@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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- # Clinical Decision Algorithms Guide
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-
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- ## Overview
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-
5
- Clinical decision algorithms provide systematic, step-by-step guidance for diagnosis, treatment selection, and patient management. This guide covers algorithm development, validation, and visual presentation using decision trees and flowcharts.
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-
7
- ## Algorithm Design Principles
8
-
9
- ### Key Components
10
-
11
- **Decision Nodes**
12
- - **Question/Criteria**: Clear, measurable clinical parameter
13
- - **Binary vs Multi-Way**: Yes/no (simple) vs multiple options (complex)
14
- - **Objective**: Lab value, imaging finding vs Subjective: Clinical judgment
15
-
16
- **Action Nodes**
17
- - **Treatment**: Specific intervention with dosing
18
- - **Test**: Additional diagnostic procedure
19
- - **Referral**: Specialist consultation, higher level of care
20
- - **Observation**: Watchful waiting with defined follow-up
21
-
22
- **Terminal Nodes**
23
- - **Outcome**: Final decision point
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- - **Follow-up**: Schedule for reassessment
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- - **Exit criteria**: When to exit algorithm
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-
27
- ### Design Criteria
28
-
29
- **Clarity**
30
- - Unambiguous decision points
31
- - Mutually exclusive pathways
32
- - No circular loops (unless intentional reassessment cycles)
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- - Clear entry and exit points
34
-
35
- **Clinical Validity**
36
- - Evidence-based decision criteria
37
- - Validated cut-points for biomarkers
38
- - Guideline-concordant recommendations
39
- - Expert consensus where evidence limited
40
-
41
- **Usability**
42
- - Maximum 7 decision points per pathway (cognitive load)
43
- - Visual hierarchy (most common path highlighted)
44
- - Printable single-page format preferred
45
- - Color coding for urgency/safety
46
-
47
- **Completeness**
48
- - All possible scenarios covered
49
- - Default pathway for edge cases
50
- - Safety-net provisions for unusual presentations
51
- - Escalation criteria clearly stated
52
-
53
- ## Clinical Decision Trees
54
-
55
- ### Diagnostic Algorithms
56
-
57
- **Chest Pain Evaluation Algorithm**
58
-
59
- ```
60
- Entry: Patient with chest pain
61
-
62
- ├─ STEMI Criteria? (ST elevation ≥1mm in ≥2 contiguous leads)
63
- │ ├─ YES → Activate cath lab, aspirin 325mg, heparin, clopidogrel 600mg
64
- │ │ Transfer for primary PCI (goal door-to-balloon <90 minutes)
65
- │ └─ NO → Continue evaluation
66
-
67
- ├─ High-Risk Features? (Hemodynamic instability, arrhythmia, troponin elevation)
68
- │ ├─ YES → Admit CCU, serial troponins, cardiology consultation
69
- │ │ Consider early angiography if NSTEMI
70
- │ └─ NO → Calculate TIMI or HEART score
71
-
72
- ├─ TIMI Score 0-1 or HEART Score 0-3? (Low risk)
73
- │ ├─ YES → Observe 6-12 hours, serial troponins, stress test if negative
74
- │ │ Discharge if all negative with cardiology follow-up in 72 hours
75
- │ └─ NO → TIMI 2-4 or HEART 4-6 (Intermediate risk)
76
-
77
- ├─ TIMI Score 2-4 or HEART Score 4-6? (Intermediate risk)
78
- │ ├─ YES → Admit telemetry, serial troponins, stress imaging vs CT angiography
79
- │ │ Medical management: Aspirin, statin, beta-blocker
80
- │ └─ NO → TIMI ≥5 or HEART ≥7 (High risk) → Treat as NSTEMI
81
-
82
- Decision Endpoint: Risk-stratified pathway with 30-day event rate documented
83
- ```
84
-
85
- **Pulmonary Embolism Diagnostic Algorithm (Wells Criteria)**
86
-
87
- ```
88
- Entry: Suspected PE
89
-
90
- Step 1: Calculate Wells Score
91
- Clinical features points:
92
- - Clinical signs of DVT: 3 points
93
- - PE more likely than alternative diagnosis: 3 points
94
- - Heart rate >100: 1.5 points
95
- - Immobilization/surgery in past 4 weeks: 1.5 points
96
- - Previous PE/DVT: 1.5 points
97
- - Hemoptysis: 1 point
98
- - Malignancy: 1 point
99
-
100
- Step 2: Risk Stratify
101
- ├─ Wells Score ≤4 (PE unlikely)
102
- │ └─ D-dimer test
103
- │ ├─ D-dimer negative (<500 ng/mL) → PE excluded, consider alternative diagnosis
104
- │ └─ D-dimer positive (≥500 ng/mL) → CTPA
105
-
106
- └─ Wells Score >4 (PE likely)
107
- └─ CTPA (skip D-dimer)
108
-
109
- Step 3: CTPA Results
110
- ├─ Positive for PE → Risk stratify severity
111
- │ ├─ Massive PE (hypotension, shock) → Thrombolytics vs embolectomy
112
- │ ├─ Submassive PE (RV strain, troponin+) → Admit ICU, consider thrombolytics
113
- │ └─ Low-risk PE → Anticoagulation, consider outpatient management
114
-
115
- └─ Negative for PE → PE excluded, investigate alternative diagnosis
116
-
117
- Step 4: Treatment Decision (if PE confirmed)
118
- ├─ Absolute contraindication to anticoagulation?
119
- │ ├─ YES → IVC filter placement, treat underlying condition
120
- │ └─ NO → Anticoagulation therapy
121
-
122
- ├─ Cancer-associated thrombosis?
123
- │ ├─ YES → LMWH preferred (edoxaban alternative)
124
- │ └─ NO → DOAC preferred (apixaban, rivaroxaban, edoxaban)
125
-
126
- └─ Duration: Minimum 3 months, extended if unprovoked or recurrent
127
- ```
128
-
129
- ### Treatment Selection Algorithms
130
-
131
- **NSCLC First-Line Treatment Algorithm**
132
-
133
- ```
134
- Entry: Advanced/Metastatic NSCLC, adequate PS (ECOG 0-2)
135
-
136
- Step 1: Biomarker Testing Complete?
137
- ├─ NO → Reflex testing: EGFR, ALK, ROS1, BRAF, PD-L1, consider NGS
138
- │ Hold systemic therapy pending results (unless rapidly progressive)
139
- └─ YES → Proceed to Step 2
140
-
141
- Step 2: Actionable Genomic Alteration?
142
- ├─ EGFR exon 19 deletion or L858R → Osimertinib 80mg daily
143
- │ └─ Alternative: Erlotinib, gefitinib, afatinib (less preferred)
144
-
145
- ├─ ALK rearrangement → Alectinib 600mg BID
146
- │ └─ Alternatives: Brigatinib, lorlatinib, crizotinib (less preferred)
147
-
148
- ├─ ROS1 rearrangement → Crizotinib 250mg BID or entrectinib
149
-
150
- ├─ BRAF V600E → Dabrafenib + trametinib
151
-
152
- ├─ MET exon 14 skipping → Capmatinib or tepotinib
153
-
154
- ├─ RET rearrangement → Selpercatinib or pralsetinib
155
-
156
- ├─ NTRK fusion → Larotrectinib or entrectinib
157
-
158
- ├─ KRAS G12C → Sotorasib or adagrasib (if no other options)
159
-
160
- └─ NO actionable alteration → Proceed to Step 3
161
-
162
- Step 3: PD-L1 Testing Result?
163
- ├─ PD-L1 ≥50% (TPS)
164
- │ ├─ Option 1: Pembrolizumab 200mg Q3W (monotherapy, NCCN Category 1)
165
- │ ├─ Option 2: Pembrolizumab + platinum doublet chemotherapy
166
- │ └─ Option 3: Atezolizumab + bevacizumab + carboplatin + paclitaxel
167
-
168
- ├─ PD-L1 1-49% (TPS)
169
- │ ├─ Preferred: Pembrolizumab + platinum doublet chemotherapy
170
- │ └─ Alternative: Platinum doublet chemotherapy alone
171
-
172
- └─ PD-L1 <1% (TPS)
173
- ├─ Preferred: Pembrolizumab + platinum doublet chemotherapy
174
- └─ Alternative: Platinum doublet chemotherapy ± bevacizumab
175
-
176
- Step 4: Platinum Doublet Selection (if applicable)
177
- ├─ Squamous histology
178
- │ └─ Carboplatin AUC 6 + paclitaxel 200 mg/m² Q3W (4 cycles)
179
- │ or Carboplatin AUC 5 + nab-paclitaxel 100 mg/m² D1,8,15 Q4W
180
-
181
- └─ Non-squamous histology
182
- └─ Carboplatin AUC 6 + pemetrexed 500 mg/m² Q3W (4 cycles)
183
- Continue pemetrexed maintenance if responding
184
- Add bevacizumab 15 mg/kg if eligible (no hemoptysis, brain mets)
185
-
186
- Step 5: Monitoring and Response Assessment
187
- - Imaging every 6 weeks for first 12 weeks, then every 9 weeks
188
- - Continue until progression or unacceptable toxicity
189
- - At progression, proceed to second-line algorithm
190
- ```
191
-
192
- **Heart Failure Management Algorithm (AHA/ACC Guidelines)**
193
-
194
- ```
195
- Entry: Heart Failure Diagnosis Confirmed
196
-
197
- Step 1: Determine HF Type
198
- ├─ HFrEF (EF ≤40%)
199
- │ └─ Proceed to Guideline-Directed Medical Therapy (GDMT)
200
-
201
- ├─ HFpEF (EF ≥50%)
202
- │ └─ Treat comorbidities, diuretics for congestion, consider SGLT2i
203
-
204
- └─ HFmrEF (EF 41-49%)
205
- └─ Consider HFrEF GDMT, evidence less robust
206
-
207
- Step 2: GDMT for HFrEF (All patients unless contraindicated)
208
-
209
- Quadruple Therapy (Class 1 recommendations):
210
-
211
- 1. ACE Inhibitor/ARB/ARNI
212
- ├─ Preferred: Sacubitril-valsartan 49/51mg BID → titrate to 97/103mg BID
213
- │ └─ If ACE-I naïve or taking <10mg enalapril equivalent
214
- ├─ Alternative: ACE-I (enalapril, lisinopril, ramipril) to target dose
215
- └─ Alternative: ARB (losartan, valsartan) if ACE-I intolerant
216
-
217
- 2. Beta-Blocker (start low, titrate slowly)
218
- ├─ Bisoprolol 1.25mg daily → 10mg daily target
219
- ├─ Metoprolol succinate 12.5mg daily → 200mg daily target
220
- └─ Carvedilol 3.125mg BID → 25mg BID target (50mg BID if >85kg)
221
-
222
- 3. Mineralocorticoid Receptor Antagonist (MRA)
223
- ├─ Spironolactone 12.5-25mg daily → 50mg daily target
224
- └─ Eplerenone 25mg daily → 50mg daily target
225
- └─ Contraindications: K >5.0, CrCl <30 mL/min
226
-
227
- 4. SGLT2 Inhibitor (regardless of diabetes status)
228
- ├─ Dapagliflozin 10mg daily
229
- └─ Empagliflozin 10mg daily
230
-
231
- Step 3: Additional Therapies Based on Phenotype
232
-
233
- ├─ Sinus rhythm + HR ≥70 despite beta-blocker?
234
- │ └─ YES: Add ivabradine 5mg BID → 7.5mg BID target
235
-
236
- ├─ African American + NYHA III-IV?
237
- │ └─ YES: Add hydralazine 37.5mg TID + isosorbide dinitrate 20mg TID
238
- │ (Target: hydralazine 75mg TID + ISDN 40mg TID)
239
-
240
- ├─ Atrial fibrillation?
241
- │ ├─ Rate control (target <80 bpm at rest, <110 bpm with activity)
242
- │ └─ Anticoagulation (DOAC preferred, warfarin if valvular)
243
-
244
- └─ Iron deficiency (ferritin <100 or <300 with TSAT <20%)?
245
- └─ YES: IV iron supplementation (ferric carboxymaltose)
246
-
247
- Step 4: Device Therapy Evaluation
248
-
249
- ├─ EF ≤35%, NYHA II-III, LBBB with QRS ≥150 ms, sinus rhythm?
250
- │ └─ YES: Cardiac resynchronization therapy (CRT-D)
251
-
252
- ├─ EF ≤35%, NYHA II-III, on GDMT ≥3 months?
253
- │ └─ YES: ICD for primary prevention
254
- │ (if life expectancy >1 year with good functional status)
255
-
256
- └─ EF ≤35%, NYHA IV despite GDMT, or advanced HF?
257
- └─ Refer to advanced HF specialist
258
- ├─ LVAD evaluation
259
- ├─ Heart transplant evaluation
260
- └─ Palliative care consultation
261
-
262
- Step 5: Monitoring and Titration
263
-
264
- Weekly to biweekly visits during titration:
265
- - Blood pressure (target SBP ≥90 mmHg)
266
- - Heart rate (target 50-60 bpm)
267
- - Potassium (target 4.0-5.0 mEq/L, hold MRA if >5.5)
268
- - Creatinine (expect 10-20% increase, acceptable if <30% and stable)
269
- - Symptoms and congestion status (daily weights, NYHA class)
270
-
271
- Stable on GDMT:
272
- - Visits every 3-6 months
273
- - Echocardiogram at 3-6 months after GDMT optimization, then annually
274
- - NT-proBNP or BNP trending (biomarker-guided therapy investigational)
275
- ```
276
-
277
- ## Risk Stratification Tools
278
-
279
- ### Cardiovascular Risk Scores
280
-
281
- **TIMI Risk Score (NSTEMI/Unstable Angina)**
282
-
283
- ```
284
- Score Calculation (0-7 points):
285
- ☐ Age ≥65 years (1 point)
286
- ☐ ≥3 cardiac risk factors (HTN, hyperlipidemia, diabetes, smoking, family history) (1)
287
- ☐ Known CAD (stenosis ≥50%) (1)
288
- ☐ ASA use in past 7 days (1)
289
- ☐ Severe angina (≥2 episodes in 24 hours) (1)
290
- ☐ ST deviation ≥0.5 mm (1)
291
- ☐ Elevated cardiac biomarkers (1)
292
-
293
- Risk Stratification:
294
- ├─ Score 0-1: 5% risk of death/MI/urgent revasc at 14 days (Low)
295
- │ └─ Management: Observation, stress test, outpatient follow-up
296
-
297
- ├─ Score 2: 8% risk (Low-intermediate)
298
- │ └─ Management: Admission, medical therapy, stress imaging
299
-
300
- ├─ Score 3-4: 13-20% risk (Intermediate-high)
301
- │ └─ Management: Admission, aggressive medical therapy, early invasive strategy
302
-
303
- └─ Score 5-7: 26-41% risk (High)
304
- └─ Management: Aggressive treatment, urgent angiography (<24 hours)
305
- ```
306
-
307
- **CHA2DS2-VASc Score (Stroke Risk in Atrial Fibrillation)**
308
-
309
- ```
310
- Score Calculation:
311
- ☐ Congestive heart failure (1 point)
312
- ☐ Hypertension (1)
313
- ☐ Age ≥75 years (2)
314
- ☐ Diabetes mellitus (1)
315
- ☐ Prior stroke/TIA/thromboembolism (2)
316
- ☐ Vascular disease (MI, PAD, aortic plaque) (1)
317
- ☐ Age 65-74 years (1)
318
- ☐ Sex category (female) (1)
319
-
320
- Maximum score: 9 points
321
-
322
- Treatment Algorithm:
323
- ├─ Score 0 (male) or 1 (female): 0-1.3% annual stroke risk
324
- │ └─ No anticoagulation or aspirin (Class IIb)
325
-
326
- ├─ Score 1 (male): 1.3% annual stroke risk
327
- │ └─ Consider anticoagulation (Class IIa)
328
- │ Factors: Patient preference, bleeding risk, comorbidities
329
-
330
- └─ Score ≥2 (male) or ≥3 (female): ≥2.2% annual stroke risk
331
- └─ Anticoagulation recommended (Class I)
332
- ├─ Preferred: DOAC (apixaban, rivaroxaban, edoxaban, dabigatran)
333
- └─ Alternative: Warfarin (INR 2-3) if DOAC contraindicated
334
-
335
- Bleeding Risk Assessment (HAS-BLED):
336
- H - Hypertension (SBP >160)
337
- A - Abnormal renal/liver function (1 point each)
338
- S - Stroke history
339
- B - Bleeding history or predisposition
340
- L - Labile INR (if on warfarin)
341
- E - Elderly (age >65)
342
- D - Drugs (antiplatelet, NSAIDs) or alcohol (1 point each)
343
-
344
- HAS-BLED ≥3: High bleeding risk → Modifiable factors, consider DOAC over warfarin
345
- ```
346
-
347
- ### Oncology Risk Calculators
348
-
349
- **MELD Score (Hepatocellular Carcinoma Eligibility)**
350
-
351
- ```
352
- MELD = 3.78×ln(bilirubin mg/dL) + 11.2×ln(INR) + 9.57×ln(creatinine mg/dL) + 6.43
353
-
354
- Interpretation:
355
- ├─ MELD <10: 1.9% 3-month mortality (Low)
356
- │ └─ Consider resection or ablation for HCC
357
-
358
- ├─ MELD 10-19: 6-20% 3-month mortality (Moderate)
359
- │ └─ Transplant evaluation if within Milan criteria
360
- │ Milan: Single ≤5cm or ≤3 lesions each ≤3cm, no vascular invasion
361
-
362
- ├─ MELD 20-29: 20-45% 3-month mortality (High)
363
- │ └─ Urgent transplant evaluation, bridge therapy (TACE, ablation)
364
-
365
- └─ MELD ≥30: 50-70% 3-month mortality (Very high)
366
- └─ Transplant vs palliative care discussion
367
- Too ill for transplant if MELD >35-40 typically
368
- ```
369
-
370
- **Adjuvant! Online (Breast Cancer Recurrence Risk)**
371
-
372
- ```
373
- Input Variables:
374
- - Age at diagnosis
375
- - Tumor size
376
- - Tumor grade (1-3)
377
- - ER status
378
- - Node status (0, 1-3, 4-9, ≥10)
379
- - HER2 status
380
- - Comorbidity index
381
-
382
- Output: 10-year risk of:
383
- - Recurrence
384
- - Breast cancer mortality
385
- - Overall mortality
386
-
387
- Treatment Benefit Estimates:
388
- - Chemotherapy: Absolute reduction in recurrence
389
- - Endocrine therapy: Absolute reduction in recurrence
390
- - Trastuzumab: Absolute reduction (if HER2+)
391
-
392
- Clinical Application:
393
- ├─ Low risk (<10% recurrence): Consider endocrine therapy alone if ER+
394
- ├─ Intermediate risk (10-20%): Chemotherapy discussion, genomic assay
395
- │ └─ Oncotype DX score <26: Endocrine therapy alone
396
- │ └─ Oncotype DX score ≥26: Chemotherapy + endocrine therapy
397
- └─ High risk (>20%): Chemotherapy + endocrine therapy if ER+
398
- ```
399
-
400
- ## TikZ Flowchart Best Practices
401
-
402
- ### Visual Design Principles
403
-
404
- **Node Styling**
405
- ```latex
406
- % Decision nodes (diamond)
407
- \tikzstyle{decision} = [diamond, draw, fill=yellow!20, text width=4.5em, text centered, inner sep=0pt]
408
-
409
- % Process nodes (rectangle)
410
- \tikzstyle{process} = [rectangle, draw, fill=blue!20, text width=5em, text centered, rounded corners, minimum height=3em]
411
-
412
- % Terminal nodes (rounded rectangle)
413
- \tikzstyle{terminal} = [rectangle, draw, fill=green!20, text width=5em, text centered, rounded corners=1em, minimum height=3em]
414
-
415
- % Input/Output (parallelogram)
416
- \tikzstyle{io} = [trapezium, draw, fill=purple!20, text width=5em, text centered, minimum height=3em]
417
- ```
418
-
419
- **Color Coding by Urgency**
420
- - **Red**: Life-threatening, immediate action required
421
- - **Orange**: Urgent, action within hours
422
- - **Yellow**: Semi-urgent, action within 24-48 hours
423
- - **Green**: Routine, stable clinical situation
424
- - **Blue**: Informational, monitoring only
425
-
426
- **Pathway Emphasis**
427
- - Bold arrows for most common pathway
428
- - Dashed arrows for rare scenarios
429
- - Arrow thickness proportional to pathway frequency
430
- - Highlight boxes around critical decision points
431
-
432
- ### LaTeX TikZ Template
433
-
434
- ```latex
435
- \documentclass{article}
436
- \usepackage{tikz}
437
- \usetikzlibrary{shapes, arrows, positioning}
438
-
439
- \begin{document}
440
-
441
- \tikzstyle{decision} = [diamond, draw, fill=yellow!20, text width=4em, text centered, inner sep=2pt, font=\small]
442
- \tikzstyle{process} = [rectangle, draw, fill=blue!20, text width=6em, text centered, rounded corners, minimum height=2.5em, font=\small]
443
- \tikzstyle{terminal} = [rectangle, draw, fill=green!20, text width=6em, text centered, rounded corners=8pt, minimum height=2.5em, font=\small]
444
- \tikzstyle{alert} = [rectangle, draw=red, line width=1.5pt, fill=red!10, text width=6em, text centered, rounded corners, minimum height=2.5em, font=\small\bfseries]
445
- \tikzstyle{arrow} = [thick,->,>=stealth]
446
-
447
- \begin{tikzpicture}[node distance=2cm, auto]
448
- % Nodes
449
- \node [terminal] (start) {Patient presents with symptom X};
450
- \node [decision, below of=start] (decision1) {Criterion A met?};
451
- \node [alert, below of=decision1, node distance=2.5cm] (alert1) {Immediate action};
452
- \node [process, right of=decision1, node distance=4cm] (process1) {Standard evaluation};
453
- \node [terminal, below of=process1, node distance=2.5cm] (end) {Outcome};
454
-
455
- % Arrows
456
- \draw [arrow] (start) -- (decision1);
457
- \draw [arrow] (decision1) -- node {Yes} (alert1);
458
- \draw [arrow] (decision1) -- node {No} (process1);
459
- \draw [arrow] (process1) -- (end);
460
- \draw [arrow] (alert1) -| (end);
461
- \end{tikzpicture}
462
-
463
- \end{document}
464
- ```
465
-
466
- ## Algorithm Validation
467
-
468
- ### Development Process
469
-
470
- **Step 1: Literature Review and Evidence Synthesis**
471
- - Systematic review of guidelines (NCCN, ASCO, ESMO, AHA/ACC)
472
- - Meta-analyses of clinical trials
473
- - Expert consensus statements
474
- - Local practice patterns and resource availability
475
-
476
- **Step 2: Draft Algorithm Development**
477
- - Multidisciplinary team input (physicians, nurses, pharmacists)
478
- - Define decision nodes and criteria
479
- - Specify actions and outcomes
480
- - Identify areas of uncertainty
481
-
482
- **Step 3: Pilot Testing**
483
- - Retrospective application to historical cases (n=20-50)
484
- - Identify scenarios not covered by algorithm
485
- - Refine decision criteria
486
- - Usability testing with end-users
487
-
488
- **Step 4: Prospective Validation**
489
- - Implement in clinical practice with data collection
490
- - Track adherence rate (target >80%)
491
- - Monitor outcomes vs historical controls
492
- - User satisfaction surveys
493
-
494
- **Step 5: Continuous Quality Improvement**
495
- - Quarterly review of algorithm performance
496
- - Update based on new evidence
497
- - Address deviations and reasons for non-adherence
498
- - Version control and change documentation
499
-
500
- ### Performance Metrics
501
-
502
- **Process Metrics**
503
- - Algorithm adherence rate (% cases following algorithm)
504
- - Time to decision (median time from presentation to treatment start)
505
- - Completion rate (% cases reaching terminal node)
506
-
507
- **Outcome Metrics**
508
- - Appropriateness of care (concordance with guidelines)
509
- - Clinical outcomes (mortality, morbidity, readmissions)
510
- - Resource utilization (length of stay, unnecessary tests)
511
- - Safety (adverse events, errors)
512
-
513
- **User Experience Metrics**
514
- - Ease of use (Likert scale survey)
515
- - Time to use (median time to navigate algorithm)
516
- - Perceived utility (% users reporting algorithm helpful)
517
- - Barriers to use (qualitative feedback)
518
-
519
- ## Implementation Strategies
520
-
521
- ### Integration into Clinical Workflow
522
-
523
- **Electronic Health Record Integration**
524
- - Clinical decision support (CDS) alerts at key decision points
525
- - Order sets linked to algorithm pathways
526
- - Auto-population of risk scores from EHR data
527
- - Documentation templates following algorithm structure
528
-
529
- **Point-of-Care Tools**
530
- - Pocket cards for quick reference
531
- - Mobile apps with interactive algorithms
532
- - Wall posters in clinical areas
533
- - QR codes linking to full algorithm
534
-
535
- **Education and Training**
536
- - Didactic presentation of algorithm rationale
537
- - Case-based exercises
538
- - Simulation scenarios
539
- - Audit and feedback on adherence
540
-
541
- ### Overcoming Barriers
542
-
543
- **Common Barriers**
544
- - Algorithm complexity (too many decision points)
545
- - Lack of awareness (not disseminated effectively)
546
- - Disagreement with recommendations (perceived as cookbook medicine)
547
- - Competing priorities (time pressure, multiple patients)
548
- - Resource limitations (recommended tests/treatments not available)
549
-
550
- **Mitigation Strategies**
551
- - Simplify algorithms (≤7 decision points per pathway preferred)
552
- - Champion network (local opinion leaders promoting algorithm)
553
- - Customize to local context (allow flexibility for clinical judgment)
554
- - Measure and report outcomes (demonstrate value)
555
- - Provide resources (ensure algorithm-recommended options available)
556
-
557
- ## Algorithm Maintenance and Updates
558
-
559
- ### Version Control
560
-
561
- **Change Log Documentation**
562
- ```
563
- Algorithm: NSCLC First-Line Treatment
564
- Version: 3.2
565
- Effective Date: January 1, 2024
566
- Previous Version: 3.1 (effective July 1, 2023)
567
-
568
- Changes in Version 3.2:
569
- 1. Added KRAS G12C-mutated pathway (sotorasib, adagrasib)
570
- - Evidence: FDA approval May 2021/2022
571
- - Guideline: NCCN v4.2023
572
-
573
- 2. Updated PD-L1 ≥50% recommendation to include pembrolizumab monotherapy as Option 1
574
- - Evidence: KEYNOTE-024 5-year follow-up
575
- - Guideline: NCCN Category 1 preferred
576
-
577
- 3. Removed crizotinib as preferred ALK inhibitor, moved to alternative
578
- - Evidence: ALEX, CROWN trials showing superiority of alectinib, lorlatinib
579
- - Guideline: NCCN/ESMO Category 1 for alectinib as first-line
580
-
581
- Reviewed by: Thoracic Oncology Committee
582
- Approved by: Dr. [Name], Medical Director
583
- Next Review Date: July 1, 2024
584
- ```
585
-
586
- ### Trigger for Updates
587
-
588
- **Mandatory Updates (Within 3 Months)**
589
- - FDA approval of new drug for algorithm indication
590
- - Guideline change (NCCN, ASCO, ESMO Category 1 recommendation)
591
- - Safety alert or black box warning added to recommended agent
592
- - Major clinical trial results changing standard of care
593
-
594
- **Routine Updates (Annually)**
595
- - Minor evidence updates
596
- - Optimization based on local performance data
597
- - Formatting or usability improvements
598
- - Addition of new clinical scenarios encountered
599
-
600
- **Emergency Updates (Within 1 Week)**
601
- - Drug shortage requiring alternative pathways
602
- - Drug recall or safety withdrawal
603
- - Outbreak or pandemic requiring modified protocols
604
-