@synsci/cli-darwin-x64 1.1.97 → 1.1.99

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1549) hide show
  1. package/bin/synsc +0 -0
  2. package/package.json +1 -1
  3. package/bin/skills/accelerate/SKILL.md +0 -332
  4. package/bin/skills/accelerate/references/custom-plugins.md +0 -453
  5. package/bin/skills/accelerate/references/megatron-integration.md +0 -489
  6. package/bin/skills/accelerate/references/performance.md +0 -525
  7. package/bin/skills/adaptyv/SKILL.md +0 -114
  8. package/bin/skills/adaptyv/reference/api_reference.md +0 -308
  9. package/bin/skills/adaptyv/reference/examples.md +0 -913
  10. package/bin/skills/adaptyv/reference/experiments.md +0 -360
  11. package/bin/skills/adaptyv/reference/protein_optimization.md +0 -637
  12. package/bin/skills/aeon/SKILL.md +0 -374
  13. package/bin/skills/aeon/references/anomaly_detection.md +0 -154
  14. package/bin/skills/aeon/references/classification.md +0 -144
  15. package/bin/skills/aeon/references/clustering.md +0 -123
  16. package/bin/skills/aeon/references/datasets_benchmarking.md +0 -387
  17. package/bin/skills/aeon/references/distances.md +0 -256
  18. package/bin/skills/aeon/references/forecasting.md +0 -140
  19. package/bin/skills/aeon/references/networks.md +0 -289
  20. package/bin/skills/aeon/references/regression.md +0 -118
  21. package/bin/skills/aeon/references/segmentation.md +0 -163
  22. package/bin/skills/aeon/references/similarity_search.md +0 -187
  23. package/bin/skills/aeon/references/transformations.md +0 -246
  24. package/bin/skills/alphafold-database/SKILL.md +0 -513
  25. package/bin/skills/alphafold-database/references/api_reference.md +0 -423
  26. package/bin/skills/anndata/SKILL.md +0 -400
  27. package/bin/skills/anndata/references/best_practices.md +0 -525
  28. package/bin/skills/anndata/references/concatenation.md +0 -396
  29. package/bin/skills/anndata/references/data_structure.md +0 -314
  30. package/bin/skills/anndata/references/io_operations.md +0 -404
  31. package/bin/skills/anndata/references/manipulation.md +0 -516
  32. package/bin/skills/arboreto/SKILL.md +0 -243
  33. package/bin/skills/arboreto/references/algorithms.md +0 -138
  34. package/bin/skills/arboreto/references/basic_inference.md +0 -151
  35. package/bin/skills/arboreto/references/distributed_computing.md +0 -242
  36. package/bin/skills/arboreto/scripts/basic_grn_inference.py +0 -97
  37. package/bin/skills/astropy/SKILL.md +0 -331
  38. package/bin/skills/astropy/references/coordinates.md +0 -273
  39. package/bin/skills/astropy/references/cosmology.md +0 -307
  40. package/bin/skills/astropy/references/fits.md +0 -396
  41. package/bin/skills/astropy/references/tables.md +0 -489
  42. package/bin/skills/astropy/references/time.md +0 -404
  43. package/bin/skills/astropy/references/units.md +0 -178
  44. package/bin/skills/astropy/references/wcs_and_other_modules.md +0 -373
  45. package/bin/skills/audiocraft/SKILL.md +0 -564
  46. package/bin/skills/audiocraft/references/advanced-usage.md +0 -666
  47. package/bin/skills/audiocraft/references/troubleshooting.md +0 -504
  48. package/bin/skills/autogpt/SKILL.md +0 -403
  49. package/bin/skills/autogpt/references/advanced-usage.md +0 -535
  50. package/bin/skills/autogpt/references/troubleshooting.md +0 -420
  51. package/bin/skills/awq/SKILL.md +0 -310
  52. package/bin/skills/awq/references/advanced-usage.md +0 -324
  53. package/bin/skills/awq/references/troubleshooting.md +0 -344
  54. package/bin/skills/axolotl/SKILL.md +0 -158
  55. package/bin/skills/axolotl/references/api.md +0 -5548
  56. package/bin/skills/axolotl/references/dataset-formats.md +0 -1029
  57. package/bin/skills/axolotl/references/index.md +0 -15
  58. package/bin/skills/axolotl/references/other.md +0 -3563
  59. package/bin/skills/benchling-integration/SKILL.md +0 -480
  60. package/bin/skills/benchling-integration/references/api_endpoints.md +0 -883
  61. package/bin/skills/benchling-integration/references/authentication.md +0 -379
  62. package/bin/skills/benchling-integration/references/sdk_reference.md +0 -774
  63. package/bin/skills/bigcode-evaluation-harness/SKILL.md +0 -405
  64. package/bin/skills/bigcode-evaluation-harness/references/benchmarks.md +0 -393
  65. package/bin/skills/bigcode-evaluation-harness/references/custom-tasks.md +0 -424
  66. package/bin/skills/bigcode-evaluation-harness/references/issues.md +0 -394
  67. package/bin/skills/biopython/SKILL.md +0 -443
  68. package/bin/skills/biopython/references/advanced.md +0 -577
  69. package/bin/skills/biopython/references/alignment.md +0 -362
  70. package/bin/skills/biopython/references/blast.md +0 -455
  71. package/bin/skills/biopython/references/databases.md +0 -484
  72. package/bin/skills/biopython/references/phylogenetics.md +0 -566
  73. package/bin/skills/biopython/references/sequence_io.md +0 -285
  74. package/bin/skills/biopython/references/structure.md +0 -564
  75. package/bin/skills/biorxiv-database/SKILL.md +0 -483
  76. package/bin/skills/biorxiv-database/references/api_reference.md +0 -280
  77. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +0 -445
  78. package/bin/skills/bioservices/SKILL.md +0 -361
  79. package/bin/skills/bioservices/references/identifier_mapping.md +0 -685
  80. package/bin/skills/bioservices/references/services_reference.md +0 -636
  81. package/bin/skills/bioservices/references/workflow_patterns.md +0 -811
  82. package/bin/skills/bioservices/scripts/batch_id_converter.py +0 -347
  83. package/bin/skills/bioservices/scripts/compound_cross_reference.py +0 -378
  84. package/bin/skills/bioservices/scripts/pathway_analysis.py +0 -309
  85. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +0 -408
  86. package/bin/skills/bitsandbytes/SKILL.md +0 -411
  87. package/bin/skills/bitsandbytes/references/memory-optimization.md +0 -521
  88. package/bin/skills/bitsandbytes/references/qlora-training.md +0 -521
  89. package/bin/skills/bitsandbytes/references/quantization-formats.md +0 -447
  90. package/bin/skills/blip-2/SKILL.md +0 -564
  91. package/bin/skills/blip-2/references/advanced-usage.md +0 -680
  92. package/bin/skills/blip-2/references/troubleshooting.md +0 -526
  93. package/bin/skills/brenda-database/SKILL.md +0 -719
  94. package/bin/skills/brenda-database/references/api_reference.md +0 -537
  95. package/bin/skills/brenda-database/scripts/brenda_queries.py +0 -844
  96. package/bin/skills/brenda-database/scripts/brenda_visualization.py +0 -772
  97. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +0 -1053
  98. package/bin/skills/cellxgene-census/SKILL.md +0 -511
  99. package/bin/skills/cellxgene-census/references/census_schema.md +0 -182
  100. package/bin/skills/cellxgene-census/references/common_patterns.md +0 -351
  101. package/bin/skills/chembl-database/SKILL.md +0 -389
  102. package/bin/skills/chembl-database/references/api_reference.md +0 -272
  103. package/bin/skills/chembl-database/scripts/example_queries.py +0 -278
  104. package/bin/skills/chroma/SKILL.md +0 -406
  105. package/bin/skills/chroma/references/integration.md +0 -38
  106. package/bin/skills/cirq/SKILL.md +0 -346
  107. package/bin/skills/cirq/references/building.md +0 -307
  108. package/bin/skills/cirq/references/experiments.md +0 -572
  109. package/bin/skills/cirq/references/hardware.md +0 -515
  110. package/bin/skills/cirq/references/noise.md +0 -515
  111. package/bin/skills/cirq/references/simulation.md +0 -350
  112. package/bin/skills/cirq/references/transformation.md +0 -416
  113. package/bin/skills/citation-management/SKILL.md +0 -1109
  114. package/bin/skills/citation-management/assets/bibtex_template.bib +0 -264
  115. package/bin/skills/citation-management/assets/citation_checklist.md +0 -386
  116. package/bin/skills/citation-management/references/bibtex_formatting.md +0 -908
  117. package/bin/skills/citation-management/references/citation_validation.md +0 -794
  118. package/bin/skills/citation-management/references/google_scholar_search.md +0 -725
  119. package/bin/skills/citation-management/references/metadata_extraction.md +0 -870
  120. package/bin/skills/citation-management/references/pubmed_search.md +0 -839
  121. package/bin/skills/citation-management/scripts/doi_to_bibtex.py +0 -182
  122. package/bin/skills/citation-management/scripts/extract_metadata.py +0 -570
  123. package/bin/skills/citation-management/scripts/format_bibtex.py +0 -349
  124. package/bin/skills/citation-management/scripts/search_google_scholar.py +0 -251
  125. package/bin/skills/citation-management/scripts/search_pubmed.py +0 -348
  126. package/bin/skills/citation-management/scripts/validate_citations.py +0 -494
  127. package/bin/skills/clinical-decision-support/README.md +0 -129
  128. package/bin/skills/clinical-decision-support/SKILL.md +0 -506
  129. package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +0 -380
  130. package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +0 -222
  131. package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +0 -359
  132. package/bin/skills/clinical-decision-support/assets/color_schemes.tex +0 -149
  133. package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +0 -208
  134. package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +0 -328
  135. package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +0 -529
  136. package/bin/skills/clinical-decision-support/references/biomarker_classification.md +0 -719
  137. package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +0 -604
  138. package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +0 -840
  139. package/bin/skills/clinical-decision-support/references/outcome_analysis.md +0 -640
  140. package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +0 -427
  141. package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +0 -521
  142. package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +0 -383
  143. package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +0 -417
  144. package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +0 -509
  145. package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +0 -441
  146. package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +0 -326
  147. package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +0 -641
  148. package/bin/skills/clinical-reports/README.md +0 -236
  149. package/bin/skills/clinical-reports/SKILL.md +0 -1127
  150. package/bin/skills/clinical-reports/assets/case_report_template.md +0 -352
  151. package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +0 -353
  152. package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +0 -359
  153. package/bin/skills/clinical-reports/assets/consult_note_template.md +0 -305
  154. package/bin/skills/clinical-reports/assets/discharge_summary_template.md +0 -453
  155. package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +0 -395
  156. package/bin/skills/clinical-reports/assets/history_physical_template.md +0 -305
  157. package/bin/skills/clinical-reports/assets/lab_report_template.md +0 -309
  158. package/bin/skills/clinical-reports/assets/pathology_report_template.md +0 -249
  159. package/bin/skills/clinical-reports/assets/quality_checklist.md +0 -338
  160. package/bin/skills/clinical-reports/assets/radiology_report_template.md +0 -318
  161. package/bin/skills/clinical-reports/assets/soap_note_template.md +0 -253
  162. package/bin/skills/clinical-reports/references/case_report_guidelines.md +0 -570
  163. package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +0 -693
  164. package/bin/skills/clinical-reports/references/data_presentation.md +0 -530
  165. package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -629
  166. package/bin/skills/clinical-reports/references/medical_terminology.md +0 -588
  167. package/bin/skills/clinical-reports/references/patient_documentation.md +0 -744
  168. package/bin/skills/clinical-reports/references/peer_review_standards.md +0 -585
  169. package/bin/skills/clinical-reports/references/regulatory_compliance.md +0 -577
  170. package/bin/skills/clinical-reports/scripts/check_deidentification.py +0 -332
  171. package/bin/skills/clinical-reports/scripts/compliance_checker.py +0 -78
  172. package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +0 -97
  173. package/bin/skills/clinical-reports/scripts/format_adverse_events.py +0 -97
  174. package/bin/skills/clinical-reports/scripts/generate_report_template.py +0 -149
  175. package/bin/skills/clinical-reports/scripts/terminology_validator.py +0 -126
  176. package/bin/skills/clinical-reports/scripts/validate_case_report.py +0 -323
  177. package/bin/skills/clinical-reports/scripts/validate_trial_report.py +0 -88
  178. package/bin/skills/clinicaltrials-database/SKILL.md +0 -507
  179. package/bin/skills/clinicaltrials-database/references/api_reference.md +0 -358
  180. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +0 -215
  181. package/bin/skills/clinpgx-database/SKILL.md +0 -638
  182. package/bin/skills/clinpgx-database/references/api_reference.md +0 -757
  183. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +0 -518
  184. package/bin/skills/clinvar-database/SKILL.md +0 -362
  185. package/bin/skills/clinvar-database/references/api_reference.md +0 -227
  186. package/bin/skills/clinvar-database/references/clinical_significance.md +0 -218
  187. package/bin/skills/clinvar-database/references/data_formats.md +0 -358
  188. package/bin/skills/clip/SKILL.md +0 -253
  189. package/bin/skills/clip/references/applications.md +0 -207
  190. package/bin/skills/cobrapy/SKILL.md +0 -463
  191. package/bin/skills/cobrapy/references/api_quick_reference.md +0 -655
  192. package/bin/skills/cobrapy/references/workflows.md +0 -593
  193. package/bin/skills/colab-finetuning/SKILL.md +0 -153
  194. package/bin/skills/colab-finetuning/references/bridge-setup.md +0 -68
  195. package/bin/skills/colab-finetuning/references/gpu-tiers.md +0 -54
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  197. package/bin/skills/constitutional-ai/SKILL.md +0 -290
  198. package/bin/skills/cosmic-database/SKILL.md +0 -336
  199. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +0 -220
  200. package/bin/skills/cosmic-database/scripts/download_cosmic.py +0 -231
  201. package/bin/skills/crewai/SKILL.md +0 -498
  202. package/bin/skills/crewai/references/flows.md +0 -438
  203. package/bin/skills/crewai/references/tools.md +0 -429
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  205. package/bin/skills/dask/SKILL.md +0 -456
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  209. package/bin/skills/dask/references/dataframes.md +0 -368
  210. package/bin/skills/dask/references/futures.md +0 -541
  211. package/bin/skills/dask/references/schedulers.md +0 -504
  212. package/bin/skills/datacommons-client/SKILL.md +0 -255
  213. package/bin/skills/datacommons-client/references/getting_started.md +0 -417
  214. package/bin/skills/datacommons-client/references/node.md +0 -250
  215. package/bin/skills/datacommons-client/references/observation.md +0 -185
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  217. package/bin/skills/datamol/SKILL.md +0 -706
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  224. package/bin/skills/deepchem/SKILL.md +0 -597
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  227. package/bin/skills/deepchem/scripts/graph_neural_network.py +0 -338
  228. package/bin/skills/deepchem/scripts/predict_solubility.py +0 -224
  229. package/bin/skills/deepchem/scripts/transfer_learning.py +0 -375
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- # Specialty-Specific Treatment Plan Guidelines
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-
3
- ## Overview
4
-
5
- This reference provides detailed guidelines for developing treatment plans specific to each of the six template types: general medical, rehabilitation, mental health, chronic disease management, perioperative, and pain management. Each section includes specialty-specific considerations, clinical pearls, and best practices.
6
-
7
- ## Concise Documentation Examples by Specialty
8
-
9
- ### Foundation Medicine Model: Concise vs. Verbose
10
-
11
- **PRINCIPLE**: Focus on actionable information; eliminate redundancy; use bullet points and short paragraphs.
12
-
13
- ### General Medical - Diabetes Example
14
-
15
- **VERBOSE (Avoid)**:
16
- > "Patient education was provided on the pathophysiology of Type 2 Diabetes Mellitus, including detailed explanation of insulin resistance, pancreatic beta-cell dysfunction, and the progressive nature of the disease. The patient was educated about the various potential complications of diabetes including microvascular complications such as diabetic retinopathy which can lead to blindness, diabetic nephropathy which can progress to end-stage renal disease requiring dialysis, and diabetic neuropathy which can cause pain and sensory loss. Additionally, macrovascular complications were discussed including increased risk of myocardial infarction, stroke, and peripheral arterial disease."
17
-
18
- **CONCISE (Preferred - 75% shorter)**:
19
- > "Key Education: Disease understanding, micro/macrovascular complication risks, self-monitoring techniques (glucose, BP), medication timing, diet basics, exercise safety, sick day management. Critical warnings: Hypoglycemia (shakiness, confusion - treat with 15g carbs), severe hyperglycemia >300 (call office), chest pain/stroke symptoms (911)."
20
-
21
- ### Mental Health - Depression Example
22
-
23
- **VERBOSE (Avoid)**:
24
- > "The patient will participate in individual psychotherapy sessions utilizing Cognitive Behavioral Therapy techniques. Sessions will be scheduled on a weekly basis for a duration of 50 minutes each. The therapist will work with the patient to identify negative thought patterns, challenge cognitive distortions, develop behavioral activation strategies, and build coping skills for managing depressive symptoms."
25
-
26
- **CONCISE (Preferred - 60% shorter)**:
27
- > "CBT weekly × 16 sessions (50 min) focusing on: identifying/challenging negative thoughts, behavioral activation, coping skills development. Goals: PHQ-9 <10, return to work, 3 effective stress management strategies."
28
-
29
- ### Rehabilitation - Post-Stroke Example
30
-
31
- **VERBOSE (Avoid)**:
32
- > "Expected outcomes include improvement in upper extremity function with anticipated achievement of the ability to perform self-care activities including bathing, dressing, and grooming with minimal assistance or independently. The patient is expected to demonstrate improved ambulation capabilities with progression from wheelchair mobility to ambulation with a rolling walker under supervision, with eventual goal of independent ambulation with a straight cane for distances up to 300 feet."
33
-
34
- **CONCISE (Preferred - 70% shorter)**:
35
- > "Expected outcomes (8 weeks): Independent ADLs with adaptive equipment, ambulation 300+ feet with walker/supervision, stair negotiation with handrail, safe home discharge. Timeline: Week 2 - transfers with supervision; Week 4 - ambulate 150 feet; Week 8 - community ambulation, discharge ready."
36
-
37
- ### Perioperative - Laparoscopic Surgery Example
38
-
39
- **VERBOSE (Avoid)**:
40
- > "Postoperative pain management will utilize a multimodal approach to analgesia in order to minimize opioid consumption and reduce the risk of opioid-related adverse effects including nausea, vomiting, constipation, and respiratory depression. The multimodal regimen will include scheduled acetaminophen administered at a dose of 1000 milligrams every 6 hours, ibuprofen 600 milligrams every 6 hours as needed, and opioid analgesics reserved for breakthrough pain only."
41
-
42
- **CONCISE (Preferred - 65% shorter)**:
43
- > "Multimodal analgesia: Acetaminophen 1000mg Q6H scheduled, ibuprofen 600mg Q6H PRN, opioids for breakthrough only. Goal: Pain <4/10, minimize opioid use, early mobilization."
44
-
45
- ### Key Principles for Concise Documentation
46
-
47
- 1. **Use abbreviations appropriately**: Q6H, PRN, ADLs, BP (define on first use if uncommon)
48
- 2. **Bullet points over paragraphs**: Easier to scan, more actionable
49
- 3. **Combine related information**: Group similar items together
50
- 4. **Eliminate filler words**: "The patient will...", "It is anticipated that..."
51
- 5. **Focus on "what, when, why"**: Action, timing, rationale in minimal words
52
- 6. **Use tables for complex data**: Medication lists, monitoring schedules
53
- 7. **Prioritize critical information**: Safety warnings, emergency actions
54
-
55
- ## 1. General Medical Treatment Plans
56
-
57
- ### Applicable Conditions
58
- - Chronic diseases: Diabetes, hypertension, heart failure, COPD, asthma
59
- - Common acute conditions requiring structured follow-up
60
- - Primary care management of stable chronic conditions
61
-
62
- ### Key Assessment Components
63
-
64
- **Baseline Status**:
65
- - Vital signs, BMI, functional status
66
- - Disease-specific metrics (HbA1c, BP, lipids, PFTs)
67
- - Comorbidity assessment
68
- - Medication reconciliation
69
- - Social determinants of health screening
70
-
71
- **Disease Severity Staging**:
72
- - Use validated staging systems when available
73
- - Examples: CKD stages 1-5, GOLD COPD stages I-IV, NYHA heart failure classes I-IV, ADA diabetes complications
74
- - Document severity to guide treatment intensity
75
-
76
- ### Treatment Goal Specifics
77
-
78
- **Guideline-Based Targets**:
79
- - HbA1c <7% for most diabetics (<8% if elderly, limited life expectancy)
80
- - BP <130/80 for most; <140/90 if elderly or low cardiovascular risk
81
- - LDL <70 mg/dL if ASCVD, <100 mg/dL moderate risk
82
- - Use individualized targets based on patient factors
83
-
84
- **Functional Goals**:
85
- - Maintain independence in ADLs
86
- - Return to work if applicable
87
- - Engage in valued activities
88
- - Quality of life improvement
89
-
90
- ### Pharmacotherapy Considerations
91
-
92
- **Polypharmacy Management**:
93
- - Consider deprescribing when possible (Beers Criteria for elderly)
94
- - Medication reconciliation at each visit
95
- - Simplify regimens (once-daily dosing, combination pills)
96
- - Address adherence barriers (cost, side effects, complexity)
97
-
98
- **Drug-Disease Interactions**:
99
- - Avoid NSAIDs if CKD, heart failure
100
- - Caution with metformin if eGFR <30
101
- - Beta-blockers contraindicated in severe COPD/asthma (use cardioselective if needed)
102
-
103
- ### Monitoring Schedules by Condition
104
-
105
- **Diabetes**:
106
- - HbA1c every 3 months if not at goal, every 6 months if stable
107
- - Annual: dilated eye exam, foot exam, urine ACR, lipids
108
- - Each visit: BP, weight, medication adherence
109
-
110
- **Hypertension**:
111
- - Home BP monitoring (HBPM) - most accurate, average of multiple readings
112
- - Office BP at each visit
113
- - Labs (BMP for K+, creatinine) 1-2 weeks after ACE/ARB initiation, then annually
114
-
115
- **Heart Failure**:
116
- - Daily weights (report gain >2-3 lbs in 2 days)
117
- - BNP/NT-proBNP when clinically changing
118
- - Echo annually or if EF change suspected
119
- - Medication titration every 2 weeks during optimization phase
120
-
121
- ### Primary Care Integration
122
-
123
- **Preventive Care**:
124
- - Include age-appropriate cancer screenings
125
- - Vaccination schedule (flu, pneumococcal, zoster, COVID)
126
- - Lifestyle counseling (tobacco, alcohol, diet, exercise)
127
-
128
- **Chronic Disease Management Models**:
129
- - Chronic Care Model components: Self-management support, delivery system redesign, clinical information systems, decision support
130
- - Team-based care: Involvement of nurses, pharmacists, dietitians, care coordinators
131
-
132
- ---
133
-
134
- ## 2. Rehabilitation Treatment Plans
135
-
136
- ### Applicable Settings
137
- - Post-acute inpatient rehabilitation
138
- - Outpatient PT/OT/SLP
139
- - Home health therapy
140
- - Skilled nursing facility rehabilitation
141
-
142
- ### Key Assessment Components
143
-
144
- **Functional Assessments (use validated tools)**:
145
- - **FIM** (Functional Independence Measure): 18 items, 7-point scale, 126 total - most widely used
146
- - **Barthel Index**: 10 ADLs, 100-point scale - simpler than FIM
147
- - **Berg Balance Scale**: 14 tasks, 56 points - fall risk (score <45 = high risk)
148
- - **6-Minute Walk Test**: Distance walked in 6 minutes - cardiopulmonary endurance
149
- - **Timed Up and Go (TUG)**: Time to stand, walk 3 meters, turn, return, sit - fall risk (>12 sec = high risk)
150
- - **9-Hole Peg Test**: Upper extremity fine motor speed
151
- - **ROM**: Goniometric measurement for each joint
152
- - **Manual Muscle Testing**: 0-5 scale (0=no contraction, 5=normal strength)
153
-
154
- **ICF Framework Goals**:
155
- - **Body Functions/Structures**: Impairments (ROM, strength, balance)
156
- - **Activity**: Task performance (walk 150 feet, dress independently)
157
- - **Participation**: Life roles (return to work, community engagement)
158
-
159
- ### Rehabilitation Goals Specifics
160
-
161
- **Goal Levels**:
162
- 1. **Impairment Goals**: Increase knee ROM 90→110°, improve MMT 3/5→4/5
163
- 2. **Activity Goals**: Ambulate 300 feet with walker, transfer bed-chair independently
164
- 3. **Participation Goals**: Return to work, resume hobbies, live independently
165
-
166
- **Assistance Levels** (document current and goal):
167
- - I = Independent
168
- - SV = Supervision (cues, no physical assist)
169
- - CG = Contact Guard (hands close, no assist)
170
- - Min A = Minimal Assist (patient does 75%+)
171
- - Mod A = Moderate Assist (patient does 50-74%)
172
- - Max A = Maximal Assist (patient does 25-49%)
173
- - Total A = Total Assist (patient does <25%)
174
-
175
- ### Therapy Interventions
176
-
177
- **Physical Therapy**:
178
- - Therapeutic exercise dose: Specify sets, reps, resistance, frequency
179
- - Gait training: Distance, assistive device, supervision level
180
- - Balance training: Static, dynamic, perturbation-based
181
- - Modalities: Heat, ice, TENS, E-stim - adjuncts only, not primary intervention
182
-
183
- **Occupational Therapy**:
184
- - ADL training: Use of adaptive equipment (reacher, sock aid, built-up utensils)
185
- - Upper extremity strengthening: Functional tasks, fine motor activities
186
- - Cognitive retraining: Memory strategies, attention training, executive function
187
-
188
- **Speech-Language Pathology**:
189
- - Dysphagia: Diet texture modifications (IDDSI levels), swallow strategies (chin tuck, multiple swallows)
190
- - Aphasia therapy: Constraint-induced language therapy, semantic feature analysis
191
- - Dysarthria: Articulation drills, rate control, augmentative communication
192
-
193
- ### Home Exercise Program (HEP)
194
-
195
- **Essentials**:
196
- - Illustrated handout with pictures/descriptions
197
- - Specific dosage (e.g., "2 sets x 10 reps, daily")
198
- - Progression criteria
199
- - Safety precautions
200
- - Patient/caregiver demonstrates understanding
201
-
202
- ### DME and Environmental Modifications
203
-
204
- **Common DME**:
205
- - Ambulation: Walker, cane, crutches (specify type, e.g., front-wheeled walker)
206
- - Bathroom: Raised toilet seat, shower chair, grab bars
207
- - Dressing: Reacher, sock aid, long shoe horn, button hook, elastic laces
208
- - Mobility: Hospital bed, wheelchair (if needed)
209
-
210
- **Home Modifications**:
211
- - Ramp for stairs
212
- - Stair lift if multiple levels
213
- - Remove scatter rugs (fall hazard)
214
- - Improve lighting
215
- - Rearrange for accessibility
216
-
217
- ### Discharge Planning
218
-
219
- **Discharge Criteria**:
220
- - Functional plateau reached or goals met
221
- - Safe for discharge setting
222
- - Patient/caregiver educated
223
- - DME obtained and home modifications complete
224
- - Follow-up arranged
225
-
226
- **Discharge Destination**:
227
- - Home with outpatient therapy
228
- - Home with home health
229
- - Skilled nursing facility
230
- - Long-term acute care hospital (if medically complex)
231
-
232
- ---
233
-
234
- ## 3. Mental Health Treatment Plans
235
-
236
- ### Applicable Conditions
237
- - Major depressive disorder, dysthymia
238
- - Anxiety disorders (GAD, panic, social anxiety, specific phobias)
239
- - Bipolar disorder
240
- - Schizophrenia and psychotic disorders
241
- - PTSD and trauma-related disorders
242
- - Eating disorders
243
- - Substance use disorders
244
- - Personality disorders
245
-
246
- ### Key Assessment Components
247
-
248
- **Diagnostic Assessment**:
249
- - Meet DSM-5 criteria for diagnosis
250
- - Symptom severity assessment (use validated scales)
251
- - Functional impairment (work, relationships, self-care)
252
- - Psychiatric history (prior episodes, treatments, hospitalizations)
253
- - Substance use assessment (AUDIT, DAST)
254
- - Trauma history
255
- - Family psychiatric history
256
-
257
- **Validated Assessment Tools**:
258
- - **PHQ-9**: Depression severity (0-27, scores ≥10 indicate moderate-severe depression)
259
- - **GAD-7**: Anxiety severity (0-21, scores ≥10 indicate moderate-severe anxiety)
260
- - **MDQ** (Mood Disorder Questionnaire): Bipolar screening
261
- - **PC-PTSD-5**: PTSD screening, then full PCL-5 if positive
262
- - **AUDIT**: Alcohol use (0-40, ≥8 indicates hazardous drinking)
263
- - **PHQ-15**: Somatic symptoms
264
- - **WHODAS 2.0**: Functional disability
265
-
266
- **Risk Assessment**:
267
- - **Suicide Risk**: Use Columbia Suicide Severity Rating Scale (C-SSRS)
268
- - Ideation (passive, active, plan, intent)
269
- - Protective factors (reasons for living, social support)
270
- - Risk factors (prior attempts, impulsivity, access to means)
271
- - **Violence/Homicide Risk**: History of violence, current ideation, access to weapons
272
-
273
- ### Treatment Goals Specifics
274
-
275
- **Symptom Goals**:
276
- - Reduction in standardized scale scores (e.g., PHQ-9 from 18→<10→<5 for remission)
277
- - Specific symptom targets (sleep 7 hours, reduce panic attacks from 3/week→0)
278
-
279
- **Functional Goals**:
280
- - Return to work/school
281
- - Resume social activities
282
- - Improve relationships
283
- - Self-care independence
284
-
285
- **Recovery-Oriented Goals**:
286
- - Personal meaning and purpose
287
- - Hope and empowerment
288
- - Social connections and community integration
289
- - Independent living
290
-
291
- ### Evidence-Based Psychotherapies
292
-
293
- **Depression**:
294
- - **CBT**: 12-16 sessions, homework between sessions
295
- - **Behavioral Activation**: Focus on increasing rewarding activities
296
- - **Interpersonal Therapy (IPT)**: 12-16 sessions, focus on relationships
297
- - **Problem-Solving Therapy**: Brief (6-8 sessions), structured approach
298
-
299
- **Anxiety**:
300
- - **CBT with exposure**: Gold standard for anxiety disorders
301
- - **Panic Control Therapy**: Interoceptive exposure, cognitive restructuring
302
- - **Social skills training**: For social anxiety
303
-
304
- **PTSD**:
305
- - **Prolonged Exposure (PE)**: 8-15 sessions, imaginal and in vivo exposure
306
- - **Cognitive Processing Therapy (CPT)**: 12 sessions, challenge trauma-related cognitions
307
- - **EMDR** (Eye Movement Desensitization and Reprocessing): Alternative, less evidence than PE/CPT
308
-
309
- **Bipolar**:
310
- - **Family-Focused Therapy**: Psychoeducation, communication, problem-solving
311
- - **Interpersonal and Social Rhythm Therapy**: Stabilize daily routines, sleep
312
-
313
- **Borderline Personality Disorder**:
314
- - **DBT** (Dialectical Behavior Therapy): 1 year program, individual + group + phone coaching
315
- - Skills: Mindfulness, distress tolerance, emotion regulation, interpersonal effectiveness
316
-
317
- ### Psychopharmacology Specifics
318
-
319
- **Antidepressants**:
320
- - First-line: SSRIs (sertraline, escitalopram, fluoxetine)
321
- - 2-4 weeks for initial response, 6-8 weeks for full effect
322
- - Titrate after 2-4 weeks if partial response
323
- - Switch if no response after full trial
324
- - Augmentation strategies if partial response (second antidepressant, atypical antipsychotic, lithium)
325
- - Continue 6-12 months after remission (longer if recurrent)
326
-
327
- **Antipsychotics**:
328
- - First-generation (typical): Haloperidol - high EPS risk, use second-generation preferred
329
- - Second-generation (atypical): Risperidone, olanzapine, quetiapine, aripiprazole, lurasidone
330
- - Monitoring: Metabolic syndrome (weight, glucose, lipids), EPS, prolactin, QTc
331
-
332
- **Mood Stabilizers**:
333
- - Lithium: Narrow therapeutic window, monitor levels (0.6-1.2 mEq/L), TSH, renal function
334
- - Valproic acid: Monitor levels, LFTs, CBC (thrombocytopenia)
335
- - Lamotrigine: Titrate slowly (risk of Stevens-Johnson syndrome if too fast)
336
-
337
- ### Safety Planning
338
-
339
- **Essential for All Mental Health Plans**:
340
- - Warning signs (thoughts, feelings, behaviors)
341
- - Internal coping strategies
342
- - Social support contacts
343
- - Professional contacts (therapist, psychiatrist, crisis line)
344
- - Means restriction (firearms removed, medications limited)
345
- - Reason for living
346
-
347
- **Crisis Resources**:
348
- - 988 Suicide & Crisis Lifeline
349
- - Crisis Text Line (text HOME to 741741)
350
- - Local mobile crisis team
351
- - Emergency department
352
-
353
- ---
354
-
355
- ## 4. Chronic Disease Management Plans
356
-
357
- ### Multiple Comorbidities Management
358
-
359
- **Common Clusters**:
360
- - Cardiometabolic: Diabetes + hypertension + hyperlipidemia + obesity
361
- - Cardiopulmonary: Heart failure + COPD
362
- - Renal-cardiovascular: CKD + hypertension + diabetes
363
- - Mental-physical: Depression + chronic pain + chronic disease
364
-
365
- ### Prioritization Strategies
366
-
367
- **When Multiple Goals Compete**:
368
- 1. **Life-threatening issues first**: Unstable angina, uncontrolled heart failure
369
- 2. **High-impact, modifiable conditions**: Diabetes with HbA1c 10% (significant reduction possible)
370
- 3. **Synergistic treatments**: Medications that help multiple conditions (SGLT2i for diabetes + heart failure + CKD)
371
- 4. **Patient priorities**: What matters most to patient
372
-
373
- ### Medication Optimization for Multimorbidity
374
-
375
- **Synergistic Medications** (dual/triple benefit):
376
- - **SGLT2 inhibitors**: Diabetes + heart failure + CKD
377
- - **ACE inhibitors/ARBs**: Hypertension + diabetes (renal protection) + heart failure
378
- - **Beta-blockers**: Hypertension + heart failure + CAD
379
- - **Statins**: Hyperlipidemia + ASCVD prevention + diabetes
380
- - **GLP-1 agonists**: Diabetes + weight loss + cardiovascular benefit
381
-
382
- **Deprescribing**:
383
- - Identify medications with limited benefit (e.g., strict glycemic control in limited life expectancy)
384
- - Discontinue medications with more harm than benefit
385
- - Simplify regimens (reduce pill burden)
386
-
387
- ### Care Coordination
388
-
389
- **Team-Based Care**:
390
- - Primary care coordinates
391
- - Specialists co-manage (cardiologist for HF, endocrinologist for diabetes)
392
- - Care coordinator facilitates (schedules, education, barrier identification)
393
- - Pharmacist reviews medications, optimizes therapy
394
- - Dietitian provides medical nutrition therapy
395
- - Social worker addresses social needs
396
-
397
- **Communication**:
398
- - Shared EHR when possible
399
- - Care plan accessible to all team members
400
- - Medication reconciliation after specialist visits
401
- - Regular team meetings or e-consultations
402
-
403
- ### Population Health Integration
404
-
405
- **Registry Management**:
406
- - Identify patients due for care (HbA1c testing, diabetic eye exam)
407
- - Outreach for overdue preventive care
408
- - Risk stratification (high-utilizers, complex patients)
409
-
410
- **Transition Management**:
411
- - Hospital discharge follow-up within 7 days
412
- - Medication reconciliation post-discharge
413
- - Red flags review
414
- - Escalation plan if decompensating
415
-
416
- ---
417
-
418
- ## 5. Perioperative Care Plans
419
-
420
- ### Preoperative Risk Assessment
421
-
422
- **Cardiac Risk** (Revised Cardiac Risk Index - RCRI):
423
- - High-risk surgery, ischemic heart disease, heart failure, CVD, diabetes on insulin, creatinine >2
424
- - 0 points = <1% risk, 1 point = 1%, 2 points = 2.4%, ≥3 points = 5.4% risk of cardiac event
425
-
426
- **If High Risk**: Consider further testing (stress test, echo), cardiology consultation, perioperative beta-blockade.
427
-
428
- **Pulmonary Risk** (ARISCAT score):
429
- - Age, SpO2, respiratory infection recent, preop anemia, surgical incision, duration, emergency
430
- - Higher risk: Smoking cessation, incentive spirometry, early mobilization
431
-
432
- **VTE Risk** (Caprini Score):
433
- - Age, surgery type, mobility, prior VTE, obesity, cancer
434
- - Stratify to guide prophylaxis (none, mechanical, pharmacologic, or both)
435
-
436
- ### Preoperative Optimization
437
-
438
- **Diabetes**:
439
- - Target HbA1c <8% for elective surgery (delay if >9%)
440
- - Hold metformin 24-48 hours before (risk of lactic acidosis)
441
- - Hold SGLT2i 3-4 days before (DKA risk)
442
- - Insulin: Reduce long-acting by 20-25% day of surgery, hold short-acting
443
-
444
- **Hypertension**:
445
- - Continue most medications through surgery
446
- - Hold ACE/ARB morning of surgery (avoid intraop hypotension)
447
- - Continue beta-blocker (avoid withdrawal)
448
-
449
- **Anticoagulation**:
450
- - Warfarin: Hold 5 days before, bridge with LMWH if high VTE risk
451
- - DOACs: Hold 24-48 hours (based on renal function and bleeding risk)
452
- - Antiplatelet: Continue aspirin for most surgeries, hold P2Y12 inhibitors (clopidogrel) 5-7 days if high bleeding risk
453
-
454
- **Anemia**:
455
- - Optimize iron stores preop (IV iron if time limited)
456
- - Avoid transfusion triggers if possible (restrictive strategy)
457
-
458
- ### Enhanced Recovery After Surgery (ERAS)
459
-
460
- **Preoperative**:
461
- - Patient education, expectation setting
462
- - No prolonged fasting (clear liquids 2 hours before)
463
- - Carbohydrate loading (reduces insulin resistance)
464
- - No routine premedication
465
-
466
- **Intraoperative**:
467
- - Multimodal analgesia (minimize opioids)
468
- - Goal-directed fluid therapy (avoid overhydration)
469
- - Normothermia (prevent hypothermia)
470
- - Antiemetic prophylaxis
471
-
472
- **Postoperative**:
473
- - Early mobilization (out of bed day of surgery)
474
- - Early oral nutrition (resume diet POD 0-1)
475
- - Multimodal analgesia (acetaminophen, NSAIDs, regional blocks)
476
- - Remove tubes/drains early (Foley, NG tube, surgical drains)
477
- - DVT prophylaxis
478
-
479
- ### Postoperative Milestones
480
-
481
- **Day of Surgery (POD 0)**:
482
- - Out of bed to chair 4-6 hours post-op
483
- - Sips of clear liquids if appropriate
484
- - Pain controlled on multimodal regimen
485
-
486
- **POD 1**:
487
- - Ambulate in hallway
488
- - Regular diet
489
- - Foley catheter removed
490
- - Transition to oral pain medications
491
-
492
- **POD 2-3** (typical discharge for many surgeries):
493
- - Ambulate 150+ feet
494
- - Adequate oral intake
495
- - Pain controlled on oral meds
496
- - No complications requiring hospitalization
497
-
498
- ### Discharge Readiness
499
-
500
- **Criteria**:
501
- - Adequate pain control on oral medications
502
- - Tolerating regular diet
503
- - Mobile (ambulate, transfers)
504
- - Voiding spontaneously
505
- - Stable vital signs
506
- - No active complications
507
- - Safe discharge plan (home support, DME arranged)
508
-
509
- ---
510
-
511
- ## 6. Pain Management Plans
512
-
513
- ### Pain Assessment
514
-
515
- **Comprehensive Pain Evaluation**:
516
- - Location, radiation
517
- - Quality (sharp, dull, burning, aching, shooting)
518
- - Intensity (0-10 NRS)
519
- - Temporal pattern (constant, intermittent, episodic)
520
- - Aggravating/alleviating factors
521
- - Functional impact (Brief Pain Inventory - BPI interference items)
522
- - Prior treatments and responses
523
-
524
- **Pain Classification**:
525
- - **Nociceptive**: Somatic (MSK) or visceral (organ)
526
- - **Neuropathic**: Nerve injury/dysfunction (burning, shooting, electric, numbness/tingling)
527
- - **Nociplastic**: Central sensitization, fibromyalgia
528
- - **Mixed**: Combination
529
-
530
- ### Multimodal Analgesia Principles
531
-
532
- **Goal**: Additive/synergistic pain relief from multiple mechanisms, opioid-sparing.
533
-
534
- **Components**:
535
- 1. Non-opioid analgesics (acetaminophen, NSAIDs)
536
- 2. Adjuvant analgesics (gabapentinoids, SNRIs, TCAs for neuropathic)
537
- 3. Topical agents (lidocaine patches, diclofenac gel, capsaicin)
538
- 4. Interventional procedures (injections, nerve blocks, RFA, SCS)
539
- 5. Physical therapies (PT, exercise, TENS)
540
- 6. Psychological therapies (CBT-CP, mindfulness, biofeedback)
541
- 7. Complementary therapies (acupuncture, massage, yoga)
542
- 8. Opioids (if other modalities insufficient) - lowest dose, reassess frequently
543
-
544
- ### Neuropathic Pain Specific Treatments
545
-
546
- **First-Line**:
547
- - Gabapentin 300mg titrate to 1800-3600mg/day divided TID
548
- - Pregabalin 75mg BID titrate to 150-300mg BID
549
- - Duloxetine 60mg daily (also for fibromyalgia, chronic MSK pain)
550
- - TCAs (amitriptyline, nortriptyline) 10-75mg QHS - second-line due to side effects
551
-
552
- **Topical**:
553
- - Lidocaine patches 5% (localized neuropathic pain)
554
- - Capsaicin 8% patch (high-concentration, applied by provider)
555
-
556
- **Refractory**:
557
- - Tramadol (dual mechanism - opioid + SNRI)
558
- - Opioids (if severe and function-limiting despite above)
559
-
560
- ### Opioid Prescribing (CDC Guidelines)
561
-
562
- **Before Initiating**:
563
- - Non-opioid multimodal therapies tried and inadequate
564
- - Functional goals established (not just pain scores)
565
- - Risks vs. benefits discussed and documented
566
- - Opioid risk assessment (ORT, SOAPP)
567
- - Informed consent discussion
568
- - Treatment agreement signed
569
- - PDMP checked
570
- - Baseline UDS
571
-
572
- **During Opioid Therapy**:
573
- - Start low dose (<50 MME/day), short-acting
574
- - Reassess frequently (every 1-3 months)
575
- - Functional improvement expected (not just pain scores)
576
- - UDS every 3-6 months (check for adherence and illicit substances)
577
- - PDMP check each prescription or at least every 3 months
578
- - Naloxone co-prescribed
579
- - Avoid concurrent benzodiazepines
580
- - If dose approaching 50 MME, reassess; avoid >90 MME if possible
581
-
582
- **Tapering**:
583
- - If not meeting functional goals
584
- - Serious adverse effects
585
- - Aberrant behaviors
586
- - Patient request
587
- - Slow taper: 10-25% dose reduction per week to month (faster if safety concern)
588
-
589
- ### Interventional Pain Procedures
590
-
591
- **Indications and Evidence**:
592
- - **Epidural Steroid Injection**: Radicular pain from disc herniation/stenosis - short-term benefit
593
- - **Facet Joint Injections**: Diagnostic (if >50% relief, proceed to RFA)
594
- - **Radiofrequency Ablation**: 6-12 months relief for facet-mediated pain
595
- - **Spinal Cord Stimulation**: Refractory neuropathic pain (FBSS, CRPS) - 50-60% success
596
- - **Intrathecal Pump**: Severe refractory pain, cancer pain - delivers medication to CSF
597
-
598
- **Documentation for Procedures**:
599
- - Indication, prior conservative treatments tried
600
- - Expected benefit and duration
601
- - Risks discussed
602
- - Number of injections/procedures allowed per year
603
-
604
- ### Functional Goals Emphasis
605
-
606
- **Shift from Pain Scores to Function**:
607
- - "Reduce pain to 3/10" is less meaningful than "Walk 1 mile, return to work, play with grandchildren"
608
- - BPI interference scores track functional impact
609
- - SMART functional goals (see Goal Setting reference)
610
-
611
- ### Psychological Integration
612
-
613
- **CBT for Chronic Pain (CBT-CP)**:
614
- - Pain education and reconceptualization (pain ≠ harm)
615
- - Cognitive restructuring (challenge catastrophizing, all-or-nothing thinking)
616
- - Activity pacing and graded exposure (increase activity without flares)
617
- - Relaxation techniques
618
- - Acceptance and mindfulness
619
-
620
- **Essential for Chronic Pain**: Psychological factors (depression, anxiety, catastrophizing) perpetuate pain; must be addressed.
621
-
622
- ---
623
-
624
- ## Cross-Cutting Considerations for All Treatment Plans
625
-
626
- ### Cultural Competence
627
- - Ask about cultural health beliefs, practices
628
- - Use interpreter services when language barriers exist
629
- - Respect religious/spiritual practices in treatment
630
- - Adapt interventions to cultural context when possible
631
-
632
- ### Health Literacy
633
- - Assess understanding (teach-back method)
634
- - Use plain language, avoid jargon
635
- - Visual aids, written materials at 5th-6th grade reading level
636
- - Confirm patient can execute plan (demonstrate inhaler use, insulin injection, etc.)
637
-
638
- ### Social Determinants of Health (SDOH)
639
- - Screen for food insecurity, housing instability, transportation barriers
640
- - Connect to community resources (SNAP, Medicaid, patient assistance programs)
641
- - Address barriers in treatment plan (e.g., medication cost → generic alternatives, patient assistance)
642
-
643
- ### Advance Care Planning
644
- - Appropriate for serious illness, elderly, declining function
645
- - Goals of care discussion
646
- - Healthcare proxy designation
647
- - Advance directive completion
648
- - Preferences for resuscitation, intubation, dialysis, etc.
649
-
650
- ---
651
-
652
- **Document Version**: 1.0
653
- **Last Updated**: January 2025
654
- **Next Review**: January 2026
655
-