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.
- package/LICENSE +50 -0
- package/README.md +602 -0
- package/README_FIRST.md +27 -0
- package/bin/medsci-skills.js +159 -0
- package/installers/install-macos.command +19 -0
- package/installers/install-windows.cmd +26 -0
- package/installers/install-windows.ps1 +17 -0
- package/installers/install.py +218 -0
- package/metadata/skills_catalog.json +452 -0
- package/package.json +48 -0
- package/skills/academic-aio/SKILL.md +408 -0
- package/skills/academic-aio/references/case_studies/kjr_mllm_2025.md +82 -0
- package/skills/academic-aio/references/checklists/AIO_GENERAL.md +354 -0
- package/skills/academic-aio/references/journal_summarybox_templates.yaml +126 -0
- package/skills/academic-aio/references/oac_funding_checklist.yaml +129 -0
- package/skills/academic-aio/references/reporting_guideline_mapping.md +39 -0
- package/skills/academic-aio/references/schema_markup_templates/CodeRepository.jsonld +32 -0
- package/skills/academic-aio/references/schema_markup_templates/Dataset.jsonld +36 -0
- package/skills/academic-aio/references/schema_markup_templates/Person.jsonld +30 -0
- package/skills/academic-aio/references/schema_markup_templates/README.md +43 -0
- package/skills/academic-aio/references/schema_markup_templates/ScholarlyArticle.jsonld +55 -0
- package/skills/academic-aio/scripts/batch_metadata_audit.py +169 -0
- package/skills/academic-aio/scripts/validate_schema.py +118 -0
- package/skills/academic-aio/skill.yml +36 -0
- package/skills/academic-aio/templates/aio_audit_checklist.md.j2 +108 -0
- package/skills/add-journal/SKILL.md +482 -0
- package/skills/add-journal/skill.yml +33 -0
- package/skills/analyze-stats/SKILL.md +598 -0
- package/skills/analyze-stats/references/analysis_guides/missing_data.md +109 -0
- package/skills/analyze-stats/references/analysis_guides/nhis_icd10_mapping.md +247 -0
- package/skills/analyze-stats/references/analysis_guides/propensity_score.md +132 -0
- package/skills/analyze-stats/references/analysis_guides/regression.md +115 -0
- package/skills/analyze-stats/references/analysis_guides/repeated_measures.md +160 -0
- package/skills/analyze-stats/references/analysis_guides/survey_weighted.md +366 -0
- package/skills/analyze-stats/references/analysis_guides/test_selection.md +86 -0
- package/skills/analyze-stats/references/style/figure_style.mplstyle +69 -0
- package/skills/analyze-stats/references/style/theme_publication.R +147 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/ajr.yaml +51 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/european_radiology.yaml +55 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/jama.yaml +66 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/lancet.yaml +57 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/nejm.yaml +51 -0
- package/skills/analyze-stats/references/table-standards/journal-profiles/radiology.yaml +66 -0
- package/skills/analyze-stats/references/table-standards/table-standards.md +287 -0
- package/skills/analyze-stats/references/table-standards/table-types/diagnostic_accuracy.md +36 -0
- package/skills/analyze-stats/references/table-standards/table-types/meta_analysis.md +58 -0
- package/skills/analyze-stats/references/table-standards/table-types/model_comparison.md +36 -0
- package/skills/analyze-stats/references/table-standards/table-types/regression_results.md +50 -0
- package/skills/analyze-stats/references/table-standards/table-types/table1_demographics.md +51 -0
- package/skills/analyze-stats/references/table-standards/tool-comparison.md +79 -0
- package/skills/analyze-stats/references/templates/agreement_analysis.py +436 -0
- package/skills/analyze-stats/references/templates/dca_plot.R +237 -0
- package/skills/analyze-stats/references/templates/diagnostic_accuracy.py +401 -0
- package/skills/analyze-stats/references/templates/dta_meta_analysis.R +384 -0
- package/skills/analyze-stats/references/templates/forest_plot.py +412 -0
- package/skills/analyze-stats/references/templates/likert_summary.py +356 -0
- package/skills/analyze-stats/references/templates/meta_analysis.R +365 -0
- package/skills/analyze-stats/references/templates/propensity_score.py +478 -0
- package/skills/analyze-stats/references/templates/regression.py +425 -0
- package/skills/analyze-stats/references/templates/repeated_measures.py +434 -0
- package/skills/analyze-stats/references/templates/sample_size.R +382 -0
- package/skills/analyze-stats/references/templates/survey_weighted_analysis.py +411 -0
- package/skills/analyze-stats/references/templates/survival_analysis.py +325 -0
- package/skills/analyze-stats/references/templates/table1_demographics.py +287 -0
- package/skills/analyze-stats/scripts/check_generated_code.py +335 -0
- package/skills/analyze-stats/skill.yml +38 -0
- package/skills/analyze-stats/tests/fixtures/gen_bad.R +16 -0
- package/skills/analyze-stats/tests/fixtures/gen_bad.py +24 -0
- package/skills/analyze-stats/tests/fixtures/gen_clean.py +21 -0
- package/skills/analyze-stats/tests/test_generated_code.sh +59 -0
- package/skills/analyze-stats/tests/test_survival_template.sh +53 -0
- package/skills/author-strategy/SKILL.md +117 -0
- package/skills/author-strategy/analyze_patterns.py +303 -0
- package/skills/author-strategy/fetch_pubmed.py +374 -0
- package/skills/author-strategy/skill.yml +34 -0
- package/skills/batch-cohort/SKILL.md +223 -0
- package/skills/batch-cohort/references/base_template_knhanes.R +210 -0
- package/skills/batch-cohort/references/batch_template_generator.R +222 -0
- package/skills/batch-cohort/references/variable_coding_registry.md +136 -0
- package/skills/batch-cohort/skill.yml +35 -0
- package/skills/calc-sample-size/SKILL.md +491 -0
- package/skills/calc-sample-size/references/formulas.md +655 -0
- package/skills/calc-sample-size/references/observational_cohort.md +49 -0
- package/skills/calc-sample-size/skill.yml +51 -0
- package/skills/check-reporting/SKILL.md +534 -0
- package/skills/check-reporting/references/LICENSES.md +41 -0
- package/skills/check-reporting/references/checklists/AMSTAR2.md +54 -0
- package/skills/check-reporting/references/checklists/ARRIVE_2.md +234 -0
- package/skills/check-reporting/references/checklists/CARE.md +102 -0
- package/skills/check-reporting/references/checklists/CLAIM_2024.md +128 -0
- package/skills/check-reporting/references/checklists/CLEAR.md +113 -0
- package/skills/check-reporting/references/checklists/CONSORT.md +86 -0
- package/skills/check-reporting/references/checklists/COSMIN_RoB.md +136 -0
- package/skills/check-reporting/references/checklists/GRRAS.md +61 -0
- package/skills/check-reporting/references/checklists/MI_CLEAR_LLM.md +167 -0
- package/skills/check-reporting/references/checklists/MOOSE.md +85 -0
- package/skills/check-reporting/references/checklists/NOS.md +88 -0
- package/skills/check-reporting/references/checklists/PRISMA_2020.md +135 -0
- package/skills/check-reporting/references/checklists/PRISMA_DTA.md +36 -0
- package/skills/check-reporting/references/checklists/PRISMA_P.md +56 -0
- package/skills/check-reporting/references/checklists/PROBAST.md +75 -0
- package/skills/check-reporting/references/checklists/PROBAST_AI.md +130 -0
- package/skills/check-reporting/references/checklists/QUADAS2.md +77 -0
- package/skills/check-reporting/references/checklists/QUADAS_C.md +131 -0
- package/skills/check-reporting/references/checklists/ROBINS_E.md +179 -0
- package/skills/check-reporting/references/checklists/ROBINS_I.md +87 -0
- package/skills/check-reporting/references/checklists/ROBIS.md +114 -0
- package/skills/check-reporting/references/checklists/ROB_ME.md +126 -0
- package/skills/check-reporting/references/checklists/RoB2.md +79 -0
- package/skills/check-reporting/references/checklists/RoB_NMA.md +96 -0
- package/skills/check-reporting/references/checklists/SPIRIT.md +112 -0
- package/skills/check-reporting/references/checklists/SQUIRE_2.md +68 -0
- package/skills/check-reporting/references/checklists/STARD.md +129 -0
- package/skills/check-reporting/references/checklists/STARD_AI.md +211 -0
- package/skills/check-reporting/references/checklists/STROBE.md +80 -0
- package/skills/check-reporting/references/checklists/SWiM.md +33 -0
- package/skills/check-reporting/references/checklists/TRIPOD.md +157 -0
- package/skills/check-reporting/references/checklists/TRIPOD_AI.md +140 -0
- package/skills/check-reporting/references/step4c_registration_timing.md +93 -0
- package/skills/check-reporting/references/step4d_prisma_figure_audit.md +137 -0
- package/skills/check-reporting/scripts/check_checklist_exists.py +183 -0
- package/skills/check-reporting/scripts/check_checklist_version.py +168 -0
- package/skills/check-reporting/scripts/check_framework_naming.py +206 -0
- package/skills/check-reporting/scripts/check_prisma_figure.py +209 -0
- package/skills/check-reporting/scripts/prisma_cascade_check.py +274 -0
- package/skills/check-reporting/skill.yml +41 -0
- package/skills/check-reporting/tests/fixtures/framework_bad.md +8 -0
- package/skills/check-reporting/tests/fixtures/framework_clean.md +7 -0
- package/skills/check-reporting/tests/test_checklist_fail_fast.sh +77 -0
- package/skills/check-reporting/tests/test_checklist_version.sh +72 -0
- package/skills/check-reporting/tests/test_framework_naming.sh +45 -0
- package/skills/check-reporting/tests/test_prisma_cascade.sh +104 -0
- package/skills/clean-data/SKILL.md +180 -0
- package/skills/clean-data/references/cleaning_patterns.md +299 -0
- package/skills/clean-data/references/profiling_template.py +304 -0
- package/skills/clean-data/scripts/check_structural_zero.py +174 -0
- package/skills/clean-data/skill.yml +35 -0
- package/skills/clean-data/tests/fixtures/smoking.csv +8 -0
- package/skills/clean-data/tests/test_structural_zero.sh +49 -0
- package/skills/cross-national/SKILL.md +264 -0
- package/skills/cross-national/skill.yml +37 -0
- package/skills/define-variables/SKILL.md +146 -0
- package/skills/define-variables/references/common_definitions.md +190 -0
- package/skills/define-variables/skill.yml +34 -0
- package/skills/define-variables/templates/variable_operationalization.md +64 -0
- package/skills/deidentify/SKILL.md +203 -0
- package/skills/deidentify/deidentify.py +1224 -0
- package/skills/deidentify/locales/_template.json +45 -0
- package/skills/deidentify/locales/au.json +43 -0
- package/skills/deidentify/locales/ca.json +44 -0
- package/skills/deidentify/locales/cn.json +47 -0
- package/skills/deidentify/locales/de.json +48 -0
- package/skills/deidentify/locales/fr.json +48 -0
- package/skills/deidentify/locales/in.json +48 -0
- package/skills/deidentify/locales/jp.json +48 -0
- package/skills/deidentify/locales/kr.json +48 -0
- package/skills/deidentify/locales/uk.json +45 -0
- package/skills/deidentify/locales/us.json +43 -0
- package/skills/deidentify/references/date_shift_guide.md +82 -0
- package/skills/deidentify/references/hipaa_18_identifiers.md +48 -0
- package/skills/deidentify/references/korean_phi_patterns.md +135 -0
- package/skills/deidentify/skill.yml +43 -0
- package/skills/deidentify/tests/README.md +26 -0
- package/skills/deidentify/tests/test_clean.csv +16 -0
- package/skills/deidentify/tests/test_edge_cases.csv +11 -0
- package/skills/deidentify/tests/test_phi_korean.csv +11 -0
- package/skills/design-ai-benchmarking/SKILL.md +214 -0
- package/skills/design-ai-benchmarking/references/benchmark_export_schema.json +69 -0
- package/skills/design-ai-benchmarking/references/elicitation_rubric_template.md +37 -0
- package/skills/design-ai-benchmarking/skill.yml +38 -0
- package/skills/design-study/SKILL.md +298 -0
- package/skills/design-study/skill.yml +33 -0
- package/skills/fill-icmje-coi/SKILL.md +216 -0
- package/skills/fill-icmje-coi/scripts/fill_icmje_coi.py +140 -0
- package/skills/fill-icmje-coi/skill.yml +35 -0
- package/skills/fill-icmje-coi/templates/icmje_coi_seed_synthetic.docx +0 -0
- package/skills/fill-protocol/SKILL.md +248 -0
- package/skills/fill-protocol/examples/example_irb_template.yaml +53 -0
- package/skills/fill-protocol/references/best_practices.md +121 -0
- package/skills/fill-protocol/scripts/doc_to_docx.py +111 -0
- package/skills/fill-protocol/scripts/fill_form.py +611 -0
- package/skills/fill-protocol/scripts/inspect_template.py +61 -0
- package/skills/fill-protocol/setup.sh +162 -0
- package/skills/fill-protocol/skill.yml +37 -0
- package/skills/find-cohort-gap/SKILL.md +309 -0
- package/skills/find-cohort-gap/references/cohort_profile_template.md +93 -0
- package/skills/find-cohort-gap/references/onepager_template.md +84 -0
- package/skills/find-cohort-gap/references/pattern_scoring_rubric.md +169 -0
- package/skills/find-cohort-gap/references/saturation_query_templates.md +143 -0
- package/skills/find-cohort-gap/skill.yml +35 -0
- package/skills/find-journal/POLICY.md +87 -0
- package/skills/find-journal/SKILL.md +340 -0
- package/skills/find-journal/references/journal_profiles/AJNR.md +29 -0
- package/skills/find-journal/references/journal_profiles/AJR.md +30 -0
- package/skills/find-journal/references/journal_profiles/Abdominal_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Academic_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Annals_of_Internal_Medicine.md +33 -0
- package/skills/find-journal/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +28 -0
- package/skills/find-journal/references/journal_profiles/BMC_Medicine.md +31 -0
- package/skills/find-journal/references/journal_profiles/British_Journal_of_Radiology.md +39 -0
- package/skills/find-journal/references/journal_profiles/CVIR.md +30 -0
- package/skills/find-journal/references/journal_profiles/Chest.md +39 -0
- package/skills/find-journal/references/journal_profiles/Clinical_Radiology.md +30 -0
- package/skills/find-journal/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +32 -0
- package/skills/find-journal/references/journal_profiles/Diabetes_Metabolism_Journal.md +36 -0
- package/skills/find-journal/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +32 -0
- package/skills/find-journal/references/journal_profiles/Endocrinology_and_Metabolism.md +37 -0
- package/skills/find-journal/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +39 -0
- package/skills/find-journal/references/journal_profiles/European_Radiology.md +29 -0
- package/skills/find-journal/references/journal_profiles/Hepatology_Communications.md +40 -0
- package/skills/find-journal/references/journal_profiles/Hepatology_International.md +37 -0
- package/skills/find-journal/references/journal_profiles/IEEE_JBHI.md +28 -0
- package/skills/find-journal/references/journal_profiles/IEEE_TMI.md +28 -0
- package/skills/find-journal/references/journal_profiles/INSI.md +29 -0
- package/skills/find-journal/references/journal_profiles/Investigative_Radiology.md +25 -0
- package/skills/find-journal/references/journal_profiles/JACC_Advances.md +41 -0
- package/skills/find-journal/references/journal_profiles/JACC_Asia.md +30 -0
- package/skills/find-journal/references/journal_profiles/JACR.md +28 -0
- package/skills/find-journal/references/journal_profiles/JAMA.md +40 -0
- package/skills/find-journal/references/journal_profiles/JAMA_Network_Open.md +30 -0
- package/skills/find-journal/references/journal_profiles/JCSM.md +39 -0
- package/skills/find-journal/references/journal_profiles/JKMS.md +32 -0
- package/skills/find-journal/references/journal_profiles/JMIR.md +29 -0
- package/skills/find-journal/references/journal_profiles/JMIR_Medical_Education.md +29 -0
- package/skills/find-journal/references/journal_profiles/JNIS.md +35 -0
- package/skills/find-journal/references/journal_profiles/JVIR.md +31 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Biomedical_Informatics.md +29 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +40 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Magnetic_Resonance_Imaging.md +30 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Nuclear_Medicine.md +31 -0
- package/skills/find-journal/references/journal_profiles/Journal_of_Stroke.md +32 -0
- package/skills/find-journal/references/journal_profiles/KJR.md +38 -0
- package/skills/find-journal/references/journal_profiles/Korean_Circulation_Journal.md +38 -0
- package/skills/find-journal/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +36 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Diabetes_and_Endocrinology.md +40 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +49 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Infectious_Diseases.md +38 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Neurology.md +39 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Oncology.md +40 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Psychiatry.md +38 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Public_Health.md +30 -0
- package/skills/find-journal/references/journal_profiles/Lancet_Respiratory_Medicine.md +39 -0
- package/skills/find-journal/references/journal_profiles/Liver_International.md +33 -0
- package/skills/find-journal/references/journal_profiles/Medical_Image_Analysis.md +28 -0
- package/skills/find-journal/references/journal_profiles/NEJM.md +33 -0
- package/skills/find-journal/references/journal_profiles/Nature_Machine_Intelligence.md +31 -0
- package/skills/find-journal/references/journal_profiles/Nature_Medicine.md +39 -0
- package/skills/find-journal/references/journal_profiles/Neuroradiology.md +31 -0
- package/skills/find-journal/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +39 -0
- package/skills/find-journal/references/journal_profiles/PLOS_Medicine.md +32 -0
- package/skills/find-journal/references/journal_profiles/RYAI.md +28 -0
- package/skills/find-journal/references/journal_profiles/Radiology.md +29 -0
- package/skills/find-journal/references/journal_profiles/Skeletal_Radiology.md +31 -0
- package/skills/find-journal/references/journal_profiles/Stroke.md +37 -0
- package/skills/find-journal/references/journal_profiles/The_BMJ.md +31 -0
- package/skills/find-journal/references/journal_profiles/The_Lancet.md +31 -0
- package/skills/find-journal/references/journal_profiles/The_Lancet_Digital_Health.md +29 -0
- package/skills/find-journal/references/journal_profiles/World_Journal_of_Hepatology.md +53 -0
- package/skills/find-journal/references/journal_profiles/npj_Digital_Medicine.md +29 -0
- package/skills/find-journal/skill.yml +34 -0
- package/skills/fulltext-retrieval/SKILL.md +174 -0
- package/skills/fulltext-retrieval/fetch_oa.py +433 -0
- package/skills/fulltext-retrieval/pdf_to_md.py +160 -0
- package/skills/fulltext-retrieval/skill.yml +41 -0
- package/skills/generate-codebook/SKILL.md +155 -0
- package/skills/generate-codebook/references/codebook_schema.md +76 -0
- package/skills/generate-codebook/scripts/generate_codebook.py +278 -0
- package/skills/generate-codebook/skill.yml +35 -0
- package/skills/generate-codebook/tests/test_generate_codebook.sh +76 -0
- package/skills/grant-builder/SKILL.md +251 -0
- package/skills/grant-builder/skill.yml +34 -0
- package/skills/humanize/SKILL.md +251 -0
- package/skills/humanize/references/ai_patterns.md +571 -0
- package/skills/humanize/skill.yml +33 -0
- package/skills/intake-project/SKILL.md +264 -0
- package/skills/intake-project/skill.yml +34 -0
- package/skills/lit-sync/SKILL.md +448 -0
- package/skills/lit-sync/references/locale/ko/note_templates.md +110 -0
- package/skills/lit-sync/skill.yml +52 -0
- package/skills/lit-sync/tests/test_poll_logic.sh +92 -0
- package/skills/ma-scout/SKILL.md +640 -0
- package/skills/ma-scout/references/project_readme_template.md +95 -0
- package/skills/ma-scout/references/project_readme_template_ko.md +82 -0
- package/skills/ma-scout/skill.yml +33 -0
- package/skills/make-figures/SKILL.md +957 -0
- package/skills/make-figures/references/critic_rubrics/data_plot.md +166 -0
- package/skills/make-figures/references/critic_rubrics/flow_diagram.md +169 -0
- package/skills/make-figures/references/design_principles.md +181 -0
- package/skills/make-figures/references/exemplar_diagrams/README.md +65 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/README.md +15 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_input.yaml +37 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_output.pdf +0 -0
- package/skills/make-figures/references/exemplar_diagrams/consort/template_output.png +0 -0
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# Paper Type: Case Report
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## Overview
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- **Reporting guideline:** CARE 2016 (mandatory)
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- **Typical word count:** 1000–1500 words (short-form) or 2000–3000 words (extended with literature review)
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- **Default mode:** Short-form (1000-1500 words). Use `--extended` for longer format.
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- **Structure:** Title → Abstract → Introduction → Case Presentation → Discussion → Conclusions → Patient Perspective (optional) → Informed Consent
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- **Key requirement:** Patient consent/anonymization documented
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---
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## CARE 2016 Checklist Quick Reference
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| # | Item | Section | Description |
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| 1 | Title | Title | Diagnosis or main symptom AND "case report" |
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| 2 | Key words | Abstract | 2-5 keywords covering the case |
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| 3 | Abstract | Abstract | Structured: Introduction, Case Presentation, Conclusion |
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| 4 | Introduction | Introduction | Background with references, why this case is reportable |
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| 5 | Patient information | Case Presentation | Demographics, main symptoms, medical history |
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| 6 | Clinical findings | Case Presentation | Physical examination, key clinical findings |
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| 7 | Timeline | Case Presentation | Important dates and events in table or figure |
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| 8 | Diagnostic assessment | Case Presentation | Methods, pathological findings, challenges, reasoning |
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| 9 | Therapeutic intervention | Case Presentation | Types, administration, duration, changes |
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| 10 | Follow-up and outcomes | Case Presentation | Clinician-assessed and patient-assessed outcomes, adherence, adverse events |
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| 11 | Discussion | Discussion | Strengths, limitations, relevant literature, rationale for conclusions |
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| 12 | Patient perspective | Optional | Patient's own views when available |
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| 13 | Informed consent | End | Documentation that consent was obtained |
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> Full CARE checklist: https://www.care-statement.org/checklist
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---
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## When to Write a Case Report
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Case reports are appropriate when the case demonstrates:
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- A rare or previously unreported condition or presentation
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- An unusual complication of a known condition or procedure
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- A novel diagnostic approach or therapeutic intervention
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- An important teaching point with clinical relevance
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- A paradoxical or unexpected finding
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---
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## Title
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---
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## Structured Abstract (150–250 words)
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```
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Introduction: [Why this case is being reported — one sentence on rarity or teaching value]
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Case Presentation: [Age, sex, key presenting complaint, key imaging/lab findings, diagnosis]
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Clinical Findings: [Key examination and investigation results]
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Treatment/Intervention: [What was done]
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---
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## Case Presentation (600–1200 words)
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### Patient Information
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- Chief complaint
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- Relevant medical history, medications, allergies, family history, social history
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[Modality and technique]: [Acquisition parameters if relevant]
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→ Findings: [Location, size, morphology, signal/density characteristics,
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enhancement pattern, associated findings]
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"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."
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## Discussion (400–800 words)
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2. **Pathophysiology:** Explain the underlying mechanism if relevant.
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3. **Diagnostic challenge:** Why was this case difficult to diagnose, or what did imaging add?
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4. **Management rationale:** Why was this treatment chosen? What are the alternatives?
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5. **Learning points:** What should clinicians take from this case?
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Learning Points
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• [Imaging finding or pattern to recognize]
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• [Management principle or pitfall to avoid]
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• [When to consider this diagnosis]
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---
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## Conclusion (100–200 words)
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"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]."
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## Informed Consent Statement
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At the end of the case report, include one of these statements:
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**Option A (patient consented):**
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**Option C (minor patient):**
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| Item | Content |
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| Table 1 | Clinical and laboratory data at presentation |
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| Author (Year) | Age/Sex | Key Presentation | Diagnosis Method | Treatment | Outcome |
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| Current case | ... | ... | ... | ... | ... |
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---
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## Common Case Report Pitfalls
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3. **Identifying information in images** — check DICOM metadata, remove patient labels from figures.
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4. **Vague imaging descriptions** — give exact size, location, signal characteristics, and enhancement pattern.
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5. **Overclaiming in Discussion** — case reports cannot establish causality; use "may," "suggest," "is consistent with."
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6. **Insufficient literature context** — do a PubMed search for similar cases; cite all relevant ones.
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7. **Too long a Discussion** — case reports are not reviews; keep Discussion focused on this case's lessons.
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@@ -0,0 +1,328 @@
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# Cross-National Comparison Study — Paper Type Template
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## Overview
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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.
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---
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## Title
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- Include "Cross-National," "Binational," or country names.
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- Specify the study design in a subtitle.
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- Under 20 words preferred.
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### Title Templates
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| Pattern | Example |
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|---------|---------|
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| `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 |
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| `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 |
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| `Maternal {exposure} and {outcome} in offspring: a binational cohort study` | Pregestational diabetes and neuropsychiatric risk |
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| `Burden of {outcome} after {exposure} in {Country A} and {Country B}: a binational population-based cohort study` | Cardiovascular outcomes after infection |
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| `Trends in {outcome} among {population}, {year range}: a nationwide representative study` | Physical activity trends (single-country variant) |
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Notes:
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- "Binational" is increasingly preferred over "Cross-national" for two-country studies.
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- Always include the year range for trend studies.
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- The subtitle pattern is consistent: "a nationwide representative {comparative/cross-sectional/cohort} study."
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---
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## Abstract (Structured, 250 words max)
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### Background
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- State the known relationship and the cross-national evidence gap.
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- Template: "Although {known relationship} has been suggested, evidence remains limited across cultural contexts. This study {compared/examined} {association} in {Country A} and {Country B}."
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### Methods
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- Name both datasets with years and sample sizes.
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- State that datasets were analyzed independently.
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- Name the harmonization approach and statistical methods.
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### Results
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- Report sample sizes from each dataset.
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- Key findings with weighted odds ratios (wOR) or aHRs and 95% CIs from each country.
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- Highlight convergent or divergent findings across countries.
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### Conclusion
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- Main conclusion emphasizing cross-national consistency or divergence.
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- Implication for policy or future research.
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#### Discovery/Validation Variant
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- Results structure: "In the {weighted} discovery cohort, {N} individuals were included... Similar patterns were observed in the validation cohort."
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---
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## Introduction (3-4 paragraphs, ~400-500 words)
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### Paragraph 1: Global Burden Statement
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- Cite GBD or WHO prevalence figures with projections.
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- Template: "{Condition} remains a {highly prevalent / growing} global health {threat/challenge}."
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|
+
|
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### Paragraph 2: Prior Evidence (Single-Country Limitations)
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- Summarize existing single-country evidence.
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- Flag limitations: "were limited to single-country cohorts," "did not adjust for key confounders," "have not taken broad population approaches."
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- If relevant, cite Mendelian randomization evidence showing ancestral or population differences.
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|
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### Paragraph 3: Cross-National Gap and Study Aim
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+
- Template: "To our knowledge, no prior study has evaluated {association} within a cross-national comparative framework."
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|
+
- 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}."
|
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+
- Optional: justify the country pairing with cultural, genetic, or healthcare system differences.
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|
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|
+
|
|
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### Variation: Trend Studies
|
|
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|
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- 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."
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|
+
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---
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|
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## Materials and Methods (~1000-1400 words)
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|
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### 3.1 Data Sources
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+
|
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Describe each dataset separately with parallel structure:
|
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|
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Template:
|
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|
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> This study utilized {Dataset A} for {years} and {Dataset B} for {years}.
|
|
86
|
+
>
|
|
87
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> {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
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+
> {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
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+
>
|
|
91
|
+
> Both surveys include standardized health interviews, physical examinations, and laboratory tests, and collect extensive information on sociodemographic characteristics, health behaviors, and medical conditions.
|
|
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|
+
|
|
93
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+
#### Common Dataset Pairings
|
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|
+
|
|
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 |
|
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+
|
|
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+
Notes:
|
|
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+
- Survey years may be non-consecutive if specific variables are only collected in certain cycles. Always explain excluded years.
|
|
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- 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}."
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|
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|
+
|
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106
|
+
### 3.2 Ethics Approval
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|
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+
|
|
108
|
+
- Separate IRB approvals per country, listed together.
|
|
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|
+
- 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."
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|
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+
|
|
111
|
+
### 3.3 Variable Harmonization
|
|
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|
+
|
|
113
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+
Three-layer harmonization framework:
|
|
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|
+
|
|
115
|
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#### Layer 1: Identical Instruments
|
|
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- Variables measured with the same validated instrument in both datasets (e.g., PHQ-9 for depression, fasting glucose + HbA1c for diabetes).
|
|
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|
+
- Template: "{Instrument} was used in both {Dataset A} and {Dataset B}."
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+
|
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119
|
+
#### Layer 2: Country-Specific Cutoffs with Clinical Justification
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|
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- Variables where clinical thresholds differ by national guidelines.
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- Template: "{Variable} was defined using country-specific standards: {cutoff A} in {Country A} and {cutoff B} in {Country B}, reflecting established national guidelines."
|
|
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+
- Common example: BMI >=25 in East Asia (Asia-Pacific cutoff) vs. BMI >=30 in US/Europe (WHO Western cutoff).
|
|
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|
+
|
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|
+
#### Layer 3: Operationally Different Variables Mapped to Equivalent Categories
|
|
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|
+
- Variables measured differently but mappable to equivalent categories.
|
|
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|
+
- Common examples:
|
|
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|
+
- Income: quintiles (Korea) vs. poverty-income ratio (US) → binary high/low.
|
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|
+
- Smoking/alcohol: mapped to equivalent categorical levels.
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|
+
|
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130
|
+
#### Key Harmonization Decisions (Reference Table)
|
|
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|
+
|
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|
+
| Variable | Typical Resolution |
|
|
133
|
+
|----------|-------------------|
|
|
134
|
+
| Obesity | Country-specific BMI cutoffs with justification |
|
|
135
|
+
| Income | Equivalent binary or tertile split |
|
|
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|
+
| Depression | Identical instrument (PHQ-9) with same cutoff |
|
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|
+
| 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
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+
- Compare with prior single-country and cross-national studies.
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- Discuss population-specific factors (cultural, genetic, healthcare system) that may explain differences.
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### Paragraph 4: Clinical and Policy Implications
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- Policy relevance across different healthcare systems.
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- Public health recommendations.
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### Paragraph 5: Limitations
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Standard limitation categories for cross-national studies:
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| # | Category | Template |
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|---|----------|----------|
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| 1 | Cross-sectional design | "The cross-sectional design precludes inference of causality." Mitigation: "the dose-response relationship and consistency across subgroups support plausibility." |
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| 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." |
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| 3 | Temporal coverage mismatch | "{Dataset A} included selected survey years, whereas {Dataset B} provided continuous data." Mitigation: "appropriate sampling weights and consistent analytic criteria." |
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| 4 | Self-report bias | "The use of self-reported data may introduce recall bias." Mitigation: "both surveys utilize validated instruments administered by trained personnel." |
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| 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." |
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| 6 | Multiple comparisons | "Subgroup analyses were not adjusted for multiple comparisons." Mitigation: "based on prespecified variables of clinical and epidemiological relevance." |
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| 7 | Unmeasured confounders | "Differences in healthcare systems, cultural factors, and unmeasured confounders may influence the relationship." |
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| 8 | Population representativeness | "Both cohorts are from East Asian and Western populations; extrapolation to other regions requires caution." |
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+
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+
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."
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+
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### Conclusion
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275
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+
- Citable statement emphasizing cross-national convergence or divergence.
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- Specific policy or clinical recommendation.
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+
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+
---
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+
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## Tables
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281
|
+
|
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282
|
+
- **Table 1**: Baseline characteristics by country (separate columns per dataset).
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283
|
+
- **Table 2**: Primary association results (wOR or aHR with 95% CI) from both countries in parallel columns.
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284
|
+
- **Table 3**: Subgroup analyses by country.
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285
|
+
- **Table S1+**: Variable harmonization details, ICD-10 codes, sensitivity analysis results.
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286
|
+
|
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287
|
+
## Figures
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288
|
+
|
|
289
|
+
- **Figure 1**: Study flow diagram (per country or combined with country-specific branches).
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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."
|
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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
|