{"id":"W4404799564","doi":"10.1016/j.lanmic.2024.06.003","title":"Signatures of transmission in within-host Mycobacterium tuberculosis complex variation: a retrospective genomic epidemiology study","year":2024,"lang":"en","type":"article","venue":"The Lancet Microbe","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"Sanofi Pasteur; Coalition for Epidemic Preparedness Innovations; Sanofi; National Institutes of Health; National Center for Advancing Translational Sciences; Moderna; National Institute of Allergy and Infectious Diseases; Pfizer","keywords":"Host (biology); Mycobacterium tuberculosis; Epidemiology; Transmission (telecommunications); Tuberculosis; Biology; Variation (astronomy); Mycobacterium tuberculosis complex; Evolutionary biology; Genetics; Medicine; Pathology; Computer science","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003206445,0.0001996153,0.001070344,0.0001937237,0.00006186286,0.00001094747,0.0002462249,0.0001635988,0.0003178015],"category_scores_gemma":[0.0006133249,0.0001208217,0.0001491241,0.0004356277,0.0001766923,0.00005187019,0.0001008604,0.0008246407,0.00004510003],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001966832,"about_ca_system_score_gemma":0.0001096739,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008413701,"about_ca_topic_score_gemma":0.0001665391,"domain_scores_codex":[0.9971457,0.001092218,0.0006714109,0.0004548145,0.000134433,0.0005014673],"domain_scores_gemma":[0.9982392,0.001009422,0.0000962273,0.0004825382,0.00007639973,0.00009625829],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.001167934,0.0003361808,0.2195858,0.0003368759,0.0005422606,0.00007483522,0.006045386,0.0001175503,0.7584199,0.001761473,0.01100926,0.0006025727],"study_design_scores_gemma":[0.001203089,0.0006643662,0.9890037,0.0001863938,0.0001219333,0.00006933715,0.000219586,0.002226377,0.0009115981,0.001161105,0.004113622,0.0001188535],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9677053,0.004227333,0.000271581,0.02590125,0.0002017254,0.0009259695,0.00005353971,0.00007374742,0.0006395353],"genre_scores_gemma":[0.9955571,0.0006562247,0.0009788219,0.00214055,0.0004448945,0.00004564725,0.0000391357,0.00002713237,0.0001104788],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7694179,"threshold_uncertainty_score":0.4926964,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05395585285588553,"score_gpt":0.3534894523925419,"score_spread":0.2995335995366564,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}