scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

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.

Potentially problematic release.


This version of scientific-writer might be problematic. Click here for more details.

Files changed (311) hide show
  1. scientific_writer/.claude/settings.local.json +30 -0
  2. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  3. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  4. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  5. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  6. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  7. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  8. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  9. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  10. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  16. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  17. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  18. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  19. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  31. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  39. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  47. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  48. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  49. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  50. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  98. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  106. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  118. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  174. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  177. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  182. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  183. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  184. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  188. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  189. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  192. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  193. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  194. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  195. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  196. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  197. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
  200. scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  201. scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
  202. scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  203. scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
  204. scientific_writer/.claude/skills/markitdown/README.md +184 -0
  205. scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
  206. scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
  207. scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
  208. scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
  209. scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
  210. scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
  211. scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
  212. scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
  213. scientific_writer/.claude/skills/paper-2-web/SKILL.md +455 -0
  214. scientific_writer/.claude/skills/paper-2-web/references/installation.md +141 -0
  215. scientific_writer/.claude/skills/paper-2-web/references/paper2poster.md +346 -0
  216. scientific_writer/.claude/skills/paper-2-web/references/paper2video.md +305 -0
  217. scientific_writer/.claude/skills/paper-2-web/references/paper2web.md +187 -0
  218. scientific_writer/.claude/skills/paper-2-web/references/usage_examples.md +436 -0
  219. scientific_writer/.claude/skills/peer-review/SKILL.md +375 -0
  220. scientific_writer/.claude/skills/peer-review/references/common_issues.md +552 -0
  221. scientific_writer/.claude/skills/peer-review/references/reporting_standards.md +290 -0
  222. scientific_writer/.claude/skills/research-grants/README.md +285 -0
  223. scientific_writer/.claude/skills/research-grants/SKILL.md +896 -0
  224. scientific_writer/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
  225. scientific_writer/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  226. scientific_writer/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  227. scientific_writer/.claude/skills/research-grants/references/broader_impacts.md +392 -0
  228. scientific_writer/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
  229. scientific_writer/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
  230. scientific_writer/.claude/skills/research-grants/references/nih_guidelines.md +851 -0
  231. scientific_writer/.claude/skills/research-grants/references/nsf_guidelines.md +570 -0
  232. scientific_writer/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
  233. scientific_writer/.claude/skills/research-lookup/README.md +116 -0
  234. scientific_writer/.claude/skills/research-lookup/SKILL.md +443 -0
  235. scientific_writer/.claude/skills/research-lookup/examples.py +174 -0
  236. scientific_writer/.claude/skills/research-lookup/lookup.py +93 -0
  237. scientific_writer/.claude/skills/research-lookup/research_lookup.py +335 -0
  238. scientific_writer/.claude/skills/research-lookup/scripts/research_lookup.py +261 -0
  239. scientific_writer/.claude/skills/scholar-evaluation/SKILL.md +254 -0
  240. scientific_writer/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  241. scientific_writer/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  242. scientific_writer/.claude/skills/scientific-critical-thinking/SKILL.md +530 -0
  243. scientific_writer/.claude/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  244. scientific_writer/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
  245. scientific_writer/.claude/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  246. scientific_writer/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  247. scientific_writer/.claude/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  248. scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  249. scientific_writer/.claude/skills/scientific-schematics/SKILL.md +2035 -0
  250. scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
  251. scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
  252. scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
  253. scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
  254. scientific_writer/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
  255. scientific_writer/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
  256. scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
  257. scientific_writer/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
  258. scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
  259. scientific_writer/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
  260. scientific_writer/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
  261. scientific_writer/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
  262. scientific_writer/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
  263. scientific_writer/.claude/skills/scientific-writing/SKILL.md +443 -0
  264. scientific_writer/.claude/skills/scientific-writing/references/citation_styles.md +720 -0
  265. scientific_writer/.claude/skills/scientific-writing/references/figures_tables.md +806 -0
  266. scientific_writer/.claude/skills/scientific-writing/references/imrad_structure.md +658 -0
  267. scientific_writer/.claude/skills/scientific-writing/references/reporting_guidelines.md +748 -0
  268. scientific_writer/.claude/skills/scientific-writing/references/writing_principles.md +824 -0
  269. scientific_writer/.claude/skills/treatment-plans/README.md +483 -0
  270. scientific_writer/.claude/skills/treatment-plans/SKILL.md +817 -0
  271. scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +636 -0
  272. scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +616 -0
  273. scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +745 -0
  274. scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +770 -0
  275. scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +724 -0
  276. scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
  277. scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +727 -0
  278. scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  279. scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  280. scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  281. scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +607 -0
  282. scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -0
  283. scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
  284. scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
  285. scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  286. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  287. scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
  288. scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  289. scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  290. scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  291. scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  292. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  293. scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  294. scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
  295. scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  296. scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  297. scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
  298. scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
  299. scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  300. scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  301. scientific_writer/CLAUDE.md +748 -0
  302. scientific_writer/__init__.py +2 -2
  303. scientific_writer/api.py +14 -7
  304. scientific_writer/cli.py +12 -7
  305. scientific_writer/core.py +27 -5
  306. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/METADATA +5 -1
  307. scientific_writer-2.2.2.dist-info/RECORD +312 -0
  308. scientific_writer-2.1.1.dist-info/RECORD +0 -11
  309. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/WHEEL +0 -0
  310. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/entry_points.txt +0 -0
  311. {scientific_writer-2.1.1.dist-info → scientific_writer-2.2.2.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,476 @@
1
+ # Regulatory Compliance for Treatment Plans
2
+
3
+ ## Overview
4
+
5
+ Treatment plans must comply with multiple federal and state regulations governing healthcare documentation, patient privacy, billing practices, and quality standards. This reference provides comprehensive guidance on regulatory requirements affecting treatment plan development and implementation.
6
+
7
+ ## HIPAA Privacy and Security
8
+
9
+ ### Health Insurance Portability and Accountability Act (HIPAA)
10
+
11
+ **Applicable Rules**:
12
+ - Privacy Rule (45 CFR Part 164, Subpart E)
13
+ - Security Rule (45 CFR Part 164, Subparts A and C)
14
+ - Breach Notification Rule (45 CFR Part 164, Subpart D)
15
+
16
+ ### Protected Health Information (PHI)
17
+
18
+ **Definition**: Any information about health status, provision of healthcare, or payment for healthcare that can be linked to a specific individual.
19
+
20
+ **18 HIPAA Identifiers** (Safe Harbor Method):
21
+ 1. Names
22
+ 2. Geographic subdivisions smaller than state (street address, city, county, ZIP code if <20,000 people)
23
+ 3. Dates (birth, admission, discharge, death) - except year
24
+ 4. Telephone numbers
25
+ 5. Fax numbers
26
+ 6. Email addresses
27
+ 7. Social Security numbers
28
+ 8. Medical record numbers
29
+ 9. Health plan beneficiary numbers
30
+ 10. Account numbers
31
+ 11. Certificate/license numbers
32
+ 12. Vehicle identifiers and serial numbers (license plate)
33
+ 13. Device identifiers and serial numbers
34
+ 14. Web URLs
35
+ 15. IP addresses
36
+ 16. Biometric identifiers (fingerprints, voice prints)
37
+ 17. Full-face photographs
38
+ 18. Any other unique identifying number, characteristic, or code
39
+
40
+ ### De-identification for Sharing Treatment Plans
41
+
42
+ **Safe Harbor Method**: Remove all 18 identifiers listed above
43
+
44
+ **Practical De-identification**:
45
+ - **Name**: Use "Patient" or de-identified code (e.g., "PT-001")
46
+ - **Age**: Use age range (e.g., "60-65 years") instead of exact age
47
+ - **Dates**: Use relative timelines (e.g., "3 months ago") or month/year only
48
+ - **Location**: State only, remove city, address, specific facility names
49
+ - **Identifiers**: Remove MRN, account numbers, SSN
50
+ - **Dates of Service**: Refer to "Month/Year" or "recent visit"
51
+
52
+ **Example**:
53
+ - **Before**: "John Smith, DOB 3/15/1965 (58 years old), MRN 123456, address 123 Main St, Anytown, CA 12345, seen 1/15/2025"
54
+ - **After**: "Patient, age range 55-60 years, seen Month/Year 2025, California"
55
+
56
+ ### Permitted Uses and Disclosures
57
+
58
+ **Without Patient Authorization**:
59
+ - **Treatment**: Sharing PHI among healthcare providers for patient care
60
+ - **Payment**: Disclosing PHI to obtain payment for services
61
+ - **Healthcare Operations**: Quality improvement, training, accreditation
62
+
63
+ **With Patient Authorization**:
64
+ - Marketing
65
+ - Research (unless IRB waiver granted)
66
+ - Sharing with non-covered entities (e.g., patient's employer)
67
+ - Psychotherapy notes (special protection)
68
+
69
+ ### Minimum Necessary Standard
70
+
71
+ Use, disclose, or request only the minimum amount of PHI necessary to accomplish the purpose.
72
+
73
+ **Exception**: Does NOT apply to treatment - providers may share all relevant information for patient care.
74
+
75
+ ### Patient Rights Under HIPAA
76
+
77
+ - Right to access own medical records (within 30 days)
78
+ - Right to request amendments to records
79
+ - Right to accounting of disclosures
80
+ - Right to request restrictions on uses/disclosures (provider may deny)
81
+ - Right to confidential communications
82
+ - Right to be notified of privacy practices (Notice of Privacy Practices)
83
+
84
+ ### Breach Notification
85
+
86
+ **Breach**: Unauthorized acquisition, access, use, or disclosure of PHI that compromises security or privacy.
87
+
88
+ **Notification Requirements**:
89
+ - **Individual**: Notify affected individuals within 60 days
90
+ - **HHS**: If $\geq$500 individuals affected, notify HHS and media
91
+ - **Business Associates**: Must notify covered entity of breaches
92
+
93
+ ### HIPAA Violations and Penalties
94
+
95
+ **Civil Penalties**: $100 to $50,000 per violation (up to $1.5 million per year for identical violations)
96
+
97
+ **Criminal Penalties**: Up to $250,000 fine and 10 years imprisonment for knowing misuse with intent to sell/transfer PHI
98
+
99
+ ## 42 CFR Part 2 (Substance Use Disorder Records)
100
+
101
+ ### Applicability
102
+
103
+ **Scope**: Federally assisted substance use disorder (SUD) treatment programs
104
+
105
+ **More Restrictive than HIPAA**: Provides additional confidentiality protections for SUD treatment records.
106
+
107
+ ### Key Requirements
108
+
109
+ **Patient Consent Required** for most disclosures (even for treatment, payment, operations - differs from HIPAA).
110
+
111
+ **Prohibition on Re-disclosure**: Recipients of 42 CFR Part 2-protected information cannot re-disclose without patient consent.
112
+
113
+ **Documentation**: Patient consent must be written, specific to the information disclosed, and include expiration date.
114
+
115
+ **Exceptions** (Disclosure without consent allowed):
116
+ - Medical emergency
117
+ - Court order (not subpoena alone)
118
+ - Suspected child abuse/neglect (per state law)
119
+ - Crime on premises or against personnel
120
+
121
+ ### Integration with HIPAA
122
+
123
+ **HIPAA Compliance**: Covered entities must comply with both HIPAA and 42 CFR Part 2 (whichever is more protective applies).
124
+
125
+ **Note in Treatment Plans**: If patient has SUD and received treatment at 42 CFR Part 2 program, annotate: "Substance use information subject to 42 CFR Part 2 confidentiality protections."
126
+
127
+ ## 21 CFR Part 11 (Electronic Records - FDA)
128
+
129
+ ### Applicability
130
+
131
+ **Scope**: Clinical trials, research involving FDA-regulated products, drug/device manufacturers.
132
+
133
+ **Requirements for Electronic Records and Signatures**:
134
+ - Validation of systems
135
+ - Audit trails (who accessed, when, what changed)
136
+ - Electronic signatures equivalent to handwritten
137
+ - Controls to prevent unauthorized access
138
+
139
+ ### Treatment Plan Implications
140
+
141
+ **If part of clinical trial**: Treatment plans must meet 21 CFR Part 11 requirements for electronic documentation.
142
+
143
+ **Non-Research Clinical Care**: Typically NOT subject to 21 CFR Part 11 (HIPAA Security Rule applies instead).
144
+
145
+ ## Medicare and Medicaid (CMS) Requirements
146
+
147
+ ### Conditions of Participation (CoPs)
148
+
149
+ **Hospitals, Skilled Nursing Facilities, Home Health Agencies** must meet CoPs to receive Medicare/Medicaid reimbursement.
150
+
151
+ **Documentation Requirements**:
152
+ - Physician orders for treatments
153
+ - Comprehensive care plans
154
+ - Periodic reassessment and revision
155
+ - Interdisciplinary team involvement
156
+ - Patient/family involvement
157
+
158
+ ### Meaningful Use / Promoting Interoperability
159
+
160
+ **EHR Requirements** (for eligible providers to receive incentive payments):
161
+ - Use of certified EHR technology
162
+ - Electronic prescribing
163
+ - Clinical decision support
164
+ - Patient portal access to health information
165
+ - Care plan documentation with patient goals
166
+
167
+ ### Documentation for Billing
168
+
169
+ **Medical Necessity**: Documentation must support the medical necessity of services billed.
170
+
171
+ **Elements to Document**:
172
+ - Diagnosis (ICD-10 codes)
173
+ - Treatments provided (CPT codes)
174
+ - Rationale for treatments
175
+ - Patient response to treatment
176
+ - Plans for ongoing care
177
+
178
+ **E/M Coding Support**: Treatment plans support Evaluation and Management (E/M) coding levels:
179
+ - Low complexity: Stable chronic conditions, limited treatment options
180
+ - Moderate complexity: Multiple conditions, moderate-risk medications/procedures
181
+ - High complexity: Severe conditions, high-risk treatments, poor response to therapy
182
+
183
+ ## Quality Measure Reporting
184
+
185
+ ### HEDIS (Healthcare Effectiveness Data and Information Set)
186
+
187
+ **Used by**: Health plans to measure quality
188
+
189
+ **Treatment Plan Elements Supporting HEDIS**:
190
+
191
+ **Diabetes**:
192
+ - HbA1c testing (at least annually, quarterly if not controlled)
193
+ - Eye exam (annual dilated retinal exam)
194
+ - Kidney disease monitoring (urine albumin-to-creatinine ratio annually)
195
+ - BP control (<140/90)
196
+
197
+ **Cardiovascular**:
198
+ - Statin therapy for patients with diabetes or ASCVD
199
+ - ACE/ARB for patients with diabetes and hypertension
200
+ - Beta-blocker for patients with prior MI or HFrEF
201
+
202
+ **Preventive Care**:
203
+ - Flu vaccine annually
204
+ - Colorectal cancer screening
205
+ - Breast cancer screening
206
+ - Cervical cancer screening
207
+
208
+ ### MIPS (Merit-Based Incentive Payment System)
209
+
210
+ **Eligible Clinicians**: Medicare Part B providers
211
+
212
+ **Performance Categories**:
213
+ 1. **Quality**: Reporting on quality measures relevant to specialty
214
+ 2. **Improvement Activities**: Participation in improvement activities
215
+ 3. **Promoting Interoperability**: EHR meaningful use
216
+ 4. **Cost**: Resource use/cost of care
217
+
218
+ **Treatment Plan Documentation**: Supports quality measure reporting (e.g., diabetes HbA1c control, depression screening and follow-up).
219
+
220
+ ### Accountable Care Organizations (ACOs)
221
+
222
+ **Quality Measures**: 33+ measures across patient experience, care coordination, preventive health, at-risk populations.
223
+
224
+ **Treatment Plans**: Facilitate care coordination, chronic disease management to meet ACO quality benchmarks.
225
+
226
+ ## Opioid Prescribing Regulations
227
+
228
+ ### CDC Opioid Prescribing Guidelines (2022)
229
+
230
+ **Recommendations**:
231
+ - Non-opioid therapies preferred for chronic pain
232
+ - If opioids used: Lowest effective dose, shortest duration
233
+ - Assess risk before starting opioids (ORT, SOAPP)
234
+ - Prescribe naloxone for patients at increased overdose risk
235
+ - Urine drug testing before and during opioid therapy
236
+ - Check PDMP (Prescription Drug Monitoring Program) before prescribing
237
+ - Avoid concurrent benzodiazepines and opioids
238
+ - Reassess risk/benefit at each increase in dose (especially if approaching $\geq$50 MME/day)
239
+
240
+ **Treatment Plan Requirements**:
241
+ - Document indication for opioid therapy
242
+ - Informed consent discussion (risks, benefits, alternatives)
243
+ - Treatment agreement/opioid contract
244
+ - Plan for monitoring (UDS frequency, PDMP checks)
245
+ - Functional goals (not just pain scores)
246
+ - Exit strategy/tapering plan
247
+
248
+ ### State Opioid Regulations
249
+
250
+ **Vary by State**, common elements:
251
+ - MME limits (e.g., 90 MME/day max without exemption)
252
+ - Prescription limits for acute pain (e.g., 7-day supply)
253
+ - Mandatory PDMP checks before prescribing
254
+ - Continuing medical education (CME) requirements for prescribers
255
+ - Co-prescription of naloxone required in some states
256
+
257
+ **Prescribers must know state-specific laws**.
258
+
259
+ ### PDMP (Prescription Drug Monitoring Program)
260
+
261
+ **Purpose**: State databases tracking controlled substance prescriptions to identify doctor shopping, overprescribing.
262
+
263
+ **Requirements**: Most states require PDMP check before initial opioid prescription and periodically during treatment (e.g., every 3-6 months).
264
+
265
+ **Documentation**: Note in treatment plan that PDMP was checked and findings (e.g., "PDMP reviewed, no other controlled substances from other prescribers").
266
+
267
+ ## State Medical Board Requirements
268
+
269
+ ### Scope of Practice
270
+
271
+ **Prescribers**: Must operate within scope of practice defined by state law.
272
+ - Physicians (MD/DO): Full prescriptive authority
273
+ - Nurse Practitioners (NP): Varies by state (full practice, reduced practice, or restricted practice authority)
274
+ - Physician Assistants (PA): Supervision requirements vary
275
+
276
+ **Controlled Substances**: DEA registration required, state regulations apply.
277
+
278
+ ### Standard of Care
279
+
280
+ **Definition**: Degree of care and skill ordinarily employed by similar practitioners under similar circumstances.
281
+
282
+ **Deviations from Standard**: Must be documented with rationale (e.g., patient-specific factors, shared decision-making, evidence supporting alternative approach).
283
+
284
+ ### Informed Consent Documentation
285
+
286
+ **Required for**: Procedures, surgeries, medications with significant risks, research.
287
+
288
+ **Elements to Document**:
289
+ - Nature of condition and proposed treatment
290
+ - Risks and benefits
291
+ - Alternatives
292
+ - Likely outcome if no treatment
293
+ - Patient questions answered
294
+ - Patient capacity to consent
295
+ - Voluntary consent
296
+
297
+ **In Treatment Plans**: Note informed consent discussion occurred, especially for high-risk treatments (e.g., opioids, chemotherapy, surgery).
298
+
299
+ ### Documentation Retention
300
+
301
+ **Medical Records**: State laws vary (typically 7-10 years from last encounter; longer for minors - often until age of majority + statute of limitations).
302
+
303
+ **Electronic Records**: Same retention requirements as paper.
304
+
305
+ ## Accreditation Standards
306
+
307
+ ### The Joint Commission
308
+
309
+ **Applicable to**: Hospitals, ambulatory care, behavioral health, long-term care, laboratories.
310
+
311
+ **Standards Relevant to Treatment Plans**:
312
+
313
+ **Patient-Centered Care (PC)**:
314
+ - Individualized care planning
315
+ - Patient and family involvement
316
+ - Cultural and language needs addressed
317
+ - Patient preferences incorporated
318
+
319
+ **Care Coordination (CC)**:
320
+ - Comprehensive assessment
321
+ - Care plan addresses all identified needs
322
+ - Interdisciplinary coordination
323
+ - Transitions of care managed
324
+
325
+ **Medication Management (MM)**:
326
+ - Medication reconciliation at transitions
327
+ - High-risk medication monitoring (anticoagulants, opioids, insulin)
328
+ - Patient education on medications
329
+
330
+ **National Patient Safety Goals (NPSG)**:
331
+ - Accurate patient identification
332
+ - Effective communication among caregivers
333
+ - Safe medication use
334
+ - Reduce healthcare-associated infections
335
+ - Prevent falls
336
+
337
+ ### CARF (Commission on Accreditation of Rehabilitation Facilities)
338
+
339
+ **Applicable to**: Rehabilitation, behavioral health, employment services.
340
+
341
+ **Standards for Treatment Plans**:
342
+ - Comprehensive assessment drives plan
343
+ - Individualized goals
344
+ - Measurable, time-specific objectives
345
+ - Regular team review and updates
346
+ - Person-centered (patient directs goals)
347
+ - Transition and discharge planning
348
+ - Outcomes measurement
349
+
350
+ ## Billing and Reimbursement Compliance
351
+
352
+ ### Coding Accuracy
353
+
354
+ **ICD-10-CM Diagnosis Codes**:
355
+ - Code to highest level of specificity
356
+ - Code all documented conditions affecting care during encounter
357
+ - Primary diagnosis is reason for visit
358
+ - Uncertain diagnoses coded as symptoms (outpatient); can code "probable" if inpatient
359
+
360
+ **CPT Procedure Codes**:
361
+ - Specific codes for services provided
362
+ - Modifiers when appropriate
363
+ - Unbundling prohibited (billing separately for bundled services)
364
+
365
+ ### Documentation Supports Billing
366
+
367
+ **Medical Necessity**: Treatment must be medically appropriate for diagnosis, meet standard of care, expected to improve condition.
368
+
369
+ **Treatment Plan Link**: Plan documents rationale for tests, treatments, referrals → supports medical necessity.
370
+
371
+ **Avoid**:
372
+ - Upcoding (billing higher level service than provided)
373
+ - Duplicate billing
374
+ - Billing for services not rendered
375
+
376
+ **Anti-Kickback Statute**: Prohibits offering, paying, soliciting, or receiving remuneration for patient referrals for services reimbursed by federal healthcare programs.
377
+
378
+ **Stark Law**: Prohibits physician self-referral for designated health services (DHS) covered by Medicare/Medicaid.
379
+
380
+ ## Clinical Research and Trials
381
+
382
+ ### Informed Consent (21 CFR Part 50)
383
+
384
+ **Required Elements**:
385
+ - Research procedures described
386
+ - Risks and discomforts
387
+ - Potential benefits
388
+ - Alternative treatments
389
+ - Confidentiality protections
390
+ - Voluntary participation, can withdraw
391
+ - Contact information for questions/problems
392
+
393
+ **Documentation**: Signed consent form, copy given to participant.
394
+
395
+ ### IRB Review (21 CFR Part 56)
396
+
397
+ **Institutional Review Board** reviews and approves research involving human subjects.
398
+
399
+ **Treatment Plans in Research**: If part of clinical trial protocol, must be approved by IRB, follow protocol exactly, documented per 21 CFR Part 11.
400
+
401
+ ### Good Clinical Practice (ICH-GCP)
402
+
403
+ **International Standard** for ethical and scientific quality in clinical trials.
404
+
405
+ **Relevant to Treatment Plans**: Detailed protocol adherence, documentation of interventions, adverse event reporting.
406
+
407
+ ## Mental Health Specific Regulations
408
+
409
+ ### Duty to Warn/Protect
410
+
411
+ **Tarasoff Rule** (varies by state): If patient poses credible threat to identifiable person, provider must:
412
+ - Warn intended victim
413
+ - Notify police
414
+ - Take steps to protect
415
+
416
+ **Documentation**: Document threat assessment, steps taken to protect.
417
+
418
+ ### Involuntary Commitment
419
+
420
+ **Criteria** (vary by state): Typically requires patient to be:
421
+ - Mentally ill, AND
422
+ - Danger to self or others OR gravely disabled
423
+
424
+ **Due Process**: Emergency hold (24-72 hours), followed by court hearing for longer commitment.
425
+
426
+ **Documentation**: Clear documentation of dangerousness, efforts at least restrictive intervention.
427
+
428
+ ### Parity Laws
429
+
430
+ **Mental Health Parity and Addiction Equity Act (MHPAEA)**: Health plans must provide mental health/substance use disorder benefits comparable to medical/surgical benefits.
431
+
432
+ **Implications**: Cannot limit therapy visits or impose higher copays for mental health vs. medical care.
433
+
434
+ ## Compliance Best Practices
435
+
436
+ ### 1. Know Applicable Regulations
437
+ - Federal (HIPAA, 42 CFR Part 2, CDC guidelines, CMS CoPs)
438
+ - State (medical practice act, opioid laws, consent requirements)
439
+ - Accreditation (Joint Commission, CARF if applicable)
440
+
441
+ ### 2. Document Thoroughly
442
+ - Complete all required elements
443
+ - Clear rationale for clinical decisions
444
+ - Informed consent discussions
445
+ - Regulatory compliance (PDMP checks, etc.)
446
+
447
+ ### 3. Privacy Protection
448
+ - De-identify before sharing outside treatment team
449
+ - Minimum necessary principle
450
+ - Secure storage and transmission of records
451
+
452
+ ### 4. Quality Measure Integration
453
+ - Include elements that support quality reporting (preventive care, chronic disease metrics)
454
+ - Structured data enables measure extraction
455
+
456
+ ### 5. Regular Training
457
+ - HIPAA training annually for all staff
458
+ - Updates on regulation changes
459
+ - Specialty-specific compliance (opioid prescribing, mental health)
460
+
461
+ ### 6. Audit and Monitor
462
+ - Internal audits for documentation compliance
463
+ - Billing compliance reviews
464
+ - Privacy breach monitoring
465
+
466
+ ### 7. Policies and Procedures
467
+ - Written policies on treatment planning, consent, privacy
468
+ - Regularly reviewed and updated
469
+
470
+ ---
471
+
472
+ **Document Version**: 1.0
473
+ **Last Updated**: January 2025
474
+ **Next Review**: January 2026
475
+ **Note**: Regulations subject to change; verify current requirements.
476
+