medsci-skills 4.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (702) hide show
  1. package/LICENSE +50 -0
  2. package/README.md +602 -0
  3. package/README_FIRST.md +27 -0
  4. package/bin/medsci-skills.js +159 -0
  5. package/installers/install-macos.command +19 -0
  6. package/installers/install-windows.cmd +26 -0
  7. package/installers/install-windows.ps1 +17 -0
  8. package/installers/install.py +218 -0
  9. package/metadata/skills_catalog.json +452 -0
  10. package/package.json +48 -0
  11. package/skills/academic-aio/SKILL.md +408 -0
  12. package/skills/academic-aio/references/case_studies/kjr_mllm_2025.md +82 -0
  13. package/skills/academic-aio/references/checklists/AIO_GENERAL.md +354 -0
  14. package/skills/academic-aio/references/journal_summarybox_templates.yaml +126 -0
  15. package/skills/academic-aio/references/oac_funding_checklist.yaml +129 -0
  16. package/skills/academic-aio/references/reporting_guideline_mapping.md +39 -0
  17. package/skills/academic-aio/references/schema_markup_templates/CodeRepository.jsonld +32 -0
  18. package/skills/academic-aio/references/schema_markup_templates/Dataset.jsonld +36 -0
  19. package/skills/academic-aio/references/schema_markup_templates/Person.jsonld +30 -0
  20. package/skills/academic-aio/references/schema_markup_templates/README.md +43 -0
  21. package/skills/academic-aio/references/schema_markup_templates/ScholarlyArticle.jsonld +55 -0
  22. package/skills/academic-aio/scripts/batch_metadata_audit.py +169 -0
  23. package/skills/academic-aio/scripts/validate_schema.py +118 -0
  24. package/skills/academic-aio/skill.yml +36 -0
  25. package/skills/academic-aio/templates/aio_audit_checklist.md.j2 +108 -0
  26. package/skills/add-journal/SKILL.md +482 -0
  27. package/skills/add-journal/skill.yml +33 -0
  28. package/skills/analyze-stats/SKILL.md +598 -0
  29. package/skills/analyze-stats/references/analysis_guides/missing_data.md +109 -0
  30. package/skills/analyze-stats/references/analysis_guides/nhis_icd10_mapping.md +247 -0
  31. package/skills/analyze-stats/references/analysis_guides/propensity_score.md +132 -0
  32. package/skills/analyze-stats/references/analysis_guides/regression.md +115 -0
  33. package/skills/analyze-stats/references/analysis_guides/repeated_measures.md +160 -0
  34. package/skills/analyze-stats/references/analysis_guides/survey_weighted.md +366 -0
  35. package/skills/analyze-stats/references/analysis_guides/test_selection.md +86 -0
  36. package/skills/analyze-stats/references/style/figure_style.mplstyle +69 -0
  37. package/skills/analyze-stats/references/style/theme_publication.R +147 -0
  38. package/skills/analyze-stats/references/table-standards/journal-profiles/ajr.yaml +51 -0
  39. package/skills/analyze-stats/references/table-standards/journal-profiles/european_radiology.yaml +55 -0
  40. package/skills/analyze-stats/references/table-standards/journal-profiles/jama.yaml +66 -0
  41. package/skills/analyze-stats/references/table-standards/journal-profiles/lancet.yaml +57 -0
  42. package/skills/analyze-stats/references/table-standards/journal-profiles/nejm.yaml +51 -0
  43. package/skills/analyze-stats/references/table-standards/journal-profiles/radiology.yaml +66 -0
  44. package/skills/analyze-stats/references/table-standards/table-standards.md +287 -0
  45. package/skills/analyze-stats/references/table-standards/table-types/diagnostic_accuracy.md +36 -0
  46. package/skills/analyze-stats/references/table-standards/table-types/meta_analysis.md +58 -0
  47. package/skills/analyze-stats/references/table-standards/table-types/model_comparison.md +36 -0
  48. package/skills/analyze-stats/references/table-standards/table-types/regression_results.md +50 -0
  49. package/skills/analyze-stats/references/table-standards/table-types/table1_demographics.md +51 -0
  50. package/skills/analyze-stats/references/table-standards/tool-comparison.md +79 -0
  51. package/skills/analyze-stats/references/templates/agreement_analysis.py +436 -0
  52. package/skills/analyze-stats/references/templates/dca_plot.R +237 -0
  53. package/skills/analyze-stats/references/templates/diagnostic_accuracy.py +401 -0
  54. package/skills/analyze-stats/references/templates/dta_meta_analysis.R +384 -0
  55. package/skills/analyze-stats/references/templates/forest_plot.py +412 -0
  56. package/skills/analyze-stats/references/templates/likert_summary.py +356 -0
  57. package/skills/analyze-stats/references/templates/meta_analysis.R +365 -0
  58. package/skills/analyze-stats/references/templates/propensity_score.py +478 -0
  59. package/skills/analyze-stats/references/templates/regression.py +425 -0
  60. package/skills/analyze-stats/references/templates/repeated_measures.py +434 -0
  61. package/skills/analyze-stats/references/templates/sample_size.R +382 -0
  62. package/skills/analyze-stats/references/templates/survey_weighted_analysis.py +411 -0
  63. package/skills/analyze-stats/references/templates/survival_analysis.py +325 -0
  64. package/skills/analyze-stats/references/templates/table1_demographics.py +287 -0
  65. package/skills/analyze-stats/scripts/check_generated_code.py +335 -0
  66. package/skills/analyze-stats/skill.yml +38 -0
  67. package/skills/analyze-stats/tests/fixtures/gen_bad.R +16 -0
  68. package/skills/analyze-stats/tests/fixtures/gen_bad.py +24 -0
  69. package/skills/analyze-stats/tests/fixtures/gen_clean.py +21 -0
  70. package/skills/analyze-stats/tests/test_generated_code.sh +59 -0
  71. package/skills/analyze-stats/tests/test_survival_template.sh +53 -0
  72. package/skills/author-strategy/SKILL.md +117 -0
  73. package/skills/author-strategy/analyze_patterns.py +303 -0
  74. package/skills/author-strategy/fetch_pubmed.py +374 -0
  75. package/skills/author-strategy/skill.yml +34 -0
  76. package/skills/batch-cohort/SKILL.md +223 -0
  77. package/skills/batch-cohort/references/base_template_knhanes.R +210 -0
  78. package/skills/batch-cohort/references/batch_template_generator.R +222 -0
  79. package/skills/batch-cohort/references/variable_coding_registry.md +136 -0
  80. package/skills/batch-cohort/skill.yml +35 -0
  81. package/skills/calc-sample-size/SKILL.md +491 -0
  82. package/skills/calc-sample-size/references/formulas.md +655 -0
  83. package/skills/calc-sample-size/references/observational_cohort.md +49 -0
  84. package/skills/calc-sample-size/skill.yml +51 -0
  85. package/skills/check-reporting/SKILL.md +534 -0
  86. package/skills/check-reporting/references/LICENSES.md +41 -0
  87. package/skills/check-reporting/references/checklists/AMSTAR2.md +54 -0
  88. package/skills/check-reporting/references/checklists/ARRIVE_2.md +234 -0
  89. package/skills/check-reporting/references/checklists/CARE.md +102 -0
  90. package/skills/check-reporting/references/checklists/CLAIM_2024.md +128 -0
  91. package/skills/check-reporting/references/checklists/CLEAR.md +113 -0
  92. package/skills/check-reporting/references/checklists/CONSORT.md +86 -0
  93. package/skills/check-reporting/references/checklists/COSMIN_RoB.md +136 -0
  94. package/skills/check-reporting/references/checklists/GRRAS.md +61 -0
  95. package/skills/check-reporting/references/checklists/MI_CLEAR_LLM.md +167 -0
  96. package/skills/check-reporting/references/checklists/MOOSE.md +85 -0
  97. package/skills/check-reporting/references/checklists/NOS.md +88 -0
  98. package/skills/check-reporting/references/checklists/PRISMA_2020.md +135 -0
  99. package/skills/check-reporting/references/checklists/PRISMA_DTA.md +36 -0
  100. package/skills/check-reporting/references/checklists/PRISMA_P.md +56 -0
  101. package/skills/check-reporting/references/checklists/PROBAST.md +75 -0
  102. package/skills/check-reporting/references/checklists/PROBAST_AI.md +130 -0
  103. package/skills/check-reporting/references/checklists/QUADAS2.md +77 -0
  104. package/skills/check-reporting/references/checklists/QUADAS_C.md +131 -0
  105. package/skills/check-reporting/references/checklists/ROBINS_E.md +179 -0
  106. package/skills/check-reporting/references/checklists/ROBINS_I.md +87 -0
  107. package/skills/check-reporting/references/checklists/ROBIS.md +114 -0
  108. package/skills/check-reporting/references/checklists/ROB_ME.md +126 -0
  109. package/skills/check-reporting/references/checklists/RoB2.md +79 -0
  110. package/skills/check-reporting/references/checklists/RoB_NMA.md +96 -0
  111. package/skills/check-reporting/references/checklists/SPIRIT.md +112 -0
  112. package/skills/check-reporting/references/checklists/SQUIRE_2.md +68 -0
  113. package/skills/check-reporting/references/checklists/STARD.md +129 -0
  114. package/skills/check-reporting/references/checklists/STARD_AI.md +211 -0
  115. package/skills/check-reporting/references/checklists/STROBE.md +80 -0
  116. package/skills/check-reporting/references/checklists/SWiM.md +33 -0
  117. package/skills/check-reporting/references/checklists/TRIPOD.md +157 -0
  118. package/skills/check-reporting/references/checklists/TRIPOD_AI.md +140 -0
  119. package/skills/check-reporting/references/step4c_registration_timing.md +93 -0
  120. package/skills/check-reporting/references/step4d_prisma_figure_audit.md +137 -0
  121. package/skills/check-reporting/scripts/check_checklist_exists.py +183 -0
  122. package/skills/check-reporting/scripts/check_checklist_version.py +168 -0
  123. package/skills/check-reporting/scripts/check_framework_naming.py +206 -0
  124. package/skills/check-reporting/scripts/check_prisma_figure.py +209 -0
  125. package/skills/check-reporting/scripts/prisma_cascade_check.py +274 -0
  126. package/skills/check-reporting/skill.yml +41 -0
  127. package/skills/check-reporting/tests/fixtures/framework_bad.md +8 -0
  128. package/skills/check-reporting/tests/fixtures/framework_clean.md +7 -0
  129. package/skills/check-reporting/tests/test_checklist_fail_fast.sh +77 -0
  130. package/skills/check-reporting/tests/test_checklist_version.sh +72 -0
  131. package/skills/check-reporting/tests/test_framework_naming.sh +45 -0
  132. package/skills/check-reporting/tests/test_prisma_cascade.sh +104 -0
  133. package/skills/clean-data/SKILL.md +180 -0
  134. package/skills/clean-data/references/cleaning_patterns.md +299 -0
  135. package/skills/clean-data/references/profiling_template.py +304 -0
  136. package/skills/clean-data/scripts/check_structural_zero.py +174 -0
  137. package/skills/clean-data/skill.yml +35 -0
  138. package/skills/clean-data/tests/fixtures/smoking.csv +8 -0
  139. package/skills/clean-data/tests/test_structural_zero.sh +49 -0
  140. package/skills/cross-national/SKILL.md +264 -0
  141. package/skills/cross-national/skill.yml +37 -0
  142. package/skills/define-variables/SKILL.md +146 -0
  143. package/skills/define-variables/references/common_definitions.md +190 -0
  144. package/skills/define-variables/skill.yml +34 -0
  145. package/skills/define-variables/templates/variable_operationalization.md +64 -0
  146. package/skills/deidentify/SKILL.md +203 -0
  147. package/skills/deidentify/deidentify.py +1224 -0
  148. package/skills/deidentify/locales/_template.json +45 -0
  149. package/skills/deidentify/locales/au.json +43 -0
  150. package/skills/deidentify/locales/ca.json +44 -0
  151. package/skills/deidentify/locales/cn.json +47 -0
  152. package/skills/deidentify/locales/de.json +48 -0
  153. package/skills/deidentify/locales/fr.json +48 -0
  154. package/skills/deidentify/locales/in.json +48 -0
  155. package/skills/deidentify/locales/jp.json +48 -0
  156. package/skills/deidentify/locales/kr.json +48 -0
  157. package/skills/deidentify/locales/uk.json +45 -0
  158. package/skills/deidentify/locales/us.json +43 -0
  159. package/skills/deidentify/references/date_shift_guide.md +82 -0
  160. package/skills/deidentify/references/hipaa_18_identifiers.md +48 -0
  161. package/skills/deidentify/references/korean_phi_patterns.md +135 -0
  162. package/skills/deidentify/skill.yml +43 -0
  163. package/skills/deidentify/tests/README.md +26 -0
  164. package/skills/deidentify/tests/test_clean.csv +16 -0
  165. package/skills/deidentify/tests/test_edge_cases.csv +11 -0
  166. package/skills/deidentify/tests/test_phi_korean.csv +11 -0
  167. package/skills/design-ai-benchmarking/SKILL.md +214 -0
  168. package/skills/design-ai-benchmarking/references/benchmark_export_schema.json +69 -0
  169. package/skills/design-ai-benchmarking/references/elicitation_rubric_template.md +37 -0
  170. package/skills/design-ai-benchmarking/skill.yml +38 -0
  171. package/skills/design-study/SKILL.md +298 -0
  172. package/skills/design-study/skill.yml +33 -0
  173. package/skills/fill-icmje-coi/SKILL.md +216 -0
  174. package/skills/fill-icmje-coi/scripts/fill_icmje_coi.py +140 -0
  175. package/skills/fill-icmje-coi/skill.yml +35 -0
  176. package/skills/fill-icmje-coi/templates/icmje_coi_seed_synthetic.docx +0 -0
  177. package/skills/fill-protocol/SKILL.md +248 -0
  178. package/skills/fill-protocol/examples/example_irb_template.yaml +53 -0
  179. package/skills/fill-protocol/references/best_practices.md +121 -0
  180. package/skills/fill-protocol/scripts/doc_to_docx.py +111 -0
  181. package/skills/fill-protocol/scripts/fill_form.py +611 -0
  182. package/skills/fill-protocol/scripts/inspect_template.py +61 -0
  183. package/skills/fill-protocol/setup.sh +162 -0
  184. package/skills/fill-protocol/skill.yml +37 -0
  185. package/skills/find-cohort-gap/SKILL.md +309 -0
  186. package/skills/find-cohort-gap/references/cohort_profile_template.md +93 -0
  187. package/skills/find-cohort-gap/references/onepager_template.md +84 -0
  188. package/skills/find-cohort-gap/references/pattern_scoring_rubric.md +169 -0
  189. package/skills/find-cohort-gap/references/saturation_query_templates.md +143 -0
  190. package/skills/find-cohort-gap/skill.yml +35 -0
  191. package/skills/find-journal/POLICY.md +87 -0
  192. package/skills/find-journal/SKILL.md +340 -0
  193. package/skills/find-journal/references/journal_profiles/AJNR.md +29 -0
  194. package/skills/find-journal/references/journal_profiles/AJR.md +30 -0
  195. package/skills/find-journal/references/journal_profiles/Abdominal_Radiology.md +30 -0
  196. package/skills/find-journal/references/journal_profiles/Academic_Radiology.md +30 -0
  197. package/skills/find-journal/references/journal_profiles/Annals_of_Internal_Medicine.md +33 -0
  198. package/skills/find-journal/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +28 -0
  199. package/skills/find-journal/references/journal_profiles/BMC_Medicine.md +31 -0
  200. package/skills/find-journal/references/journal_profiles/British_Journal_of_Radiology.md +39 -0
  201. package/skills/find-journal/references/journal_profiles/CVIR.md +30 -0
  202. package/skills/find-journal/references/journal_profiles/Chest.md +39 -0
  203. package/skills/find-journal/references/journal_profiles/Clinical_Radiology.md +30 -0
  204. package/skills/find-journal/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +32 -0
  205. package/skills/find-journal/references/journal_profiles/Diabetes_Metabolism_Journal.md +36 -0
  206. package/skills/find-journal/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +32 -0
  207. package/skills/find-journal/references/journal_profiles/Endocrinology_and_Metabolism.md +37 -0
  208. package/skills/find-journal/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +39 -0
  209. package/skills/find-journal/references/journal_profiles/European_Radiology.md +29 -0
  210. package/skills/find-journal/references/journal_profiles/Hepatology_Communications.md +40 -0
  211. package/skills/find-journal/references/journal_profiles/Hepatology_International.md +37 -0
  212. package/skills/find-journal/references/journal_profiles/IEEE_JBHI.md +28 -0
  213. package/skills/find-journal/references/journal_profiles/IEEE_TMI.md +28 -0
  214. package/skills/find-journal/references/journal_profiles/INSI.md +29 -0
  215. package/skills/find-journal/references/journal_profiles/Investigative_Radiology.md +25 -0
  216. package/skills/find-journal/references/journal_profiles/JACC_Advances.md +41 -0
  217. package/skills/find-journal/references/journal_profiles/JACC_Asia.md +30 -0
  218. package/skills/find-journal/references/journal_profiles/JACR.md +28 -0
  219. package/skills/find-journal/references/journal_profiles/JAMA.md +40 -0
  220. package/skills/find-journal/references/journal_profiles/JAMA_Network_Open.md +30 -0
  221. package/skills/find-journal/references/journal_profiles/JCSM.md +39 -0
  222. package/skills/find-journal/references/journal_profiles/JKMS.md +32 -0
  223. package/skills/find-journal/references/journal_profiles/JMIR.md +29 -0
  224. package/skills/find-journal/references/journal_profiles/JMIR_Medical_Education.md +29 -0
  225. package/skills/find-journal/references/journal_profiles/JNIS.md +35 -0
  226. package/skills/find-journal/references/journal_profiles/JVIR.md +31 -0
  227. package/skills/find-journal/references/journal_profiles/Journal_of_Biomedical_Informatics.md +29 -0
  228. package/skills/find-journal/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +40 -0
  229. package/skills/find-journal/references/journal_profiles/Journal_of_Magnetic_Resonance_Imaging.md +30 -0
  230. package/skills/find-journal/references/journal_profiles/Journal_of_Nuclear_Medicine.md +31 -0
  231. package/skills/find-journal/references/journal_profiles/Journal_of_Stroke.md +32 -0
  232. package/skills/find-journal/references/journal_profiles/KJR.md +38 -0
  233. package/skills/find-journal/references/journal_profiles/Korean_Circulation_Journal.md +38 -0
  234. package/skills/find-journal/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +36 -0
  235. package/skills/find-journal/references/journal_profiles/Lancet_Diabetes_and_Endocrinology.md +40 -0
  236. package/skills/find-journal/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +49 -0
  237. package/skills/find-journal/references/journal_profiles/Lancet_Infectious_Diseases.md +38 -0
  238. package/skills/find-journal/references/journal_profiles/Lancet_Neurology.md +39 -0
  239. package/skills/find-journal/references/journal_profiles/Lancet_Oncology.md +40 -0
  240. package/skills/find-journal/references/journal_profiles/Lancet_Psychiatry.md +38 -0
  241. package/skills/find-journal/references/journal_profiles/Lancet_Public_Health.md +30 -0
  242. package/skills/find-journal/references/journal_profiles/Lancet_Respiratory_Medicine.md +39 -0
  243. package/skills/find-journal/references/journal_profiles/Liver_International.md +33 -0
  244. package/skills/find-journal/references/journal_profiles/Medical_Image_Analysis.md +28 -0
  245. package/skills/find-journal/references/journal_profiles/NEJM.md +33 -0
  246. package/skills/find-journal/references/journal_profiles/Nature_Machine_Intelligence.md +31 -0
  247. package/skills/find-journal/references/journal_profiles/Nature_Medicine.md +39 -0
  248. package/skills/find-journal/references/journal_profiles/Neuroradiology.md +31 -0
  249. package/skills/find-journal/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +39 -0
  250. package/skills/find-journal/references/journal_profiles/PLOS_Medicine.md +32 -0
  251. package/skills/find-journal/references/journal_profiles/RYAI.md +28 -0
  252. package/skills/find-journal/references/journal_profiles/Radiology.md +29 -0
  253. package/skills/find-journal/references/journal_profiles/Skeletal_Radiology.md +31 -0
  254. package/skills/find-journal/references/journal_profiles/Stroke.md +37 -0
  255. package/skills/find-journal/references/journal_profiles/The_BMJ.md +31 -0
  256. package/skills/find-journal/references/journal_profiles/The_Lancet.md +31 -0
  257. package/skills/find-journal/references/journal_profiles/The_Lancet_Digital_Health.md +29 -0
  258. package/skills/find-journal/references/journal_profiles/World_Journal_of_Hepatology.md +53 -0
  259. package/skills/find-journal/references/journal_profiles/npj_Digital_Medicine.md +29 -0
  260. package/skills/find-journal/skill.yml +34 -0
  261. package/skills/fulltext-retrieval/SKILL.md +174 -0
  262. package/skills/fulltext-retrieval/fetch_oa.py +433 -0
  263. package/skills/fulltext-retrieval/pdf_to_md.py +160 -0
  264. package/skills/fulltext-retrieval/skill.yml +41 -0
  265. package/skills/generate-codebook/SKILL.md +155 -0
  266. package/skills/generate-codebook/references/codebook_schema.md +76 -0
  267. package/skills/generate-codebook/scripts/generate_codebook.py +278 -0
  268. package/skills/generate-codebook/skill.yml +35 -0
  269. package/skills/generate-codebook/tests/test_generate_codebook.sh +76 -0
  270. package/skills/grant-builder/SKILL.md +251 -0
  271. package/skills/grant-builder/skill.yml +34 -0
  272. package/skills/humanize/SKILL.md +251 -0
  273. package/skills/humanize/references/ai_patterns.md +571 -0
  274. package/skills/humanize/skill.yml +33 -0
  275. package/skills/intake-project/SKILL.md +264 -0
  276. package/skills/intake-project/skill.yml +34 -0
  277. package/skills/lit-sync/SKILL.md +448 -0
  278. package/skills/lit-sync/references/locale/ko/note_templates.md +110 -0
  279. package/skills/lit-sync/skill.yml +52 -0
  280. package/skills/lit-sync/tests/test_poll_logic.sh +92 -0
  281. package/skills/ma-scout/SKILL.md +640 -0
  282. package/skills/ma-scout/references/project_readme_template.md +95 -0
  283. package/skills/ma-scout/references/project_readme_template_ko.md +82 -0
  284. package/skills/ma-scout/skill.yml +33 -0
  285. package/skills/make-figures/SKILL.md +957 -0
  286. package/skills/make-figures/references/critic_rubrics/data_plot.md +166 -0
  287. package/skills/make-figures/references/critic_rubrics/flow_diagram.md +169 -0
  288. package/skills/make-figures/references/design_principles.md +181 -0
  289. package/skills/make-figures/references/exemplar_diagrams/README.md +65 -0
  290. package/skills/make-figures/references/exemplar_diagrams/consort/README.md +15 -0
  291. package/skills/make-figures/references/exemplar_diagrams/consort/template_input.yaml +37 -0
  292. package/skills/make-figures/references/exemplar_diagrams/consort/template_output.pdf +0 -0
  293. package/skills/make-figures/references/exemplar_diagrams/consort/template_output.png +0 -0
  294. package/skills/make-figures/references/exemplar_diagrams/consort/template_output_600.png +0 -0
  295. package/skills/make-figures/references/exemplar_diagrams/other/other_02.meta.yaml +4 -0
  296. package/skills/make-figures/references/exemplar_diagrams/other/other_02.png +0 -0
  297. package/skills/make-figures/references/exemplar_diagrams/other/other_02_why.md +13 -0
  298. package/skills/make-figures/references/exemplar_diagrams/pipeline/README.md +15 -0
  299. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_01.meta.yaml +4 -0
  300. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_01.png +0 -0
  301. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_01_why.md +13 -0
  302. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_03.meta.yaml +4 -0
  303. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_03.png +0 -0
  304. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_03_why.md +13 -0
  305. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_04.meta.yaml +4 -0
  306. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_04.png +0 -0
  307. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_04_why.md +13 -0
  308. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_05.meta.yaml +4 -0
  309. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_05.png +0 -0
  310. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_05_why.md +13 -0
  311. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_06.meta.yaml +4 -0
  312. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_06.png +0 -0
  313. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_06_why.md +13 -0
  314. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_07.meta.yaml +4 -0
  315. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_07.png +0 -0
  316. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_07_why.md +13 -0
  317. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_08.meta.yaml +4 -0
  318. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_08.png +0 -0
  319. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_08_why.md +13 -0
  320. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_09.meta.yaml +4 -0
  321. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_09.png +0 -0
  322. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_09_why.md +13 -0
  323. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_10.meta.yaml +4 -0
  324. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_10.png +0 -0
  325. package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_10_why.md +13 -0
  326. package/skills/make-figures/references/exemplar_diagrams/prisma/README.md +15 -0
  327. package/skills/make-figures/references/exemplar_diagrams/prisma/template_input.yaml +47 -0
  328. package/skills/make-figures/references/exemplar_diagrams/prisma/template_output.pdf +0 -0
  329. package/skills/make-figures/references/exemplar_diagrams/prisma/template_output.png +0 -0
  330. package/skills/make-figures/references/exemplar_diagrams/prisma/template_output_600.png +0 -0
  331. package/skills/make-figures/references/exemplar_diagrams/stard/README.md +15 -0
  332. package/skills/make-figures/references/exemplar_diagrams/stard/template_input.yaml +40 -0
  333. package/skills/make-figures/references/exemplar_diagrams/stard/template_output.pdf +0 -0
  334. package/skills/make-figures/references/exemplar_diagrams/stard/template_output.png +0 -0
  335. package/skills/make-figures/references/exemplar_diagrams/stard/template_output_600.png +0 -0
  336. package/skills/make-figures/references/exemplar_diagrams/strobe/template_input.yaml +43 -0
  337. package/skills/make-figures/references/exemplar_diagrams/strobe/template_input_pptx.yaml +43 -0
  338. package/skills/make-figures/references/exemplar_diagrams/strobe/template_output.pdf +0 -0
  339. package/skills/make-figures/references/exemplar_diagrams/strobe/template_output.png +0 -0
  340. package/skills/make-figures/references/exemplar_diagrams/strobe/template_output.pptx +0 -0
  341. package/skills/make-figures/references/exemplar_diagrams/strobe/template_output_600.png +0 -0
  342. package/skills/make-figures/references/figure_specs.md +291 -0
  343. package/skills/make-figures/references/flow_diagram_lessons.md +164 -0
  344. package/skills/make-figures/references/jacc_central_illustration_principles.md +91 -0
  345. package/skills/make-figures/references/medical_illustration_sources.md +98 -0
  346. package/skills/make-figures/references/pipeline_concepts_medical_ai.md +240 -0
  347. package/skills/make-figures/references/reporting_guideline_figure_map.md +104 -0
  348. package/skills/make-figures/references/visual_abstract_templates/european_radiology.pptx +0 -0
  349. package/skills/make-figures/references/visual_abstract_templates/jacc_central_illustration.pptx +0 -0
  350. package/skills/make-figures/references/visual_abstract_templates/medsci_default.pptx +0 -0
  351. package/skills/make-figures/references/visual_abstract_templates/template_guide.md +114 -0
  352. package/skills/make-figures/scripts/build_jacc_template.py +77 -0
  353. package/skills/make-figures/scripts/build_prisma2020_template.py +371 -0
  354. package/skills/make-figures/scripts/build_strobe_template.py +351 -0
  355. package/skills/make-figures/scripts/critic_figure.py +264 -0
  356. package/skills/make-figures/scripts/derive_figure_legend_counts.py +138 -0
  357. package/skills/make-figures/scripts/extract_exemplar_from_pdf.py +186 -0
  358. package/skills/make-figures/scripts/fetch_official_templates.sh +88 -0
  359. package/skills/make-figures/scripts/fill_prisma_template.py +142 -0
  360. package/skills/make-figures/scripts/generate_flow_diagram.R +133 -0
  361. package/skills/make-figures/scripts/generate_image.py +99 -0
  362. package/skills/make-figures/scripts/generate_visual_abstract.py +438 -0
  363. package/skills/make-figures/scripts/validate_pptx_mac_compat.py +233 -0
  364. package/skills/make-figures/skill.yml +52 -0
  365. package/skills/make-figures/templates/official/NOTES.md +62 -0
  366. package/skills/make-figures/templates/official/consort2010/CONSORT_2025_editable_checklist.docx +0 -0
  367. package/skills/make-figures/templates/official/consort2010/CONSORT_2025_flow_diagram.docx +0 -0
  368. package/skills/make-figures/templates/official/prisma2020/PRISMA_2020_flow_new_v1.pptx +0 -0
  369. package/skills/make-figures/templates/official/prisma2020/PRISMA_2020_flow_new_v2.pptx +0 -0
  370. package/skills/make-figures/templates/official/prisma2020/PRISMA_2020_flow_updated_v2.pptx +0 -0
  371. package/skills/make-figures/templates/official/spirit2013/SPIRIT_2025_editable_checklist.docx +0 -0
  372. package/skills/make-figures/templates/official/spirit2013/SPIRIT_2025_participant_timeline.docx +0 -0
  373. package/skills/make-figures/templates/official/stard2015/STARD_2015_checklist.docx +0 -0
  374. package/skills/make-figures/templates/official/stard2015/STARD_2015_flow_diagram.pdf +0 -0
  375. package/skills/make-figures/tests/fixtures/figure1_flow.yaml +8 -0
  376. package/skills/make-figures/tests/fixtures/manuscript_ok.md +9 -0
  377. package/skills/make-figures/tests/fixtures/manuscript_stale.md +4 -0
  378. package/skills/make-figures/tests/test_legend_reconcile.sh +36 -0
  379. package/skills/manage-project/SKILL.md +358 -0
  380. package/skills/manage-project/references/pre_submission_checklist.md +53 -0
  381. package/skills/manage-project/references/project_state_template.json +37 -0
  382. package/skills/manage-project/references/scaffold_templates.md +118 -0
  383. package/skills/manage-project/references/status_output_format.md +44 -0
  384. package/skills/manage-project/references/timeline_example.md +20 -0
  385. package/skills/manage-project/skill.yml +36 -0
  386. package/skills/manage-project/templates/SSOT.yaml.template +41 -0
  387. package/skills/manage-refs/LICENSE.zotero-mcp +21 -0
  388. package/skills/manage-refs/NOTICE.md +29 -0
  389. package/skills/manage-refs/SKILL.md +289 -0
  390. package/skills/manage-refs/citation_styles/README.md +40 -0
  391. package/skills/manage-refs/citation_styles/american-journal-of-roentgenology.csl +211 -0
  392. package/skills/manage-refs/citation_styles/cardiovascular-and-interventional-radiology.csl +19 -0
  393. package/skills/manage-refs/citation_styles/european-radiology.csl +19 -0
  394. package/skills/manage-refs/citation_styles/journal-of-cachexia-sarcopenia-and-muscle.csl +150 -0
  395. package/skills/manage-refs/citation_styles/journal-of-korean-medical-science-strict.csl +533 -0
  396. package/skills/manage-refs/citation_styles/journal-of-korean-medical-science.csl +16 -0
  397. package/skills/manage-refs/citation_styles/korean-journal-of-radiology.csl +155 -0
  398. package/skills/manage-refs/citation_styles/nature.csl +189 -0
  399. package/skills/manage-refs/citation_styles/nlm-citation-sequence.csl +535 -0
  400. package/skills/manage-refs/citation_styles/radiology.csl +228 -0
  401. package/skills/manage-refs/citation_styles/springer-basic-brackets.csl +187 -0
  402. package/skills/manage-refs/citation_styles/springer-vancouver-brackets.csl +276 -0
  403. package/skills/manage-refs/citation_styles/vancouver-superscript.csl +536 -0
  404. package/skills/manage-refs/citation_styles/vancouver.csl +535 -0
  405. package/skills/manage-refs/references/REFERENCE_STYLE_SPECS.md +59 -0
  406. package/skills/manage-refs/references/check_xref_symptoms.md +35 -0
  407. package/skills/manage-refs/scripts/_vendor_citation_writer.py +600 -0
  408. package/skills/manage-refs/scripts/check_citation_keys.py +112 -0
  409. package/skills/manage-refs/scripts/check_csl_render.py +102 -0
  410. package/skills/manage-refs/scripts/check_xref.py +633 -0
  411. package/skills/manage-refs/scripts/fill_journal_abbrev.py +104 -0
  412. package/skills/manage-refs/scripts/inject_zotero_cwyw.py +133 -0
  413. package/skills/manage-refs/scripts/md_marker_convert.py +193 -0
  414. package/skills/manage-refs/scripts/pre_submission_gate.sh +238 -0
  415. package/skills/manage-refs/scripts/render_pandoc.sh +88 -0
  416. package/skills/manage-refs/skill.yml +70 -0
  417. package/skills/manage-refs/tests/fixtures/pre_submission_gate/README.md +32 -0
  418. package/skills/manage-refs/tests/fixtures/pre_submission_gate/manuscript.md +10 -0
  419. package/skills/manage-refs/tests/fixtures/pre_submission_gate/refs.bib +34 -0
  420. package/skills/manage-refs/tests/fixtures/pre_submission_gate/run.sh +117 -0
  421. package/skills/manage-refs/tests/test_vN_docx_check.sh +145 -0
  422. package/skills/meta-analysis/SKILL.md +739 -0
  423. package/skills/meta-analysis/references/LICENSES.md +21 -0
  424. package/skills/meta-analysis/references/PROSPERO_template.md +221 -0
  425. package/skills/meta-analysis/references/ai_pre_screening_template.py +245 -0
  426. package/skills/meta-analysis/references/checklists/JBI_Case_Series.md +45 -0
  427. package/skills/meta-analysis/references/checklists/NOS.md +88 -0
  428. package/skills/meta-analysis/references/checklists/PRISMA_DTA.md +36 -0
  429. package/skills/meta-analysis/references/checklists/PROBAST.md +75 -0
  430. package/skills/meta-analysis/references/checklists/QUADAS2.md +77 -0
  431. package/skills/meta-analysis/references/checklists/ROBINS_I.md +87 -0
  432. package/skills/meta-analysis/references/checklists/RoB2.md +79 -0
  433. package/skills/meta-analysis/references/data_integrity_checklist.md +57 -0
  434. package/skills/meta-analysis/references/icmje_coi_guide.md +181 -0
  435. package/skills/meta-analysis/references/phase10_recovery.md +136 -0
  436. package/skills/meta-analysis/references/phase4_km_composite.md +58 -0
  437. package/skills/meta-analysis/references/phase6_statistical_synthesis.md +148 -0
  438. package/skills/meta-analysis/references/phase9_circulation.md +84 -0
  439. package/skills/meta-analysis/references/post_submission_release_ops.md +41 -0
  440. package/skills/meta-analysis/references/r_templates.md +132 -0
  441. package/skills/meta-analysis/references/review_orchestration.md +40 -0
  442. package/skills/meta-analysis/references/submission_package_drift.md +71 -0
  443. package/skills/meta-analysis/scripts/check_pool_consistency.py +201 -0
  444. package/skills/meta-analysis/scripts/cohort_overlap_check.py +242 -0
  445. package/skills/meta-analysis/scripts/dta_extraction_qc.py +137 -0
  446. package/skills/meta-analysis/scripts/screening_reconcile.py +160 -0
  447. package/skills/meta-analysis/skill.yml +47 -0
  448. package/skills/meta-analysis/templates/FINAL_POOL_LOCK.yaml.template +70 -0
  449. package/skills/meta-analysis/templates/extraction_form_v2.md +129 -0
  450. package/skills/meta-analysis/templates/supplementary_8file_checklist.md +94 -0
  451. package/skills/meta-analysis/tests/test_pool_consistency.sh +123 -0
  452. package/skills/orchestrate/SKILL.md +501 -0
  453. package/skills/orchestrate/references/dialogue_nodes.md +196 -0
  454. package/skills/orchestrate/references/report_template.md +109 -0
  455. package/skills/orchestrate/references/report_template_ko.md +88 -0
  456. package/skills/orchestrate/skill.yml +44 -0
  457. package/skills/peer-review/SKILL.md +381 -0
  458. package/skills/peer-review/references/aczel_2021_reviewer2_patterns.md +88 -0
  459. package/skills/peer-review/references/domain-probes/ai_overclaiming.md +47 -0
  460. package/skills/peer-review/references/domain-probes/narrative_review.md +44 -0
  461. package/skills/peer-review/references/domain-probes/observational_confounding.md +48 -0
  462. package/skills/peer-review/references/domain-probes/radiomics.md +38 -0
  463. package/skills/peer-review/references/domain-probes/sr_ma.md +87 -0
  464. package/skills/peer-review/references/domain-probes/survival_prognostic.md +68 -0
  465. package/skills/peer-review/references/exemplar_reviews/README.md +43 -0
  466. package/skills/peer-review/references/exemplar_reviews/ai_overclaiming.md +47 -0
  467. package/skills/peer-review/references/exemplar_reviews/calibration_missing.md +44 -0
  468. package/skills/peer-review/references/exemplar_reviews/data_leakage.md +48 -0
  469. package/skills/peer-review/references/exemplar_reviews/reference_standard_validity.md +45 -0
  470. package/skills/peer-review/references/narrative_review_audit.md +67 -0
  471. package/skills/peer-review/references/reviewer_calibration/README.md +34 -0
  472. package/skills/peer-review/references/reviewer_calibration/compliance_floor.md +52 -0
  473. package/skills/peer-review/references/reviewer_profiles/AJR.md +82 -0
  474. package/skills/peer-review/references/reviewer_profiles/EURE.md +64 -0
  475. package/skills/peer-review/references/reviewer_profiles/INSI.md +57 -0
  476. package/skills/peer-review/references/reviewer_profiles/KJR.md +100 -0
  477. package/skills/peer-review/references/reviewer_profiles/README.md +32 -0
  478. package/skills/peer-review/references/reviewer_profiles/RYAI.md +86 -0
  479. package/skills/peer-review/skill.yml +39 -0
  480. package/skills/present-paper/SKILL.md +675 -0
  481. package/skills/present-paper/references/critic_rubrics/slide.md +155 -0
  482. package/skills/present-paper/references/generate_pptx_templates.py +604 -0
  483. package/skills/present-paper/references/medical_presentation_templates.md +277 -0
  484. package/skills/present-paper/references/slide_design_principles.md +202 -0
  485. package/skills/present-paper/references/slide_visual_styles/nature_lancet.md +168 -0
  486. package/skills/present-paper/references/workflow-checklist.md +109 -0
  487. package/skills/present-paper/scripts/extract_pdf_figures.py +243 -0
  488. package/skills/present-paper/scripts/inject_pronunciation_notes.py +178 -0
  489. package/skills/present-paper/scripts/inject_speaker_notes.py +133 -0
  490. package/skills/present-paper/scripts/strip_notes_for_sharing.py +140 -0
  491. package/skills/present-paper/scripts/trim_caption.py +271 -0
  492. package/skills/present-paper/skill.yml +41 -0
  493. package/skills/present-paper/templates/build_pptx_nature_lancet.py +688 -0
  494. package/skills/publish-skill/SKILL.md +370 -0
  495. package/skills/publish-skill/references/license-compatibility-matrix.md +132 -0
  496. package/skills/publish-skill/references/pii-patterns.md +130 -0
  497. package/skills/publish-skill/scripts/audit_skill.sh +278 -0
  498. package/skills/publish-skill/skill.yml +35 -0
  499. package/skills/render-pdf-doc/SKILL.md +146 -0
  500. package/skills/render-pdf-doc/references/known_pitfalls.md +53 -0
  501. package/skills/render-pdf-doc/references/pandoc_korean_cheatsheet.md +77 -0
  502. package/skills/render-pdf-doc/scripts/check_deps.sh +42 -0
  503. package/skills/render-pdf-doc/scripts/infer_colwidths.py +164 -0
  504. package/skills/render-pdf-doc/scripts/render_pdf.sh +98 -0
  505. package/skills/render-pdf-doc/skill.yml +57 -0
  506. package/skills/render-pdf-doc/templates/anchor-doc.md +27 -0
  507. package/skills/render-pdf-doc/templates/anchor-doc_ko.md +25 -0
  508. package/skills/render-pdf-doc/templates/briefing-handout.md +33 -0
  509. package/skills/render-pdf-doc/templates/briefing-handout_ko.md +31 -0
  510. package/skills/render-pdf-doc/templates/proposal-cover.md +33 -0
  511. package/skills/render-pdf-doc/templates/proposal-cover_ko.md +31 -0
  512. package/skills/render-pdf-doc/templates/reference-table.md +22 -0
  513. package/skills/render-pdf-doc/templates/reference-table_ko.md +20 -0
  514. package/skills/replicate-study/SKILL.md +150 -0
  515. package/skills/replicate-study/references/harmonization_3country.csv +47 -0
  516. package/skills/replicate-study/references/harmonization_knhanes_nhanes.csv +68 -0
  517. package/skills/replicate-study/references/methodology_extraction_template.md +134 -0
  518. package/skills/replicate-study/skill.yml +37 -0
  519. package/skills/review-paper/SKILL.md +104 -0
  520. package/skills/review-paper/references/macro_skeleton.md +6 -0
  521. package/skills/review-paper/skill.yml +25 -0
  522. package/skills/revise/SKILL.md +515 -0
  523. package/skills/revise/references/r2r_voice.md +346 -0
  524. package/skills/revise/skill.yml +43 -0
  525. package/skills/search-lit/SKILL.md +443 -0
  526. package/skills/search-lit/references/parse_pubmed.py +326 -0
  527. package/skills/search-lit/references/pubmed_eutils.sh +111 -0
  528. package/skills/search-lit/skill.yml +46 -0
  529. package/skills/self-review/SKILL.md +1045 -0
  530. package/skills/self-review/references/domain-probes/ai_overclaiming.md +47 -0
  531. package/skills/self-review/references/domain-probes/narrative_review.md +44 -0
  532. package/skills/self-review/references/domain-probes/observational_confounding.md +48 -0
  533. package/skills/self-review/references/domain-probes/radiomics.md +38 -0
  534. package/skills/self-review/references/domain-probes/sr_ma.md +87 -0
  535. package/skills/self-review/references/domain-probes/survival_prognostic.md +68 -0
  536. package/skills/self-review/references/exemplar_findings/README.md +43 -0
  537. package/skills/self-review/references/exemplar_findings/cohort_arithmetic_mismatch.md +35 -0
  538. package/skills/self-review/references/exemplar_findings/estimand_drift_posthoc_primary.md +39 -0
  539. package/skills/self-review/references/exemplar_findings/scope_overreach_cross_sectional.md +35 -0
  540. package/skills/self-review/references/exemplar_findings/unadjusted_confounder.md +36 -0
  541. package/skills/self-review/references/panel_review_template.md +177 -0
  542. package/skills/self-review/scripts/check_artifact_coverage.py +301 -0
  543. package/skills/self-review/scripts/check_claim_artifact.py +248 -0
  544. package/skills/self-review/scripts/check_classical_style.py +185 -0
  545. package/skills/self-review/scripts/check_cohort_arithmetic.py +481 -0
  546. package/skills/self-review/scripts/check_confounding_completeness.py +287 -0
  547. package/skills/self-review/scripts/check_panel_diversity.py +336 -0
  548. package/skills/self-review/scripts/check_reference_adequacy.py +392 -0
  549. package/skills/self-review/scripts/check_reviewer_team_consistency.py +412 -0
  550. package/skills/self-review/scripts/check_scope_coherence.py +177 -0
  551. package/skills/self-review/skill.yml +47 -0
  552. package/skills/self-review/tests/fixtures/claim_manuscript.md +17 -0
  553. package/skills/self-review/tests/fixtures/claim_prereg.md +6 -0
  554. package/skills/self-review/tests/fixtures/cohort_bad.md +21 -0
  555. package/skills/self-review/tests/fixtures/cohort_clean.md +21 -0
  556. package/skills/self-review/tests/fixtures/cohort_partition.csv +5 -0
  557. package/skills/self-review/tests/fixtures/coverage_analysis/31_delong_nested_added_value.csv +3 -0
  558. package/skills/self-review/tests/fixtures/coverage_analysis/table1_demographics.csv +3 -0
  559. package/skills/self-review/tests/fixtures/coverage_clean.md +13 -0
  560. package/skills/self-review/tests/fixtures/coverage_manuscript.md +11 -0
  561. package/skills/self-review/tests/fixtures/panel_collapse.json +27 -0
  562. package/skills/self-review/tests/fixtures/panel_good.json +32 -0
  563. package/skills/self-review/tests/fixtures/panel_monoculture.json +32 -0
  564. package/skills/self-review/tests/fixtures/refadeq_letter.md +13 -0
  565. package/skills/self-review/tests/fixtures/refadeq_original_fixed.md +42 -0
  566. package/skills/self-review/tests/fixtures/refadeq_original_uncited.md +40 -0
  567. package/skills/self-review/tests/fixtures/scope_bad.md +9 -0
  568. package/skills/self-review/tests/fixtures/scope_clean.md +8 -0
  569. package/skills/self-review/tests/fixtures/scope_surrogate.md +8 -0
  570. package/skills/self-review/tests/fixtures/style_bad.md +13 -0
  571. package/skills/self-review/tests/fixtures/style_clean.md +11 -0
  572. package/skills/self-review/tests/fixtures/table1_by_exposure.csv +11 -0
  573. package/skills/self-review/tests/test_artifact_coverage.sh +44 -0
  574. package/skills/self-review/tests/test_claim_artifact.sh +50 -0
  575. package/skills/self-review/tests/test_classical_style.sh +44 -0
  576. package/skills/self-review/tests/test_cohort_arithmetic.sh +49 -0
  577. package/skills/self-review/tests/test_confounding_completeness.sh +66 -0
  578. package/skills/self-review/tests/test_panel_diversity.sh +55 -0
  579. package/skills/self-review/tests/test_panel_mode.sh +69 -0
  580. package/skills/self-review/tests/test_reference_adequacy.sh +68 -0
  581. package/skills/self-review/tests/test_reviewer_team_consistency.sh +138 -0
  582. package/skills/self-review/tests/test_scope_coherence.sh +46 -0
  583. package/skills/setup-medsci/SKILL.md +110 -0
  584. package/skills/setup-medsci/references/setup-checklist.md +51 -0
  585. package/skills/setup-medsci/skill.yml +30 -0
  586. package/skills/sync-submission/SKILL.md +382 -0
  587. package/skills/sync-submission/scripts/author_registry_example.yaml +36 -0
  588. package/skills/sync-submission/scripts/blind_sweep.py +203 -0
  589. package/skills/sync-submission/scripts/check_asset_anonymization.py +300 -0
  590. package/skills/sync-submission/scripts/check_cross_artifact_stale.py +211 -0
  591. package/skills/sync-submission/scripts/cover_letter_drift_check.py +451 -0
  592. package/skills/sync-submission/scripts/cross_document_n_check.py +486 -0
  593. package/skills/sync-submission/scripts/detect_copy_divergence.py +136 -0
  594. package/skills/sync-submission/scripts/preflight_gate.py +458 -0
  595. package/skills/sync-submission/scripts/scope_drift_check.py +362 -0
  596. package/skills/sync-submission/scripts/sync_submission.py +169 -0
  597. package/skills/sync-submission/skill.yml +43 -0
  598. package/skills/sync-submission/tests/fixtures/copy_ok.md +5 -0
  599. package/skills/sync-submission/tests/fixtures/copy_stale.md +5 -0
  600. package/skills/sync-submission/tests/fixtures/ssot.md +5 -0
  601. package/skills/sync-submission/tests/test_asset_anonymization.sh +99 -0
  602. package/skills/sync-submission/tests/test_copy_divergence.sh +44 -0
  603. package/skills/sync-submission/tests/test_cross_artifact_stale.sh +80 -0
  604. package/skills/sync-submission/tests/test_cross_document_n.sh +132 -0
  605. package/skills/sync-submission/tests/test_preflight_gate.sh +112 -0
  606. package/skills/sync-submission/tests/test_scope_drift.sh +122 -0
  607. package/skills/sync-submission/tests/test_vN_docx_assertion.sh +51 -0
  608. package/skills/verify-refs/SKILL.md +177 -0
  609. package/skills/verify-refs/references/manual_checkpoint_guide.md +100 -0
  610. package/skills/verify-refs/scripts/verify_cli.sh +62 -0
  611. package/skills/verify-refs/scripts/verify_refs.py +782 -0
  612. package/skills/verify-refs/skill.yml +44 -0
  613. package/skills/verify-refs/tests/fixtures/pagination_placeholder.bib +17 -0
  614. package/skills/verify-refs/tests/test_pagination_placeholder.sh +42 -0
  615. package/skills/version-dataset/SKILL.md +143 -0
  616. package/skills/version-dataset/references/manifest_schema.md +72 -0
  617. package/skills/version-dataset/scripts/version_dataset.py +242 -0
  618. package/skills/version-dataset/skill.yml +35 -0
  619. package/skills/version-dataset/tests/test_version_dataset.sh +52 -0
  620. package/skills/write-paper/SKILL.md +1148 -0
  621. package/skills/write-paper/references/exemplar_methods/README.md +38 -0
  622. package/skills/write-paper/references/exemplar_methods/ai_validation_tripod_claim.md +47 -0
  623. package/skills/write-paper/references/exemplar_methods/diagnostic_accuracy_stard.md +50 -0
  624. package/skills/write-paper/references/exemplar_methods/observational_cohort_strobe.md +43 -0
  625. package/skills/write-paper/references/journal_profiles/AJNR.md +185 -0
  626. package/skills/write-paper/references/journal_profiles/AJR.md +149 -0
  627. package/skills/write-paper/references/journal_profiles/Abdominal_Radiology.md +139 -0
  628. package/skills/write-paper/references/journal_profiles/Academic_Radiology.md +90 -0
  629. package/skills/write-paper/references/journal_profiles/Annals_of_Internal_Medicine.md +150 -0
  630. package/skills/write-paper/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +82 -0
  631. package/skills/write-paper/references/journal_profiles/British_Journal_of_Radiology.md +161 -0
  632. package/skills/write-paper/references/journal_profiles/CVIR.md +157 -0
  633. package/skills/write-paper/references/journal_profiles/Chest.md +270 -0
  634. package/skills/write-paper/references/journal_profiles/Clinical_Radiology.md +160 -0
  635. package/skills/write-paper/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +147 -0
  636. package/skills/write-paper/references/journal_profiles/Diabetes_Metabolism_Journal.md +163 -0
  637. package/skills/write-paper/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +216 -0
  638. package/skills/write-paper/references/journal_profiles/Endocrinology_and_Metabolism.md +167 -0
  639. package/skills/write-paper/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +192 -0
  640. package/skills/write-paper/references/journal_profiles/European_Radiology.md +159 -0
  641. package/skills/write-paper/references/journal_profiles/Hepatology_Communications.md +110 -0
  642. package/skills/write-paper/references/journal_profiles/Hepatology_International.md +106 -0
  643. package/skills/write-paper/references/journal_profiles/IEEE_TMI.md +180 -0
  644. package/skills/write-paper/references/journal_profiles/INSI.md +163 -0
  645. package/skills/write-paper/references/journal_profiles/Investigative_Radiology.md +86 -0
  646. package/skills/write-paper/references/journal_profiles/JACC_Advances.md +197 -0
  647. package/skills/write-paper/references/journal_profiles/JACC_Asia.md +168 -0
  648. package/skills/write-paper/references/journal_profiles/JACR.md +87 -0
  649. package/skills/write-paper/references/journal_profiles/JAMA.md +188 -0
  650. package/skills/write-paper/references/journal_profiles/JAMA_Network_Open.md +170 -0
  651. package/skills/write-paper/references/journal_profiles/JCSM.md +266 -0
  652. package/skills/write-paper/references/journal_profiles/JKMS.md +201 -0
  653. package/skills/write-paper/references/journal_profiles/JMIR.md +88 -0
  654. package/skills/write-paper/references/journal_profiles/JMIR_Medical_Education.md +86 -0
  655. package/skills/write-paper/references/journal_profiles/JNIS.md +227 -0
  656. package/skills/write-paper/references/journal_profiles/JVIR.md +158 -0
  657. package/skills/write-paper/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +191 -0
  658. package/skills/write-paper/references/journal_profiles/Journal_of_Stroke.md +176 -0
  659. package/skills/write-paper/references/journal_profiles/KJR.md +185 -0
  660. package/skills/write-paper/references/journal_profiles/Korean_Circulation_Journal.md +184 -0
  661. package/skills/write-paper/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +178 -0
  662. package/skills/write-paper/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +127 -0
  663. package/skills/write-paper/references/journal_profiles/Liver_International.md +165 -0
  664. package/skills/write-paper/references/journal_profiles/Medical_Image_Analysis.md +147 -0
  665. package/skills/write-paper/references/journal_profiles/NEJM.md +147 -0
  666. package/skills/write-paper/references/journal_profiles/Nature_Medicine.md +181 -0
  667. package/skills/write-paper/references/journal_profiles/Neuroradiology.md +151 -0
  668. package/skills/write-paper/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +184 -0
  669. package/skills/write-paper/references/journal_profiles/PLOS_Medicine.md +166 -0
  670. package/skills/write-paper/references/journal_profiles/RYAI.md +124 -0
  671. package/skills/write-paper/references/journal_profiles/Radiology.md +173 -0
  672. package/skills/write-paper/references/journal_profiles/Skeletal_Radiology.md +135 -0
  673. package/skills/write-paper/references/journal_profiles/Stroke.md +210 -0
  674. package/skills/write-paper/references/journal_profiles/The_BMJ.md +121 -0
  675. package/skills/write-paper/references/journal_profiles/The_Lancet.md +112 -0
  676. package/skills/write-paper/references/journal_profiles/The_Lancet_Digital_Health.md +104 -0
  677. package/skills/write-paper/references/journal_profiles/World_Journal_of_Hepatology.md +106 -0
  678. package/skills/write-paper/references/journal_profiles/npj_Digital_Medicine.md +93 -0
  679. package/skills/write-paper/references/paper_types/ai_validation.md +270 -0
  680. package/skills/write-paper/references/paper_types/animal_study.md +194 -0
  681. package/skills/write-paper/references/paper_types/case_report.md +237 -0
  682. package/skills/write-paper/references/paper_types/cross_national.md +328 -0
  683. package/skills/write-paper/references/paper_types/letter.md +127 -0
  684. package/skills/write-paper/references/paper_types/meta_analysis.md +181 -0
  685. package/skills/write-paper/references/paper_types/nhis_cohort.md +297 -0
  686. package/skills/write-paper/references/paper_types/original_article.md +221 -0
  687. package/skills/write-paper/references/paper_types/technical_note.md +131 -0
  688. package/skills/write-paper/references/section_guides/discussion.md +155 -0
  689. package/skills/write-paper/references/section_guides/introduction.md +108 -0
  690. package/skills/write-paper/references/section_guides/methods.md +144 -0
  691. package/skills/write-paper/references/section_guides/results.md +113 -0
  692. package/skills/write-paper/references/section_guides/step7_1_classical_qc.md +67 -0
  693. package/skills/write-paper/references/section_guides/step7_4a_audit_recovery.md +74 -0
  694. package/skills/write-paper/references/section_guides/title_abstract.md +123 -0
  695. package/skills/write-paper/references/section_templates/methods_statistical.md +147 -0
  696. package/skills/write-paper/scripts/check_placeholders.py +182 -0
  697. package/skills/write-paper/skill.yml +48 -0
  698. package/skills/write-paper/tests/test_placeholders.sh +107 -0
  699. package/skills/write-protocol/SKILL.md +243 -0
  700. package/skills/write-protocol/references/ethics_checklist.md +150 -0
  701. package/skills/write-protocol/references/protocol_template.md +304 -0
  702. package/skills/write-protocol/skill.yml +34 -0
@@ -0,0 +1,237 @@
1
+ # Paper Type: Case Report
2
+
3
+ ## Overview
4
+
5
+ - **Reporting guideline:** CARE 2016 (mandatory)
6
+ - **Typical word count:** 1000–1500 words (short-form) or 2000–3000 words (extended with literature review)
7
+ - **Default mode:** Short-form (1000-1500 words). Use `--extended` for longer format.
8
+ - **Structure:** Title → Abstract → Introduction → Case Presentation → Discussion → Conclusions → Patient Perspective (optional) → Informed Consent
9
+ - **Key requirement:** Patient consent/anonymization documented
10
+
11
+ ---
12
+
13
+ ## CARE 2016 Checklist Quick Reference
14
+
15
+ | # | Item | Section | Description |
16
+ |---|------|---------|-------------|
17
+ | 1 | Title | Title | Diagnosis or main symptom AND "case report" |
18
+ | 2 | Key words | Abstract | 2-5 keywords covering the case |
19
+ | 3 | Abstract | Abstract | Structured: Introduction, Case Presentation, Conclusion |
20
+ | 4 | Introduction | Introduction | Background with references, why this case is reportable |
21
+ | 5 | Patient information | Case Presentation | Demographics, main symptoms, medical history |
22
+ | 6 | Clinical findings | Case Presentation | Physical examination, key clinical findings |
23
+ | 7 | Timeline | Case Presentation | Important dates and events in table or figure |
24
+ | 8 | Diagnostic assessment | Case Presentation | Methods, pathological findings, challenges, reasoning |
25
+ | 9 | Therapeutic intervention | Case Presentation | Types, administration, duration, changes |
26
+ | 10 | Follow-up and outcomes | Case Presentation | Clinician-assessed and patient-assessed outcomes, adherence, adverse events |
27
+ | 11 | Discussion | Discussion | Strengths, limitations, relevant literature, rationale for conclusions |
28
+ | 12 | Patient perspective | Optional | Patient's own views when available |
29
+ | 13 | Informed consent | End | Documentation that consent was obtained |
30
+
31
+ > Full CARE checklist: https://www.care-statement.org/checklist
32
+
33
+ ---
34
+
35
+ ## When to Write a Case Report
36
+
37
+ Case reports are appropriate when the case demonstrates:
38
+ - A rare or previously unreported condition or presentation
39
+ - An unusual complication of a known condition or procedure
40
+ - A novel diagnostic approach or therapeutic intervention
41
+ - An important teaching point with clinical relevance
42
+ - A paradoxical or unexpected finding
43
+
44
+ ---
45
+
46
+ ## Title
47
+
48
+ Format: "[Condition/Diagnosis]: [What makes it unusual]" or "[Unusual presentation/complication] of [condition]"
49
+
50
+ Example: "Cerebral Venous Sinus Thrombosis Presenting as Isolated Neck Pain: A Case Report and Literature Review"
51
+
52
+ Keep ≤ 15 words. Include "Case Report" in the title or subtitle.
53
+
54
+ ---
55
+
56
+ ## Structured Abstract (150–250 words)
57
+
58
+ ```
59
+ Introduction: [Why this case is being reported — one sentence on rarity or teaching value]
60
+
61
+ Case Presentation: [Age, sex, key presenting complaint, key imaging/lab findings, diagnosis]
62
+
63
+ Clinical Findings: [Key examination and investigation results]
64
+
65
+ Treatment/Intervention: [What was done]
66
+
67
+ Outcome: [Follow-up duration, outcome at last follow-up]
68
+
69
+ Conclusion: [Take-home message — what this case adds to the literature]
70
+ ```
71
+
72
+ ---
73
+
74
+ ## Introduction (200–400 words)
75
+
76
+ 1. Clinical background: Briefly describe the condition (2–3 sentences; cite key references).
77
+ 2. Why this case is unusual: State the rarity explicitly. If known epidemiology: "The reported incidence is [X per 100,000 person-years]."
78
+ 3. Objective: "We report a case of [condition] presenting with [unusual feature] and discuss [management strategy/diagnostic approach/teaching point]."
79
+
80
+ ---
81
+
82
+ ## Case Presentation (600–1200 words)
83
+
84
+ ### Patient Information
85
+
86
+ - Age and sex (no name or specific dates — protect anonymity)
87
+ - Chief complaint
88
+ - Relevant medical history, medications, allergies, family history, social history
89
+ - Any relevant prior treatments or procedures
90
+
91
+ ### Clinical Findings
92
+
93
+ - Physical examination findings
94
+ - Vital signs (if relevant)
95
+
96
+ ### Diagnostic Assessment (Imaging — Key Section for Radiology Cases)
97
+
98
+ Structure imaging descriptions as:
99
+
100
+ ```
101
+ [Modality and technique]: [Acquisition parameters if relevant]
102
+ → Findings: [Location, size, morphology, signal/density characteristics,
103
+ enhancement pattern, associated findings]
104
+ → Impression: [Radiological diagnosis or differential]
105
+ ```
106
+
107
+ Example:
108
+ "Contrast-enhanced MRI of the brain (1.5 T, gadolinium 0.1 mmol/kg) demonstrated a 2.3 × 1.8 cm extra-axial mass in the right cerebellopontine angle with hypointense T1, hyperintense T2 signal, and homogeneous enhancement. Mass effect on the ipsilateral facial and vestibulocochlear nerves was evident."
109
+
110
+ List relevant laboratory findings in a table.
111
+
112
+ ### Clinical Timeline Table
113
+
114
+ | Date | Event |
115
+ |------|-------|
116
+ | Day 0 | Symptom onset — [description] |
117
+ | Day 3 | Emergency department presentation |
118
+ | Day 5 | Imaging: [key finding] |
119
+ | Day 7 | Diagnosis established / Procedure performed |
120
+ | Day 14 | Discharge |
121
+ | Month 3 | Follow-up: [outcome] |
122
+
123
+ ### Therapeutic Intervention
124
+
125
+ Describe exactly what was done:
126
+ - Medical management: drug names, doses, duration
127
+ - Surgical/procedural management: technique, approach, materials used, any intraoperative findings
128
+ - Multidisciplinary involvement
129
+
130
+ ### Follow-up and Outcome
131
+
132
+ - Follow-up duration (e.g., "At 6-month follow-up")
133
+ - Functional outcome (use validated scales where applicable: mRS, GCS, NIHSS, Karnofsky)
134
+ - Imaging outcome (if follow-up imaging available)
135
+ - Any complications of treatment
136
+
137
+ ---
138
+
139
+ ## Discussion (400–800 words)
140
+
141
+ 1. **Literature context:** How does this case compare to previously reported cases? Cite key papers. Include a brief systematic search if cases are very rare ("A PubMed search using the terms '[terms]' identified [N] previously reported cases").
142
+ 2. **Pathophysiology:** Explain the underlying mechanism if relevant.
143
+ 3. **Diagnostic challenge:** Why was this case difficult to diagnose, or what did imaging add?
144
+ 4. **Management rationale:** Why was this treatment chosen? What are the alternatives?
145
+ 5. **Learning points:** What should clinicians take from this case?
146
+
147
+ ---
148
+
149
+ ## Learning Points Box (Required)
150
+
151
+ 3–5 concise, specific, clinically actionable statements:
152
+
153
+ ```
154
+ Learning Points
155
+ • [Specific diagnostic or management insight]
156
+ • [Imaging finding or pattern to recognize]
157
+ • [Management principle or pitfall to avoid]
158
+ • [When to consider this diagnosis]
159
+ ```
160
+
161
+ ---
162
+
163
+ ## Conclusion (100–200 words)
164
+
165
+ "We report a case of [condition] with [unusual feature]. [Key diagnostic or management point]. This case highlights the importance of [clinical lesson]. [Any implications for practice or future research]."
166
+
167
+ ---
168
+
169
+ ## Patient Perspective (Optional)
170
+
171
+ If the patient consented to provide a statement about their experience, include a brief paragraph in their own words. This is increasingly encouraged by CARE guidelines and some journals.
172
+
173
+ ---
174
+
175
+ ## Informed Consent Statement
176
+
177
+ At the end of the case report, include one of these statements:
178
+
179
+ **Option A (patient consented):**
180
+ "Written informed consent was obtained from the patient for publication of this case report and any accompanying images."
181
+
182
+ **Option B (patient deceased/consent waiver):**
183
+ "The institutional review board waived the requirement for informed consent for this retrospective case report. All identifying information has been removed."
184
+
185
+ **Option C (minor patient):**
186
+ "Written informed consent was obtained from the patient's legal guardian for publication of this case report."
187
+
188
+ ---
189
+
190
+ ## Required Figures
191
+
192
+ | Item | Content |
193
+ |------|---------|
194
+ | Figure 1 | Key imaging findings (annotated; typically 3–6 panels) |
195
+ | Figure 2 | Timeline figure or pathology if relevant |
196
+ | Table 1 | Clinical and laboratory data at presentation |
197
+ | Table 2 | Comparison with published similar cases (if ≥5 exist) |
198
+
199
+ ---
200
+
201
+ ## Similar Case Literature Search
202
+
203
+ When writing the Discussion, systematically search for previously reported similar cases:
204
+
205
+ **Search strategy:**
206
+ 1. Primary: PubMed — `"[condition]"[Title] AND "case report"[Publication Type]`
207
+ 2. If <5 results, broaden: `"[condition]"[Title/Abstract] AND (case report[ti] OR case series[ti])`
208
+ 3. Optional: Google Scholar for non-indexed case reports
209
+
210
+ **Data extraction from each similar case:**
211
+ - Author and year
212
+ - Patient age and sex
213
+ - Key presenting features
214
+ - Diagnostic method
215
+ - Treatment approach
216
+ - Outcome at follow-up
217
+
218
+ **Comparison table (include if >=5 similar cases found):**
219
+
220
+ | Author (Year) | Age/Sex | Key Presentation | Diagnosis Method | Treatment | Outcome |
221
+ |---------------|---------|-----------------|-----------------|-----------|---------|
222
+ | Current case | ... | ... | ... | ... | ... |
223
+ | [Prior case 1] | ... | ... | ... | ... | ... |
224
+
225
+ If <5 similar cases exist, state explicitly: "To our knowledge, only [N] similar cases have been reported in the English literature [citations]."
226
+
227
+ ---
228
+
229
+ ## Common Case Report Pitfalls
230
+
231
+ 1. **Failing to explain why the case is unusual** — state rarity explicitly with epidemiological data.
232
+ 2. **Missing patient consent statement** — most journals will reject without this.
233
+ 3. **Identifying information in images** — check DICOM metadata, remove patient labels from figures.
234
+ 4. **Vague imaging descriptions** — give exact size, location, signal characteristics, and enhancement pattern.
235
+ 5. **Overclaiming in Discussion** — case reports cannot establish causality; use "may," "suggest," "is consistent with."
236
+ 6. **Insufficient literature context** — do a PubMed search for similar cases; cite all relevant ones.
237
+ 7. **Too long a Discussion** — case reports are not reviews; keep Discussion focused on this case's lessons.
@@ -0,0 +1,328 @@
1
+ # Cross-National Comparison Study — Paper Type Template
2
+
3
+ ## Overview
4
+
5
+ Template for cross-national (binational) comparative studies using nationally representative datasets from two or more countries. Covers three study architectures: (A) Parallel Survey Analysis using cross-sectional surveys (e.g., KNHANES + NHANES), (B) Discovery/Validation Cohort using claims databases (e.g., NHIS + JMDC), and (C) Binational Birth/Longitudinal Cohort with sibling comparison. Applicable to prevalence comparisons, association studies, trend analyses, and composite health metric evaluations.
6
+
7
+ ---
8
+
9
+ ## Title
10
+
11
+ - Include "Cross-National," "Binational," or country names.
12
+ - Specify the study design in a subtitle.
13
+ - Under 20 words preferred.
14
+
15
+ ### Title Templates
16
+
17
+ | Pattern | Example |
18
+ |---------|---------|
19
+ | `Cross-national comparison of {X} and {Y} in {Country A} and {Country B}: a nationwide representative comparative study` | Depression and diabetes in Korea and the US |
20
+ | `Binational association between {X} and {Y} in {Country A} and {Country B}: a nationally representative cross-sectional study` | PUFA and depression in Korea and the US |
21
+ | `Maternal {exposure} and {outcome} in offspring: a binational cohort study` | Pregestational diabetes and neuropsychiatric risk |
22
+ | `Burden of {outcome} after {exposure} in {Country A} and {Country B}: a binational population-based cohort study` | Cardiovascular outcomes after infection |
23
+ | `Trends in {outcome} among {population}, {year range}: a nationwide representative study` | Physical activity trends (single-country variant) |
24
+
25
+ Notes:
26
+ - "Binational" is increasingly preferred over "Cross-national" for two-country studies.
27
+ - Always include the year range for trend studies.
28
+ - The subtitle pattern is consistent: "a nationwide representative {comparative/cross-sectional/cohort} study."
29
+
30
+ ---
31
+
32
+ ## Abstract (Structured, 250 words max)
33
+
34
+ ### Background
35
+ - State the known relationship and the cross-national evidence gap.
36
+ - Template: "Although {known relationship} has been suggested, evidence remains limited across cultural contexts. This study {compared/examined} {association} in {Country A} and {Country B}."
37
+
38
+ ### Methods
39
+ - Name both datasets with years and sample sizes.
40
+ - State that datasets were analyzed independently.
41
+ - Name the harmonization approach and statistical methods.
42
+
43
+ ### Results
44
+ - Report sample sizes from each dataset.
45
+ - Key findings with weighted odds ratios (wOR) or aHRs and 95% CIs from each country.
46
+ - Highlight convergent or divergent findings across countries.
47
+
48
+ ### Conclusion
49
+ - Main conclusion emphasizing cross-national consistency or divergence.
50
+ - Implication for policy or future research.
51
+
52
+ #### Discovery/Validation Variant
53
+ - Results structure: "In the {weighted} discovery cohort, {N} individuals were included... Similar patterns were observed in the validation cohort."
54
+
55
+ ---
56
+
57
+ ## Introduction (3-4 paragraphs, ~400-500 words)
58
+
59
+ ### Paragraph 1: Global Burden Statement
60
+ - Cite GBD or WHO prevalence figures with projections.
61
+ - Template: "{Condition} remains a {highly prevalent / growing} global health {threat/challenge}."
62
+
63
+ ### Paragraph 2: Prior Evidence (Single-Country Limitations)
64
+ - Summarize existing single-country evidence.
65
+ - Flag limitations: "were limited to single-country cohorts," "did not adjust for key confounders," "have not taken broad population approaches."
66
+ - If relevant, cite Mendelian randomization evidence showing ancestral or population differences.
67
+
68
+ ### Paragraph 3: Cross-National Gap and Study Aim
69
+ - Template: "To our knowledge, no prior study has evaluated {association} within a cross-national comparative framework."
70
+ - Template: "To address this gap, we analyzed nationally representative data from {Dataset A} and {Dataset B} collected between {years} to compare {outcome} in {Country A} and {Country B}."
71
+ - Optional: justify the country pairing with cultural, genetic, or healthcare system differences.
72
+
73
+ ### Variation: Trend Studies
74
+ - Replace the cross-national gap with a temporal gap: "there is a lack of large-scale studies examining how {X} patterns have evolved across pre-, intra-, and post-pandemic periods."
75
+
76
+ ---
77
+
78
+ ## Materials and Methods (~1000-1400 words)
79
+
80
+ ### 3.1 Data Sources
81
+
82
+ Describe each dataset separately with parallel structure:
83
+
84
+ Template:
85
+ > This study utilized {Dataset A} for {years} and {Dataset B} for {years}.
86
+ >
87
+ > {Dataset A} is a {population-based, cross-sectional / cohort} survey conducted by {Agency A} using a stratified, multistage probability sampling design to assess the health and nutritional status of the noninstitutionalized {Country A} population.
88
+ >
89
+ > {Dataset B}, administered by {Agency B}, is a {biennial / annual} survey designed to represent the noninstitutionalized {Country B} population using a similar multistage probability sampling approach.
90
+ >
91
+ > Both surveys include standardized health interviews, physical examinations, and laboratory tests, and collect extensive information on sociodemographic characteristics, health behaviors, and medical conditions.
92
+
93
+ #### Common Dataset Pairings
94
+
95
+ | Country A Dataset | Country B Dataset | Use Case |
96
+ |-------------------|-------------------|----------|
97
+ | KNHANES (Korea) | NHANES (US) | Nutrition, metabolic, mental health, composite score comparisons |
98
+ | NHIS (Korea) | JMDC (Japan) | Claims-based cohort and birth cohort studies |
99
+ | K-COV-N (NHIS+KDCA) | JMDC (Japan) | Disease-specific cohort (discovery/validation) |
100
+ | KCHS (Korea) | — (single-country) | National trend studies with temporal phases |
101
+
102
+ Notes:
103
+ - Survey years may be non-consecutive if specific variables are only collected in certain cycles. Always explain excluded years.
104
+ - For claims-based binational studies, shift the description to: "This binational cohort study included {N} individuals from {Country A} and {N} from {Country B}, from {start} to {end}."
105
+
106
+ ### 3.2 Ethics Approval
107
+
108
+ - Separate IRB approvals per country, listed together.
109
+ - Template: "The {Dataset A} protocol was approved by {IRB A} ({numbers}), and the {Dataset B} protocol was approved by {IRB B} ({numbers}). All participants provided written informed consent. Both surveys comply with the ethical principles outlined in the Declaration of Helsinki, and their de-identified data are publicly accessible for research purposes."
110
+
111
+ ### 3.3 Variable Harmonization
112
+
113
+ Three-layer harmonization framework:
114
+
115
+ #### Layer 1: Identical Instruments
116
+ - Variables measured with the same validated instrument in both datasets (e.g., PHQ-9 for depression, fasting glucose + HbA1c for diabetes).
117
+ - Template: "{Instrument} was used in both {Dataset A} and {Dataset B}."
118
+
119
+ #### Layer 2: Country-Specific Cutoffs with Clinical Justification
120
+ - Variables where clinical thresholds differ by national guidelines.
121
+ - Template: "{Variable} was defined using country-specific standards: {cutoff A} in {Country A} and {cutoff B} in {Country B}, reflecting established national guidelines."
122
+ - Common example: BMI >=25 in East Asia (Asia-Pacific cutoff) vs. BMI >=30 in US/Europe (WHO Western cutoff).
123
+
124
+ #### Layer 3: Operationally Different Variables Mapped to Equivalent Categories
125
+ - Variables measured differently but mappable to equivalent categories.
126
+ - Common examples:
127
+ - Income: quintiles (Korea) vs. poverty-income ratio (US) → binary high/low.
128
+ - Smoking/alcohol: mapped to equivalent categorical levels.
129
+
130
+ #### Key Harmonization Decisions (Reference Table)
131
+
132
+ | Variable | Typical Resolution |
133
+ |----------|-------------------|
134
+ | Obesity | Country-specific BMI cutoffs with justification |
135
+ | Income | Equivalent binary or tertile split |
136
+ | Depression | Identical instrument (PHQ-9) with same cutoff |
137
+ | Diabetes | Identical lab criteria (FG >=126 or HbA1c >=6.5%) |
138
+ | Physical activity | Identical framework (IPAQ-SF → MET-min/week) |
139
+
140
+ #### Core Principle
141
+ > "We applied harmonized variable definitions and conducted weighting and preprocessing separately for each dataset to preserve internal validity."
142
+
143
+ **Never pool raw data across countries.** Each dataset is analyzed independently.
144
+
145
+ #### ICD-10-Level Harmonization (Claims-Based Studies)
146
+ For binational cohort studies using claims databases, harmonization is done at the ICD-10 code level rather than questionnaire items. Apply the same code definitions, exposure/outcome assessments, and analytical approaches to both cohorts.
147
+
148
+ ### 3.4 Study Population
149
+
150
+ - State inclusion/exclusion criteria applied to each dataset separately.
151
+ - For composite score studies (e.g., Life's Essential 8): calculate the score identically in both countries.
152
+ - For cohort studies: apply parallel exclusion cascades to each country's dataset.
153
+
154
+ ### 3.5 Statistical Analysis
155
+
156
+ #### Architecture A: Parallel Survey Analysis
157
+
158
+ ```
159
+ Step 1 — Separate analysis per country
160
+ "Data from {Dataset A} and {Dataset B} were analyzed separately."
161
+ Complex survey design: "appropriate stratification, clustering, and sampling weights were applied."
162
+
163
+ Step 2 — Sequential model building
164
+ Model 1: adjusted for age and sex
165
+ Model 2: additionally adjusted for {income, education, smoking, alcohol, BMI, comorbidities}
166
+ Results as weighted odds ratios (wOR) with 95% CI
167
+
168
+ Step 3 — Subgroup / interaction analyses
169
+ Stratified by: sex, age group, education, income, alcohol, smoking, obesity, comorbidities
170
+ "Weighted odds ratios are adjusted for all covariates except the stratification variable."
171
+
172
+ Step 4 — Advanced modeling (choose as appropriate)
173
+ - Restricted cubic spline (RCS) with 3 knots for nonlinear dose-response
174
+ - Weighted quantile sum (WQS) regression for composite exposure component contribution
175
+ - Beta-coefficient comparison across time periods (trend studies)
176
+ ```
177
+
178
+ Notes:
179
+ - Never pool datasets into a single regression.
180
+ - Compare results side-by-side in the same table.
181
+ - Multicollinearity: check via VIF; values <2.0 acceptable.
182
+ - Missing data: variables with <5% missingness → complete case; higher → multiple imputation (5 datasets).
183
+
184
+ #### Architecture B: Discovery/Validation Cohort
185
+
186
+ ```
187
+ Step 1 — Full analysis in discovery cohort
188
+ PS-based balancing (overlap weighting, SIPTW, or matching)
189
+ Cox proportional hazards → aHR with 95% CI
190
+ Stratification and time-dependent analyses
191
+
192
+ Step 2 — Replication in validation cohort
193
+ "The study applied similar methodologies to the {validation cohort} as those used for the discovery cohort."
194
+ Same ICD-10 codes, exposure/outcome definitions, follow-up duration, and PS approach.
195
+
196
+ Step 3 — Subgroup analyses
197
+ Disease severity, treatment dosage, temporal era stratification
198
+ ```
199
+
200
+ #### Architecture C: Binational Birth/Longitudinal Cohort
201
+
202
+ ```
203
+ Step 1 — Full-cohort SIPTW-weighted Cox regression (primary)
204
+ Step 2 — Sibling comparison analysis (addresses unmeasured familial confounding)
205
+ Step 3 — Independent validation in second country (sibling pairs or full cohort)
206
+ ```
207
+
208
+ For multiple primary outcomes: apply Bonferroni correction (p < 0.05/K).
209
+
210
+ #### Software and Significance
211
+ - SAS for survey-weighted analyses and Cox regression.
212
+ - R for WQS regression and advanced modeling.
213
+ - Python for ML components if applicable.
214
+ - "A two-sided p value of less than 0.05 was considered statistically significant."
215
+
216
+ ---
217
+
218
+ ## Results (~800-1200 words)
219
+
220
+ ### 4.1 Study Population
221
+ - Report sample sizes from each dataset: "{N_A} from {Dataset A} and {N_B} from {Dataset B}."
222
+ - Demographics table (Table 1) with columns per country.
223
+
224
+ ### 4.2 Primary Findings
225
+ - Present results from each country in parallel.
226
+ - For parallel survey studies: wORs from both countries in the same table.
227
+ - For discovery/validation: primary results from discovery, confirmation from validation.
228
+
229
+ ### 4.3 Subgroup and Advanced Analyses
230
+ - Stratification results by country.
231
+ - Dose-response (RCS) or component contribution (WQS) results.
232
+ - Time-dependent or era-specific results if applicable.
233
+
234
+ ### 4.4 Sensitivity Analyses
235
+ - Confirm findings with alternative definitions, negative controls, or sibling comparisons.
236
+
237
+ ### Rules
238
+ - Same as original article: no interpretation, no causal language.
239
+ - Present both countries' results for every analysis.
240
+
241
+ ---
242
+
243
+ ## Discussion (4-5 paragraphs, ~800-1200 words)
244
+
245
+ ### Paragraph 1: Summary of Key Findings
246
+ - Highlight cross-national consistency or divergence.
247
+ - State whether findings were replicated across countries.
248
+
249
+ ### Paragraphs 2-3: Comparison with Prior Literature
250
+ - Compare with prior single-country and cross-national studies.
251
+ - Discuss population-specific factors (cultural, genetic, healthcare system) that may explain differences.
252
+
253
+ ### Paragraph 4: Clinical and Policy Implications
254
+ - Policy relevance across different healthcare systems.
255
+ - Public health recommendations.
256
+
257
+ ### Paragraph 5: Limitations
258
+
259
+ Standard limitation categories for cross-national studies:
260
+
261
+ | # | Category | Template |
262
+ |---|----------|----------|
263
+ | 1 | Cross-sectional design | "The cross-sectional design precludes inference of causality." Mitigation: "the dose-response relationship and consistency across subgroups support plausibility." |
264
+ | 2 | Dataset differences | "Differences exist between {Dataset A} and {Dataset B} in data collection methods, diagnostic criteria, and survey protocols." Mitigation: "we applied harmonized variable definitions and conducted weighting and preprocessing separately for each dataset to preserve internal validity." |
265
+ | 3 | Temporal coverage mismatch | "{Dataset A} included selected survey years, whereas {Dataset B} provided continuous data." Mitigation: "appropriate sampling weights and consistent analytic criteria." |
266
+ | 4 | Self-report bias | "The use of self-reported data may introduce recall bias." Mitigation: "both surveys utilize validated instruments administered by trained personnel." |
267
+ | 5 | Country-specific definitions | "Obesity and income were defined using country-specific standards." Mitigation: "these definitions reflect established national guidelines and were applied consistently within each dataset, allowing for valid within-country comparisons." |
268
+ | 6 | Multiple comparisons | "Subgroup analyses were not adjusted for multiple comparisons." Mitigation: "based on prespecified variables of clinical and epidemiological relevance." |
269
+ | 7 | Unmeasured confounders | "Differences in healthcare systems, cultural factors, and unmeasured confounders may influence the relationship." |
270
+ | 8 | Population representativeness | "Both cohorts are from East Asian and Western populations; extrapolation to other regions requires caution." |
271
+
272
+ Each limitation followed by mitigation. End with strength-as-buffer: "our use of large, nationally representative samples allows for a broad understanding of population-level trends."
273
+
274
+ ### Conclusion
275
+ - Citable statement emphasizing cross-national convergence or divergence.
276
+ - Specific policy or clinical recommendation.
277
+
278
+ ---
279
+
280
+ ## Tables
281
+
282
+ - **Table 1**: Baseline characteristics by country (separate columns per dataset).
283
+ - **Table 2**: Primary association results (wOR or aHR with 95% CI) from both countries in parallel columns.
284
+ - **Table 3**: Subgroup analyses by country.
285
+ - **Table S1+**: Variable harmonization details, ICD-10 codes, sensitivity analysis results.
286
+
287
+ ## Figures
288
+
289
+ - **Figure 1**: Study flow diagram (per country or combined with country-specific branches).
290
+ - **Figure 2**: Forest plot of primary associations by country and subgroup.
291
+ - **Figure 3**: Restricted cubic spline dose-response curves (if applicable).
292
+ - Optional: Trend plots for temporal studies, WQS component weight bar charts.
293
+
294
+ ---
295
+
296
+ ## Boilerplate Sentences (Reusable)
297
+
298
+ ### Survey Design
299
+ > "To account for the complex survey designs and ensure nationally representative estimates, appropriate stratification, clustering, and sampling weights were applied."
300
+
301
+ ### Ethical
302
+ > "Both surveys comply with the ethical principles outlined in the Declaration of Helsinki, and their de-identified data are publicly accessible for research purposes."
303
+
304
+ ### Separate Analysis Justification
305
+ > "For cross-national comparisons, data from {Dataset A} and {Dataset B} were analyzed separately."
306
+
307
+ ### Within-Country Validity Defense
308
+ > "These definitions reflect established national guidelines and were applied consistently within each dataset, allowing for valid within-country comparisons and minimizing potential bias in the overall findings."
309
+
310
+ ### Data Availability
311
+ > "Study protocol and statistical code: available from the corresponding author. Dataset: {public access URLs}."
312
+
313
+ ---
314
+
315
+ ## Checklist Before Submission
316
+
317
+ - [ ] Both datasets described with sampling design, years, and agency
318
+ - [ ] Separate IRB approvals per country listed
319
+ - [ ] Harmonization approach explicitly stated for all key variables
320
+ - [ ] Country-specific cutoffs justified with national guideline references
321
+ - [ ] Datasets analyzed independently (never pooled)
322
+ - [ ] Survey weights applied for cross-sectional surveys
323
+ - [ ] Results presented in parallel for both countries
324
+ - [ ] Subgroup analyses consistent across both datasets
325
+ - [ ] Limitations address dataset differences and temporal mismatch
326
+ - [ ] Within-country validity defense included
327
+ - [ ] Numbers consistent between text, tables, and figures
328
+ - [ ] Reporting guideline (STROBE) items addressed