scientific-writer 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

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  1. scientific_writer/.claude/WRITER.md +748 -0
  2. scientific_writer/.claude/settings.local.json +30 -0
  3. scientific_writer/.claude/skills/citation-management/SKILL.md +1046 -0
  4. scientific_writer/.claude/skills/citation-management/assets/bibtex_template.bib +264 -0
  5. scientific_writer/.claude/skills/citation-management/assets/citation_checklist.md +386 -0
  6. scientific_writer/.claude/skills/citation-management/references/bibtex_formatting.md +908 -0
  7. scientific_writer/.claude/skills/citation-management/references/citation_validation.md +794 -0
  8. scientific_writer/.claude/skills/citation-management/references/google_scholar_search.md +725 -0
  9. scientific_writer/.claude/skills/citation-management/references/metadata_extraction.md +870 -0
  10. scientific_writer/.claude/skills/citation-management/references/pubmed_search.md +839 -0
  11. scientific_writer/.claude/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  12. scientific_writer/.claude/skills/citation-management/scripts/extract_metadata.py +569 -0
  13. scientific_writer/.claude/skills/citation-management/scripts/format_bibtex.py +349 -0
  14. scientific_writer/.claude/skills/citation-management/scripts/search_google_scholar.py +282 -0
  15. scientific_writer/.claude/skills/citation-management/scripts/search_pubmed.py +398 -0
  16. scientific_writer/.claude/skills/citation-management/scripts/validate_citations.py +497 -0
  17. scientific_writer/.claude/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +641 -0
  18. scientific_writer/.claude/skills/clinical-reports/README.md +236 -0
  19. scientific_writer/.claude/skills/clinical-reports/SKILL.md +1088 -0
  20. scientific_writer/.claude/skills/clinical-reports/assets/case_report_template.md +352 -0
  21. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  22. scientific_writer/.claude/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  23. scientific_writer/.claude/skills/clinical-reports/assets/consult_note_template.md +305 -0
  24. scientific_writer/.claude/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  25. scientific_writer/.claude/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  26. scientific_writer/.claude/skills/clinical-reports/assets/history_physical_template.md +305 -0
  27. scientific_writer/.claude/skills/clinical-reports/assets/lab_report_template.md +309 -0
  28. scientific_writer/.claude/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  29. scientific_writer/.claude/skills/clinical-reports/assets/quality_checklist.md +338 -0
  30. scientific_writer/.claude/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  31. scientific_writer/.claude/skills/clinical-reports/assets/soap_note_template.md +253 -0
  32. scientific_writer/.claude/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  33. scientific_writer/.claude/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  34. scientific_writer/.claude/skills/clinical-reports/references/data_presentation.md +530 -0
  35. scientific_writer/.claude/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  36. scientific_writer/.claude/skills/clinical-reports/references/medical_terminology.md +588 -0
  37. scientific_writer/.claude/skills/clinical-reports/references/patient_documentation.md +744 -0
  38. scientific_writer/.claude/skills/clinical-reports/references/peer_review_standards.md +585 -0
  39. scientific_writer/.claude/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  40. scientific_writer/.claude/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  41. scientific_writer/.claude/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  42. scientific_writer/.claude/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  43. scientific_writer/.claude/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  44. scientific_writer/.claude/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  45. scientific_writer/.claude/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  46. scientific_writer/.claude/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  47. scientific_writer/.claude/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  48. scientific_writer/.claude/skills/document-skills/docx/LICENSE.txt +30 -0
  49. scientific_writer/.claude/skills/document-skills/docx/SKILL.md +197 -0
  50. scientific_writer/.claude/skills/document-skills/docx/docx-js.md +350 -0
  51. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  52. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  53. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  54. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  55. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  56. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  57. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  58. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  59. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  60. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  61. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  62. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  63. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  64. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  65. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  66. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  67. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  68. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  69. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  70. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  71. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  72. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  73. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  74. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  75. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  76. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  77. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  78. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  79. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  80. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  81. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  82. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  83. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  84. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  85. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  86. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  87. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  88. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  89. scientific_writer/.claude/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  90. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  91. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  92. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  93. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  94. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  95. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  96. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  97. scientific_writer/.claude/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  98. scientific_writer/.claude/skills/document-skills/docx/ooxml.md +610 -0
  99. scientific_writer/.claude/skills/document-skills/docx/scripts/__init__.py +1 -0
  100. scientific_writer/.claude/skills/document-skills/docx/scripts/document.py +1276 -0
  101. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  102. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  103. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  104. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  105. scientific_writer/.claude/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  106. scientific_writer/.claude/skills/document-skills/docx/scripts/utilities.py +374 -0
  107. scientific_writer/.claude/skills/document-skills/pdf/LICENSE.txt +30 -0
  108. scientific_writer/.claude/skills/document-skills/pdf/SKILL.md +294 -0
  109. scientific_writer/.claude/skills/document-skills/pdf/forms.md +205 -0
  110. scientific_writer/.claude/skills/document-skills/pdf/reference.md +612 -0
  111. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  112. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  113. scientific_writer/.claude/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  114. scientific_writer/.claude/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  115. scientific_writer/.claude/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  116. scientific_writer/.claude/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  117. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  118. scientific_writer/.claude/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  119. scientific_writer/.claude/skills/document-skills/pptx/LICENSE.txt +30 -0
  120. scientific_writer/.claude/skills/document-skills/pptx/SKILL.md +484 -0
  121. scientific_writer/.claude/skills/document-skills/pptx/html2pptx.md +625 -0
  122. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  123. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  124. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  125. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  126. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  127. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  128. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  129. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  130. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  131. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  132. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  133. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  134. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  135. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  136. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  137. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  138. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  139. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  140. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  141. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  142. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  143. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  144. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  145. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  146. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  147. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  148. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  149. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  150. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  151. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  152. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  153. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  154. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  155. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  156. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  157. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  158. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  159. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  160. scientific_writer/.claude/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  161. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  162. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  163. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  164. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  165. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  166. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  167. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  168. scientific_writer/.claude/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  169. scientific_writer/.claude/skills/document-skills/pptx/ooxml.md +427 -0
  170. scientific_writer/.claude/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  171. scientific_writer/.claude/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  172. scientific_writer/.claude/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  173. scientific_writer/.claude/skills/document-skills/pptx/scripts/replace.py +385 -0
  174. scientific_writer/.claude/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  175. scientific_writer/.claude/skills/document-skills/xlsx/LICENSE.txt +30 -0
  176. scientific_writer/.claude/skills/document-skills/xlsx/SKILL.md +289 -0
  177. scientific_writer/.claude/skills/document-skills/xlsx/recalc.py +178 -0
  178. scientific_writer/.claude/skills/hypothesis-generation/SKILL.md +155 -0
  179. scientific_writer/.claude/skills/hypothesis-generation/assets/hypothesis_output_template.md +302 -0
  180. scientific_writer/.claude/skills/hypothesis-generation/references/experimental_design_patterns.md +327 -0
  181. scientific_writer/.claude/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +196 -0
  182. scientific_writer/.claude/skills/hypothesis-generation/references/literature_search_strategies.md +505 -0
  183. scientific_writer/.claude/skills/latex-posters/README.md +417 -0
  184. scientific_writer/.claude/skills/latex-posters/SKILL.md +919 -0
  185. scientific_writer/.claude/skills/latex-posters/assets/baposter_template.tex +257 -0
  186. scientific_writer/.claude/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  187. scientific_writer/.claude/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  188. scientific_writer/.claude/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  189. scientific_writer/.claude/skills/latex-posters/references/latex_poster_packages.md +745 -0
  190. scientific_writer/.claude/skills/latex-posters/references/poster_content_guide.md +748 -0
  191. scientific_writer/.claude/skills/latex-posters/references/poster_design_principles.md +806 -0
  192. scientific_writer/.claude/skills/latex-posters/references/poster_layout_design.md +900 -0
  193. scientific_writer/.claude/skills/latex-posters/scripts/review_poster.sh +214 -0
  194. scientific_writer/.claude/skills/literature-review/SKILL.md +546 -0
  195. scientific_writer/.claude/skills/literature-review/assets/review_template.md +412 -0
  196. scientific_writer/.claude/skills/literature-review/references/citation_styles.md +166 -0
  197. scientific_writer/.claude/skills/literature-review/references/database_strategies.md +381 -0
  198. scientific_writer/.claude/skills/literature-review/scripts/generate_pdf.py +176 -0
  199. scientific_writer/.claude/skills/literature-review/scripts/search_databases.py +303 -0
  200. scientific_writer/.claude/skills/literature-review/scripts/verify_citations.py +222 -0
  201. scientific_writer/.claude/skills/markitdown/INSTALLATION_GUIDE.md +318 -0
  202. scientific_writer/.claude/skills/markitdown/LICENSE.txt +22 -0
  203. scientific_writer/.claude/skills/markitdown/OPENROUTER_INTEGRATION.md +359 -0
  204. scientific_writer/.claude/skills/markitdown/QUICK_REFERENCE.md +309 -0
  205. scientific_writer/.claude/skills/markitdown/README.md +184 -0
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  207. scientific_writer/.claude/skills/markitdown/SKILL_SUMMARY.md +307 -0
  208. scientific_writer/.claude/skills/markitdown/assets/example_usage.md +463 -0
  209. scientific_writer/.claude/skills/markitdown/references/api_reference.md +399 -0
  210. scientific_writer/.claude/skills/markitdown/references/file_formats.md +542 -0
  211. scientific_writer/.claude/skills/markitdown/scripts/batch_convert.py +228 -0
  212. scientific_writer/.claude/skills/markitdown/scripts/convert_literature.py +283 -0
  213. scientific_writer/.claude/skills/markitdown/scripts/convert_with_ai.py +243 -0
  214. scientific_writer/.claude/skills/paper-2-web/SKILL.md +455 -0
  215. scientific_writer/.claude/skills/paper-2-web/references/installation.md +141 -0
  216. scientific_writer/.claude/skills/paper-2-web/references/paper2poster.md +346 -0
  217. scientific_writer/.claude/skills/paper-2-web/references/paper2video.md +305 -0
  218. scientific_writer/.claude/skills/paper-2-web/references/paper2web.md +187 -0
  219. scientific_writer/.claude/skills/paper-2-web/references/usage_examples.md +436 -0
  220. scientific_writer/.claude/skills/peer-review/SKILL.md +375 -0
  221. scientific_writer/.claude/skills/peer-review/references/common_issues.md +552 -0
  222. scientific_writer/.claude/skills/peer-review/references/reporting_standards.md +290 -0
  223. scientific_writer/.claude/skills/research-grants/README.md +285 -0
  224. scientific_writer/.claude/skills/research-grants/SKILL.md +896 -0
  225. scientific_writer/.claude/skills/research-grants/assets/budget_justification_template.md +453 -0
  226. scientific_writer/.claude/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  227. scientific_writer/.claude/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  228. scientific_writer/.claude/skills/research-grants/references/broader_impacts.md +392 -0
  229. scientific_writer/.claude/skills/research-grants/references/darpa_guidelines.md +636 -0
  230. scientific_writer/.claude/skills/research-grants/references/doe_guidelines.md +586 -0
  231. scientific_writer/.claude/skills/research-grants/references/nih_guidelines.md +851 -0
  232. scientific_writer/.claude/skills/research-grants/references/nsf_guidelines.md +570 -0
  233. scientific_writer/.claude/skills/research-grants/references/specific_aims_guide.md +458 -0
  234. scientific_writer/.claude/skills/research-lookup/README.md +116 -0
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  236. scientific_writer/.claude/skills/research-lookup/examples.py +174 -0
  237. scientific_writer/.claude/skills/research-lookup/lookup.py +93 -0
  238. scientific_writer/.claude/skills/research-lookup/research_lookup.py +335 -0
  239. scientific_writer/.claude/skills/research-lookup/scripts/research_lookup.py +261 -0
  240. scientific_writer/.claude/skills/scholar-evaluation/SKILL.md +254 -0
  241. scientific_writer/.claude/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  242. scientific_writer/.claude/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  243. scientific_writer/.claude/skills/scientific-critical-thinking/SKILL.md +530 -0
  244. scientific_writer/.claude/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  245. scientific_writer/.claude/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
  246. scientific_writer/.claude/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  247. scientific_writer/.claude/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  248. scientific_writer/.claude/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  249. scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  250. scientific_writer/.claude/skills/scientific-schematics/SKILL.md +2035 -0
  251. scientific_writer/.claude/skills/scientific-schematics/assets/block_diagram_template.tex +199 -0
  252. scientific_writer/.claude/skills/scientific-schematics/assets/circuit_template.tex +159 -0
  253. scientific_writer/.claude/skills/scientific-schematics/assets/flowchart_template.tex +161 -0
  254. scientific_writer/.claude/skills/scientific-schematics/assets/pathway_template.tex +162 -0
  255. scientific_writer/.claude/skills/scientific-schematics/assets/tikz_styles.tex +422 -0
  256. scientific_writer/.claude/skills/scientific-schematics/references/best_practices.md +562 -0
  257. scientific_writer/.claude/skills/scientific-schematics/references/diagram_types.md +637 -0
  258. scientific_writer/.claude/skills/scientific-schematics/references/python_libraries.md +791 -0
  259. scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md +734 -0
  260. scientific_writer/.claude/skills/scientific-schematics/scripts/circuit_generator.py +307 -0
  261. scientific_writer/.claude/skills/scientific-schematics/scripts/compile_tikz.py +292 -0
  262. scientific_writer/.claude/skills/scientific-schematics/scripts/generate_flowchart.py +281 -0
  263. scientific_writer/.claude/skills/scientific-schematics/scripts/pathway_diagram.py +406 -0
  264. scientific_writer/.claude/skills/scientific-writing/SKILL.md +443 -0
  265. scientific_writer/.claude/skills/scientific-writing/references/citation_styles.md +720 -0
  266. scientific_writer/.claude/skills/scientific-writing/references/figures_tables.md +806 -0
  267. scientific_writer/.claude/skills/scientific-writing/references/imrad_structure.md +658 -0
  268. scientific_writer/.claude/skills/scientific-writing/references/reporting_guidelines.md +748 -0
  269. scientific_writer/.claude/skills/scientific-writing/references/writing_principles.md +824 -0
  270. scientific_writer/.claude/skills/treatment-plans/README.md +483 -0
  271. scientific_writer/.claude/skills/treatment-plans/SKILL.md +817 -0
  272. scientific_writer/.claude/skills/treatment-plans/assets/chronic_disease_management_plan.tex +636 -0
  273. scientific_writer/.claude/skills/treatment-plans/assets/general_medical_treatment_plan.tex +616 -0
  274. scientific_writer/.claude/skills/treatment-plans/assets/mental_health_treatment_plan.tex +745 -0
  275. scientific_writer/.claude/skills/treatment-plans/assets/pain_management_plan.tex +770 -0
  276. scientific_writer/.claude/skills/treatment-plans/assets/perioperative_care_plan.tex +724 -0
  277. scientific_writer/.claude/skills/treatment-plans/assets/quality_checklist.md +471 -0
  278. scientific_writer/.claude/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +727 -0
  279. scientific_writer/.claude/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  280. scientific_writer/.claude/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  281. scientific_writer/.claude/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  282. scientific_writer/.claude/skills/treatment-plans/references/specialty_specific_guidelines.md +607 -0
  283. scientific_writer/.claude/skills/treatment-plans/references/treatment_plan_standards.md +456 -0
  284. scientific_writer/.claude/skills/treatment-plans/scripts/check_completeness.py +318 -0
  285. scientific_writer/.claude/skills/treatment-plans/scripts/generate_template.py +244 -0
  286. scientific_writer/.claude/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  287. scientific_writer/.claude/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  288. scientific_writer/.claude/skills/venue-templates/SKILL.md +590 -0
  289. scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  290. scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  291. scientific_writer/.claude/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  292. scientific_writer/.claude/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  293. scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  294. scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  295. scientific_writer/.claude/skills/venue-templates/references/conferences_formatting.md +564 -0
  296. scientific_writer/.claude/skills/venue-templates/references/grants_requirements.md +787 -0
  297. scientific_writer/.claude/skills/venue-templates/references/journals_formatting.md +486 -0
  298. scientific_writer/.claude/skills/venue-templates/references/posters_guidelines.md +628 -0
  299. scientific_writer/.claude/skills/venue-templates/scripts/customize_template.py +206 -0
  300. scientific_writer/.claude/skills/venue-templates/scripts/query_template.py +260 -0
  301. scientific_writer/.claude/skills/venue-templates/scripts/validate_format.py +255 -0
  302. scientific_writer/__init__.py +1 -1
  303. scientific_writer/api.py +9 -5
  304. scientific_writer/cli.py +9 -5
  305. scientific_writer/core.py +28 -5
  306. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/METADATA +1 -1
  307. scientific_writer-2.2.3.dist-info/RECORD +312 -0
  308. scientific_writer-2.2.1.dist-info/RECORD +0 -11
  309. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/WHEEL +0 -0
  310. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/entry_points.txt +0 -0
  311. {scientific_writer-2.2.1.dist-info → scientific_writer-2.2.3.dist-info}/licenses/LICENSE +0 -0
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+ % Chronic Disease Management Plan Template
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+ % For long-term management of multiple chronic conditions
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+ % Last updated: 2025
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+
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+ \documentclass[11pt,letterpaper]{article}
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+
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+ % Packages
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+ \usepackage[top=1in,bottom=1in,left=1in,right=1in]{geometry}
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+ \usepackage{amsmath,amssymb}
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+ \usepackage[utf8]{inputenc}
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+ \usepackage{graphicx}
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+ \usepackage{array}
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+ \usepackage{longtable}
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+ \usepackage{booktabs}
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+ \usepackage{enumitem}
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+ \usepackage{xcolor}
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+ \usepackage{fancyhdr}
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+ \usepackage{lastpage}
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+ \usepackage{tabularx}
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+
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+ % Header and footer
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+ \pagestyle{fancy}
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+ \fancyhf{}
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+ \lhead{Chronic Disease Management Plan}
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+ \rhead{Page \thepage\ of \pageref{LastPage}}
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+ \lfoot{Date Created: \today}
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+ \rfoot{Confidential Patient Information}
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+
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+ % Title formatting
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+ \usepackage{titlesec}
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+ \titleformat{\section}{\large\bfseries}{\thesection}{1em}{}
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+ \titleformat{\subsection}{\normalsize\bfseries}{\thesubsection}{1em}{}
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+
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+ \begin{document}
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+
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+ % Title
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+ \begin{center}
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+ {\Large\bfseries CHRONIC DISEASE MANAGEMENT PLAN}\\[0.5em]
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+ {\large Comprehensive Long-Term Care Coordination}\\[0.5em]
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+ \rule{\textwidth}{1pt}
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+ \end{center}
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+
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+ \vspace{1em}
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+
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+ % ===== SECTION 1: PATIENT INFORMATION =====
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+ \section*{1. Patient Information and Problem List}
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+
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+ \textbf{HIPAA Notice}: De-identify all protected health information before sharing.
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+
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+ \vspace{0.5em}
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+
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+ \begin{tabularx}{\textwidth}{|l|X|}
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+ \hline
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+ \textbf{Patient ID} & [De-identified code, e.g., CDM-001] \\ \hline
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+ \textbf{Age Range} & [e.g., 60-65 years] \\ \hline
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+ \textbf{Sex} & [Male/Female/Other] \\ \hline
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+ \textbf{Date of Plan} & [Month/Year only] \\ \hline
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+ \textbf{Primary Care Provider} & [Name, MD/DO, Credentials] \\ \hline
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+ \textbf{Care Coordinator} & [Name, RN/NP/PA, if applicable] \\ \hline
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+ \textbf{Facility/System} & [Healthcare organization] \\ \hline
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+ \end{tabularx}
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+
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+ \vspace{1em}
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+
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+ \subsection*{Active Problem List (Prioritized)}
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+
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+ \begin{longtable}{|c|p{4cm}|c|p{3cm}|p{3.5cm}|}
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+ \hline
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+ \textbf{\#} & \textbf{Condition} & \textbf{ICD-10} & \textbf{Status} & \textbf{Specialists} \\ \hline
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+ \endfirsthead
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+ \hline
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+ \textbf{\#} & \textbf{Condition} & \textbf{ICD-10} & \textbf{Status} & \textbf{Specialists} \\ \hline
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+ \endhead
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+ 1 & Type 2 Diabetes Mellitus & E11.65 & Suboptimal control (HbA1c 8.2\%) & Endocrinology \\ \hline
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+ 2 & Chronic Heart Failure (HFrEF) & I50.22 & Stable, NYHA Class II & Cardiology \\ \hline
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+ 3 & Chronic Kidney Disease Stage 3b & N18.31 & Stable, eGFR 38 & Nephrology (as needed) \\ \hline
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+ 4 & Hypertension & I10 & Well-controlled on meds & PCP \\ \hline
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+ 5 & Hyperlipidemia & E78.5 & On statin, LDL at goal & PCP \\ \hline
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+ 6 & Obstructive Sleep Apnea & G47.33 & On CPAP, adherent & Sleep Medicine \\ \hline
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+ 7 & Obesity & E66.9 & BMI 34, stable weight & PCP, Nutrition \\ \hline
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+ 8 & Osteoarthritis, bilateral knees & M17.0 & Managed conservatively & Ortho (prn) \\ \hline
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+ [Add rows] & & & & \\ \hline
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+ \end{longtable}
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+
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+ \subsection*{Current Medication List}
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+
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+ \textit{Reconciled as of [Date]. Total: [X] medications}
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+
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+ \begin{longtable}{|p{3cm}|p{2cm}|p{1.8cm}|p{3cm}|p{3.5cm}|}
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+ \hline
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+ \textbf{Medication} & \textbf{Dose} & \textbf{Frequency} & \textbf{Indication} & \textbf{Prescriber} \\ \hline
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+ \endfirsthead
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+ \hline
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+ \textbf{Medication} & \textbf{Dose} & \textbf{Frequency} & \textbf{Indication} & \textbf{Prescriber} \\ \hline
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+ \endhead
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+ Metformin ER & 1000mg & BID & Diabetes & PCP \\ \hline
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+ Insulin glargine & 24 units & QHS & Diabetes & Endocrinology \\ \hline
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+ Carvedilol & 12.5mg & BID & Heart failure, HTN & Cardiology \\ \hline
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+ Lisinopril & 40mg & Daily & Heart failure, HTN, CKD protection & Cardiology \\ \hline
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+ Furosemide & 40mg & Daily & Heart failure (diuresis) & Cardiology \\ \hline
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+ Atorvastatin & 40mg & QHS & Hyperlipidemia, ASCVD prevention & PCP \\ \hline
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+ Aspirin & 81mg & Daily & ASCVD prevention & PCP \\ \hline
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+ [Continue list] & & & & \\ \hline
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+ \end{longtable}
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+
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+ \subsection*{Care Team and Specialists}
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+
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Primary Care Provider}: [Name, practice] - Coordinates overall care
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+ \item \textbf{Cardiology}: [Name] - Heart failure management
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+ \item \textbf{Endocrinology}: [Name] - Diabetes optimization
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+ \item \textbf{Nephrology}: [Name if engaged] - CKD monitoring
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+ \item \textbf{Care Coordinator/Navigator}: [Name] - Appointment coordination, patient education
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+ \item \textbf{Pharmacist}: [Clinical pharmacist if available] - Medication reconciliation, optimization
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+ \item \textbf{Registered Dietitian}: [Name] - Medical nutrition therapy
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+ \item \textbf{Social Worker}: [Name if engaged] - Psychosocial support, resources
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+ \end{itemize}
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+
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+ % ===== SECTION 2: DISEASE-SPECIFIC ASSESSMENTS =====
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+ \section*{2. Disease-Specific Assessments and Status}
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+
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+ \subsection*{2.1 Type 2 Diabetes Mellitus}
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+
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+ \textbf{Current Status}: Suboptimal control
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{HbA1c}: 8.2\% (target $<$7\%)
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+ \item \textbf{Fasting Glucose}: Average 165 mg/dL (target 80-130)
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+ \item \textbf{Time in Range}: Approximately 55\% (target $>$70\%)
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+ \item \textbf{Hypoglycemia}: Infrequent, 1-2 episodes/month (BG 65-70)
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+ \item \textbf{Duration}: 12 years
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+ \item \textbf{Complications Screening}:
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+ \begin{itemize}
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+ \item Retinopathy: Mild NPDR, followed by ophthalmology
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+ \item Nephropathy: CKD stage 3b, urine ACR 180 mg/g (albuminuria)
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+ \item Neuropathy: Mild peripheral neuropathy, no foot ulcers
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+ \item Cardiovascular: History of heart failure
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+ \end{itemize}
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+ \end{itemize}
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+
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+ \subsection*{2.2 Chronic Heart Failure (HFrEF)}
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+
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+ \textbf{Current Status}: Stable, NYHA Class II
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Ejection Fraction}: 35\% (reduced, HFrEF)
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+ \item \textbf{Etiology}: Ischemic cardiomyopathy (prior MI 5 years ago)
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+ \item \textbf{NYHA Class}: II - Slight limitation, comfortable at rest, symptoms with ordinary activity
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+ \item \textbf{Symptoms}: Mild dyspnea on exertion, no orthopnea/PND, occasional LE edema
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+ \item \textbf{Weight}: Stable, patient monitors daily
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+ \item \textbf{GDMT Status}:
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+ \begin{itemize}
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+ \item ACE inhibitor: Lisinopril 40mg daily (at target dose)
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+ \item Beta-blocker: Carvedilol 12.5mg BID (target 25mg BID - limited by fatigue)
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+ \item Diuretic: Furosemide 40mg daily
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+ \item Need to consider: SGLT2 inhibitor (also beneficial for diabetes), ARNI
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+ \end{itemize}
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+ \item \textbf{Device Therapy}: No ICD/CRT currently, discussed with cardiology
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+ \end{itemize}
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+
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+ \subsection*{2.3 Chronic Kidney Disease Stage 3b}
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+
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+ \textbf{Current Status}: Stable
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{eGFR}: 38 mL/min/1.73m² (Stage 3b, moderate-severe decrease)
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+ \item \textbf{Creatinine}: 1.8 mg/dL (stable)
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+ \item \textbf{Urine Albumin}: ACR 180 mg/g (albuminuria, from diabetes)
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+ \item \textbf{Etiology}: Diabetic nephropathy, hypertensive nephropathy
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+ \item \textbf{Progression Risk}: Moderate-high (diabetes, albuminuria)
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+ \item \textbf{Complications}: Anemia (Hgb 11.2), managed with iron supplementation
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+ \item \textbf{Renal Protection}: ACE inhibitor, BP control, glucose control, limit nephrotoxins
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+ \end{itemize}
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+
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+ \subsection*{2.4 Additional Conditions Summary}
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+
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Hypertension}: Well-controlled, average home BP 128/78 mmHg
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+ \item \textbf{Hyperlipidemia}: LDL 65 mg/dL (at goal $<$70 for ASCVD), on statin
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+ \item \textbf{Obstructive Sleep Apnea}: On CPAP nightly, AHI reduced from 32 to 4, good adherence
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+ \item \textbf{Obesity}: BMI 34, weight stable, difficulty with weight loss due to HF exercise limitations
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+ \item \textbf{Osteoarthritis}: Bilateral knee pain, managed with acetaminophen, PT, avoid NSAIDs (CKD)
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+ \end{itemize}
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+
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+ % ===== SECTION 3: INTEGRATED GOALS =====
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+ \section*{3. Integrated Treatment Goals (SMART Format)}
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+
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+ \subsection*{3.1 Short-Term Goals (3-6 months)}
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+
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+ \textbf{Diabetes Goals}:
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+ \begin{enumerate}[leftmargin=*]
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+ \item Reduce HbA1c from 8.2\% to $<$7.5\% within 3 months by optimizing insulin dosing and medication adherence.
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+ \item Improve fasting glucose to 100-140 mg/dL range through medication adjustment and dietary changes within 3 months.
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+ \item Complete annual diabetic eye exam and foot exam within 1 month.
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+ \end{enumerate}
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+
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+ \textbf{Heart Failure Goals}:
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+ \begin{enumerate}[leftmargin=*]
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+ \item Maintain NYHA Class II status (no worsening) with daily weight monitoring and adherence to fluid/sodium restrictions.
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+ \item Add SGLT2 inhibitor for dual diabetes and heart failure benefit within 1 month.
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+ \item Improve exercise tolerance: Walk 15 minutes daily without dyspnea within 3 months.
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+ \end{enumerate}
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+
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+ \textbf{CKD Goals}:
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+ \begin{enumerate}[leftmargin=*]
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+ \item Maintain eGFR stability ($\pm$5 mL/min from baseline 38) over 6 months.
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+ \item Reduce urine albumin-to-creatinine ratio from 180 to $<$100 mg/g with BP and glucose control.
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+ \item Avoid nephrotoxic agents (NSAIDs, contrast without prophylaxis).
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+ \end{enumerate}
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+
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+ \textbf{Cross-Cutting Goals}:
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+ \begin{enumerate}[leftmargin=*]
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+ \item Medication adherence $>$90\% measured by refill rates and pill counts within 3 months.
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+ \item Weight loss of 5\% body weight (10 lbs) through diet modification within 6 months.
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+ \item Blood pressure maintenance at $<$130/80 mmHg (home average).
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+ \end{enumerate}
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+
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+ \subsection*{3.2 Long-Term Goals (6-12 months)}
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+
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+ \begin{enumerate}[leftmargin=*]
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+ \item \textbf{Diabetes}: Achieve HbA1c $<$7\% and prevent progression of microvascular complications.
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+ \item \textbf{Heart Failure}: Optimize GDMT, prevent hospitalizations, maintain functional status.
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+ \item \textbf{CKD}: Slow progression (goal: $<$2 mL/min/year eGFR decline), delay need for dialysis.
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+ \item \textbf{Quality of Life}: Maintain independence in ADLs, engage in meaningful activities (gardening, grandchildren visits).
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+ \item \textbf{Prevention}: Up-to-date with all preventive care (vaccinations, cancer screenings).
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+ \item \textbf{Coordination}: Seamless care transitions, all providers aware of care plan, no conflicting treatments.
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+ \end{enumerate}
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+
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+ \subsection*{3.3 Patient-Centered Priorities}
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+
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Priority 1}: "I don't want to end up on dialysis like my brother"
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+ \item \textbf{Priority 2}: "I want to keep up with my grandkids"
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+ \item \textbf{Priority 3}: "I want to reduce my medications if possible" (pill burden concern)
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+ \item \textbf{Priority 4}: "I want to avoid being hospitalized again"
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+ \end{itemize}
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+
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+ % ===== SECTION 4: COMPREHENSIVE INTERVENTIONS =====
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+ \section*{4. Comprehensive Interventions}
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+
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+ \subsection*{4.1 Medication Management and Optimization}
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+
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+ \textbf{Current Regimen Optimization}:
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+
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+ \begin{enumerate}[leftmargin=*]
243
+ \item \textbf{ADD: Empagliflozin (Jardiance) 10mg daily}
244
+ \begin{itemize}
245
+ \item \textit{Rationale}: SGLT2 inhibitor provides dual benefit - improves diabetes control AND reduces HF hospitalizations/mortality (EMPEROR-Reduced trial). Also slows CKD progression.
246
+ \item \textit{Monitoring}: eGFR (hold if $<$20), volume status, UTI symptoms, DKA risk (low in T2DM)
247
+ \item \textit{Expected benefit}: HbA1c reduction 0.5-0.8\%, reduced HF events 25-30\%
248
+ \end{itemize}
249
+
250
+ \item \textbf{TITRATE: Insulin glargine}
251
+ \begin{itemize}
252
+ \item \textit{Current}: 24 units QHS, fasting BG averaging 165
253
+ \item \textit{Plan}: Increase by 2 units every 3 days until fasting BG 100-130, patient to self-titrate with daily phone/portal check-ins
254
+ \item \textit{Expected dose}: Likely 30-36 units
255
+ \end{itemize}
256
+
257
+ \item \textbf{OPTIMIZE: Beta-blocker (carvedilol)}
258
+ \begin{itemize}
259
+ \item \textit{Current}: 12.5mg BID (patient reports fatigue at higher doses)
260
+ \item \textit{Plan}: Trial slow up-titration to 18.75mg BID, monitor for tolerance
261
+ \item \textit{Goal}: Target dose 25mg BID for HFrEF mortality benefit
262
+ \item \textit{Alternative}: Consider switching to different beta-blocker if intolerable
263
+ \end{itemize}
264
+
265
+ \item \textbf{CONTINUE}: ACE inhibitor (lisinopril 40mg) - at target dose
266
+
267
+ \item \textbf{CONSIDER FUTURE}: Sacubitril/valsartan (Entresto) to replace lisinopril if HF symptoms progress
268
+ \end{enumerate}
269
+
270
+ \textbf{Medication Safety}:
271
+ \begin{itemize}[leftmargin=*]
272
+ \item \textbf{Polypharmacy Review}: Current medication count [X], review quarterly for deprescribing opportunities
273
+ \item \textbf{Renal Dosing}: All medications reviewed for CKD Stage 3b, adjust as needed
274
+ \item \textbf{Drug Interactions}: Monitor K+ with ACE + diuretic, avoid NSAIDs (CKD, HF)
275
+ \item \textbf{Adherence Support}: Pill organizer, medication list wallet card, automatic refills, pharmacy synchronization
276
+ \end{itemize}
277
+
278
+ \subsection*{4.2 Lifestyle and Self-Management Interventions}
279
+
280
+ \textbf{Dietary Management}:
281
+ \begin{itemize}[leftmargin=*]
282
+ \item \textbf{Diabetes}:
283
+ \begin{itemize}
284
+ \item Carbohydrate consistency: 45-60g per meal
285
+ \item Mediterranean diet pattern
286
+ \item Limit refined sugars and processed carbohydrates
287
+ \end{itemize}
288
+ \item \textbf{Heart Failure}:
289
+ \begin{itemize}
290
+ \item Sodium restriction: $<$2000mg daily (low-sodium products, avoid processed foods)
291
+ \item Fluid restriction: 1.5-2L daily if needed for volume management
292
+ \end{itemize}
293
+ \item \textbf{CKD}:
294
+ \begin{itemize}
295
+ \item Moderate protein intake: 0.8-1.0 g/kg/day
296
+ \item Phosphorus and potassium awareness (but not severely restricted at Stage 3b)
297
+ \end{itemize}
298
+ \item \textbf{Weight Loss}: 500 kcal/day deficit for gradual weight loss
299
+ \item \textbf{Referral}: Registered dietitian for medical nutrition therapy
300
+ \end{itemize}
301
+
302
+ \textbf{Physical Activity}:
303
+ \begin{itemize}[leftmargin=*]
304
+ \item \textbf{Goal}: 150 min/week moderate activity (walking, swimming)
305
+ \item \textbf{Heart Failure Considerations}: Start with 10-15 min sessions, gradually increase, monitor symptoms
306
+ \item \textbf{Diabetes Benefits}: Improves insulin sensitivity, glucose control
307
+ \item \textbf{Cardiac Rehabilitation}: Consider referral if not previously completed
308
+ \item \textbf{Progression}: Track with pedometer/activity tracker, goal 7000-10,000 steps daily
309
+ \end{itemize}
310
+
311
+ \textbf{Self-Monitoring}:
312
+ \begin{itemize}[leftmargin=*]
313
+ \item \textbf{Daily}:
314
+ \begin{itemize}
315
+ \item Weight (same time, same scale) - report gain $>$2-3 lbs in 2 days
316
+ \item Blood glucose: Fasting and pre-dinner
317
+ \item Blood pressure: Morning and evening
318
+ \end{itemize}
319
+ \item \textbf{Weekly}:
320
+ \begin{itemize}
321
+ \item Symptom check (dyspnea, edema, chest pain, hypoglycemia frequency)
322
+ \item Medication adherence review
323
+ \end{itemize}
324
+ \item \textbf{Recording}: Use logbook or smartphone app (MyChart, Apple Health)
325
+ \end{itemize}
326
+
327
+ \textbf{Other Lifestyle Factors}:
328
+ \begin{itemize}[leftmargin=*]
329
+ \item \textbf{CPAP Adherence}: Continue nightly use, download compliance data quarterly
330
+ \item \textbf{Smoking}: [If applicable - cessation interventions]
331
+ \item \textbf{Alcohol}: Limit to $\leq$1 drink/day (heart failure, diabetes management)
332
+ \item \textbf{Stress Management}: Mindfulness, adequate sleep, social engagement
333
+ \end{itemize}
334
+
335
+ \subsection*{4.3 Disease-Specific Monitoring and Screening}
336
+
337
+ \textbf{Diabetes Monitoring}:
338
+ \begin{itemize}[leftmargin=*]
339
+ \item HbA1c every 3 months until at goal, then every 6 months
340
+ \item Lipid panel annually
341
+ \item Urine albumin-to-creatinine ratio annually
342
+ \item Comprehensive foot exam every visit, monofilament testing annually
343
+ \item Dilated eye exam annually (ophthalmology)
344
+ \item Dental exam every 6 months (periodontal disease link)
345
+ \end{itemize}
346
+
347
+ \textbf{Heart Failure Monitoring}:
348
+ \begin{itemize}[leftmargin=*]
349
+ \item Daily weights, report significant changes
350
+ \item BNP or NT-proBNP when symptoms change
351
+ \item Echocardiogram annually or if clinical change
352
+ \item EKG annually
353
+ \item Functional assessment (6-minute walk test) periodically
354
+ \end{itemize}
355
+
356
+ \textbf{CKD Monitoring}:
357
+ \begin{itemize}[leftmargin=*]
358
+ \item eGFR and creatinine every 3-6 months
359
+ \item Urine ACR annually
360
+ \item CBC (anemia), CMP (electrolytes, calcium, phosphorus) every 6 months
361
+ \item Vitamin D, PTH if indicated
362
+ \item Bone density scan (increased fracture risk)
363
+ \end{itemize}
364
+
365
+ \textbf{Preventive Care}:
366
+ \begin{itemize}[leftmargin=*]
367
+ \item Influenza vaccine annually
368
+ \item Pneumococcal vaccines (PCV20 or PCV15+PPSV23) per ACIP guidelines
369
+ \item COVID-19 vaccination per current recommendations
370
+ \item Zoster vaccine (Shingrix)
371
+ \item Colorectal cancer screening per age guidelines
372
+ \item [Other age/sex-appropriate screenings]
373
+ \end{itemize}
374
+
375
+ % ===== SECTION 5: CARE COORDINATION =====
376
+ \section*{5. Care Coordination and Communication}
377
+
378
+ \subsection*{Provider Communication Plan}
379
+
380
+ \begin{tabularx}{\textwidth}{|l|X|X|}
381
+ \hline
382
+ \textbf{Provider} & \textbf{Visit Frequency} & \textbf{Communication/Coordination} \\ \hline
383
+ Primary Care & Every 3 months & Care plan coordinator, medication reconciliation, preventive care \\ \hline
384
+ Cardiology & Every 4-6 months & HF medication optimization, EF monitoring, device consideration \\ \hline
385
+ Endocrinology & Every 3-4 months & Diabetes management, insulin titration, complications screening \\ \hline
386
+ Nephrology & As needed (if eGFR $<$30 or rapid decline) & CKD management, dialysis planning if needed \\ \hline
387
+ Dietitian & Monthly x3, then quarterly & Nutrition counseling, meal planning \\ \hline
388
+ Pharmacist & Quarterly & Medication review, adherence counseling, cost optimization \\ \hline
389
+ Care Coordinator & Monthly phone check-in & Appointment scheduling, barrier identification, education \\ \hline
390
+ \end{tabularx}
391
+
392
+ \subsection*{Information Sharing}
393
+
394
+ \begin{itemize}[leftmargin=*]
395
+ \item Shared EHR access for all providers in health system
396
+ \item Medication reconciliation after each specialist visit
397
+ \item Lab results shared via patient portal and provider notifications
398
+ \item Care plan accessible to all team members
399
+ \item Patient carries medication list and problem list
400
+ \end{itemize}
401
+
402
+ \subsection*{Care Transitions Management}
403
+
404
+ \textbf{Hospital Discharge Protocol}:
405
+ \begin{itemize}[leftmargin=*]
406
+ \item PCP notified within 24 hours of admission and discharge
407
+ \item Follow-up appointment within 7 days of discharge
408
+ \item Medication reconciliation at discharge and first follow-up
409
+ \item Red flags review: HF exacerbation signs, hyperglycemia, AKI
410
+ \end{itemize}
411
+
412
+ \textbf{Specialty Referral Coordination}:
413
+ \begin{itemize}[leftmargin=*]
414
+ \item Care coordinator ensures specialist appointments scheduled
415
+ \item Specialist notes reviewed by PCP within 1 week
416
+ \item Treatment recommendations integrated into care plan
417
+ \item Conflicting recommendations discussed among providers
418
+ \end{itemize}
419
+
420
+ % ===== SECTION 6: MONITORING AND OUTCOMES =====
421
+ \section*{6. Monitoring Parameters and Quality Measures}
422
+
423
+ \subsection*{Clinical Outcomes Dashboard}
424
+
425
+ \begin{longtable}{|p{3.5cm}|p{2.5cm}|p{2cm}|p{2cm}|p{3cm}|}
426
+ \hline
427
+ \textbf{Parameter} & \textbf{Baseline} & \textbf{Target} & \textbf{Current} & \textbf{Frequency} \\ \hline
428
+ \endfirsthead
429
+ \hline
430
+ \textbf{Parameter} & \textbf{Baseline} & \textbf{Target} & \textbf{Current} & \textbf{Frequency} \\ \hline
431
+ \endhead
432
+ HbA1c & 8.2\% & $<$7\% & [update] & Q3-6 months \\ \hline
433
+ Fasting Glucose & 165 mg/dL & 100-130 & [update] & Daily (patient), labs Q3mo \\ \hline
434
+ Blood Pressure & 142/86 & $<$130/80 & [update] & Daily (patient), each visit \\ \hline
435
+ LDL Cholesterol & 65 mg/dL & $<$70 & At goal & Annually \\ \hline
436
+ eGFR & 38 mL/min & Stable ($\pm$5) & [update] & Every 3-6 months \\ \hline
437
+ Urine ACR & 180 mg/g & $<$100 & [update] & Annually \\ \hline
438
+ Weight & [baseline] lbs & -10 lbs (5\%) & [update] & Daily (patient), each visit \\ \hline
439
+ BNP/NT-proBNP & [if available] & Stable & [update] & When symptomatic \\ \hline
440
+ Ejection Fraction & 35\% & Monitor & [date of last echo] & Annually or if change \\ \hline
441
+ \end{longtable}
442
+
443
+ \subsection*{Quality Measure Tracking (HEDIS/CMS)}
444
+
445
+ \begin{itemize}[leftmargin=*]
446
+ \item ✓ Diabetes HbA1c testing (every 6 months)
447
+ \item ☐ Diabetes HbA1c control ($<$8\%) - \textit{Target: achieve}
448
+ \item ✓ Diabetes eye exam (annual dilated)
449
+ \item ☐ Diabetes medical attention for nephropathy (urine ACR) - \textit{Due [month]}
450
+ \item ✓ Blood pressure control ($<$140/90 for diabetes)
451
+ \item ✓ Statin therapy for ASCVD
452
+ \item ✓ ACE/ARB therapy for diabetes with hypertension
453
+ \item ✓ Beta-blocker for HFrEF
454
+ \item ☐ Flu vaccine current year - \textit{Due [month]}
455
+ \item ✓ Pneumococcal vaccine
456
+ \end{itemize}
457
+
458
+ % ===== SECTION 7: PATIENT EDUCATION AND ACTIVATION =====
459
+ \section*{7. Patient Education and Self-Management Support}
460
+
461
+ \subsection*{Disease Education Completed}
462
+
463
+ \begin{itemize}[leftmargin=*]
464
+ \item \textbf{Diabetes}: Pathophysiology, complications, importance of glucose control, hypoglycemia recognition
465
+ \item \textbf{Heart Failure}: How heart failure affects body, medication importance, fluid/sodium restrictions, warning signs
466
+ \item \textbf{CKD}: Kidney function, progression risk, renal protection strategies, medication precautions
467
+ \item \textbf{Medication Purposes}: Why each medication is prescribed, expected benefits
468
+ \item \textbf{Lifestyle Impact}: How diet, exercise, weight loss benefit all conditions
469
+ \end{itemize}
470
+
471
+ \subsection*{Self-Management Skills Training}
472
+
473
+ \begin{itemize}[leftmargin=*]
474
+ \item ✓ Blood glucose monitoring technique
475
+ \item ✓ Insulin injection technique and storage
476
+ \item ✓ Home blood pressure monitoring
477
+ \item ✓ Daily weight tracking and interpretation
478
+ \item ✓ Symptom recognition (HF exacerbation, hypoglycemia, hyperglycemia)
479
+ \item ✓ Medication organization (pill box use)
480
+ \item ☐ Dietary skills: Carb counting, label reading, low-sodium food selection
481
+ \item ☐ Sick day management (when to call, medication adjustments)
482
+ \end{itemize}
483
+
484
+ \subsection*{Warning Signs - When to Call Provider}
485
+
486
+ \textbf{Call office same day or go to ED if}:
487
+ \begin{itemize}[leftmargin=*]
488
+ \item Weight gain $>$2-3 lbs in 2 days or 5 lbs in 1 week (heart failure)
489
+ \item Increased shortness of breath, cannot lie flat, new leg swelling
490
+ \item Chest pain or pressure
491
+ \item Blood glucose consistently $>$300 or $<$60 mg/dL
492
+ \item Decreased urine output, dark urine, swelling
493
+ \item Dizziness, lightheadedness, syncope
494
+ \end{itemize}
495
+
496
+ \subsection*{Resources and Support}
497
+
498
+ \begin{itemize}[leftmargin=*]
499
+ \item Diabetes self-management education program (DSMES)
500
+ \item Cardiac rehabilitation program
501
+ \item Patient portal for lab results, messaging, educational materials
502
+ \item American Diabetes Association (diabetes.org) resources
503
+ \item American Heart Association (heart.org) HF information
504
+ \item National Kidney Foundation (kidney.org) CKD education
505
+ \item Local support groups [if available]
506
+ \end{itemize}
507
+
508
+ % ===== SECTION 8: CONTINGENCY PLANNING =====
509
+ \section*{8. Contingency Planning and Risk Mitigation}
510
+
511
+ \subsection*{Hospital Readmission Prevention}
512
+
513
+ \textbf{High-Risk Period}: 30 days post-discharge
514
+
515
+ \textbf{Prevention Strategies}:
516
+ \begin{itemize}[leftmargin=*]
517
+ \item Early follow-up appointment (within 7 days)
518
+ \item Medication reconciliation and adherence check
519
+ \item Symptom monitoring escalation
520
+ \item Care coordinator phone call within 48 hours of discharge
521
+ \item Access to nurse advice line 24/7
522
+ \end{itemize}
523
+
524
+ \subsection*{Disease Progression Planning}
525
+
526
+ \textbf{If CKD progresses to Stage 4-5}:
527
+ \begin{itemize}[leftmargin=*]
528
+ \item Nephrology referral for CKD education and dialysis planning
529
+ \item Vascular access planning if eGFR $<$20
530
+ \item Medication adjustments for reduced renal clearance
531
+ \item Anemia management optimization (ESA if needed)
532
+ \item Advance care planning discussions
533
+ \end{itemize}
534
+
535
+ \textbf{If HF worsens to NYHA Class III-IV}:
536
+ \begin{itemize}[leftmargin=*]
537
+ \item Consider ICD/CRT device evaluation
538
+ \item Advanced therapies discussion (LVAD, transplant evaluation if appropriate)
539
+ \item Palliative care consultation for symptom management
540
+ \item Home health nursing for weight/symptom monitoring
541
+ \end{itemize}
542
+
543
+ \subsection*{Advance Care Planning}
544
+
545
+ \begin{itemize}[leftmargin=*]
546
+ \item Goals of care discussion: [Patient preferences documented]
547
+ \item Healthcare proxy: [Name, relationship] designated
548
+ \item Advance directive: ☐ Completed / ☐ To complete
549
+ \item CPR preferences: [Discussed, documented in chart]
550
+ \item Dialysis preferences: Patient expresses desire to avoid if possible
551
+ \end{itemize}
552
+
553
+ % ===== SECTION 9: FOLLOW-UP SCHEDULE =====
554
+ \section*{9. Follow-Up and Reassessment Schedule}
555
+
556
+ \subsection*{Appointment Calendar}
557
+
558
+ \begin{longtable}{|l|l|p{7cm}|}
559
+ \hline
560
+ \textbf{Timeframe} & \textbf{Provider} & \textbf{Purpose} \\ \hline
561
+ \endfirsthead
562
+ \hline
563
+ \textbf{Timeframe} & \textbf{Provider} & \textbf{Purpose} \\ \hline
564
+ \endhead
565
+ Week 2 & Care Coordinator (phone) & Check medication tolerability, answer questions, reinforce education \\ \hline
566
+ Month 1 & PCP & Add empagliflozin, assess insulin titration, review home monitoring logs \\ \hline
567
+ Month 2 & Dietitian & Nutrition counseling, meal planning, sodium/carb education \\ \hline
568
+ Month 3 & PCP & HbA1c check, labs (CMP, lipids), medication review, preventive care update \\ \hline
569
+ Month 3-4 & Cardiology & HF assessment, beta-blocker titration, consider ARNI \\ \hline
570
+ Month 3-4 & Endocrinology & Diabetes management review, complications screening \\ \hline
571
+ Month 6 & PCP & Comprehensive reassessment, all labs, update care plan, goal review \\ \hline
572
+ Ongoing & Quarterly PCP & Chronic disease management visits \\ \hline
573
+ \end{longtable}
574
+
575
+ \subsection*{Plan Reassessment}
576
+
577
+ This care plan will be formally reassessed and updated:
578
+ \begin{itemize}[leftmargin=*]
579
+ \item Every 6 months (routine)
580
+ \item After hospitalization or ED visit
581
+ \item With significant change in clinical status
582
+ \item When new diagnoses are added
583
+ \item When treatment goals are achieved or modified
584
+ \item At patient or provider request
585
+ \end{itemize}
586
+
587
+ % ===== SECTION 10: SIGNATURES =====
588
+ \vspace{2em}
589
+
590
+ \section*{10. Provider Signature and Attestation}
591
+
592
+ This comprehensive chronic disease management plan has been reviewed with the patient. The patient demonstrates understanding of all chronic conditions, treatment goals, medications, lifestyle recommendations, self-monitoring requirements, warning signs, and when to seek care. Patient's values and preferences have been incorporated through shared decision-making.
593
+
594
+ \vspace{1em}
595
+
596
+ \begin{tabular}{ll}
597
+ Provider Signature: & \rule{7cm}{0.5pt} \\[1em]
598
+ Provider Name/Credentials: & \rule{7cm}{0.5pt} \\[1em]
599
+ Date: & \rule{4cm}{0.5pt} \\[2em]
600
+ \end{tabular}
601
+
602
+ \subsection*{Care Team Acknowledgment (Optional)}
603
+
604
+ Care team members have reviewed this integrated care plan and will coordinate care accordingly.
605
+
606
+ \vspace{0.5em}
607
+
608
+ \textit{[Additional signature lines for cardiologist, endocrinologist, care coordinator as appropriate]}
609
+
610
+ \vspace{2em}
611
+ \begin{center}
612
+ \rule{\textwidth}{1pt}\\
613
+ \textbf{End of Chronic Disease Management Plan}\\
614
+ This document contains confidential patient information protected by HIPAA.
615
+ \end{center}
616
+
617
+ \end{document}
618
+
619
+ % ========== NOTES FOR USERS ==========
620
+ %
621
+ % KEY FEATURES:
622
+ % - Integrates multiple chronic conditions into unified plan
623
+ % - Addresses medication interactions and contraindications across conditions
624
+ % - Coordinates care across multiple specialistsUtilizes shared goals when conditions overlap (e.g., SGLT2i for DM + HF + CKD)
625
+ % - Emphasizes patient self-management and activation
626
+ % - Tracks quality measures and outcomes
627
+ %
628
+ % CUSTOMIZATION:
629
+ % - Adjust problem list based on patient's specific conditions
630
+ % - Modify goals for disease severity and patient capabilities
631
+ % - Adapt medication regimen to formulary and patient tolerance
632
+ % - Coordinate specialist involvement based on availability and need
633
+ %
634
+ % COMPILATION:
635
+ % pdflatex chronic_disease_management_plan.tex
636
+