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
  206. scientific_writer/.claude/skills/markitdown/SKILL.md +450 -0
  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
  235. scientific_writer/.claude/skills/research-lookup/SKILL.md +443 -0
  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
@@ -0,0 +1,616 @@
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+ % General Medical Treatment Plan Template
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+ % For primary care and chronic disease management
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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{General Medical Treatment 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 MEDICAL TREATMENT PLAN}\\[0.5em]
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+ {\large General Medicine \& Chronic Disease Management}\\[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}
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+
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+ \textbf{HIPAA Notice}: All identifiable information must be removed or de-identified per Safe Harbor method before sharing this document. Remove: name, dates (except year), addresses, phone/fax, email, SSN, medical record numbers, account numbers, photos, and other unique identifiers.
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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., PT-001] \\ \hline
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+ \textbf{Age Range} & [e.g., 55-60 years] \\ \hline
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+ \textbf{Sex} & [Male/Female/Other] \\ \hline
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+ \textbf{Race/Ethnicity} & [If relevant to treatment] \\ \hline
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+ \textbf{Date of Plan} & [Month/Year only] \\ \hline
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+ \textbf{Provider} & [Name, MD/DO/NP/PA, Credentials] \\ \hline
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+ \textbf{Facility} & [Healthcare facility name] \\ \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 Medical Conditions}
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Primary Diagnosis}: [Condition with ICD-10 code]
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+ \item \textbf{Secondary Diagnoses}:
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+ \begin{itemize}
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+ \item [Comorbidity 1 with ICD-10 code]
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+ \item [Comorbidity 2 with ICD-10 code]
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+ \item [Additional conditions as needed]
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+ \end{itemize}
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+ \end{itemize}
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+
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+ \subsection*{Current Medications}
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+ \begin{longtable}{|p{3.5cm}|p{2cm}|p{2cm}|p{5cm}|}
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+ \hline
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+ \textbf{Medication} & \textbf{Dose} & \textbf{Frequency} & \textbf{Indication} \\ \hline
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+ \endfirsthead
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+ \hline
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+ \textbf{Medication} & \textbf{Dose} & \textbf{Frequency} & \textbf{Indication} \\ \hline
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+ \endhead
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+ Medication 1 & [e.g., 10mg] & [e.g., daily] & [Indication] \\ \hline
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+ Medication 2 & [e.g., 50mg] & [e.g., BID] & [Indication] \\ \hline
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+ [Add rows as needed] & & & \\ \hline
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+ \end{longtable}
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+
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+ \subsection*{Allergies}
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Drug Allergies}: [List medications and reactions, or NKDA]
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+ \item \textbf{Food/Environmental}: [If relevant to treatment]
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+ \end{itemize}
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+
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+ \subsection*{Baseline Assessment}
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Functional Status}: [Independent/requires assistance/dependent for ADLs]
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+ \item \textbf{Cognitive Status}: [Alert and oriented/impairment if present]
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+ \item \textbf{Social Support}: [Lives alone/with family, support system]
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+ \item \textbf{Key Baseline Values}: [e.g., HbA1c 8.5\%, BP 145/90, BMI 32, eGFR 55]
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+ \end{itemize}
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+
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+ % ===== SECTION 2: DIAGNOSIS AND ASSESSMENT =====
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+ \section*{2. Diagnosis and Assessment Summary}
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+
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+ \subsection*{Primary Diagnosis}
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+ \textbf{Diagnosis}: [Full diagnosis name]\\
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+ \textbf{ICD-10 Code}: [e.g., E11.9 for Type 2 Diabetes Mellitus without complications]\\
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+ \textbf{Severity}: [Mild/Moderate/Severe or stage classification]\\
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+ \textbf{Duration}: [Time since diagnosis]
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+
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+ \subsection*{Clinical Presentation}
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+ [Describe current symptoms, functional limitations, and impact on quality of life. Include relevant exam findings and diagnostic test results.]
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+
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+ \subsection*{Risk Stratification}
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Cardiovascular Risk}: [e.g., ASCVD 10-year risk 15\%]
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+ \item \textbf{Complications Risk}: [e.g., high risk for diabetic nephropathy]
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+ \item \textbf{Other Risk Factors}: [e.g., fall risk, frailty, polypharmacy]
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+ \end{itemize}
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+
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+ \subsection*{Prognostic Considerations}
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+ [Discuss expected disease course, factors affecting prognosis, and rationale for treatment intensity.]
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+
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+ % ===== SECTION 3: TREATMENT GOALS =====
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+ \section*{3. Treatment Goals (SMART Format)}
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+
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+ \textbf{SMART Criteria}: All goals should be \textbf{S}pecific, \textbf{M}easurable, \textbf{A}chievable, \textbf{R}elevant, and \textbf{T}ime-bound.
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+
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+ \subsection*{Short-Term Goals (1-3 months)}
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+
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+ \begin{enumerate}[leftmargin=*]
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+ \item \textbf{Goal 1}: [e.g., Reduce HbA1c from 8.5\% to $<$7.5\%]
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+ \begin{itemize}
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+ \item \textit{Specific}: Reduce HbA1c by at least 1 percentage point
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+ \item \textit{Measurable}: HbA1c lab value
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+ \item \textit{Achievable}: With medication initiation and lifestyle changes
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+ \item \textit{Relevant}: Reduce microvascular complication risk
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+ \item \textit{Time-bound}: Achieve within 3 months (next follow-up)
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+ \end{itemize}
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+
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+ \item \textbf{Goal 2}: [e.g., Decrease systolic blood pressure to $<$130 mmHg]
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+ \begin{itemize}
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+ \item \textit{Specific}: Achieve BP $<$130/80 mmHg
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+ \item \textit{Measurable}: Office and home BP measurements
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+ \item \textit{Achievable}: With medication optimization
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+ \item \textit{Relevant}: Reduce cardiovascular event risk
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+ \item \textit{Time-bound}: Within 8 weeks
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+ \end{itemize}
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+
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+ \item \textbf{Goal 3}: [Additional short-term goal]
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+ \end{enumerate}
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+
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+ \subsection*{Long-Term Goals (6-12 months)}
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+
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+ \begin{enumerate}[leftmargin=*]
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+ \item \textbf{Goal 1}: [e.g., Maintain HbA1c $<$7\% and prevent diabetic complications]
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+ \begin{itemize}
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+ \item \textit{Success criteria}: HbA1c $<$7\%, no new retinopathy/nephropathy/neuropathy
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+ \item \textit{Timeline}: Ongoing, assessed every 3-6 months
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+ \end{itemize}
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+
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+ \item \textbf{Goal 2}: [e.g., Weight loss of 15 pounds (7\% body weight)]
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+ \begin{itemize}
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+ \item \textit{Success criteria}: BMI reduction from 32 to $<$30
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+ \item \textit{Timeline}: 6-12 months at 1-2 lbs/week
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+ \end{itemize}
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+
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+ \item \textbf{Goal 3}: [e.g., Achieve LDL cholesterol $<$70 mg/dL]
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+
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+ \item \textbf{Goal 4}: [Additional long-term goal as needed]
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+ \end{enumerate}
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+
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+ \subsection*{Patient-Centered Goals}
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Patient Priority 1}: [e.g., "Feel more energetic throughout the day"]
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+ \item \textbf{Patient Priority 2}: [e.g., "Avoid insulin injections if possible"]
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+ \item \textbf{Patient Priority 3}: [e.g., "Continue working full-time"]
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+ \end{itemize}
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+
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+ % ===== SECTION 4: INTERVENTIONS =====
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+ \section*{4. Interventions}
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+
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+ \subsection*{4.1 Pharmacological Interventions}
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+
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+ \begin{longtable}{|p{3cm}|p{2cm}|p{2cm}|p{6.5cm}|}
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+ \hline
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+ \textbf{Medication} & \textbf{Dose} & \textbf{Frequency} & \textbf{Instructions \& Rationale} \\ \hline
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+ \endfirsthead
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+ \hline
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+ \textbf{Medication} & \textbf{Dose} & \textbf{Frequency} & \textbf{Instructions \& Rationale} \\ \hline
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+ \endhead
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+
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+ [e.g., Metformin] & 500mg & BID & \textbf{Start:} Take with meals to reduce GI upset. \textbf{Titration:} Increase to 1000mg BID after 2 weeks if tolerated. \textbf{Target:} 2000mg daily. \textbf{Rationale:} First-line for T2DM, reduces hepatic glucose production. \\ \hline
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+
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+ [e.g., Lisinopril] & 10mg & Daily & \textbf{Instructions:} Take in morning. Monitor BP at home. \textbf{Titration:} May increase to 20mg if BP not at goal in 4 weeks. \textbf{Rationale:} ACE inhibitor for HTN and renal protection in diabetes. \\ \hline
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+
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+ [Additional medications] & & & \\ \hline
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+ \end{longtable}
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+
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+ \textbf{Medication Safety Considerations}:
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Drug Interactions}: [List relevant interactions to monitor]
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+ \item \textbf{Adverse Effects to Monitor}: [e.g., metformin - GI upset, lactic acidosis; lisinopril - cough, hyperkalemia, angioedema]
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+ \item \textbf{Contraindications}: [e.g., metformin if eGFR $<$30]
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+ \item \textbf{Pregnancy Category}: [If relevant to patient]
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+ \end{itemize}
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+
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+ \subsection*{4.2 Non-Pharmacological Interventions}
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+
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+ \textbf{Lifestyle Modifications}:
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Diet}:
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+ \begin{itemize}
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+ \item Mediterranean or DASH diet pattern
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+ \item Carbohydrate counting: 45-60g per meal
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+ \item Reduce saturated fat $<$7\% of calories
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+ \item Sodium restriction $<$2300mg daily
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+ \item Referral to registered dietitian
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+ \end{itemize}
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+
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+ \item \textbf{Exercise}:
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+ \begin{itemize}
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+ \item Aerobic exercise: 150 minutes/week moderate intensity (e.g., brisk walking 30 min 5x/week)
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+ \item Resistance training: 2-3 sessions/week
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+ \item Reduce sedentary time, stand/move every 30 minutes
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+ \end{itemize}
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+
229
+ \item \textbf{Smoking Cessation}: [If applicable]
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+ \begin{itemize}
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+ \item Nicotine replacement therapy (patch, gum, lozenge)
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+ \item Consider varenicline or bupropion
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+ \item Behavioral counseling: 1-800-QUIT-NOW
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+ \item Target quit date: [specific date within 1 month]
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+ \end{itemize}
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+
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+ \item \textbf{Weight Management}:
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+ \begin{itemize}
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+ \item Target: 7-10\% body weight loss over 6 months
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+ \item Caloric deficit: 500-750 kcal/day
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+ \item Weekly self-weighing and food diary
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+ \item Consider weight loss program or app
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+ \end{itemize}
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+
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+ \item \textbf{Sleep Hygiene}:
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+ \begin{itemize}
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+ \item Target 7-9 hours nightly
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+ \item Consistent sleep schedule
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+ \item Screen for sleep apnea if indicated
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+ \end{itemize}
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+
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+ \item \textbf{Stress Management}:
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+ \begin{itemize}
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+ \item Mindfulness or meditation practice
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+ \item Stress reduction techniques
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+ \item Adequate social support
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+ \end{itemize}
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+ \end{itemize}
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+
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+ \textbf{Self-Management and Monitoring}:
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+ \begin{itemize}[leftmargin=*]
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+ \item \textbf{Blood Glucose Monitoring}: [Frequency, e.g., fasting and 2hr post-prandial 3x/week]
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+ \item \textbf{Home Blood Pressure}: [Frequency, e.g., daily in AM, record in log]
264
+ \item \textbf{Weight Tracking}: [e.g., weekly on same day/time]
265
+ \item \textbf{Symptom Diary}: [Track relevant symptoms]
266
+ \item \textbf{Medication Adherence}: [Pill box, reminder app]
267
+ \end{itemize}
268
+
269
+ \subsection*{4.3 Procedural and Referral Interventions}
270
+
271
+ \begin{itemize}[leftmargin=*]
272
+ \item \textbf{Specialist Referrals}:
273
+ \begin{itemize}
274
+ \item [e.g., Endocrinology consultation for diabetes management]
275
+ \item [e.g., Ophthalmology for annual dilated eye exam]
276
+ \item [e.g., Podiatry for diabetic foot exam]
277
+ \item [e.g., Nephrology if eGFR $<$30 or proteinuria]
278
+ \end{itemize}
279
+
280
+ \item \textbf{Diagnostic Testing Schedule}:
281
+ \begin{itemize}
282
+ \item [e.g., HbA1c every 3 months until at goal, then every 6 months]
283
+ \item [e.g., Lipid panel annually]
284
+ \item [e.g., Urine albumin-to-creatinine ratio annually]
285
+ \item [e.g., Comprehensive metabolic panel every 6 months]
286
+ \end{itemize}
287
+
288
+ \item \textbf{Preventive Care}:
289
+ \begin{itemize}
290
+ \item Influenza vaccine annually
291
+ \item Pneumococcal vaccines (PCV20 or PCV15+PPSV23)
292
+ \item COVID-19 vaccination per current guidelines
293
+ \item Age-appropriate cancer screenings
294
+ \item [Other preventive measures as indicated]
295
+ \end{itemize}
296
+ \end{itemize}
297
+
298
+ % ===== SECTION 5: TIMELINE AND SCHEDULE =====
299
+ \section*{5. Timeline and Schedule}
300
+
301
+ \subsection*{Treatment Phases}
302
+
303
+ \begin{tabularx}{\textwidth}{|l|X|X|}
304
+ \hline
305
+ \textbf{Phase} & \textbf{Timeframe} & \textbf{Focus} \\ \hline
306
+ Intensive Initiation & Weeks 1-4 & Medication titration, lifestyle education, baseline monitoring \\ \hline
307
+ Adjustment & Weeks 5-12 & Optimize medications, reinforce lifestyle changes, assess goal progress \\ \hline
308
+ Maintenance & Months 4-12 & Sustain improvements, prevent complications, long-term adherence \\ \hline
309
+ Ongoing & $>$12 months & Chronic disease management, annual assessments, update goals \\ \hline
310
+ \end{tabularx}
311
+
312
+ \subsection*{Appointment Schedule}
313
+
314
+ \begin{tabularx}{\textwidth}{|l|X|X|}
315
+ \hline
316
+ \textbf{Timepoint} & \textbf{Visit Type} & \textbf{Key Activities} \\ \hline
317
+ Week 2 & Phone/telehealth & Check medication tolerance, answer questions \\ \hline
318
+ Week 4 & Office visit & Medication adjustment, BP check, labs, review monitoring \\ \hline
319
+ Week 8 & Office visit & Assess progress toward goals, reinforce lifestyle \\ \hline
320
+ Month 3 & Office visit & HbA1c, comprehensive assessment, goal evaluation \\ \hline
321
+ Month 6 & Office visit & Reassess all goals, update plan, labs \\ \hline
322
+ Month 12 & Annual exam & Comprehensive evaluation, preventive care, specialty referrals \\ \hline
323
+ Ongoing & Every 3-6 months & Per chronic disease management protocol \\ \hline
324
+ \end{tabularx}
325
+
326
+ \subsection*{Milestone Assessments}
327
+
328
+ \begin{itemize}[leftmargin=*]
329
+ \item \textbf{Month 1}: Medication tolerance, lifestyle initiation, home monitoring established
330
+ \item \textbf{Month 3}: HbA1c $<$7.5\%, BP $<$130/80, 3-5 lb weight loss
331
+ \item \textbf{Month 6}: HbA1c $<$7\%, sustained BP control, 8-10 lb weight loss
332
+ \item \textbf{Month 12}: All long-term goals achieved or revised, complication screening complete
333
+ \end{itemize}
334
+
335
+ % ===== SECTION 6: MONITORING PARAMETERS =====
336
+ \section*{6. Monitoring Parameters}
337
+
338
+ \subsection*{Clinical Outcomes to Track}
339
+
340
+ \begin{longtable}{|p{4cm}|p{3cm}|p{3cm}|p{4cm}|}
341
+ \hline
342
+ \textbf{Parameter} & \textbf{Baseline} & \textbf{Target} & \textbf{Frequency} \\ \hline
343
+ \endfirsthead
344
+ \hline
345
+ \textbf{Parameter} & \textbf{Baseline} & \textbf{Target} & \textbf{Frequency} \\ \hline
346
+ \endhead
347
+
348
+ HbA1c & [e.g., 8.5\%] & $<$7\% & Every 3 months until stable, then every 6 months \\ \hline
349
+ Fasting Glucose & [e.g., 165 mg/dL] & 80-130 mg/dL & Home monitoring per schedule \\ \hline
350
+ Blood Pressure & [e.g., 145/90] & $<$130/80 mmHg & Daily home, every office visit \\ \hline
351
+ Weight/BMI & [e.g., 210 lb, BMI 32] & 195 lb, BMI $<$30 & Weekly at home, every visit \\ \hline
352
+ LDL Cholesterol & [e.g., 135 mg/dL] & $<$70 mg/dL & Every 6-12 months \\ \hline
353
+ eGFR & [e.g., 55 mL/min] & Stable, $>$45 & Every 6 months \\ \hline
354
+ Urine ACR & [e.g., normal] & $<$30 mg/g & Annually \\ \hline
355
+ [Add additional parameters] & & & \\ \hline
356
+ \end{longtable}
357
+
358
+ \subsection*{Assessment Tools and Scales}
359
+
360
+ \begin{itemize}[leftmargin=*]
361
+ \item \textbf{Diabetes Distress Scale}: [Assess emotional burden of diabetes management]
362
+ \item \textbf{SF-12 or PROMIS}: [Quality of life assessment]
363
+ \item \textbf{Medication Adherence}: [Morisky scale or refill tracking]
364
+ \item \textbf{[Other relevant scales]}: [e.g., PHQ-2 for depression screening]
365
+ \end{itemize}
366
+
367
+ \subsection*{Safety Monitoring}
368
+
369
+ \begin{itemize}[leftmargin=*]
370
+ \item \textbf{Hypoglycemia}: Frequency of blood glucose $<$70 mg/dL, symptoms
371
+ \item \textbf{Medication Adverse Effects}: GI upset, cough, dizziness, other symptoms
372
+ \item \textbf{Hyperkalemia}: Potassium level if on ACE inhibitor/ARB
373
+ \item \textbf{Renal Function}: Monitor eGFR for metformin safety, ACE/ARB effects
374
+ \end{itemize}
375
+
376
+ \subsection*{Thresholds for Intervention}
377
+
378
+ \begin{itemize}[leftmargin=*]
379
+ \item \textbf{Urgent}: Blood glucose $>$300 or $<$50, BP $>$180/110, chest pain, severe symptoms
380
+ \item \textbf{Escalate Treatment}: No improvement in HbA1c after 3 months, BP above goal after 8 weeks
381
+ \item \textbf{Modify Plan}: Intolerable side effects, patient preference change, new comorbidities
382
+ \end{itemize}
383
+
384
+ % ===== SECTION 7: EXPECTED OUTCOMES =====
385
+ \section*{7. Expected Outcomes}
386
+
387
+ \subsection*{Primary Outcome Measures}
388
+
389
+ \begin{itemize}[leftmargin=*]
390
+ \item \textbf{Glycemic Control}: HbA1c reduction of 1.5\% expected with metformin + lifestyle
391
+ \item \textbf{Blood Pressure Control}: SBP reduction of 10-15 mmHg with ACE inhibitor
392
+ \item \textbf{Weight Reduction}: 7-10\% body weight loss over 6-12 months
393
+ \item \textbf{Lipid Control}: LDL reduction of 30-40\% with statin therapy
394
+ \end{itemize}
395
+
396
+ \subsection*{Timeline for Improvement}
397
+
398
+ \begin{itemize}[leftmargin=*]
399
+ \item \textbf{Weeks 1-2}: Improved fasting glucose, initial weight loss
400
+ \item \textbf{Weeks 4-8}: BP at goal, medication tolerance established
401
+ \item \textbf{Month 3}: HbA1c improvement visible
402
+ \item \textbf{Months 6-12}: Sustained control, complication risk reduction
403
+ \end{itemize}
404
+
405
+ \subsection*{Long-Term Prognosis}
406
+
407
+ With adherence to this treatment plan, expected outcomes include:
408
+ \begin{itemize}[leftmargin=*]
409
+ \item Reduced microvascular complication risk (retinopathy, nephropathy, neuropathy)
410
+ \item Decreased cardiovascular event risk (MI, stroke)
411
+ \item Improved quality of life and functional status
412
+ \item Maintained independence and ability to work
413
+ \item [Additional expected benefits]
414
+ \end{itemize}
415
+
416
+ % ===== SECTION 8: FOLLOW-UP PLAN =====
417
+ \section*{8. Follow-Up Plan}
418
+
419
+ \subsection*{Scheduled Appointments}
420
+
421
+ \begin{itemize}[leftmargin=*]
422
+ \item \textbf{Next Visit}: [Date/timeframe - e.g., 4 weeks from today]
423
+ \item \textbf{Visit Purpose}: [Medication adjustment, lab review, goal assessment]
424
+ \item \textbf{Ongoing Schedule}: See Appointment Schedule in Section 5
425
+ \end{itemize}
426
+
427
+ \subsection*{Communication Plan}
428
+
429
+ \begin{itemize}[leftmargin=*]
430
+ \item \textbf{Between-Visit Contact}: Phone call at 2 weeks to assess medication tolerance
431
+ \item \textbf{Lab Results}: Will call with results within 3-5 business days
432
+ \item \textbf{Questions}: Call office at [phone], patient portal messaging
433
+ \item \textbf{Prescription Refills}: Via patient portal or pharmacy automated refill
434
+ \end{itemize}
435
+
436
+ \subsection*{Emergency Procedures}
437
+
438
+ \textbf{Call 911 immediately for}:
439
+ \begin{itemize}[leftmargin=*]
440
+ \item Chest pain, shortness of breath, or stroke symptoms
441
+ \item Severe hypoglycemia with confusion or loss of consciousness
442
+ \item Severe allergic reaction (angioedema, anaphylaxis)
443
+ \end{itemize}
444
+
445
+ \textbf{Call office same day for}:
446
+ \begin{itemize}[leftmargin=*]
447
+ \item Blood glucose consistently $>$300 or $<$60 mg/dL
448
+ \item Blood pressure $>$180/110 mmHg
449
+ \item Persistent severe medication side effects
450
+ \item Fever, infection, or acute illness (may need medication adjustment)
451
+ \end{itemize}
452
+
453
+ \subsection*{Transition Planning}
454
+
455
+ \begin{itemize}[leftmargin=*]
456
+ \item \textbf{If Hospitalized}: Provide this treatment plan to hospital team, resume medications on discharge
457
+ \item \textbf{Specialist Co-Management}: Share plan with all specialists, coordinate medication changes
458
+ \item \textbf{Future Considerations}: [e.g., may need insulin if oral medications insufficient]
459
+ \end{itemize}
460
+
461
+ % ===== SECTION 9: PATIENT EDUCATION =====
462
+ \section*{9. Patient Education}
463
+
464
+ \subsection*{Condition Understanding}
465
+
466
+ Patient education provided on:
467
+ \begin{itemize}[leftmargin=*]
468
+ \item \textbf{Disease Pathophysiology}: [e.g., How Type 2 diabetes affects blood sugar and organs]
469
+ \item \textbf{Natural History}: [Course without treatment vs. with optimal management]
470
+ \item \textbf{Complication Risks}: [Microvascular and macrovascular complications]
471
+ \item \textbf{Treatment Rationale}: [Why each intervention is recommended]
472
+ \end{itemize}
473
+
474
+ \subsection*{Self-Management Skills}
475
+
476
+ Training provided on:
477
+ \begin{itemize}[leftmargin=*]
478
+ \item \textbf{Glucose Monitoring}: How to use glucometer, when to test, target ranges, record keeping
479
+ \item \textbf{Blood Pressure Monitoring}: Proper technique, timing, logging
480
+ \item \textbf{Medication Administration}: How to take each medication, timing with meals
481
+ \item \textbf{Diet and Nutrition}: Carb counting, meal planning, label reading
482
+ \item \textbf{Exercise Safety}: Starting gradually, checking glucose before/after exercise
483
+ \item \textbf{Sick Day Management}: When to call, medication adjustments during illness
484
+ \end{itemize}
485
+
486
+ \subsection*{Warning Signs}
487
+
488
+ Patient instructed to recognize and respond to:
489
+ \begin{itemize}[leftmargin=*]
490
+ \item \textbf{Hypoglycemia}: Shakiness, sweating, confusion - treat with 15g fast carbs
491
+ \item \textbf{Hyperglycemia}: Excessive thirst, urination, fatigue - check glucose, call if $>$300
492
+ \item \textbf{Cardiovascular Symptoms}: Chest pain, SOB, leg swelling - seek immediate care
493
+ \item \textbf{Diabetic Foot Problems}: Wounds, numbness, pain - immediate podiatry evaluation
494
+ \item \textbf{Medication Side Effects}: [Specific symptoms requiring dose adjustment or discontinuation]
495
+ \end{itemize}
496
+
497
+ \subsection*{Resources and Support}
498
+
499
+ \begin{itemize}[leftmargin=*]
500
+ \item \textbf{Educational Materials}: [Handouts provided on diabetes, diet, medications]
501
+ \item \textbf{Diabetes Self-Management Education}: Referral to DSMES program
502
+ \item \textbf{Nutrition Counseling}: Registered dietitian appointment scheduled
503
+ \item \textbf{Support Groups}: [Local or online diabetes support groups]
504
+ \item \textbf{Technology}: [Glucose tracking app, BP log app, medication reminder]
505
+ \item \textbf{Financial Assistance}: [Medication assistance programs, community resources]
506
+ \end{itemize}
507
+
508
+ % ===== SECTION 10: RISK MITIGATION =====
509
+ \section*{10. Risk Mitigation and Safety}
510
+
511
+ \subsection*{Medication Safety}
512
+
513
+ \begin{itemize}[leftmargin=*]
514
+ \item \textbf{Hypoglycemia Risk}:
515
+ \begin{itemize}
516
+ \item Low risk with metformin alone (no insulin/sulfonylureas)
517
+ \item Patient educated on symptoms and treatment (15-15 rule)
518
+ \item Glucose monitoring more frequent if starting insulin in future
519
+ \end{itemize}
520
+
521
+ \item \textbf{Lactic Acidosis Risk} (metformin):
522
+ \begin{itemize}
523
+ \item Monitor renal function every 6 months
524
+ \item Hold metformin if eGFR $<$30 or during acute illness/dehydration
525
+ \item Discontinue 48 hours before contrast procedures
526
+ \end{itemize}
527
+
528
+ \item \textbf{Hyperkalemia/Renal Impairment} (ACE inhibitor):
529
+ \begin{itemize}
530
+ \item Check potassium and creatinine 1-2 weeks after initiation
531
+ \item Monitor every 6 months ongoing
532
+ \item Hold during severe dehydration or acute kidney injury
533
+ \end{itemize}
534
+ \end{itemize}
535
+
536
+ \subsection*{Complication Prevention}
537
+
538
+ \begin{itemize}[leftmargin=*]
539
+ \item \textbf{Cardiovascular}: Aspirin 81mg if ASCVD risk $>$10\%, BP/lipid control
540
+ \item \textbf{Retinopathy}: Annual dilated eye exam, glucose control
541
+ \item \textbf{Nephropathy}: ACE inhibitor renal protection, annual urine ACR, BP control
542
+ \item \textbf{Neuropathy}: Annual foot exam, glucose control, foot care education
543
+ \item \textbf{Falls}: Screen for orthostatic hypotension, avoid overtreatment
544
+ \end{itemize}
545
+
546
+ \subsection*{Polypharmacy and Drug Interactions}
547
+
548
+ \begin{itemize}[leftmargin=*]
549
+ \item Regular medication reconciliation at each visit
550
+ \item Screen for drug-drug interactions with new medications
551
+ \item Deprescribe unnecessary medications
552
+ \item Consider pill burden and simplify regimen when possible
553
+ \end{itemize}
554
+
555
+ \subsection*{Emergency Action Plan}
556
+
557
+ \begin{tabularx}{\textwidth}{|l|X|}
558
+ \hline
559
+ \textbf{Situation} & \textbf{Action} \\ \hline
560
+ Severe hypoglycemia ($<$50, confusion) & Give glucagon injection if available, call 911 \\ \hline
561
+ Hyperglycemia $>$300 with symptoms & Drink water, check ketones if T1DM, call office \\ \hline
562
+ Chest pain or stroke symptoms & Call 911 immediately \\ \hline
563
+ Medication side effect & Stop medication, call office same day \\ \hline
564
+ Acute illness/vomiting & Sick day protocol, call office for guidance \\ \hline
565
+ \end{tabularx}
566
+
567
+ % ===== SECTION 11: PROVIDER SIGNATURE =====
568
+ \vspace{2em}
569
+
570
+ \section*{11. Provider Signature and Attestation}
571
+
572
+ I have reviewed this treatment plan with the patient. The patient demonstrates understanding of the diagnosis, treatment rationale, goals, interventions, self-management requirements, warning signs, and when to seek emergency care. The patient agrees to this treatment plan and has had the opportunity to ask questions. Shared decision-making was employed, and patient preferences were incorporated.
573
+
574
+ \vspace{1em}
575
+
576
+ \begin{tabular}{ll}
577
+ Provider Signature: & \rule{7cm}{0.5pt} \\[1em]
578
+ Provider Name/Credentials: & \rule{7cm}{0.5pt} \\[1em]
579
+ Date: & \rule{4cm}{0.5pt} \\[2em]
580
+ \end{tabular}
581
+
582
+ \subsection*{Patient Acknowledgment (Optional)}
583
+
584
+ I have reviewed this treatment plan with my healthcare provider. I understand my diagnosis, treatment goals, medications, lifestyle recommendations, self-monitoring requirements, and when to seek medical attention. I agree to follow this plan and contact my provider with questions or concerns.
585
+
586
+ \vspace{1em}
587
+
588
+ \begin{tabular}{ll}
589
+ Patient/Representative Signature: & \rule{7cm}{0.5pt} \\[1em]
590
+ Date: & \rule{4cm}{0.5pt} \\
591
+ \end{tabular}
592
+
593
+ \vspace{2em}
594
+ \begin{center}
595
+ \rule{\textwidth}{1pt}\\
596
+ \textbf{End of Treatment Plan}\\
597
+ This document contains confidential patient information protected by HIPAA.
598
+ \end{center}
599
+
600
+ \end{document}
601
+
602
+ % ========== NOTES FOR USERS ==========
603
+ %
604
+ % CUSTOMIZATION INSTRUCTIONS:
605
+ % 1. Replace all bracketed placeholders [like this] with patient-specific information
606
+ % 2. Remove or add sections as appropriate for the clinical condition
607
+ % 3. Ensure all SMART goals meet criteria (Specific, Measurable, Achievable, Relevant, Time-bound)
608
+ % 4. Include evidence-based interventions per current clinical guidelines
609
+ % 5. De-identify all protected health information before sharing
610
+ %
611
+ % COMPILATION:
612
+ % pdflatex general_medical_treatment_plan.tex
613
+ %
614
+ % VALIDATION:
615
+ % Run check_completeness.py and validate_treatment_plan.py before finalizing
616
+