@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.
- package/bin/synsc +0 -0
- package/package.json +1 -1
- package/bin/skills/accelerate/SKILL.md +0 -332
- package/bin/skills/accelerate/references/custom-plugins.md +0 -453
- package/bin/skills/accelerate/references/megatron-integration.md +0 -489
- package/bin/skills/accelerate/references/performance.md +0 -525
- package/bin/skills/adaptyv/SKILL.md +0 -114
- package/bin/skills/adaptyv/reference/api_reference.md +0 -308
- package/bin/skills/adaptyv/reference/examples.md +0 -913
- package/bin/skills/adaptyv/reference/experiments.md +0 -360
- package/bin/skills/adaptyv/reference/protein_optimization.md +0 -637
- package/bin/skills/aeon/SKILL.md +0 -374
- package/bin/skills/aeon/references/anomaly_detection.md +0 -154
- package/bin/skills/aeon/references/classification.md +0 -144
- package/bin/skills/aeon/references/clustering.md +0 -123
- package/bin/skills/aeon/references/datasets_benchmarking.md +0 -387
- package/bin/skills/aeon/references/distances.md +0 -256
- package/bin/skills/aeon/references/forecasting.md +0 -140
- package/bin/skills/aeon/references/networks.md +0 -289
- package/bin/skills/aeon/references/regression.md +0 -118
- package/bin/skills/aeon/references/segmentation.md +0 -163
- package/bin/skills/aeon/references/similarity_search.md +0 -187
- package/bin/skills/aeon/references/transformations.md +0 -246
- package/bin/skills/alphafold-database/SKILL.md +0 -513
- package/bin/skills/alphafold-database/references/api_reference.md +0 -423
- package/bin/skills/anndata/SKILL.md +0 -400
- package/bin/skills/anndata/references/best_practices.md +0 -525
- package/bin/skills/anndata/references/concatenation.md +0 -396
- package/bin/skills/anndata/references/data_structure.md +0 -314
- package/bin/skills/anndata/references/io_operations.md +0 -404
- package/bin/skills/anndata/references/manipulation.md +0 -516
- package/bin/skills/arboreto/SKILL.md +0 -243
- package/bin/skills/arboreto/references/algorithms.md +0 -138
- package/bin/skills/arboreto/references/basic_inference.md +0 -151
- package/bin/skills/arboreto/references/distributed_computing.md +0 -242
- package/bin/skills/arboreto/scripts/basic_grn_inference.py +0 -97
- package/bin/skills/astropy/SKILL.md +0 -331
- package/bin/skills/astropy/references/coordinates.md +0 -273
- package/bin/skills/astropy/references/cosmology.md +0 -307
- package/bin/skills/astropy/references/fits.md +0 -396
- package/bin/skills/astropy/references/tables.md +0 -489
- package/bin/skills/astropy/references/time.md +0 -404
- package/bin/skills/astropy/references/units.md +0 -178
- package/bin/skills/astropy/references/wcs_and_other_modules.md +0 -373
- package/bin/skills/audiocraft/SKILL.md +0 -564
- package/bin/skills/audiocraft/references/advanced-usage.md +0 -666
- package/bin/skills/audiocraft/references/troubleshooting.md +0 -504
- package/bin/skills/autogpt/SKILL.md +0 -403
- package/bin/skills/autogpt/references/advanced-usage.md +0 -535
- package/bin/skills/autogpt/references/troubleshooting.md +0 -420
- package/bin/skills/awq/SKILL.md +0 -310
- package/bin/skills/awq/references/advanced-usage.md +0 -324
- package/bin/skills/awq/references/troubleshooting.md +0 -344
- package/bin/skills/axolotl/SKILL.md +0 -158
- package/bin/skills/axolotl/references/api.md +0 -5548
- package/bin/skills/axolotl/references/dataset-formats.md +0 -1029
- package/bin/skills/axolotl/references/index.md +0 -15
- package/bin/skills/axolotl/references/other.md +0 -3563
- package/bin/skills/benchling-integration/SKILL.md +0 -480
- package/bin/skills/benchling-integration/references/api_endpoints.md +0 -883
- package/bin/skills/benchling-integration/references/authentication.md +0 -379
- package/bin/skills/benchling-integration/references/sdk_reference.md +0 -774
- package/bin/skills/bigcode-evaluation-harness/SKILL.md +0 -405
- package/bin/skills/bigcode-evaluation-harness/references/benchmarks.md +0 -393
- package/bin/skills/bigcode-evaluation-harness/references/custom-tasks.md +0 -424
- package/bin/skills/bigcode-evaluation-harness/references/issues.md +0 -394
- package/bin/skills/biopython/SKILL.md +0 -443
- package/bin/skills/biopython/references/advanced.md +0 -577
- package/bin/skills/biopython/references/alignment.md +0 -362
- package/bin/skills/biopython/references/blast.md +0 -455
- package/bin/skills/biopython/references/databases.md +0 -484
- package/bin/skills/biopython/references/phylogenetics.md +0 -566
- package/bin/skills/biopython/references/sequence_io.md +0 -285
- package/bin/skills/biopython/references/structure.md +0 -564
- package/bin/skills/biorxiv-database/SKILL.md +0 -483
- package/bin/skills/biorxiv-database/references/api_reference.md +0 -280
- package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +0 -445
- package/bin/skills/bioservices/SKILL.md +0 -361
- package/bin/skills/bioservices/references/identifier_mapping.md +0 -685
- package/bin/skills/bioservices/references/services_reference.md +0 -636
- package/bin/skills/bioservices/references/workflow_patterns.md +0 -811
- package/bin/skills/bioservices/scripts/batch_id_converter.py +0 -347
- package/bin/skills/bioservices/scripts/compound_cross_reference.py +0 -378
- package/bin/skills/bioservices/scripts/pathway_analysis.py +0 -309
- package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +0 -408
- package/bin/skills/bitsandbytes/SKILL.md +0 -411
- package/bin/skills/bitsandbytes/references/memory-optimization.md +0 -521
- package/bin/skills/bitsandbytes/references/qlora-training.md +0 -521
- package/bin/skills/bitsandbytes/references/quantization-formats.md +0 -447
- package/bin/skills/blip-2/SKILL.md +0 -564
- package/bin/skills/blip-2/references/advanced-usage.md +0 -680
- package/bin/skills/blip-2/references/troubleshooting.md +0 -526
- package/bin/skills/brenda-database/SKILL.md +0 -719
- package/bin/skills/brenda-database/references/api_reference.md +0 -537
- package/bin/skills/brenda-database/scripts/brenda_queries.py +0 -844
- package/bin/skills/brenda-database/scripts/brenda_visualization.py +0 -772
- package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +0 -1053
- package/bin/skills/cellxgene-census/SKILL.md +0 -511
- package/bin/skills/cellxgene-census/references/census_schema.md +0 -182
- package/bin/skills/cellxgene-census/references/common_patterns.md +0 -351
- package/bin/skills/chembl-database/SKILL.md +0 -389
- package/bin/skills/chembl-database/references/api_reference.md +0 -272
- package/bin/skills/chembl-database/scripts/example_queries.py +0 -278
- package/bin/skills/chroma/SKILL.md +0 -406
- package/bin/skills/chroma/references/integration.md +0 -38
- package/bin/skills/cirq/SKILL.md +0 -346
- package/bin/skills/cirq/references/building.md +0 -307
- package/bin/skills/cirq/references/experiments.md +0 -572
- package/bin/skills/cirq/references/hardware.md +0 -515
- package/bin/skills/cirq/references/noise.md +0 -515
- package/bin/skills/cirq/references/simulation.md +0 -350
- package/bin/skills/cirq/references/transformation.md +0 -416
- package/bin/skills/citation-management/SKILL.md +0 -1109
- package/bin/skills/citation-management/assets/bibtex_template.bib +0 -264
- package/bin/skills/citation-management/assets/citation_checklist.md +0 -386
- package/bin/skills/citation-management/references/bibtex_formatting.md +0 -908
- package/bin/skills/citation-management/references/citation_validation.md +0 -794
- package/bin/skills/citation-management/references/google_scholar_search.md +0 -725
- package/bin/skills/citation-management/references/metadata_extraction.md +0 -870
- package/bin/skills/citation-management/references/pubmed_search.md +0 -839
- package/bin/skills/citation-management/scripts/doi_to_bibtex.py +0 -182
- package/bin/skills/citation-management/scripts/extract_metadata.py +0 -570
- package/bin/skills/citation-management/scripts/format_bibtex.py +0 -349
- package/bin/skills/citation-management/scripts/search_google_scholar.py +0 -251
- package/bin/skills/citation-management/scripts/search_pubmed.py +0 -348
- package/bin/skills/citation-management/scripts/validate_citations.py +0 -494
- package/bin/skills/clinical-decision-support/README.md +0 -129
- package/bin/skills/clinical-decision-support/SKILL.md +0 -506
- package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +0 -380
- package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +0 -222
- package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +0 -359
- package/bin/skills/clinical-decision-support/assets/color_schemes.tex +0 -149
- package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +0 -208
- package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +0 -328
- package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +0 -529
- package/bin/skills/clinical-decision-support/references/biomarker_classification.md +0 -719
- package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +0 -604
- package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +0 -840
- package/bin/skills/clinical-decision-support/references/outcome_analysis.md +0 -640
- package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +0 -427
- package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +0 -521
- package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +0 -383
- package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +0 -417
- package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +0 -509
- package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +0 -441
- package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +0 -326
- package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +0 -641
- package/bin/skills/clinical-reports/README.md +0 -236
- package/bin/skills/clinical-reports/SKILL.md +0 -1127
- package/bin/skills/clinical-reports/assets/case_report_template.md +0 -352
- package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +0 -353
- package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +0 -359
- package/bin/skills/clinical-reports/assets/consult_note_template.md +0 -305
- package/bin/skills/clinical-reports/assets/discharge_summary_template.md +0 -453
- package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +0 -395
- package/bin/skills/clinical-reports/assets/history_physical_template.md +0 -305
- package/bin/skills/clinical-reports/assets/lab_report_template.md +0 -309
- package/bin/skills/clinical-reports/assets/pathology_report_template.md +0 -249
- package/bin/skills/clinical-reports/assets/quality_checklist.md +0 -338
- package/bin/skills/clinical-reports/assets/radiology_report_template.md +0 -318
- package/bin/skills/clinical-reports/assets/soap_note_template.md +0 -253
- package/bin/skills/clinical-reports/references/case_report_guidelines.md +0 -570
- package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +0 -693
- package/bin/skills/clinical-reports/references/data_presentation.md +0 -530
- package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -629
- package/bin/skills/clinical-reports/references/medical_terminology.md +0 -588
- package/bin/skills/clinical-reports/references/patient_documentation.md +0 -744
- package/bin/skills/clinical-reports/references/peer_review_standards.md +0 -585
- package/bin/skills/clinical-reports/references/regulatory_compliance.md +0 -577
- package/bin/skills/clinical-reports/scripts/check_deidentification.py +0 -332
- package/bin/skills/clinical-reports/scripts/compliance_checker.py +0 -78
- package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +0 -97
- package/bin/skills/clinical-reports/scripts/format_adverse_events.py +0 -97
- package/bin/skills/clinical-reports/scripts/generate_report_template.py +0 -149
- package/bin/skills/clinical-reports/scripts/terminology_validator.py +0 -126
- package/bin/skills/clinical-reports/scripts/validate_case_report.py +0 -323
- package/bin/skills/clinical-reports/scripts/validate_trial_report.py +0 -88
- package/bin/skills/clinicaltrials-database/SKILL.md +0 -507
- package/bin/skills/clinicaltrials-database/references/api_reference.md +0 -358
- package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +0 -215
- package/bin/skills/clinpgx-database/SKILL.md +0 -638
- package/bin/skills/clinpgx-database/references/api_reference.md +0 -757
- package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +0 -518
- package/bin/skills/clinvar-database/SKILL.md +0 -362
- package/bin/skills/clinvar-database/references/api_reference.md +0 -227
- package/bin/skills/clinvar-database/references/clinical_significance.md +0 -218
- package/bin/skills/clinvar-database/references/data_formats.md +0 -358
- package/bin/skills/clip/SKILL.md +0 -253
- package/bin/skills/clip/references/applications.md +0 -207
- package/bin/skills/cobrapy/SKILL.md +0 -463
- package/bin/skills/cobrapy/references/api_quick_reference.md +0 -655
- package/bin/skills/cobrapy/references/workflows.md +0 -593
- package/bin/skills/colab-finetuning/SKILL.md +0 -153
- package/bin/skills/colab-finetuning/references/bridge-setup.md +0 -68
- package/bin/skills/colab-finetuning/references/gpu-tiers.md +0 -54
- package/bin/skills/colab-finetuning/references/troubleshooting.md +0 -79
- package/bin/skills/constitutional-ai/SKILL.md +0 -290
- package/bin/skills/cosmic-database/SKILL.md +0 -336
- package/bin/skills/cosmic-database/references/cosmic_data_reference.md +0 -220
- package/bin/skills/cosmic-database/scripts/download_cosmic.py +0 -231
- package/bin/skills/crewai/SKILL.md +0 -498
- package/bin/skills/crewai/references/flows.md +0 -438
- package/bin/skills/crewai/references/tools.md +0 -429
- package/bin/skills/crewai/references/troubleshooting.md +0 -480
- package/bin/skills/dask/SKILL.md +0 -456
- package/bin/skills/dask/references/arrays.md +0 -497
- package/bin/skills/dask/references/bags.md +0 -468
- package/bin/skills/dask/references/best-practices.md +0 -277
- package/bin/skills/dask/references/dataframes.md +0 -368
- package/bin/skills/dask/references/futures.md +0 -541
- package/bin/skills/dask/references/schedulers.md +0 -504
- package/bin/skills/datacommons-client/SKILL.md +0 -255
- package/bin/skills/datacommons-client/references/getting_started.md +0 -417
- package/bin/skills/datacommons-client/references/node.md +0 -250
- package/bin/skills/datacommons-client/references/observation.md +0 -185
- package/bin/skills/datacommons-client/references/resolve.md +0 -246
- package/bin/skills/datamol/SKILL.md +0 -706
- package/bin/skills/datamol/references/conformers_module.md +0 -131
- package/bin/skills/datamol/references/core_api.md +0 -130
- package/bin/skills/datamol/references/descriptors_viz.md +0 -195
- package/bin/skills/datamol/references/fragments_scaffolds.md +0 -174
- package/bin/skills/datamol/references/io_module.md +0 -109
- package/bin/skills/datamol/references/reactions_data.md +0 -218
- package/bin/skills/deepchem/SKILL.md +0 -597
- package/bin/skills/deepchem/references/api_reference.md +0 -303
- package/bin/skills/deepchem/references/workflows.md +0 -491
- package/bin/skills/deepchem/scripts/graph_neural_network.py +0 -338
- package/bin/skills/deepchem/scripts/predict_solubility.py +0 -224
- package/bin/skills/deepchem/scripts/transfer_learning.py +0 -375
- package/bin/skills/deepspeed/SKILL.md +0 -141
- package/bin/skills/deepspeed/references/08.md +0 -17
- package/bin/skills/deepspeed/references/09.md +0 -173
- package/bin/skills/deepspeed/references/2020.md +0 -378
- package/bin/skills/deepspeed/references/2023.md +0 -279
- package/bin/skills/deepspeed/references/assets.md +0 -179
- package/bin/skills/deepspeed/references/index.md +0 -35
- package/bin/skills/deepspeed/references/mii.md +0 -118
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- package/bin/skills/deepspeed/references/tutorials.md +0 -6554
- package/bin/skills/deeptools/SKILL.md +0 -531
- package/bin/skills/deeptools/assets/quick_reference.md +0 -58
- package/bin/skills/deeptools/references/effective_genome_sizes.md +0 -116
- package/bin/skills/deeptools/references/normalization_methods.md +0 -410
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- package/bin/skills/deeptools/references/workflows.md +0 -474
- package/bin/skills/deeptools/scripts/validate_files.py +0 -195
- package/bin/skills/deeptools/scripts/workflow_generator.py +0 -454
- package/bin/skills/denario/SKILL.md +0 -215
- package/bin/skills/denario/references/examples.md +0 -494
- package/bin/skills/denario/references/installation.md +0 -213
- package/bin/skills/denario/references/llm_configuration.md +0 -265
- package/bin/skills/denario/references/research_pipeline.md +0 -471
- package/bin/skills/diffdock/SKILL.md +0 -483
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- package/bin/skills/diffdock/scripts/analyze_results.py +0 -334
- package/bin/skills/diffdock/scripts/prepare_batch_csv.py +0 -254
- package/bin/skills/diffdock/scripts/setup_check.py +0 -278
- package/bin/skills/dnanexus-integration/SKILL.md +0 -383
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# Clinical Decision Algorithms Guide
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## Overview
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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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## Algorithm Design Principles
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### Key Components
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**Decision Nodes**
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- **Question/Criteria**: Clear, measurable clinical parameter
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- **Binary vs Multi-Way**: Yes/no (simple) vs multiple options (complex)
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- **Objective**: Lab value, imaging finding vs Subjective: Clinical judgment
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**Action Nodes**
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- **Treatment**: Specific intervention with dosing
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- **Test**: Additional diagnostic procedure
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- **Referral**: Specialist consultation, higher level of care
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- **Observation**: Watchful waiting with defined follow-up
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**Terminal Nodes**
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- **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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### Design Criteria
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**Clarity**
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- Unambiguous decision points
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- Mutually exclusive pathways
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- No circular loops (unless intentional reassessment cycles)
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- Clear entry and exit points
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**Clinical Validity**
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- Evidence-based decision criteria
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- Validated cut-points for biomarkers
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- Guideline-concordant recommendations
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- Expert consensus where evidence limited
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**Usability**
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- Maximum 7 decision points per pathway (cognitive load)
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- Visual hierarchy (most common path highlighted)
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- Printable single-page format preferred
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- Color coding for urgency/safety
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**Completeness**
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- All possible scenarios covered
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- Default pathway for edge cases
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- Safety-net provisions for unusual presentations
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- Escalation criteria clearly stated
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## Clinical Decision Trees
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### Diagnostic Algorithms
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**Chest Pain Evaluation Algorithm**
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```
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Entry: Patient with chest pain
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├─ STEMI Criteria? (ST elevation ≥1mm in ≥2 contiguous leads)
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│ ├─ YES → Activate cath lab, aspirin 325mg, heparin, clopidogrel 600mg
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│ │ Transfer for primary PCI (goal door-to-balloon <90 minutes)
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│ └─ NO → Continue evaluation
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├─ High-Risk Features? (Hemodynamic instability, arrhythmia, troponin elevation)
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│ │ Consider early angiography if NSTEMI
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│ └─ NO → Calculate TIMI or HEART score
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├─ TIMI Score 0-1 or HEART Score 0-3? (Low risk)
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│ ├─ YES → Observe 6-12 hours, serial troponins, stress test if negative
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│ │ Discharge if all negative with cardiology follow-up in 72 hours
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│ └─ NO → TIMI 2-4 or HEART 4-6 (Intermediate risk)
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├─ TIMI Score 2-4 or HEART Score 4-6? (Intermediate risk)
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│ ├─ YES → Admit telemetry, serial troponins, stress imaging vs CT angiography
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│ │ Medical management: Aspirin, statin, beta-blocker
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│ └─ NO → TIMI ≥5 or HEART ≥7 (High risk) → Treat as NSTEMI
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Decision Endpoint: Risk-stratified pathway with 30-day event rate documented
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```
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**Pulmonary Embolism Diagnostic Algorithm (Wells Criteria)**
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Entry: Suspected PE
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Step 1: Calculate Wells Score
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Clinical features points:
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├─ Wells Score ≤4 (PE unlikely)
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│ └─ D-dimer test
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│ ├─ D-dimer negative (<500 ng/mL) → PE excluded, consider alternative diagnosis
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│ ├─ Massive PE (hypotension, shock) → Thrombolytics vs embolectomy
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│ ├─ Submassive PE (RV strain, troponin+) → Admit ICU, consider thrombolytics
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│ └─ Low-risk PE → Anticoagulation, consider outpatient management
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│ ├─ YES → LMWH preferred (edoxaban alternative)
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│
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└─ Duration: Minimum 3 months, extended if unprovoked or recurrent
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```
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### Treatment Selection Algorithms
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**NSCLC First-Line Treatment Algorithm**
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Entry: Advanced/Metastatic NSCLC, adequate PS (ECOG 0-2)
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Step 1: Biomarker Testing Complete?
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├─ NO → Reflex testing: EGFR, ALK, ROS1, BRAF, PD-L1, consider NGS
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│ Hold systemic therapy pending results (unless rapidly progressive)
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└─ YES → Proceed to Step 2
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Step 2: Actionable Genomic Alteration?
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├─ EGFR exon 19 deletion or L858R → Osimertinib 80mg daily
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│ └─ Alternative: Erlotinib, gefitinib, afatinib (less preferred)
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├─ ALK rearrangement → Alectinib 600mg BID
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│ └─ Alternatives: Brigatinib, lorlatinib, crizotinib (less preferred)
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│ ├─ Option 1: Pembrolizumab 200mg Q3W (monotherapy, NCCN Category 1)
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│ ├─ Option 2: Pembrolizumab + platinum doublet chemotherapy
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│ └─ Option 3: Atezolizumab + bevacizumab + carboplatin + paclitaxel
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Continue pemetrexed maintenance if responding
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Add bevacizumab 15 mg/kg if eligible (no hemoptysis, brain mets)
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**Heart Failure Management Algorithm (AHA/ACC Guidelines)**
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Entry: Heart Failure Diagnosis Confirmed
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Step 1: Determine HF Type
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├─ HFpEF (EF ≥50%)
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Step 2: GDMT for HFrEF (All patients unless contraindicated)
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Quadruple Therapy (Class 1 recommendations):
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├─ Preferred: Sacubitril-valsartan 49/51mg BID → titrate to 97/103mg BID
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│ └─ If ACE-I naïve or taking <10mg enalapril equivalent
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├─ Alternative: ACE-I (enalapril, lisinopril, ramipril) to target dose
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└─ Alternative: ARB (losartan, valsartan) if ACE-I intolerant
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├─ Metoprolol succinate 12.5mg daily → 200mg daily target
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└─ Carvedilol 3.125mg BID → 25mg BID target (50mg BID if >85kg)
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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
|
-
|