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
- package/skills/make-figures/references/exemplar_diagrams/consort/template_output_600.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/other/other_02.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/other/other_02.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/other/other_02_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/README.md +15 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_01.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_01.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_01_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_03.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_03.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_03_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_04.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_04.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_04_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_05.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_05.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_05_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_06.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_06.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_06_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_07.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_07.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_07_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_08.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_08.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_08_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_09.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_09.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_09_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_10.meta.yaml +4 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_10.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/pipeline/pipeline_10_why.md +13 -0
- package/skills/make-figures/references/exemplar_diagrams/prisma/README.md +15 -0
- package/skills/make-figures/references/exemplar_diagrams/prisma/template_input.yaml +47 -0
- package/skills/make-figures/references/exemplar_diagrams/prisma/template_output.pdf +0 -0
- package/skills/make-figures/references/exemplar_diagrams/prisma/template_output.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/prisma/template_output_600.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/stard/README.md +15 -0
- package/skills/make-figures/references/exemplar_diagrams/stard/template_input.yaml +40 -0
- package/skills/make-figures/references/exemplar_diagrams/stard/template_output.pdf +0 -0
- package/skills/make-figures/references/exemplar_diagrams/stard/template_output.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/stard/template_output_600.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/strobe/template_input.yaml +43 -0
- package/skills/make-figures/references/exemplar_diagrams/strobe/template_input_pptx.yaml +43 -0
- package/skills/make-figures/references/exemplar_diagrams/strobe/template_output.pdf +0 -0
- package/skills/make-figures/references/exemplar_diagrams/strobe/template_output.png +0 -0
- package/skills/make-figures/references/exemplar_diagrams/strobe/template_output.pptx +0 -0
- package/skills/make-figures/references/exemplar_diagrams/strobe/template_output_600.png +0 -0
- package/skills/make-figures/references/figure_specs.md +291 -0
- package/skills/make-figures/references/flow_diagram_lessons.md +164 -0
- package/skills/make-figures/references/jacc_central_illustration_principles.md +91 -0
- package/skills/make-figures/references/medical_illustration_sources.md +98 -0
- package/skills/make-figures/references/pipeline_concepts_medical_ai.md +240 -0
- package/skills/make-figures/references/reporting_guideline_figure_map.md +104 -0
- package/skills/make-figures/references/visual_abstract_templates/european_radiology.pptx +0 -0
- package/skills/make-figures/references/visual_abstract_templates/jacc_central_illustration.pptx +0 -0
- package/skills/make-figures/references/visual_abstract_templates/medsci_default.pptx +0 -0
- package/skills/make-figures/references/visual_abstract_templates/template_guide.md +114 -0
- package/skills/make-figures/scripts/build_jacc_template.py +77 -0
- package/skills/make-figures/scripts/build_prisma2020_template.py +371 -0
- package/skills/make-figures/scripts/build_strobe_template.py +351 -0
- package/skills/make-figures/scripts/critic_figure.py +264 -0
- package/skills/make-figures/scripts/derive_figure_legend_counts.py +138 -0
- package/skills/make-figures/scripts/extract_exemplar_from_pdf.py +186 -0
- package/skills/make-figures/scripts/fetch_official_templates.sh +88 -0
- package/skills/make-figures/scripts/fill_prisma_template.py +142 -0
- package/skills/make-figures/scripts/generate_flow_diagram.R +133 -0
- package/skills/make-figures/scripts/generate_image.py +99 -0
- package/skills/make-figures/scripts/generate_visual_abstract.py +438 -0
- package/skills/make-figures/scripts/validate_pptx_mac_compat.py +233 -0
- package/skills/make-figures/skill.yml +52 -0
- package/skills/make-figures/templates/official/NOTES.md +62 -0
- package/skills/make-figures/templates/official/consort2010/CONSORT_2025_editable_checklist.docx +0 -0
- package/skills/make-figures/templates/official/consort2010/CONSORT_2025_flow_diagram.docx +0 -0
- package/skills/make-figures/templates/official/prisma2020/PRISMA_2020_flow_new_v1.pptx +0 -0
- package/skills/make-figures/templates/official/prisma2020/PRISMA_2020_flow_new_v2.pptx +0 -0
- package/skills/make-figures/templates/official/prisma2020/PRISMA_2020_flow_updated_v2.pptx +0 -0
- package/skills/make-figures/templates/official/spirit2013/SPIRIT_2025_editable_checklist.docx +0 -0
- package/skills/make-figures/templates/official/spirit2013/SPIRIT_2025_participant_timeline.docx +0 -0
- package/skills/make-figures/templates/official/stard2015/STARD_2015_checklist.docx +0 -0
- package/skills/make-figures/templates/official/stard2015/STARD_2015_flow_diagram.pdf +0 -0
- package/skills/make-figures/tests/fixtures/figure1_flow.yaml +8 -0
- package/skills/make-figures/tests/fixtures/manuscript_ok.md +9 -0
- package/skills/make-figures/tests/fixtures/manuscript_stale.md +4 -0
- package/skills/make-figures/tests/test_legend_reconcile.sh +36 -0
- package/skills/manage-project/SKILL.md +358 -0
- package/skills/manage-project/references/pre_submission_checklist.md +53 -0
- package/skills/manage-project/references/project_state_template.json +37 -0
- package/skills/manage-project/references/scaffold_templates.md +118 -0
- package/skills/manage-project/references/status_output_format.md +44 -0
- package/skills/manage-project/references/timeline_example.md +20 -0
- package/skills/manage-project/skill.yml +36 -0
- package/skills/manage-project/templates/SSOT.yaml.template +41 -0
- package/skills/manage-refs/LICENSE.zotero-mcp +21 -0
- package/skills/manage-refs/NOTICE.md +29 -0
- package/skills/manage-refs/SKILL.md +289 -0
- package/skills/manage-refs/citation_styles/README.md +40 -0
- package/skills/manage-refs/citation_styles/american-journal-of-roentgenology.csl +211 -0
- package/skills/manage-refs/citation_styles/cardiovascular-and-interventional-radiology.csl +19 -0
- package/skills/manage-refs/citation_styles/european-radiology.csl +19 -0
- package/skills/manage-refs/citation_styles/journal-of-cachexia-sarcopenia-and-muscle.csl +150 -0
- package/skills/manage-refs/citation_styles/journal-of-korean-medical-science-strict.csl +533 -0
- package/skills/manage-refs/citation_styles/journal-of-korean-medical-science.csl +16 -0
- package/skills/manage-refs/citation_styles/korean-journal-of-radiology.csl +155 -0
- package/skills/manage-refs/citation_styles/nature.csl +189 -0
- package/skills/manage-refs/citation_styles/nlm-citation-sequence.csl +535 -0
- package/skills/manage-refs/citation_styles/radiology.csl +228 -0
- package/skills/manage-refs/citation_styles/springer-basic-brackets.csl +187 -0
- package/skills/manage-refs/citation_styles/springer-vancouver-brackets.csl +276 -0
- package/skills/manage-refs/citation_styles/vancouver-superscript.csl +536 -0
- package/skills/manage-refs/citation_styles/vancouver.csl +535 -0
- package/skills/manage-refs/references/REFERENCE_STYLE_SPECS.md +59 -0
- package/skills/manage-refs/references/check_xref_symptoms.md +35 -0
- package/skills/manage-refs/scripts/_vendor_citation_writer.py +600 -0
- package/skills/manage-refs/scripts/check_citation_keys.py +112 -0
- package/skills/manage-refs/scripts/check_csl_render.py +102 -0
- package/skills/manage-refs/scripts/check_xref.py +633 -0
- package/skills/manage-refs/scripts/fill_journal_abbrev.py +104 -0
- package/skills/manage-refs/scripts/inject_zotero_cwyw.py +133 -0
- package/skills/manage-refs/scripts/md_marker_convert.py +193 -0
- package/skills/manage-refs/scripts/pre_submission_gate.sh +238 -0
- package/skills/manage-refs/scripts/render_pandoc.sh +88 -0
- package/skills/manage-refs/skill.yml +70 -0
- package/skills/manage-refs/tests/fixtures/pre_submission_gate/README.md +32 -0
- package/skills/manage-refs/tests/fixtures/pre_submission_gate/manuscript.md +10 -0
- package/skills/manage-refs/tests/fixtures/pre_submission_gate/refs.bib +34 -0
- package/skills/manage-refs/tests/fixtures/pre_submission_gate/run.sh +117 -0
- package/skills/manage-refs/tests/test_vN_docx_check.sh +145 -0
- package/skills/meta-analysis/SKILL.md +739 -0
- package/skills/meta-analysis/references/LICENSES.md +21 -0
- package/skills/meta-analysis/references/PROSPERO_template.md +221 -0
- package/skills/meta-analysis/references/ai_pre_screening_template.py +245 -0
- package/skills/meta-analysis/references/checklists/JBI_Case_Series.md +45 -0
- package/skills/meta-analysis/references/checklists/NOS.md +88 -0
- package/skills/meta-analysis/references/checklists/PRISMA_DTA.md +36 -0
- package/skills/meta-analysis/references/checklists/PROBAST.md +75 -0
- package/skills/meta-analysis/references/checklists/QUADAS2.md +77 -0
- package/skills/meta-analysis/references/checklists/ROBINS_I.md +87 -0
- package/skills/meta-analysis/references/checklists/RoB2.md +79 -0
- package/skills/meta-analysis/references/data_integrity_checklist.md +57 -0
- package/skills/meta-analysis/references/icmje_coi_guide.md +181 -0
- package/skills/meta-analysis/references/phase10_recovery.md +136 -0
- package/skills/meta-analysis/references/phase4_km_composite.md +58 -0
- package/skills/meta-analysis/references/phase6_statistical_synthesis.md +148 -0
- package/skills/meta-analysis/references/phase9_circulation.md +84 -0
- package/skills/meta-analysis/references/post_submission_release_ops.md +41 -0
- package/skills/meta-analysis/references/r_templates.md +132 -0
- package/skills/meta-analysis/references/review_orchestration.md +40 -0
- package/skills/meta-analysis/references/submission_package_drift.md +71 -0
- package/skills/meta-analysis/scripts/check_pool_consistency.py +201 -0
- package/skills/meta-analysis/scripts/cohort_overlap_check.py +242 -0
- package/skills/meta-analysis/scripts/dta_extraction_qc.py +137 -0
- package/skills/meta-analysis/scripts/screening_reconcile.py +160 -0
- package/skills/meta-analysis/skill.yml +47 -0
- package/skills/meta-analysis/templates/FINAL_POOL_LOCK.yaml.template +70 -0
- package/skills/meta-analysis/templates/extraction_form_v2.md +129 -0
- package/skills/meta-analysis/templates/supplementary_8file_checklist.md +94 -0
- package/skills/meta-analysis/tests/test_pool_consistency.sh +123 -0
- package/skills/orchestrate/SKILL.md +501 -0
- package/skills/orchestrate/references/dialogue_nodes.md +196 -0
- package/skills/orchestrate/references/report_template.md +109 -0
- package/skills/orchestrate/references/report_template_ko.md +88 -0
- package/skills/orchestrate/skill.yml +44 -0
- package/skills/peer-review/SKILL.md +381 -0
- package/skills/peer-review/references/aczel_2021_reviewer2_patterns.md +88 -0
- package/skills/peer-review/references/domain-probes/ai_overclaiming.md +47 -0
- package/skills/peer-review/references/domain-probes/narrative_review.md +44 -0
- package/skills/peer-review/references/domain-probes/observational_confounding.md +48 -0
- package/skills/peer-review/references/domain-probes/radiomics.md +38 -0
- package/skills/peer-review/references/domain-probes/sr_ma.md +87 -0
- package/skills/peer-review/references/domain-probes/survival_prognostic.md +68 -0
- package/skills/peer-review/references/exemplar_reviews/README.md +43 -0
- package/skills/peer-review/references/exemplar_reviews/ai_overclaiming.md +47 -0
- package/skills/peer-review/references/exemplar_reviews/calibration_missing.md +44 -0
- package/skills/peer-review/references/exemplar_reviews/data_leakage.md +48 -0
- package/skills/peer-review/references/exemplar_reviews/reference_standard_validity.md +45 -0
- package/skills/peer-review/references/narrative_review_audit.md +67 -0
- package/skills/peer-review/references/reviewer_calibration/README.md +34 -0
- package/skills/peer-review/references/reviewer_calibration/compliance_floor.md +52 -0
- package/skills/peer-review/references/reviewer_profiles/AJR.md +82 -0
- package/skills/peer-review/references/reviewer_profiles/EURE.md +64 -0
- package/skills/peer-review/references/reviewer_profiles/INSI.md +57 -0
- package/skills/peer-review/references/reviewer_profiles/KJR.md +100 -0
- package/skills/peer-review/references/reviewer_profiles/README.md +32 -0
- package/skills/peer-review/references/reviewer_profiles/RYAI.md +86 -0
- package/skills/peer-review/skill.yml +39 -0
- package/skills/present-paper/SKILL.md +675 -0
- package/skills/present-paper/references/critic_rubrics/slide.md +155 -0
- package/skills/present-paper/references/generate_pptx_templates.py +604 -0
- package/skills/present-paper/references/medical_presentation_templates.md +277 -0
- package/skills/present-paper/references/slide_design_principles.md +202 -0
- package/skills/present-paper/references/slide_visual_styles/nature_lancet.md +168 -0
- package/skills/present-paper/references/workflow-checklist.md +109 -0
- package/skills/present-paper/scripts/extract_pdf_figures.py +243 -0
- package/skills/present-paper/scripts/inject_pronunciation_notes.py +178 -0
- package/skills/present-paper/scripts/inject_speaker_notes.py +133 -0
- package/skills/present-paper/scripts/strip_notes_for_sharing.py +140 -0
- package/skills/present-paper/scripts/trim_caption.py +271 -0
- package/skills/present-paper/skill.yml +41 -0
- package/skills/present-paper/templates/build_pptx_nature_lancet.py +688 -0
- package/skills/publish-skill/SKILL.md +370 -0
- package/skills/publish-skill/references/license-compatibility-matrix.md +132 -0
- package/skills/publish-skill/references/pii-patterns.md +130 -0
- package/skills/publish-skill/scripts/audit_skill.sh +278 -0
- package/skills/publish-skill/skill.yml +35 -0
- package/skills/render-pdf-doc/SKILL.md +146 -0
- package/skills/render-pdf-doc/references/known_pitfalls.md +53 -0
- package/skills/render-pdf-doc/references/pandoc_korean_cheatsheet.md +77 -0
- package/skills/render-pdf-doc/scripts/check_deps.sh +42 -0
- package/skills/render-pdf-doc/scripts/infer_colwidths.py +164 -0
- package/skills/render-pdf-doc/scripts/render_pdf.sh +98 -0
- package/skills/render-pdf-doc/skill.yml +57 -0
- package/skills/render-pdf-doc/templates/anchor-doc.md +27 -0
- package/skills/render-pdf-doc/templates/anchor-doc_ko.md +25 -0
- package/skills/render-pdf-doc/templates/briefing-handout.md +33 -0
- package/skills/render-pdf-doc/templates/briefing-handout_ko.md +31 -0
- package/skills/render-pdf-doc/templates/proposal-cover.md +33 -0
- package/skills/render-pdf-doc/templates/proposal-cover_ko.md +31 -0
- package/skills/render-pdf-doc/templates/reference-table.md +22 -0
- package/skills/render-pdf-doc/templates/reference-table_ko.md +20 -0
- package/skills/replicate-study/SKILL.md +150 -0
- package/skills/replicate-study/references/harmonization_3country.csv +47 -0
- package/skills/replicate-study/references/harmonization_knhanes_nhanes.csv +68 -0
- package/skills/replicate-study/references/methodology_extraction_template.md +134 -0
- package/skills/replicate-study/skill.yml +37 -0
- package/skills/review-paper/SKILL.md +104 -0
- package/skills/review-paper/references/macro_skeleton.md +6 -0
- package/skills/review-paper/skill.yml +25 -0
- package/skills/revise/SKILL.md +515 -0
- package/skills/revise/references/r2r_voice.md +346 -0
- package/skills/revise/skill.yml +43 -0
- package/skills/search-lit/SKILL.md +443 -0
- package/skills/search-lit/references/parse_pubmed.py +326 -0
- package/skills/search-lit/references/pubmed_eutils.sh +111 -0
- package/skills/search-lit/skill.yml +46 -0
- package/skills/self-review/SKILL.md +1045 -0
- package/skills/self-review/references/domain-probes/ai_overclaiming.md +47 -0
- package/skills/self-review/references/domain-probes/narrative_review.md +44 -0
- package/skills/self-review/references/domain-probes/observational_confounding.md +48 -0
- package/skills/self-review/references/domain-probes/radiomics.md +38 -0
- package/skills/self-review/references/domain-probes/sr_ma.md +87 -0
- package/skills/self-review/references/domain-probes/survival_prognostic.md +68 -0
- package/skills/self-review/references/exemplar_findings/README.md +43 -0
- package/skills/self-review/references/exemplar_findings/cohort_arithmetic_mismatch.md +35 -0
- package/skills/self-review/references/exemplar_findings/estimand_drift_posthoc_primary.md +39 -0
- package/skills/self-review/references/exemplar_findings/scope_overreach_cross_sectional.md +35 -0
- package/skills/self-review/references/exemplar_findings/unadjusted_confounder.md +36 -0
- package/skills/self-review/references/panel_review_template.md +177 -0
- package/skills/self-review/scripts/check_artifact_coverage.py +301 -0
- package/skills/self-review/scripts/check_claim_artifact.py +248 -0
- package/skills/self-review/scripts/check_classical_style.py +185 -0
- package/skills/self-review/scripts/check_cohort_arithmetic.py +481 -0
- package/skills/self-review/scripts/check_confounding_completeness.py +287 -0
- package/skills/self-review/scripts/check_panel_diversity.py +336 -0
- package/skills/self-review/scripts/check_reference_adequacy.py +392 -0
- package/skills/self-review/scripts/check_reviewer_team_consistency.py +412 -0
- package/skills/self-review/scripts/check_scope_coherence.py +177 -0
- package/skills/self-review/skill.yml +47 -0
- package/skills/self-review/tests/fixtures/claim_manuscript.md +17 -0
- package/skills/self-review/tests/fixtures/claim_prereg.md +6 -0
- package/skills/self-review/tests/fixtures/cohort_bad.md +21 -0
- package/skills/self-review/tests/fixtures/cohort_clean.md +21 -0
- package/skills/self-review/tests/fixtures/cohort_partition.csv +5 -0
- package/skills/self-review/tests/fixtures/coverage_analysis/31_delong_nested_added_value.csv +3 -0
- package/skills/self-review/tests/fixtures/coverage_analysis/table1_demographics.csv +3 -0
- package/skills/self-review/tests/fixtures/coverage_clean.md +13 -0
- package/skills/self-review/tests/fixtures/coverage_manuscript.md +11 -0
- package/skills/self-review/tests/fixtures/panel_collapse.json +27 -0
- package/skills/self-review/tests/fixtures/panel_good.json +32 -0
- package/skills/self-review/tests/fixtures/panel_monoculture.json +32 -0
- package/skills/self-review/tests/fixtures/refadeq_letter.md +13 -0
- package/skills/self-review/tests/fixtures/refadeq_original_fixed.md +42 -0
- package/skills/self-review/tests/fixtures/refadeq_original_uncited.md +40 -0
- package/skills/self-review/tests/fixtures/scope_bad.md +9 -0
- package/skills/self-review/tests/fixtures/scope_clean.md +8 -0
- package/skills/self-review/tests/fixtures/scope_surrogate.md +8 -0
- package/skills/self-review/tests/fixtures/style_bad.md +13 -0
- package/skills/self-review/tests/fixtures/style_clean.md +11 -0
- package/skills/self-review/tests/fixtures/table1_by_exposure.csv +11 -0
- package/skills/self-review/tests/test_artifact_coverage.sh +44 -0
- package/skills/self-review/tests/test_claim_artifact.sh +50 -0
- package/skills/self-review/tests/test_classical_style.sh +44 -0
- package/skills/self-review/tests/test_cohort_arithmetic.sh +49 -0
- package/skills/self-review/tests/test_confounding_completeness.sh +66 -0
- package/skills/self-review/tests/test_panel_diversity.sh +55 -0
- package/skills/self-review/tests/test_panel_mode.sh +69 -0
- package/skills/self-review/tests/test_reference_adequacy.sh +68 -0
- package/skills/self-review/tests/test_reviewer_team_consistency.sh +138 -0
- package/skills/self-review/tests/test_scope_coherence.sh +46 -0
- package/skills/setup-medsci/SKILL.md +110 -0
- package/skills/setup-medsci/references/setup-checklist.md +51 -0
- package/skills/setup-medsci/skill.yml +30 -0
- package/skills/sync-submission/SKILL.md +382 -0
- package/skills/sync-submission/scripts/author_registry_example.yaml +36 -0
- package/skills/sync-submission/scripts/blind_sweep.py +203 -0
- package/skills/sync-submission/scripts/check_asset_anonymization.py +300 -0
- package/skills/sync-submission/scripts/check_cross_artifact_stale.py +211 -0
- package/skills/sync-submission/scripts/cover_letter_drift_check.py +451 -0
- package/skills/sync-submission/scripts/cross_document_n_check.py +486 -0
- package/skills/sync-submission/scripts/detect_copy_divergence.py +136 -0
- package/skills/sync-submission/scripts/preflight_gate.py +458 -0
- package/skills/sync-submission/scripts/scope_drift_check.py +362 -0
- package/skills/sync-submission/scripts/sync_submission.py +169 -0
- package/skills/sync-submission/skill.yml +43 -0
- package/skills/sync-submission/tests/fixtures/copy_ok.md +5 -0
- package/skills/sync-submission/tests/fixtures/copy_stale.md +5 -0
- package/skills/sync-submission/tests/fixtures/ssot.md +5 -0
- package/skills/sync-submission/tests/test_asset_anonymization.sh +99 -0
- package/skills/sync-submission/tests/test_copy_divergence.sh +44 -0
- package/skills/sync-submission/tests/test_cross_artifact_stale.sh +80 -0
- package/skills/sync-submission/tests/test_cross_document_n.sh +132 -0
- package/skills/sync-submission/tests/test_preflight_gate.sh +112 -0
- package/skills/sync-submission/tests/test_scope_drift.sh +122 -0
- package/skills/sync-submission/tests/test_vN_docx_assertion.sh +51 -0
- package/skills/verify-refs/SKILL.md +177 -0
- package/skills/verify-refs/references/manual_checkpoint_guide.md +100 -0
- package/skills/verify-refs/scripts/verify_cli.sh +62 -0
- package/skills/verify-refs/scripts/verify_refs.py +782 -0
- package/skills/verify-refs/skill.yml +44 -0
- package/skills/verify-refs/tests/fixtures/pagination_placeholder.bib +17 -0
- package/skills/verify-refs/tests/test_pagination_placeholder.sh +42 -0
- package/skills/version-dataset/SKILL.md +143 -0
- package/skills/version-dataset/references/manifest_schema.md +72 -0
- package/skills/version-dataset/scripts/version_dataset.py +242 -0
- package/skills/version-dataset/skill.yml +35 -0
- package/skills/version-dataset/tests/test_version_dataset.sh +52 -0
- package/skills/write-paper/SKILL.md +1148 -0
- package/skills/write-paper/references/exemplar_methods/README.md +38 -0
- package/skills/write-paper/references/exemplar_methods/ai_validation_tripod_claim.md +47 -0
- package/skills/write-paper/references/exemplar_methods/diagnostic_accuracy_stard.md +50 -0
- package/skills/write-paper/references/exemplar_methods/observational_cohort_strobe.md +43 -0
- package/skills/write-paper/references/journal_profiles/AJNR.md +185 -0
- package/skills/write-paper/references/journal_profiles/AJR.md +149 -0
- package/skills/write-paper/references/journal_profiles/Abdominal_Radiology.md +139 -0
- package/skills/write-paper/references/journal_profiles/Academic_Radiology.md +90 -0
- package/skills/write-paper/references/journal_profiles/Annals_of_Internal_Medicine.md +150 -0
- package/skills/write-paper/references/journal_profiles/Artificial_Intelligence_in_Medicine.md +82 -0
- package/skills/write-paper/references/journal_profiles/British_Journal_of_Radiology.md +161 -0
- package/skills/write-paper/references/journal_profiles/CVIR.md +157 -0
- package/skills/write-paper/references/journal_profiles/Chest.md +270 -0
- package/skills/write-paper/references/journal_profiles/Clinical_Radiology.md +160 -0
- package/skills/write-paper/references/journal_profiles/Clinical_and_Molecular_Hepatology.md +147 -0
- package/skills/write-paper/references/journal_profiles/Diabetes_Metabolism_Journal.md +163 -0
- package/skills/write-paper/references/journal_profiles/Diagnostic_and_Interventional_Radiology.md +216 -0
- package/skills/write-paper/references/journal_profiles/Endocrinology_and_Metabolism.md +167 -0
- package/skills/write-paper/references/journal_profiles/European_Journal_of_Preventive_Cardiology.md +192 -0
- package/skills/write-paper/references/journal_profiles/European_Radiology.md +159 -0
- package/skills/write-paper/references/journal_profiles/Hepatology_Communications.md +110 -0
- package/skills/write-paper/references/journal_profiles/Hepatology_International.md +106 -0
- package/skills/write-paper/references/journal_profiles/IEEE_TMI.md +180 -0
- package/skills/write-paper/references/journal_profiles/INSI.md +163 -0
- package/skills/write-paper/references/journal_profiles/Investigative_Radiology.md +86 -0
- package/skills/write-paper/references/journal_profiles/JACC_Advances.md +197 -0
- package/skills/write-paper/references/journal_profiles/JACC_Asia.md +168 -0
- package/skills/write-paper/references/journal_profiles/JACR.md +87 -0
- package/skills/write-paper/references/journal_profiles/JAMA.md +188 -0
- package/skills/write-paper/references/journal_profiles/JAMA_Network_Open.md +170 -0
- package/skills/write-paper/references/journal_profiles/JCSM.md +266 -0
- package/skills/write-paper/references/journal_profiles/JKMS.md +201 -0
- package/skills/write-paper/references/journal_profiles/JMIR.md +88 -0
- package/skills/write-paper/references/journal_profiles/JMIR_Medical_Education.md +86 -0
- package/skills/write-paper/references/journal_profiles/JNIS.md +227 -0
- package/skills/write-paper/references/journal_profiles/JVIR.md +158 -0
- package/skills/write-paper/references/journal_profiles/Journal_of_Clinical_Endocrinology_and_Metabolism.md +191 -0
- package/skills/write-paper/references/journal_profiles/Journal_of_Stroke.md +176 -0
- package/skills/write-paper/references/journal_profiles/KJR.md +185 -0
- package/skills/write-paper/references/journal_profiles/Korean_Circulation_Journal.md +184 -0
- package/skills/write-paper/references/journal_profiles/Korean_Journal_of_Internal_Medicine.md +178 -0
- package/skills/write-paper/references/journal_profiles/Lancet_Gastroenterology_and_Hepatology.md +127 -0
- package/skills/write-paper/references/journal_profiles/Liver_International.md +165 -0
- package/skills/write-paper/references/journal_profiles/Medical_Image_Analysis.md +147 -0
- package/skills/write-paper/references/journal_profiles/NEJM.md +147 -0
- package/skills/write-paper/references/journal_profiles/Nature_Medicine.md +181 -0
- package/skills/write-paper/references/journal_profiles/Neuroradiology.md +151 -0
- package/skills/write-paper/references/journal_profiles/Nutrition_Metabolism_and_Cardiovascular_Diseases.md +184 -0
- package/skills/write-paper/references/journal_profiles/PLOS_Medicine.md +166 -0
- package/skills/write-paper/references/journal_profiles/RYAI.md +124 -0
- package/skills/write-paper/references/journal_profiles/Radiology.md +173 -0
- package/skills/write-paper/references/journal_profiles/Skeletal_Radiology.md +135 -0
- package/skills/write-paper/references/journal_profiles/Stroke.md +210 -0
- package/skills/write-paper/references/journal_profiles/The_BMJ.md +121 -0
- package/skills/write-paper/references/journal_profiles/The_Lancet.md +112 -0
- package/skills/write-paper/references/journal_profiles/The_Lancet_Digital_Health.md +104 -0
- package/skills/write-paper/references/journal_profiles/World_Journal_of_Hepatology.md +106 -0
- package/skills/write-paper/references/journal_profiles/npj_Digital_Medicine.md +93 -0
- package/skills/write-paper/references/paper_types/ai_validation.md +270 -0
- package/skills/write-paper/references/paper_types/animal_study.md +194 -0
- package/skills/write-paper/references/paper_types/case_report.md +237 -0
- package/skills/write-paper/references/paper_types/cross_national.md +328 -0
- package/skills/write-paper/references/paper_types/letter.md +127 -0
- package/skills/write-paper/references/paper_types/meta_analysis.md +181 -0
- package/skills/write-paper/references/paper_types/nhis_cohort.md +297 -0
- package/skills/write-paper/references/paper_types/original_article.md +221 -0
- package/skills/write-paper/references/paper_types/technical_note.md +131 -0
- package/skills/write-paper/references/section_guides/discussion.md +155 -0
- package/skills/write-paper/references/section_guides/introduction.md +108 -0
- package/skills/write-paper/references/section_guides/methods.md +144 -0
- package/skills/write-paper/references/section_guides/results.md +113 -0
- package/skills/write-paper/references/section_guides/step7_1_classical_qc.md +67 -0
- package/skills/write-paper/references/section_guides/step7_4a_audit_recovery.md +74 -0
- package/skills/write-paper/references/section_guides/title_abstract.md +123 -0
- package/skills/write-paper/references/section_templates/methods_statistical.md +147 -0
- package/skills/write-paper/scripts/check_placeholders.py +182 -0
- package/skills/write-paper/skill.yml +48 -0
- package/skills/write-paper/tests/test_placeholders.sh +107 -0
- package/skills/write-protocol/SKILL.md +243 -0
- package/skills/write-protocol/references/ethics_checklist.md +150 -0
- package/skills/write-protocol/references/protocol_template.md +304 -0
- package/skills/write-protocol/skill.yml +34 -0
|
@@ -0,0 +1,90 @@
|
|
|
1
|
+
# Academic Radiology
|
|
2
|
+
|
|
3
|
+
## Journal Identity
|
|
4
|
+
|
|
5
|
+
- **Full name**: Academic Radiology
|
|
6
|
+
- **Abbreviation**: Acad Radiol
|
|
7
|
+
- **Publisher**: Elsevier (Association of Academic Radiology)
|
|
8
|
+
- **ISSN**: Not specified in guidelines
|
|
9
|
+
- **Frequency**: Monthly
|
|
10
|
+
- **Impact Factor**: Not specified in guidelines
|
|
11
|
+
- **Open Access**: Hybrid (subscription + OA option)
|
|
12
|
+
- **APC**: See Elsevier OA policies
|
|
13
|
+
|
|
14
|
+
## Manuscript Types and Word Limits
|
|
15
|
+
|
|
16
|
+
| Type | Abstract | Manuscript Body | References | Figures/Tables |
|
|
17
|
+
|------|----------|----------------|------------|----------------|
|
|
18
|
+
| Original Investigation | 200 w (structured) | No strict cap | No cap | No strict cap |
|
|
19
|
+
| Clinical Review / Systematic Review | 250 w | 5,000 | 100 | 5 T + 10 F |
|
|
20
|
+
| Innovations | 200 w | 2,500 | 15 | 5 |
|
|
21
|
+
| Perspectives | None | 2,000 | 20 | 2 |
|
|
22
|
+
| Beyond Academic Radiology | None | 1,000 | 10 | 2 |
|
|
23
|
+
| White Papers | None | 5,000 | 50 | 5 |
|
|
24
|
+
| Letter to the Editor | None | 500 | 5 | 0 |
|
|
25
|
+
|
|
26
|
+
Word counts exclude abstract, references, figure legends, and tables.
|
|
27
|
+
|
|
28
|
+
## Abstract Format
|
|
29
|
+
|
|
30
|
+
Structured with four headings (for Original Investigations):
|
|
31
|
+
1. **Background**
|
|
32
|
+
2. **Methods**
|
|
33
|
+
3. **Results**
|
|
34
|
+
4. **Conclusion**
|
|
35
|
+
|
|
36
|
+
Maximum 200 words (Original Investigation) or 250 words (Clinical Review).
|
|
37
|
+
No abbreviations unless established. No references in abstract.
|
|
38
|
+
|
|
39
|
+
## Keywords
|
|
40
|
+
|
|
41
|
+
3-5 keywords on the title page.
|
|
42
|
+
|
|
43
|
+
## Required Sections
|
|
44
|
+
|
|
45
|
+
1. **Introduction**
|
|
46
|
+
2. **Material and Methods**
|
|
47
|
+
3. **Results**
|
|
48
|
+
4. **Conclusions**
|
|
49
|
+
|
|
50
|
+
Additional required elements:
|
|
51
|
+
- **Take-Home Messages**: 1-2 bullet points (max 50 words total) for Original Investigations; up to 3 for Clinical Reviews
|
|
52
|
+
- **Title page** (separate): title, authors, affiliations, corresponding author, keywords, disclosures, funding, AI declaration
|
|
53
|
+
- **Blinded manuscript** (separate): no author-identifying information (double-blind review)
|
|
54
|
+
- **Acknowledgements** (separate file)
|
|
55
|
+
|
|
56
|
+
## Citation Style
|
|
57
|
+
|
|
58
|
+
- Vancouver (numbered) style
|
|
59
|
+
- Numbered sequentially in order of first appearance
|
|
60
|
+
- DOI highly encouraged
|
|
61
|
+
- Journal abbreviations per ISSN List of Title Word Abbreviations
|
|
62
|
+
- Example: `Boyko A, Qureshi MM, Fishman MDC, Slanetz PJ. Predictors of breast cancer outcome... Acad Radiol. 2024;31(5):1727-1734. doi: 10.1016/j.acra.2023.11.037.`
|
|
63
|
+
|
|
64
|
+
## Reporting Guidelines
|
|
65
|
+
|
|
66
|
+
| Study Type | Required Guideline |
|
|
67
|
+
|------------|-------------------|
|
|
68
|
+
| Systematic reviews / meta-analyses | PRISMA |
|
|
69
|
+
| Observational studies | STROBE |
|
|
70
|
+
| Quality improvement | SQUIRE |
|
|
71
|
+
| AI/ML studies | CLAIM |
|
|
72
|
+
| Randomized trials | CONSORT |
|
|
73
|
+
|
|
74
|
+
## Statistical Reporting
|
|
75
|
+
|
|
76
|
+
Follows standard biomedical statistical reporting conventions:
|
|
77
|
+
- Report exact p-values; use P < .001 only when value is below that threshold.
|
|
78
|
+
- 95% CI required for all primary outcomes.
|
|
79
|
+
- For AI/ML studies: CLAIM checklist compliance required; discrimination and calibration both expected.
|
|
80
|
+
- Effect sizes with units; identify specific statistical tests used.
|
|
81
|
+
- Statistical software and version must be named in Methods.
|
|
82
|
+
- No journal-specific statistical reporting requirements beyond standard practice; SAMPL guidelines recommended as reference.
|
|
83
|
+
|
|
84
|
+
## Special Notes
|
|
85
|
+
|
|
86
|
+
- **Double-blind review**: author information must be completely removed from the blinded manuscript file.
|
|
87
|
+
- **AI declaration mandatory**: generative AI use must be declared; failure to disclose leads to automatic rejection and possible submission ban.
|
|
88
|
+
- **Co-first authors**: up to two allowed; no co-senior authors accepted.
|
|
89
|
+
- **Proof turnaround**: 48 hours.
|
|
90
|
+
- Drug/instrument names: use generic name first, then trade name with manufacturer and location in parentheses.
|
|
@@ -0,0 +1,150 @@
|
|
|
1
|
+
# Journal Profile: Annals of Internal Medicine
|
|
2
|
+
|
|
3
|
+
## Journal Identity
|
|
4
|
+
|
|
5
|
+
- **Full name**: Annals of Internal Medicine
|
|
6
|
+
- **Abbreviation**: Ann Intern Med
|
|
7
|
+
- **Publisher**: American College of Physicians (ACP)
|
|
8
|
+
- **ISSN**: 0003-4819 (print), 1539-3704 (online)
|
|
9
|
+
- **Frequency**: Monthly (12 issues/year + online-first)
|
|
10
|
+
- **Impact Factor**: ~39 (JCR 2023), top-5 general/internal medicine journal
|
|
11
|
+
- **Open Access**: Hybrid (optional OA; standard subscription)
|
|
12
|
+
- **Acceptance rate**: ~5% for Original Research
|
|
13
|
+
- **Peer review**: Double-blind; dedicated statistical reviewers
|
|
14
|
+
|
|
15
|
+
## Manuscript Types and Word Limits
|
|
16
|
+
|
|
17
|
+
| Type | Body Word Limit | Abstract | References | Figures/Tables |
|
|
18
|
+
|------|----------------|----------|------------|----------------|
|
|
19
|
+
| Original Research | 3000 words | 325 words (structured) | 50 | 6 |
|
|
20
|
+
| Review | 4000 words | 250 words | 75 | 6 |
|
|
21
|
+
| Research Letter | 600 words | None | 6 | 1 |
|
|
22
|
+
| Ideas and Opinions | 1200 words | None | 10 | 1 |
|
|
23
|
+
| Clinical Guidelines | By invitation | 250 words | Varies | Varies |
|
|
24
|
+
| Systematic Review | 3500 words | 325 words | 75 | 6 |
|
|
25
|
+
|
|
26
|
+
Word counts exclude abstract, references, tables, figure legends, and appendices.
|
|
27
|
+
|
|
28
|
+
---
|
|
29
|
+
|
|
30
|
+
## Abstract Requirements
|
|
31
|
+
|
|
32
|
+
**Structured abstract, 325 words maximum:**
|
|
33
|
+
|
|
34
|
+
```
|
|
35
|
+
Background: [Context and knowledge gap — 2-3 sentences]
|
|
36
|
+
Objective: [Specific aims]
|
|
37
|
+
Design: [Study design (e.g., retrospective cohort, RCT)]
|
|
38
|
+
Setting: [Single center/multi-center, country]
|
|
39
|
+
Participants: [Eligibility, sample size]
|
|
40
|
+
Intervention: [If applicable]
|
|
41
|
+
Measurements: [Primary and secondary outcomes]
|
|
42
|
+
Results: [Key results with effect sizes, CIs, P values]
|
|
43
|
+
Limitation: [1-2 key limitations]
|
|
44
|
+
Conclusion: [Main conclusion answering the Objective]
|
|
45
|
+
Primary Funding Source: [Funder name]
|
|
46
|
+
```
|
|
47
|
+
|
|
48
|
+
**Unique feature**: Annals includes "Limitation" as an abstract heading — the only major general journal to do so. Do not omit this.
|
|
49
|
+
|
|
50
|
+
---
|
|
51
|
+
|
|
52
|
+
## Required Journal-Specific Elements
|
|
53
|
+
|
|
54
|
+
### 1. Visual Abstract (Encouraged)
|
|
55
|
+
|
|
56
|
+
Annals encourages a single-page graphical summary suitable for social media. Not required but strongly recommended for visibility.
|
|
57
|
+
|
|
58
|
+
### 2. Summaries for Patients
|
|
59
|
+
|
|
60
|
+
For all Original Research articles, Annals publishes a plain-language "Summaries for Patients" companion. Authors may be asked to draft this (~300 words, written at 8th-grade reading level).
|
|
61
|
+
|
|
62
|
+
### 3. Appendix
|
|
63
|
+
|
|
64
|
+
Detailed methods, supplementary tables/figures, sensitivity analyses go in an online Appendix (no word limit). Referenced from main text.
|
|
65
|
+
|
|
66
|
+
---
|
|
67
|
+
|
|
68
|
+
## Required Sections (Original Research)
|
|
69
|
+
|
|
70
|
+
1. **Introduction** — concise (2 paragraphs); end with clear objective
|
|
71
|
+
2. **Methods**
|
|
72
|
+
- Study Design and Oversight: IRB approval, registration (ClinicalTrials.gov for RCTs)
|
|
73
|
+
- Participants and Setting: eligibility, recruitment, sites
|
|
74
|
+
- Measurements/Interventions
|
|
75
|
+
- Statistical Analysis: pre-specified, power calculation, missing data handling, sensitivity analyses
|
|
76
|
+
- Role of the Funding Source: explicit statement
|
|
77
|
+
3. **Results** — begin with participant flow; baseline table; primary then secondary outcomes
|
|
78
|
+
4. **Discussion** — start with key findings; compare with literature; Limitations paragraph; conclude with implications
|
|
79
|
+
5. **Appendix** — detailed methods, supplementary analyses
|
|
80
|
+
|
|
81
|
+
---
|
|
82
|
+
|
|
83
|
+
## Statistical Reporting
|
|
84
|
+
|
|
85
|
+
Annals of Internal Medicine has historically championed transparent statistical reporting:
|
|
86
|
+
- Report exact P values (e.g., P = .04); use P < .001 below that threshold.
|
|
87
|
+
- 95% CI required for all primary outcomes; preferred over P values alone.
|
|
88
|
+
- Effect sizes in clinically meaningful units (absolute risk difference, NNT/NNH, mean difference with units).
|
|
89
|
+
- For diagnostic accuracy: report sensitivity, specificity, and likelihood ratios with CIs.
|
|
90
|
+
- Prediction models: calibration required (Hosmer-Lemeshow or calibration plot); discrimination alone insufficient.
|
|
91
|
+
- Report both unadjusted and adjusted results for observational studies.
|
|
92
|
+
- Multiple comparisons: describe approach; secondary analyses should be labeled exploratory.
|
|
93
|
+
- Missing data: state the amount and handling method (complete case, imputation).
|
|
94
|
+
- Power calculation with assumptions stated for all prospective studies.
|
|
95
|
+
- Statistical software and version must be identified in Methods.
|
|
96
|
+
|
|
97
|
+
**Note**: Annals published the TRIPOD statement (Moons et al., 2015) and enforces its items rigorously for prediction model papers.
|
|
98
|
+
|
|
99
|
+
---
|
|
100
|
+
|
|
101
|
+
## Figures
|
|
102
|
+
|
|
103
|
+
- **Maximum 6 figures/tables combined**
|
|
104
|
+
- **Resolution**: 300 DPI (600 DPI for line art)
|
|
105
|
+
- **Format**: TIFF, EPS, or high-resolution PDF
|
|
106
|
+
- **Color**: Free online; grayscale for print
|
|
107
|
+
- **Appendix figures**: Unlimited (online only)
|
|
108
|
+
- **Multi-panel**: Counts as one figure; label A, B, C
|
|
109
|
+
|
|
110
|
+
---
|
|
111
|
+
|
|
112
|
+
## Common Rejection Reasons
|
|
113
|
+
|
|
114
|
+
1. **Too specialized for internal medicine audience** — Annals expects relevance to practicing internists; pure subspecialty or methodological papers should target specialty journals
|
|
115
|
+
2. **Missing Limitation in abstract** — unique to Annals; omission signals unfamiliarity with journal
|
|
116
|
+
3. **Underpowered or single-center** — Annals favors large multi-center studies
|
|
117
|
+
4. **Observational study with causal claims** — editors and statistical reviewers scrutinize causal language
|
|
118
|
+
5. **No clinical endpoint** — surrogate outcomes insufficient unless no alternative exists
|
|
119
|
+
6. **AI study without clinical utility demonstration** — must show impact on clinical decision-making, not just accuracy
|
|
120
|
+
7. **Incomplete reporting** — Annals requires adherence to EQUATOR guidelines; missing checklist items flagged
|
|
121
|
+
|
|
122
|
+
---
|
|
123
|
+
|
|
124
|
+
## Cover Letter
|
|
125
|
+
|
|
126
|
+
Must include:
|
|
127
|
+
- Why this study is important for Annals' readership (internists and generalists)
|
|
128
|
+
- Key finding in 1-2 sentences
|
|
129
|
+
- Statement of originality
|
|
130
|
+
- Disclosure of related submissions
|
|
131
|
+
- Suggested reviewers (optional)
|
|
132
|
+
|
|
133
|
+
---
|
|
134
|
+
|
|
135
|
+
## Author Guidelines URL
|
|
136
|
+
|
|
137
|
+
https://www.acpjournals.org/journal/aim/authors
|
|
138
|
+
|
|
139
|
+
---
|
|
140
|
+
|
|
141
|
+
## Positioning
|
|
142
|
+
|
|
143
|
+
Annals of Internal Medicine is appropriate when:
|
|
144
|
+
- Large prospective or multi-center study relevant to internal medicine practice
|
|
145
|
+
- Systematic review or meta-analysis following PRISMA rigorously
|
|
146
|
+
- Diagnostic accuracy study affecting common clinical decisions (screening, triage)
|
|
147
|
+
- Prediction model validated externally with clinical decision impact
|
|
148
|
+
- Health policy study with evidence-based recommendations
|
|
149
|
+
|
|
150
|
+
Not appropriate for: pure radiology methodology, small pilot studies, AI technical papers without clinical integration, narrow subspecialty findings.
|
|
@@ -0,0 +1,82 @@
|
|
|
1
|
+
# Artificial Intelligence in Medicine
|
|
2
|
+
|
|
3
|
+
## Journal Identity
|
|
4
|
+
|
|
5
|
+
- **Full name**: Artificial Intelligence in Medicine
|
|
6
|
+
- **Abbreviation**: Artif Intell Med
|
|
7
|
+
- **Publisher**: Elsevier
|
|
8
|
+
- **ISSN**: 0933-3657 (print) / 1873-2860 (online)
|
|
9
|
+
- **Frequency**: Continuous
|
|
10
|
+
- **Impact Factor**: ~6.2 (2024)
|
|
11
|
+
- **Open Access**: Hybrid (subscription + Gold OA option)
|
|
12
|
+
- **APC**: USD 3,310
|
|
13
|
+
|
|
14
|
+
## Manuscript Types and Word Limits
|
|
15
|
+
|
|
16
|
+
| Type | Abstract | Manuscript Body | References | Notes |
|
|
17
|
+
|------|----------|----------------|------------|-------|
|
|
18
|
+
| Original Research | 250 w | No strict cap | No cap | Must show AI novelty + medical impact |
|
|
19
|
+
| Methodological Review/Survey | 250 w | No strict cap | No cap | Classify and critically analyze methods |
|
|
20
|
+
| Position Paper | 250 w | No strict cap | No cap | Scientific challenges of a field |
|
|
21
|
+
| Letter to the Editor | 250 w | Short | No cap | Comment on recent articles |
|
|
22
|
+
| PhD Project | 250 w | Short | No cap | Overall goals, not detailed results |
|
|
23
|
+
|
|
24
|
+
Mere application of known algorithms to medical data is NOT considered original.
|
|
25
|
+
|
|
26
|
+
## Abstract Format
|
|
27
|
+
|
|
28
|
+
Unstructured, maximum 250 words.
|
|
29
|
+
State purpose, principal results, and major conclusions.
|
|
30
|
+
Must stand alone; avoid references. Define non-standard abbreviations at first mention.
|
|
31
|
+
|
|
32
|
+
## Keywords
|
|
33
|
+
|
|
34
|
+
1-7 keywords. Avoid multi-word keywords using "and"/"or". Use established abbreviations only.
|
|
35
|
+
|
|
36
|
+
## Required Sections
|
|
37
|
+
|
|
38
|
+
1. **Introduction**
|
|
39
|
+
2. **Material and Methods**
|
|
40
|
+
3. **Results**
|
|
41
|
+
4. **Discussion**
|
|
42
|
+
5. **Conclusions**
|
|
43
|
+
|
|
44
|
+
Additional required elements:
|
|
45
|
+
- **Highlights**: separate file, 3-5 bullet points, max 85 characters each (including spaces)
|
|
46
|
+
- **CRediT Author Contributions**: mandatory
|
|
47
|
+
- **Acknowledgements**: separate section before references
|
|
48
|
+
- **Numbered sections** (1, 1.1, 1.2, etc.)
|
|
49
|
+
|
|
50
|
+
## Citation Style
|
|
51
|
+
|
|
52
|
+
- Numbered [1], [2] in order of appearance
|
|
53
|
+
- No strict formatting required at submission (any consistent style accepted)
|
|
54
|
+
- After acceptance: numbered Vancouver-like style applied
|
|
55
|
+
- More than 6 authors: list first 6, then "et al."
|
|
56
|
+
- DOI recommended
|
|
57
|
+
- Example: `Van der Geer J, Hanraads JAJ, Lupton RA. The art of writing a scientific article. J Sci Commun 2020;163:51-9. https://doi.org/10.1016/j.sc.2020.00372.`
|
|
58
|
+
|
|
59
|
+
## Reporting Guidelines
|
|
60
|
+
|
|
61
|
+
- Follow ICMJE recommendations and Declaration of Helsinki for human studies
|
|
62
|
+
- Clinical trials: register before enrollment; include registration number in title page and abstract; follow CONSORT
|
|
63
|
+
- SAGER guidelines for sex/gender reporting
|
|
64
|
+
|
|
65
|
+
## Statistical Reporting
|
|
66
|
+
|
|
67
|
+
Follows ICMJE and SAGER guidelines:
|
|
68
|
+
- Report exact p-values where applicable.
|
|
69
|
+
- 95% CI for primary outcomes; effect sizes with units.
|
|
70
|
+
- For AI model evaluations: discrimination metrics (AUC, F1, accuracy) with CI; calibration expected for prediction models; external or independent test set required.
|
|
71
|
+
- Sex and gender disaggregation of results per SAGER guidelines.
|
|
72
|
+
- Statistical software and version identified in Methods.
|
|
73
|
+
- No journal-specific statistical reporting requirements beyond ICMJE and SAGER are published.
|
|
74
|
+
|
|
75
|
+
## Special Notes
|
|
76
|
+
|
|
77
|
+
- **Single-blind review** (reviewers know author identity).
|
|
78
|
+
- **AI-generated images NOT permitted** in artwork (exception: AI as part of research methods).
|
|
79
|
+
- **Clinical assessment strongly recommended**: manuscripts should demonstrate potential clinical impact.
|
|
80
|
+
- **Median review time**: submission to first decision ~12 days; to acceptance ~303 days.
|
|
81
|
+
- Preprints allowed; free posting on SSRN during submission.
|
|
82
|
+
- Self-archiving: 12-month embargo for subscription articles.
|
|
@@ -0,0 +1,161 @@
|
|
|
1
|
+
# Journal Profile: British Journal of Radiology (BJR)
|
|
2
|
+
|
|
3
|
+
## Basic Information
|
|
4
|
+
|
|
5
|
+
- **Publisher:** Oxford University Press (on behalf of The British Institute of Radiology)
|
|
6
|
+
- **Impact Factor:** [TODO: verify at journal site — typically reported in JCR]
|
|
7
|
+
- **ISSN:** 0007-1285 (print) / 1748-880X (online)
|
|
8
|
+
- **Frequency:** 12 issues per year (online)
|
|
9
|
+
- **Scope:** All subspecialties of diagnostic radiology, interventional radiology, nuclear medicine, radiation oncology, radiation physics; particular interest in clinical research, methodology, and translational radiology
|
|
10
|
+
- **Open Access:** Hybrid — optional Open Access under Creative Commons (CC BY or CC BY-NC); APC £2,393 for CC licenses; Read and Publish institutional agreements available
|
|
11
|
+
- **Language:** English only
|
|
12
|
+
|
|
13
|
+
---
|
|
14
|
+
|
|
15
|
+
## Manuscript Types and Word Limits
|
|
16
|
+
|
|
17
|
+
| Type | Body Word Limit | Abstract | Figures | Tables | References |
|
|
18
|
+
|------|----------------|----------|---------|--------|------------|
|
|
19
|
+
| Research Article | 3,000 words | 250 words (structured) | 10 | 5 | 50 |
|
|
20
|
+
| Review | 4,000 words | 200 words (unstructured) | 12 | 5 | 100 |
|
|
21
|
+
| Systematic Review | 3,000 words | 250 words (structured) | 10 | 5 | 50 |
|
|
22
|
+
| Pictorial Review | 1,500 words | 200 words (unstructured) | 15 | 4 | 15 |
|
|
23
|
+
| Guidelines | 4,000 words | 200 words (unstructured) | 12 | 5 | 100 |
|
|
24
|
+
| Short Communication | 2,000 words | 250 words (structured) | 5 | 2 | 15 |
|
|
25
|
+
| Commentary | 1,500 words | 200 words (unstructured) | 4 | 2 | 15 |
|
|
26
|
+
| Letter to Editor | 750 words | None | 2 (max) | — | 10 |
|
|
27
|
+
|
|
28
|
+
---
|
|
29
|
+
|
|
30
|
+
## Abstract Requirements
|
|
31
|
+
|
|
32
|
+
**Structured abstract** (Research Articles, Short Communications, Systematic Reviews) — 250 words, five required headings:
|
|
33
|
+
|
|
34
|
+
```
|
|
35
|
+
Objectives: [Primary aim of the study]
|
|
36
|
+
Methods: [Design, population, intervention/exposure, comparator, outcome]
|
|
37
|
+
Results: [Key findings with statistics and 95% CIs]
|
|
38
|
+
Conclusions: [Main interpretation]
|
|
39
|
+
Advances in knowledge: [What this study adds]
|
|
40
|
+
```
|
|
41
|
+
|
|
42
|
+
The "Advances in knowledge" heading is BJR-specific — it must explicitly state the novelty contribution and is checked by reviewers.
|
|
43
|
+
|
|
44
|
+
**Unstructured abstract** (Reviews, Pictorial Reviews, Guidelines, Commentary) — 200 words, single paragraph.
|
|
45
|
+
|
|
46
|
+
---
|
|
47
|
+
|
|
48
|
+
## Required Sections (Research Article)
|
|
49
|
+
|
|
50
|
+
Standard IMRAD:
|
|
51
|
+
|
|
52
|
+
1. **Introduction**
|
|
53
|
+
2. **Methods**
|
|
54
|
+
3. **Results**
|
|
55
|
+
4. **Discussion**
|
|
56
|
+
|
|
57
|
+
Ethics, funding, conflict of interest, and data availability statements are required as separate end-matter sections.
|
|
58
|
+
|
|
59
|
+
---
|
|
60
|
+
|
|
61
|
+
## Statistical Reporting
|
|
62
|
+
|
|
63
|
+
- Measures of variation must be included for all important results
|
|
64
|
+
- Estimates of differences must be provided with 95% confidence limits
|
|
65
|
+
- For diagnostic test evaluation: sensitivity, specificity, and predictive values are required
|
|
66
|
+
- p-value reporting format: [TODO: verify at journal site — follow standard convention]
|
|
67
|
+
- Statistical software identification: [TODO: verify — recommend stating software + version]
|
|
68
|
+
|
|
69
|
+
---
|
|
70
|
+
|
|
71
|
+
## Figure Requirements
|
|
72
|
+
|
|
73
|
+
- **Resolution:** 300 DPI (color), 600 DPI (grayscale/combination), 1,200 DPI (monochrome line art)
|
|
74
|
+
- **Formats accepted:** JPEG, PNG, TIFF, SVG, PDF, EPS
|
|
75
|
+
- **Color:** accepted (online publication is in color)
|
|
76
|
+
- **Maximum:** 10 figures + 5 tables for Research Articles (see manuscript-type table above)
|
|
77
|
+
|
|
78
|
+
---
|
|
79
|
+
|
|
80
|
+
## Common Rejection Reasons
|
|
81
|
+
|
|
82
|
+
1. **Insufficient novelty** — BJR Research Articles are expected to clearly state advancement over existing literature in the dedicated "Advances in knowledge" abstract heading
|
|
83
|
+
2. **Single-center study with limited generalizability** — multi-center or representative cohort designs preferred
|
|
84
|
+
3. **Missing structured abstract elements** — particularly omission of the "Advances in knowledge" line
|
|
85
|
+
4. **Inadequate statistical reporting** — confidence intervals and effect sizes required, not just p-values
|
|
86
|
+
5. **Poor English language quality** — BJR expects professional editing prior to submission
|
|
87
|
+
6. **Pictorial Review without sufficient teaching value** — pictorial submissions must demonstrate clear pedagogical contribution beyond image collection
|
|
88
|
+
|
|
89
|
+
---
|
|
90
|
+
|
|
91
|
+
## AI Writing Disclosure Policy
|
|
92
|
+
|
|
93
|
+
- **Requirement level:** Required (mandatory disclosure)
|
|
94
|
+
- **Permitted scope:** Content generation, image generation, code writing, data processing, translation — all permitted with disclosure; AI tools cannot be listed as authors
|
|
95
|
+
- **Disclosure location:** Both (a) cover letter to editors AND (b) Methods or Acknowledgements section
|
|
96
|
+
- **AI-generated images:** Must be disclosed; AI image policy aligns with COPE/ICMJE guidance
|
|
97
|
+
- **Policy URL:** https://academic.oup.com/bjr/pages/author-guidelines
|
|
98
|
+
|
|
99
|
+
---
|
|
100
|
+
|
|
101
|
+
## Cover Letter
|
|
102
|
+
|
|
103
|
+
Not mandatory per current author guidelines, but recommended; if AI tools were used in manuscript preparation, AI disclosure in the cover letter is required (see AI Writing Disclosure Policy above).
|
|
104
|
+
|
|
105
|
+
---
|
|
106
|
+
|
|
107
|
+
## Open Access and APC
|
|
108
|
+
|
|
109
|
+
- **Hybrid model**: Subscription default; optional Open Access under CC BY or CC BY-NC
|
|
110
|
+
- **APC:** £2,393 (for CC license; may vary — verify at submission)
|
|
111
|
+
- **Read and Publish agreements:** institutional waiver may apply if author's institution has an OUP Read and Publish deal
|
|
112
|
+
|
|
113
|
+
---
|
|
114
|
+
|
|
115
|
+
## Peer Review
|
|
116
|
+
|
|
117
|
+
- **Type:** Double-anonymized peer review (both author and reviewer identities blinded)
|
|
118
|
+
- **Number of reviewers:** Typically 2 reviewers
|
|
119
|
+
- **Turnaround:** [TODO: verify at journal site]
|
|
120
|
+
|
|
121
|
+
Because BJR uses double-anonymized review, manuscript files (including supplementary materials and registry record PDFs) must be blinded prior to submission. Author identifiers (names, institutions, ORCID, funding grant IDs that identify a specific group) should be removed from all uploaded files except the separately-uploaded title page.
|
|
122
|
+
|
|
123
|
+
---
|
|
124
|
+
|
|
125
|
+
## Author Guidelines URL
|
|
126
|
+
|
|
127
|
+
https://academic.oup.com/bjr/pages/author-guidelines
|
|
128
|
+
|
|
129
|
+
---
|
|
130
|
+
|
|
131
|
+
## Positioning
|
|
132
|
+
|
|
133
|
+
BJR is well-suited for:
|
|
134
|
+
- Clinical radiology research with clear translational impact
|
|
135
|
+
- Methodology and radiation-physics studies that complement clinical findings
|
|
136
|
+
- Studies with explicit "Advances in knowledge" framing
|
|
137
|
+
- Authors seeking a UK/European-oriented general radiology audience with mid-range Q1/Q2 visibility
|
|
138
|
+
|
|
139
|
+
| Dimension | British Journal of Radiology | Clinical Radiology | European Radiology |
|
|
140
|
+
|-----------|-----------------------------|-------------------|--------------------|
|
|
141
|
+
| Society | British Institute of Radiology | Royal College of Radiologists (UK) | European Society of Radiology |
|
|
142
|
+
| Scope | Diagnostic + interventional + radiation oncology + physics | Diagnostic radiology (general) | Diagnostic radiology (general) |
|
|
143
|
+
| Peer review | Double-anonymized | [varies] | Single-blind |
|
|
144
|
+
| Emphasis | "Advances in knowledge" novelty statement; methodology and physics included | UK-leaning clinical practice | European multi-center studies, AI |
|
|
145
|
+
| OA option | Hybrid (CC BY / CC BY-NC) | Hybrid | Hybrid |
|
|
146
|
+
|
|
147
|
+
---
|
|
148
|
+
|
|
149
|
+
## Formatting Notes
|
|
150
|
+
|
|
151
|
+
- References: Vancouver style (numbered)
|
|
152
|
+
- Units: SI units
|
|
153
|
+
- Abbreviations: define at first use
|
|
154
|
+
- Double-anonymized: blind all uploaded files except title page (see Peer Review section above)
|
|
155
|
+
|
|
156
|
+
|
|
157
|
+
---
|
|
158
|
+
|
|
159
|
+
## Verification
|
|
160
|
+
- **Source:** https://academic.oup.com/bjr/pages/author-guidelines
|
|
161
|
+
- **Date:** 2026-05-21
|
|
@@ -0,0 +1,157 @@
|
|
|
1
|
+
# Journal Profile: CardioVascular and Interventional Radiology (CVIR)
|
|
2
|
+
|
|
3
|
+
## Journal Identity
|
|
4
|
+
|
|
5
|
+
- **Full name**: CardioVascular and Interventional Radiology
|
|
6
|
+
- **Abbreviation**: Cardiovasc Intervent Radiol
|
|
7
|
+
- **Publisher**: Springer Nature (CIRSE — Cardiovascular and Interventional Radiological Society of Europe)
|
|
8
|
+
- **ISSN**: 0174-1551 (print), 1432-086X (online)
|
|
9
|
+
- **Frequency**: Monthly (12 issues/year)
|
|
10
|
+
- **Impact Factor**: ~3.0 (JCR 2023)
|
|
11
|
+
- **Open Access**: Hybrid (Springer transformative agreements may cover OA)
|
|
12
|
+
- **Acceptance rate**: ~25-30%
|
|
13
|
+
- **Peer review**: Single-blind; 2-3 reviewers per manuscript
|
|
14
|
+
|
|
15
|
+
## Manuscript Types and Word Limits
|
|
16
|
+
|
|
17
|
+
| Type | Body Word Limit | Abstract | References | Figures/Tables |
|
|
18
|
+
|------|----------------|----------|------------|----------------|
|
|
19
|
+
| Original Article | 3500 words | 250 words (structured) | 30 | 6 |
|
|
20
|
+
| Review Article | 5000 words | 250 words | 60 | 8 |
|
|
21
|
+
| Technical Note | 2000 words | 150 words (unstructured) | 15 | 4 |
|
|
22
|
+
| Case Report | 1500 words | 150 words (unstructured) | 10 | 4 |
|
|
23
|
+
| Letter to the Editor | 500 words | None | 5 | 1 |
|
|
24
|
+
| Systematic Review / Meta-Analysis | 4000 words | 250 words (structured) | 50 | 8 |
|
|
25
|
+
|
|
26
|
+
Word counts exclude abstract, references, tables, and figure legends.
|
|
27
|
+
|
|
28
|
+
---
|
|
29
|
+
|
|
30
|
+
## Abstract Requirements
|
|
31
|
+
|
|
32
|
+
**Structured abstract for Original Articles and SRMAs, 250 words maximum:**
|
|
33
|
+
|
|
34
|
+
```
|
|
35
|
+
Purpose: [Study aim — 1-2 sentences]
|
|
36
|
+
Materials and Methods: [Design, population, intervention/technique, outcomes,
|
|
37
|
+
statistical methods]
|
|
38
|
+
Results: [Key results with effect sizes and CIs or p-values]
|
|
39
|
+
Conclusion: [Main conclusion — 1-2 sentences]
|
|
40
|
+
```
|
|
41
|
+
|
|
42
|
+
**Unstructured abstract for Technical Notes and Case Reports, 150 words maximum.**
|
|
43
|
+
|
|
44
|
+
---
|
|
45
|
+
|
|
46
|
+
## Required Sections (Original Article)
|
|
47
|
+
|
|
48
|
+
1. **Introduction** — brief (2-3 paragraphs); end with study purpose
|
|
49
|
+
2. **Materials and Methods**
|
|
50
|
+
- Study Design: prospective/retrospective, IRB approval
|
|
51
|
+
- Patient Population: inclusion/exclusion criteria, recruitment period
|
|
52
|
+
- Procedure/Intervention: detailed technical description
|
|
53
|
+
- Outcome Measures: primary (technical success, clinical success) and secondary
|
|
54
|
+
- Follow-up: imaging and clinical follow-up protocol
|
|
55
|
+
- Statistical Analysis: software, tests, significance level
|
|
56
|
+
3. **Results** — patient demographics, technical outcomes, clinical outcomes, complications
|
|
57
|
+
4. **Discussion** — comparison with literature, limitations, clinical implications
|
|
58
|
+
5. **Conclusion** — brief (1-2 sentences)
|
|
59
|
+
|
|
60
|
+
---
|
|
61
|
+
|
|
62
|
+
## Statistical Reporting
|
|
63
|
+
|
|
64
|
+
- Report exact p-values (e.g., p = 0.032); use p < 0.001 below that threshold.
|
|
65
|
+
- 95% CI for primary outcomes.
|
|
66
|
+
- For diagnostic/technical studies: sensitivity, specificity, accuracy with CIs.
|
|
67
|
+
- For intervention studies: technical success rate, clinical success rate with definitions.
|
|
68
|
+
- Complication rates with Clavien-Dindo or SIR classification.
|
|
69
|
+
- Kaplan-Meier for time-to-event outcomes; Cox regression for multivariate analysis.
|
|
70
|
+
- For meta-analyses: I-squared, prediction intervals, funnel plot for publication bias.
|
|
71
|
+
- Statistical software and version must be identified.
|
|
72
|
+
|
|
73
|
+
---
|
|
74
|
+
|
|
75
|
+
## IR-Specific Requirements
|
|
76
|
+
|
|
77
|
+
### Complication Reporting
|
|
78
|
+
|
|
79
|
+
CVIR expects standardized complication classification:
|
|
80
|
+
- **SIR Classification** (Society of Interventional Radiology): Minor (A, B) and Major (C, D, E, F)
|
|
81
|
+
- **Clavien-Dindo** for post-procedural complications
|
|
82
|
+
- Report per-patient and per-procedure rates separately
|
|
83
|
+
|
|
84
|
+
### Technical Outcome Definitions
|
|
85
|
+
|
|
86
|
+
Define clearly:
|
|
87
|
+
- **Technical success**: procedure completed as intended (specific criteria)
|
|
88
|
+
- **Clinical success**: symptom improvement or target outcome achieved (specific criteria and timepoint)
|
|
89
|
+
- **Primary patency / secondary patency** (for vascular interventions)
|
|
90
|
+
- **Local tumor progression / technique efficacy** (for ablation studies)
|
|
91
|
+
|
|
92
|
+
### Device and Equipment
|
|
93
|
+
|
|
94
|
+
Report: device manufacturer, model, size/configuration used. CVIR readers expect this level of procedural detail.
|
|
95
|
+
|
|
96
|
+
---
|
|
97
|
+
|
|
98
|
+
## Figures
|
|
99
|
+
|
|
100
|
+
- **Maximum 6 figures/tables combined** for original articles
|
|
101
|
+
- **Resolution**: 300 DPI minimum
|
|
102
|
+
- **Format**: TIFF, EPS, or high-resolution JPEG
|
|
103
|
+
- **Color**: Free online; grayscale for print
|
|
104
|
+
- **Typical figure set for IR studies**: pre-procedure imaging, procedural images (key steps), post-procedure imaging, follow-up imaging
|
|
105
|
+
|
|
106
|
+
---
|
|
107
|
+
|
|
108
|
+
## Common Rejection Reasons
|
|
109
|
+
|
|
110
|
+
1. **Small sample size without novelty** — single-center retrospective with N < 50 needs strong technical innovation
|
|
111
|
+
2. **Inadequate complication reporting** — missing SIR classification or Clavien-Dindo grading
|
|
112
|
+
3. **Vague technical success definition** — must be operationally defined before the study
|
|
113
|
+
4. **Missing follow-up data** — IR studies need adequate follow-up duration with imaging
|
|
114
|
+
5. **No comparison with existing techniques** — CVIR favors comparative studies
|
|
115
|
+
6. **Overclaiming for observational data** — causal language in retrospective series
|
|
116
|
+
|
|
117
|
+
---
|
|
118
|
+
|
|
119
|
+
## Cover Letter
|
|
120
|
+
|
|
121
|
+
Should emphasize:
|
|
122
|
+
- Relevance to interventional radiology practice in Europe
|
|
123
|
+
- Technical innovation or comparative advantage
|
|
124
|
+
- Patient safety implications
|
|
125
|
+
- Suggested reviewers with IR expertise
|
|
126
|
+
|
|
127
|
+
---
|
|
128
|
+
|
|
129
|
+
## Author Guidelines URL
|
|
130
|
+
|
|
131
|
+
https://www.springer.com/journal/270/submission-guidelines
|
|
132
|
+
|
|
133
|
+
---
|
|
134
|
+
|
|
135
|
+
## Positioning
|
|
136
|
+
|
|
137
|
+
CVIR is appropriate when:
|
|
138
|
+
- Interventional radiology procedure with clinical outcome data (embolization, ablation, drainage, vascular)
|
|
139
|
+
- CBCT-guided interventions with technical or clinical outcomes
|
|
140
|
+
- Comparative study of IR techniques (new vs standard)
|
|
141
|
+
- Systematic review or meta-analysis of IR procedures
|
|
142
|
+
- Technical innovation in IR devices or techniques
|
|
143
|
+
|
|
144
|
+
Not appropriate for: diagnostic imaging studies without interventional component, pure AI methodology, non-vascular/non-interventional radiology.
|
|
145
|
+
|
|
146
|
+
---
|
|
147
|
+
|
|
148
|
+
## Differentiation from JVIR
|
|
149
|
+
|
|
150
|
+
| Dimension | CVIR | JVIR |
|
|
151
|
+
|-----------|------|------|
|
|
152
|
+
| Society | CIRSE (European) | SIR (American) |
|
|
153
|
+
| Geography emphasis | European and international | North American and international |
|
|
154
|
+
| Impact factor | ~3.0 | ~3.5 |
|
|
155
|
+
| Scope | Cardiovascular + interventional | Interventional (broader) |
|
|
156
|
+
| Meta-analyses | Accepts readily | Accepts readily |
|
|
157
|
+
| Review speed | ~4-6 weeks first decision | ~4-6 weeks first decision |
|