package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/algorithmic.md +18 -0
  130. package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/hypothesis.md +17 -0
  131. package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/methods.md +35 -0
  132. package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/research.md +29 -0
  133. package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/review.md +17 -0
  134. package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/abstract.md +26 -0
  135. package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/conclusion.md +15 -0
  136. package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/discussion.md +48 -0
  137. package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/intro.md +33 -0
  138. package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/methods.md +26 -0
  139. package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/results.md +61 -0
  140. package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/title.md +17 -0
  141. package/vendor/nature-skills/skills/nature-ref-verifier/README.md +44 -0
  142. package/vendor/nature-skills/skills/nature-ref-verifier/README_EN.md +44 -0
  143. package/vendor/nature-skills/skills/nature-ref-verifier/SKILL.md +196 -0
  144. package/vendor/nature-skills/skills/nature-ref-verifier/agents/openai.yaml +4 -0
  145. package/vendor/nature-skills/skills/nature-ref-verifier/manifest.yaml +19 -0
  146. package/vendor/nature-skills/skills/nature-ref-verifier/references/common-patterns.md +96 -0
  147. package/vendor/nature-skills/skills/nature-shared/README.md +43 -0
  148. package/vendor/nature-skills/skills/nature-shared/README_EN.md +43 -0
  149. package/vendor/nature-skills/skills/nature-shared/SKILL.md +33 -0
  150. package/vendor/nature-skills/skills/nature-shared/agents/openai.yaml +6 -0
  151. package/vendor/nature-skills/skills/nature-shared/core/consistency-sweep.md +122 -0
  152. package/vendor/nature-skills/skills/nature-shared/core/discussion-argument-language.md +192 -0
  153. package/vendor/nature-skills/skills/nature-shared/core/ethics.md +88 -0
  154. package/vendor/nature-skills/skills/nature-shared/core/main-text-discipline.md +179 -0
  155. package/vendor/nature-skills/skills/nature-shared/core/nature-abstract.md +171 -0
  156. package/vendor/nature-skills/skills/nature-shared/core/nature-introduction.md +164 -0
  157. package/vendor/nature-skills/skills/nature-shared/core/nature-results-discussion.md +215 -0
  158. package/vendor/nature-skills/skills/nature-shared/core/paper-type-taxonomy.md +41 -0
  159. package/vendor/nature-skills/skills/nature-shared/core/reader-workflow.md +21 -0
  160. package/vendor/nature-skills/skills/nature-shared/core/research-compliance.md +192 -0
  161. package/vendor/nature-skills/skills/nature-shared/core/terminology-ledger.md +58 -0
  162. package/vendor/nature-skills/skills/nature-shared/journal-formats/nat-comms.md +139 -0
  163. package/vendor/nature-skills/skills/nature-shared/journal-formats/nature-machine-intelligence.md +431 -0
  164. package/vendor/nature-skills/skills/nature-shared/journal-formats/nature.md +313 -0
  165. package/vendor/nature-skills/skills/nature-shared/manifest.yaml +52 -0
  166. package/vendor/nature-skills/skills/nature-shared/scripts/check_consistency.py +273 -0
  167. package/vendor/nature-skills/skills/nature-shared/tests/test_check_consistency.py +63 -0
@@ -0,0 +1,171 @@
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+ # Nature Abstract Corpus Guidance
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+
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+ Use this reference when drafting, restructuring, or polishing an abstract for
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+ flagship **Nature**, **Nature Communications**, **Nature Machine Intelligence**,
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+ or another **Nature Portfolio** title. The patterns were initially distilled
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+ from an author-supplied reading set of published NMI papers and are generalized
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+ here as Nature-style defaults. They are **corpus-derived writing guidance, not
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+ official journal requirements**. Current target-journal instructions,
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+ article-type rules, reporting standards, and the paper's actual evidence always
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+ take precedence.
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+
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+ ## Contents
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+
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+ - [Treat the abstract as the shortest evidence chain](#treat-the-abstract-as-the-shortest-evidence-chain)
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+ - [Use a discovery-centred architecture](#use-a-discovery-centred-architecture)
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+ - [Make the gap sharp and brief](#make-the-gap-sharp-and-brief)
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+ - [Keep only answer-enabling method logic](#keep-only-answer-enabling-method-logic)
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+ - [Select one main claim](#select-one-main-claim)
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+ - [Use numbers by necessity](#use-numbers-by-necessity)
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+ - [End with the conceptual payoff](#end-with-the-conceptual-payoff)
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+ - [Align the abstract with the manuscript](#align-the-abstract-with-the-manuscript)
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+ - [Run the Nature abstract audit](#run-the-nature-abstract-audit)
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+
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+ ## Treat the abstract as the shortest evidence chain
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+
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+ Do not write the abstract as a compressed Introduction or a catalogue of
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+ sections. Compress the entire paper into the shortest chain that makes the
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+ central discovery understandable, credible, and consequential:
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+
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+ `precise problem or gap -> what the study does to resolve it -> main discovery -> decisive support or boundary -> what the discovery establishes -> why it matters`
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+
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+ Draft the abstract after the Introduction question, Results evidence chain,
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+ and Discussion synthesis are stable. The abstract should reveal the paper's
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+ argument, not the chronology of the research process.
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+
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+ ## Use a discovery-centred architecture
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+
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+ Use this default move order for a Nature Portfolio research article:
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+
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+ 1. known phenomenon or important problem
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+ 2. precise unresolved question
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+ 3. study design or conceptual move used to answer it
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+ 4. main discovery
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+ 5. one or two critical supporting findings or boundaries
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+ 6. conceptual, technical, or field-level implication
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+
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+ Move rapidly into the present study. Spend only enough background to make the
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+ gap intelligible. The centre of gravity must be `we found X`, not `we evaluated
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+ many models and datasets` or `we propose a framework`.
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+
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+ This move order is rhetorical guidance, not a requirement for six sentences.
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+ Combine moves when needed to satisfy the current target-journal abstract limit.
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+
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+ ## Make the gap sharp and brief
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+
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+ Use one sentence, or at most the minimum needed, to join the known phenomenon
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+ to the exact unknown. Prefer:
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+
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+ `X is increasingly used or observed, but whether, why, or under what conditions Y remains unclear.`
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+
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+ Do not spend abstract space proving that the whole field is important,
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+ summarizing several generations of prior work, or rehearsing the Introduction
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+ funnel. Avoid generic gaps such as `existing methods still face challenges`
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+ when the paper addresses a precise source, condition, mechanism, or boundary.
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+
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+ ## Keep only answer-enabling method logic
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+
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+ Describe the method at the minimum level needed to understand why the design
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+ can answer the stated question. Include, when central:
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+
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+ - the controlled factor or contrast that identifies the claim
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+ - the perturbation, intervention, or decomposition that tests the proposed
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+ source or mechanism
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+ - the scope needed to judge generalization
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+ - the theoretical property needed to understand the contribution
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+
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+ Omit learning rates, hardware, routine data splits, implementation modules,
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+ and dataset-by-dataset detail unless one of them defines the discovery or its
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+ boundary. The abstract is not a Methods summary.
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+
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+ ## Select one main claim
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+
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+ Choose one central claim and at most one or two supporting claims. Compress the
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+ remaining Results into evidence categories or omit them.
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+
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+ Use this hierarchy:
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+
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+ | Role | Abstract decision |
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+ |---|---|
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+ | Main claim | State explicitly and give it the most space |
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+ | Decisive support | Keep when needed to make the main claim credible |
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+ | Boundary | Keep when it materially changes how the claim must be read |
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+ | Scope credential | Mention briefly only when breadth itself supports the inference |
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+ | Secondary analysis | Omit or reserve for the main text/SI |
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+
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+ Do not give every Results subsection one sentence. Experimental scale is a
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+ credibility cue, not the protagonist: use `across ... settings` only when that
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+ scope is necessary to understand generality or confidence.
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+
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+ ## Use numbers by necessity
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+
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+ Nature Portfolio abstracts do not require a numeric result merely to appear
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+ empirical.
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+ Include a number only when it performs one of these functions:
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+
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+ - defines the strength or threshold of the main discovery
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+ - is itself the paper's principal law, prediction, or selection result
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+ - makes a decisive comparison interpretable
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+ - establishes a boundary that qualitative wording would obscure
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+
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+ Omit numbers when the conceptual or mechanistic claim is the contribution and
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+ the number would displace the evidence logic. Comparative wording may be
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+ adequate when the exact effect size is not the headline claim.
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+
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+ If several numbers compete for space, keep the one that most changes the
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+ reader's understanding of the central claim. Do not report sample counts,
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+ benchmarks, models, metrics, and multiple effect sizes simply because they are
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+ available.
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+
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+ ## End with the conceptual payoff
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+
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+ Use the final sentence to state what the findings change, enable, connect, or
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+ make predictable. Prefer a bounded field-level payoff over self-evaluation:
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+
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+ - a mechanism or principle becomes identifiable
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+ - a design or architecture choice becomes predictable
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+ - a method becomes applicable to a previously inaccessible regime
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+ - two areas become conceptually connected
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+ - a practical decision gains a quantitative or mechanistic basis
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+
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+ Do not end with `the proposed method achieves superior performance` or a broad
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+ promise unsupported by the tested scope.
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+
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+ ## Align the abstract with the manuscript
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+
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+ Treat the four sections as different compressions of the same central claim:
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+
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+ - **Abstract:** the manuscript's shortest claim–evidence–implication chain
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+ - **Introduction:** why the exact question must be asked
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+ - **Results:** the full escalating evidence chain that answers it
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+ - **Discussion:** what the answers mean together
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+
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+ Every abstract claim must map to visible Results evidence. The final implication
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+ must match the Discussion synthesis without exceeding its boundaries. Do not
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+ introduce a claim, mechanism, or application in the abstract that the main text
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+ does not establish.
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+
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+ ## Run the Nature abstract audit
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+
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+ Build this compact map before sentence polishing:
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+
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+ | Abstract move | Content | Manuscript support | Keep test |
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+ |---|---|---|---|
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+ | Gap | Exact unresolved question | Introduction | Can it be stated in one sharp sentence? |
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+ | Design | Answer-enabling logic | Methods/Results | Does it explain why the question is answerable? |
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+ | Main discovery | One central claim | Results | Is this the paper's real advance? |
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+ | Support/boundary | One or two decisive findings | Results | Does each materially strengthen or bound the claim? |
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+ | Payoff | What the finding changes | Discussion | Is it important and scope-calibrated? |
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+
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+ Then delete or compress:
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+
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+ - background already implied by the title
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+ - implementation detail that does not explain identification or inference
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+ - experiment inventory presented instead of a discovery
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+ - secondary Results included only for completeness
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+ - numbers that do not define, support, or bound the main claim
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+ - a final sentence that merely says the method performs well
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+
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+ Read the abstract once with all method and dataset names hidden. If the central
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+ discovery and why it matters are no longer clear, the abstract is organized
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+ around implementation rather than insight.
@@ -0,0 +1,164 @@
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+ # Nature Introduction Corpus Guidance
2
+
3
+ Use this reference when drafting, restructuring, or polishing an Introduction
4
+ for flagship **Nature**, **Nature Communications**, **Nature Machine
5
+ Intelligence**, or another **Nature Portfolio** title. The patterns were
6
+ initially distilled from an author-supplied reading set of published NMI papers
7
+ and are generalized here as Nature-style defaults. They are **corpus-derived
8
+ writing guidance, not official journal requirements**. Current target-journal
9
+ instructions, article-type rules, reporting standards, and the paper's actual
10
+ evidence always take precedence.
11
+
12
+ ## Contents
13
+
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+ - [Make the Introduction converge](#make-the-introduction-converge)
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+ - [State an exact knowledge gap](#state-an-exact-knowledge-gap)
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+ - [Use literature to construct the gap](#use-literature-to-construct-the-gap)
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+ - [Frame a scientific question](#frame-a-scientific-question)
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+ - [Let the answer emerge late](#let-the-answer-emerge-late)
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+ - [End with a compact research route](#end-with-a-compact-research-route)
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+ - [Align Introduction, Results, and Discussion](#align-introduction-results-and-discussion)
21
+ - [Run the Nature Introduction audit](#run-the-nature-introduction-audit)
22
+
23
+ ## Make the Introduction converge
24
+
25
+ Build a narrowing argument rather than an extended topic overview:
26
+
27
+ `important problem -> specific phenomenon or difficulty -> what existing approaches establish -> unresolved limitation or tension -> exact unknown -> research question or hypothesis -> what this study does`
28
+
29
+ Move quickly. Assume the target journal's readers understand the broad field's
30
+ importance; use only enough context to make the specific unresolved problem
31
+ intelligible. By the end of the opening paragraph, expose the concrete
32
+ phenomenon, contradiction, failure condition, or bottleneck whenever the
33
+ material permits it.
34
+
35
+ Delete or compress background that neither narrows the problem nor makes the
36
+ eventual question necessary. A history of the field is not a substitute for a
37
+ problem funnel.
38
+
39
+ ## State an exact knowledge gap
40
+
41
+ Express the gap as something genuinely unknown, disputed, or untested. Prefer:
42
+
43
+ - what causes an observed advantage or failure
44
+ - under what conditions a claimed benefit appears or disappears
45
+ - which mechanism, information source, or design choice is necessary
46
+ - why two credible bodies of evidence disagree
47
+ - whether a proposed representation or signal adds information beyond the
48
+ current baseline
49
+
50
+ Avoid `existing methods have limitations` unless the next clause names the
51
+ specific limitation and why resolving it matters. The reader should be able to
52
+ complete the sentence:
53
+
54
+ > It remains unclear whether, why, or under what conditions ______.
55
+
56
+ Do not define the gap as the absence of the author's method. `No one has used
57
+ our architecture for this task` is not yet a scientific unknown.
58
+
59
+ ## Use literature to construct the gap
60
+
61
+ Organize citations by argumentative function, not as an author-by-author
62
+ catalogue:
63
+
64
+ 1. establish the known capability, phenomenon, or prevailing explanation
65
+ 2. show what prior work has already resolved
66
+ 3. expose the unresolved condition, boundary, or contradiction
67
+ 4. make the present research question unavoidable
68
+
69
+ When the literature contains tension, state both sides fairly and use the
70
+ tension to motivate a discriminating question. Avoid generic transitions such
71
+ as `substantial progress has been made, but challenges remain` when the cited
72
+ work supports a more exact conflict or boundary.
73
+
74
+ Every literature paragraph must earn its place by narrowing the question. Move
75
+ material that only demonstrates breadth to Related Work, Methods context, or a
76
+ shorter citation cluster.
77
+
78
+ ## Frame a scientific question
79
+
80
+ Prefer a question about a phenomenon, condition, mechanism, or boundary over a
81
+ method-demand claim:
82
+
83
+ - weak: `Existing methods are limited; therefore, a new method is needed.`
84
+ - stronger: `Performance improves in some settings but deteriorates in others;
85
+ which condition determines whether the proposed mechanism is beneficial?`
86
+
87
+ Let novelty arise from the unanswered question and the study design capable of
88
+ answering it. Remove unsupported novelty adjectives such as `novel`,
89
+ `groundbreaking`, `unprecedented`, or `innovative` when the question,
90
+ controlled comparison, or diagnostic perturbation already demonstrates the
91
+ advance.
92
+
93
+ ## Let the answer emerge late
94
+
95
+ Do not force the paper's preferred concept, mechanism, or framework into the
96
+ opening before the problem logic has motivated it. First establish the
97
+ phenomenon, limitation, and exact unknown; then introduce the study's conceptual
98
+ move as the natural way to resolve that unknown.
99
+
100
+ Use transitions such as `To address this question`, `To test this possibility`,
101
+ or `To this end` only after the question is explicit. Do not use the transition
102
+ to conceal a missing gap.
103
+
104
+ ## End with a compact research route
105
+
106
+ Prefer one connected closing paragraph over a ceremonial contribution list for
107
+ a Nature Portfolio research article, unless the target journal, article type,
108
+ editor, or user requires another structure. The paragraph should state:
109
+
110
+ `research question -> study design or conceptual move -> decisive evaluation route -> principal scope of inference`
111
+
112
+ Preview the logic of the Results without replaying all findings, metrics, or
113
+ figure-level detail. A restrained result-level statement is acceptable when it
114
+ clarifies the paper's answer, but do not turn the final paragraph into an
115
+ abstract or Discussion.
116
+
117
+ The route should tell the reader why the chosen comparisons, perturbations,
118
+ decompositions, or boundary tests can answer the stated question. Method names
119
+ alone do not provide that logic.
120
+
121
+ ## Align Introduction, Results, and Discussion
122
+
123
+ Treat the three sections as one story at different levels:
124
+
125
+ - **Introduction:** establish why each central question must be asked.
126
+ - **Results:** answer the questions through an escalating evidence chain.
127
+ - **Discussion:** synthesize what those answers mean together.
128
+
129
+ Draft backward from the paper's actual Results claims. For every central
130
+ Results subsection, identify the question that the Introduction must motivate.
131
+ For every question or hypothesis introduced, identify the Results subsection
132
+ that answers it. Do not create parallel stories.
133
+
134
+ A useful alignment pattern is:
135
+
136
+ `Introduction: phenomenon -> unresolved source -> necessary-condition question -> decomposition question`
137
+
138
+ `Results: establish phenomenon -> identify source -> perturb or test necessity -> decompose contributions -> establish boundaries`
139
+
140
+ `Discussion: synthesize the answers -> relate to theory and prior work -> state implications and limits`
141
+
142
+ ## Run the Nature Introduction audit
143
+
144
+ First state the paper's exact unknown in one sentence. If that sentence is
145
+ vague, repair the gap before polishing prose.
146
+
147
+ Then build this reverse-outline table:
148
+
149
+ | Introduction unit | Narrowing move | Literature function | Question motivated | Results answer |
150
+ |---|---|---|---|---|
151
+ | Paragraph or sentence block | What becomes more specific here? | Establish, resolve, contrast, or expose gap | Which exact question follows? | Which Results subsection answers it? |
152
+
153
+ Flag and revise any unit that:
154
+
155
+ - adds field background without narrowing the problem
156
+ - lists studies without constructing a known–unknown transition
157
+ - introduces the solution before the reader can see why it is needed
158
+ - claims novelty mainly through adjectives
159
+ - previews a Results claim for which no question has been motivated
160
+ - motivates a question that the Results never answer
161
+
162
+ Before finalizing, run a deletion test: if removing a paragraph leaves the
163
+ exact gap, research question, and Results roadmap intact, compress, relocate, or
164
+ delete that paragraph.
@@ -0,0 +1,215 @@
1
+ # Nature Results–Discussion Corpus Guidance
2
+
3
+ Use this reference when drafting, restructuring, or polishing Results and
4
+ Discussion for flagship **Nature**, **Nature Communications**, **Nature Machine
5
+ Intelligence**, or another **Nature Portfolio** title. The patterns were
6
+ initially distilled from an author-supplied NMI reading set and reinforced by a
7
+ second author-supplied comparison set of flagship Nature papers. They are
8
+ generalized here as Nature-style defaults and remain **corpus-derived writing
9
+ guidance, not official journal requirements**. Current target-journal
10
+ instructions, article-type rules, reporting standards, and the paper's actual
11
+ evidence always take precedence.
12
+
13
+ ## Contents
14
+
15
+ - [Core division of labour](#core-division-of-labour)
16
+ - [Build Results as claim escalation](#build-results-as-claim-escalation)
17
+ - [Choose an evidence-chain archetype](#choose-an-evidence-chain-archetype)
18
+ - [Prevent same-level repetition](#prevent-same-level-repetition)
19
+ - [Prefer diagnostic experiments when mechanism matters](#prefer-diagnostic-experiments-when-mechanism-matters)
20
+ - [End evidence units with an inference](#end-evidence-units-with-an-inference)
21
+ - [Apply the local-interpretation gate](#apply-the-local-interpretation-gate)
22
+ - [Write Discussion as synthesis, not re-demonstration](#write-discussion-as-synthesis-not-re-demonstration)
23
+ - [Run the Nature claim-escalation audit](#run-the-nature-claim-escalation-audit)
24
+
25
+ ## Core division of labour
26
+
27
+ - **Results:** establish and advance the paper's scientific claims through an
28
+ evidence chain. Results may include comparison, ablation, perturbation,
29
+ robustness, failure analysis, directly evidence-bound interpretation, and a
30
+ local inference.
31
+ - **Discussion:** synthesize several established claims into a higher-order
32
+ understanding, relate that understanding to prior work, explain its
33
+ importance, and bound its implications.
34
+
35
+ Do not enforce the mechanical split `Results = facts only` and
36
+ `Discussion = all interpretation`. The operative boundary is local versus
37
+ synthetic interpretation: keep an explanation in Results when it directly
38
+ resolves the experiment just reported; move broader theory, literature
39
+ integration, general implications, and extended speculation to Discussion.
40
+
41
+ ## Build Results as claim escalation
42
+
43
+ Make each Results subsection answer one scientific question and establish one
44
+ new claim. Prefer a conclusion-bearing heading over a procedural experiment
45
+ label when the evidence supports it.
46
+
47
+ Order adjacent subsections so that each result creates the next question:
48
+
49
+ `observation -> unresolved question -> targeted experiment -> comparison or perturbation -> local interpretation -> stronger claim -> next question`
50
+
51
+ At paper level, prefer an escalating arc such as:
52
+
53
+ `phenomenon -> source -> necessary condition or mechanism -> decomposition -> boundary or robustness`
54
+
55
+ Do not substitute repeated demonstrations of the same claim for escalation.
56
+ Two subsections may share data, conditions, or methods; they become redundant
57
+ only when they collapse to the same inferential conclusion.
58
+
59
+ ## Choose an evidence-chain archetype
60
+
61
+ Organize Results by inferential function, not by a routine inventory such as
62
+ `system description -> benchmark -> ablation`. Select or combine the archetype
63
+ that matches the scientific claim:
64
+
65
+ ### Discovery loop
66
+
67
+ Use when evidence changes what should be tested next:
68
+
69
+ `initial hypothesis -> real or decisive test -> analyse the resulting evidence -> refine the hypothesis -> next test -> architecture or mechanism validation`
70
+
71
+ The Results should preserve the epistemic loop without becoming a chronological
72
+ lab notebook. Keep only iterations that change the claim or the next scientific
73
+ question.
74
+
75
+ ### Core capability and validation envelope
76
+
77
+ Use when the paper establishes one central capability, then asks whether it is
78
+ reliable, safe, general, or confounded:
79
+
80
+ `establish core capability -> validate in decisive settings -> test safety or bias -> rule out central alternatives -> define limits`
81
+
82
+ Treat medication, subgroup, decision, bias, or perturbation analyses as the
83
+ validation envelope of the main story when they answer whether the same core
84
+ capability survives important conditions. Do not present each check as an
85
+ unrelated second discovery.
86
+
87
+ ### Capability ladder
88
+
89
+ Use when a system or model supports progressively stronger claims:
90
+
91
+ `quantitative performance -> robustness to data properties -> stronger competitors or tuned ensembles -> interpretability -> broader foundation or transfer abilities`
92
+
93
+ Each rung must justify a stronger inference. More datasets or another benchmark
94
+ at the same inferential level do not automatically create a new rung.
95
+
96
+ Across archetypes, the most common functional chain is:
97
+
98
+ `establish the phenomenon -> stress-test it -> rule out alternatives -> broaden it -> interpret it -> bound it`
99
+
100
+ Not every paper needs every move. Preserve the shortest chain sufficient for
101
+ the central claim.
102
+
103
+ ## Prevent same-level repetition
104
+
105
+ A later subsection may reuse an earlier baseline, control, or reference
106
+ contrast, but it must not present the same comparison and conclusion as a new
107
+ result. Treat reused conditions as **necessary comparators**, not as the centre
108
+ of the later subsection.
109
+
110
+ Ask what deeper discriminator the later analysis adds:
111
+
112
+ - content versus correct correspondence
113
+ - association versus necessity
114
+ - nominal performance versus robustness
115
+ - apparent gain versus a data, compute, or tuning confound
116
+ - one setting versus the boundary of generalization
117
+
118
+ Make the new perturbation, falsification, stronger comparator, or boundary test
119
+ the subsection's decisive evidence. If two adjacent subsections can both be
120
+ summarized as `X helps`, merge them, compress the repeated contrast, or move the
121
+ weaker demonstration to SI. A valid progression looks like:
122
+
123
+ `X is associated with the effect -> disrupting the proposed relation removes the effect -> therefore the relation, not merely the presence of X, is necessary within the tested design`
124
+
125
+ ## Prefer diagnostic experiments when mechanism matters
126
+
127
+ When the claim concerns why a result occurs, do more than show performance with
128
+ and without a component. Where scientifically valid, perturb, shuffle, mask,
129
+ misalign, remove, or otherwise disrupt the proposed information or mechanism,
130
+ then test whether the predicted degradation occurs.
131
+
132
+ Use the logic:
133
+
134
+ `association -> targeted disruption -> predicted degradation -> bounded mechanism inference`
135
+
136
+ Do not turn this pattern into automatic causal language. Calibrate the
137
+ inference to the intervention, controls, design, and alternative explanations.
138
+
139
+ ## End evidence units with an inference
140
+
141
+ After a coherent group of measurements, state what the evidence establishes;
142
+ do not stop at a sequence of numbers. The inference must be no broader than the
143
+ evaluated conditions.
144
+
145
+ Report failures, reversals, anomalous scaling, weak subgroups, and performance
146
+ trade-offs when they materially define where the claim holds, weakens, or
147
+ fails. Do not hide a conclusion-changing boundary in Supplementary
148
+ Information.
149
+
150
+ Place robustness in the main text when it establishes a necessary condition,
151
+ rules out a central alternative, reveals a failure boundary, or otherwise
152
+ creates an independent scientific inference. Route it to SI when it only adds
153
+ reassurance that the same conclusion survives another seed, estimator,
154
+ threshold, or secondary specification.
155
+
156
+ ## Apply the local-interpretation gate
157
+
158
+ Results may use calibrated language such as `suggests`, `indicates`, `likely
159
+ because`, `probably owing to`, or `we speculate that` only when all of the
160
+ following hold:
161
+
162
+ 1. the interpretation answers the question raised by the immediately preceding
163
+ result
164
+ 2. the evidence for it is visible in the current subsection
165
+ 3. uncertainty and alternative explanations remain explicit
166
+ 4. the passage closes the local evidence unit instead of opening a broad field
167
+ discussion
168
+
169
+ If several sentences are needed to reconcile theory, prior literature, or
170
+ competing mechanisms, state the bounded local inference in Results and move the
171
+ extended synthesis to Discussion or SI as appropriate.
172
+
173
+ ## Write Discussion as synthesis, not re-demonstration
174
+
175
+ Use the move order:
176
+
177
+ `brief central finding anchor -> cross-Results synthesis -> relation to prior work or theory -> importance -> boundary conditions and limitations -> broader implications or future directions`
178
+
179
+ Open by redefining the paper's central discovery in one compressed judgement.
180
+ A short recap—and occasionally one indispensable anchor number—is acceptable.
181
+ Then move immediately to mechanism or conceptual interpretation, significance,
182
+ limitations, and future directions. Do not repeat the full comparison, effect
183
+ size, statistical test, and inference already used to demonstrate the claim in
184
+ Results.
185
+
186
+ Distinguish:
187
+
188
+ - **necessary recap / anchor:** `Results establishes X; taken together, X implies Y`
189
+ - **redundant re-demonstration:** Results and Discussion both replay
190
+ `A versus B -> effect -> test -> therefore X`
191
+
192
+ Some published Nature Portfolio content types may use a Conclusion rather than
193
+ a standalone Discussion. Treat that as corpus variation, not permission to
194
+ ignore the current target-journal article-type instructions or an
195
+ editor-provided template.
196
+
197
+ ## Run the Nature claim-escalation audit
198
+
199
+ For each Results subsection, record:
200
+
201
+ | Audit field | Question |
202
+ |---|---|
203
+ | Scientific question | What unresolved question does this subsection answer? |
204
+ | New claim | What proposition becomes supportable here that was not supportable before? |
205
+ | Evidence-chain role | Establish, stress-test, discriminate, broaden, interpret, or bound? |
206
+ | Decisive evidence | Which comparison, perturbation, or analysis establishes it? |
207
+ | Inference gain | What independent inference would disappear if the subsection were removed? |
208
+ | Next question | What uncertainty naturally motivates the following subsection? |
209
+
210
+ Flag adjacent subsections when their `New claim` or `Inference gain` entries are
211
+ substantively identical. Merge, compress, or move the weaker repetition to SI.
212
+
213
+ Before finalizing Discussion, map every repeated claim to a distinct rhetorical
214
+ function: `anchor`, `synthesize`, `relate`, `bound`, or `extend`. Delete any
215
+ repetition that only re-demonstrates the Results evidence.
@@ -0,0 +1,41 @@
1
+ # Paper-type taxonomy
2
+
3
+ Canonical 5-type vocabulary used by both `nature-polishing` and `nature-writing` (and any future skill on the `paper_type` axis).
4
+
5
+ ## The five types
6
+
7
+ | Type | One-line definition | Reader's central question |
8
+ |---|---|---|
9
+ | **research** | Reports a phenomenon, mechanism, or finding from primary observation or experiment. | What was found and what does it mean? |
10
+ | **methods** | Proposes a new method, protocol, or measurement and demonstrates its advantage. | Does it work? Is it better? Is it reproducible? |
11
+ | **hypothesis** | Establishes or rules out a causal explanation through targeted evidence. | Is the proposed mechanism the right one? |
12
+ | **algorithmic** | Proposes a procedure, model, system, or device and shows it performs reliably and advantageously. | Does it perform under fair comparison? Where does it fail? |
13
+ | **review** | Synthesizes the state of a field, organizing the literature by argument, not by paper. | What is known, where is the disagreement, what is open? |
14
+
15
+ ## Detection guidance
16
+
17
+ - If the user names a paper type, use it.
18
+ - If the manuscript reports experiments testing a stated mechanism → **hypothesis**.
19
+ - If the manuscript proposes a procedure/model and reports comparisons → **algorithmic**.
20
+ - If the manuscript proposes a measurement or protocol and reports validation → **methods**.
21
+ - If the manuscript synthesizes prior literature without new primary data → **review**.
22
+ - Otherwise → **research** (default).
23
+
24
+ ## Notes on legacy vocab
25
+
26
+ Some older notes use a longer taxonomy (mechanism / method / resource / device / model / clinical / materials / computational / interdisciplinary). Map onto the five canonical types:
27
+
28
+ - mechanism, clinical, materials → **research** or **hypothesis** depending on whether a causal claim is central
29
+ - method → **methods**
30
+ - model, device, computational → **algorithmic**
31
+ - resource → usually **methods** (a dataset/benchmark paper) or **research**
32
+ - interdisciplinary → use the dominant argument structure, not the field label
33
+
34
+ ## Skill-specific action layers
35
+
36
+ Each skill's `static/fragments/paper_type/<type>.md` adds the **action layer** for that skill on top of this taxonomy:
37
+
38
+ - `nature-polishing` adds diagnostic rules (what to look for, what to fix).
39
+ - `nature-writing` adds constructive rules (argument chain, drafting order).
40
+
41
+ The taxonomy here is the **shared vocabulary**; the action is skill-specific.
@@ -0,0 +1,21 @@
1
+ # Reader workflow
2
+
3
+ Used by both `nature-polishing` and `nature-writing`. Always-loaded shared core.
4
+
5
+ ## The reader's question sequence
6
+
7
+ Most readers of a scientific paper follow a stable sequence:
8
+
9
+ 1. **Relevance** — Is this for me?
10
+ 2. **Novelty** — What is new here?
11
+ 3. **Trust** — Do I believe it?
12
+ 4. **Reuse** — Can I use it?
13
+ 5. **Meaning** — What does it mean, and where are the boundaries?
14
+
15
+ Whether the task is drafting from scratch or polishing existing prose, the paper should help the reader answer these questions in this order.
16
+
17
+ ## Implications
18
+
19
+ - A draft that buries novelty (question 2) behind methods detail (which serves question 3) will lose readers in the first paragraph.
20
+ - A polish that improves sentence-level fluency without surfacing relevance (question 1) earlier may still fail with broad-audience readers.
21
+ - "Where are the boundaries" (question 5) is the most commonly skipped. Both drafting and polishing should expose it, not paper over it.