{"id":"W3215251541","doi":"10.1038/s41564-021-01000-z","title":"Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis","year":2021,"lang":"en","type":"article","venue":"Nature Microbiology","topic":"Syphilis Diagnosis and Treatment","field":"Medicine","cited_by":135,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; University of Alberta; Alberta Hospital Edmonton; BC Centre for Disease Control","funders":"European and Developing Countries Clinical Trials Partnership; Programme Development Grants; National Health and Medical Research Council; National Institute of Allergy and Infectious Diseases; Medical Research Council; Centers for Disease Control and Prevention; Queensland Government; Public Health England; Medical Research Foundation; National Institute for Health and Care Research; Instituut voor Tropische Geneeskunde; UK Research and Innovation; Sahlgrenska Universitetssjukhuset; Wellcome Trust; Alberta Precision Laboratories; Wellcome; National Institutes of Health; U.S. Department of Health and Human Services","keywords":"Treponema; Biology; Population; Syphilis; Phylogenetics; Phylogenetic tree; Evolutionary biology; Genome; Molecular epidemiology; Population bottleneck; Zoology; Genetics; Virology; Demography; Gene; Genotype; Microsatellite","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004395278,0.0003031982,0.0004324958,0.001553305,0.0003216134,0.0007292791,0.0002259345,0.0003795249,0.000742005],"category_scores_gemma":[0.000969219,0.0002094107,0.0004311721,0.001465934,0.000400225,0.0004825592,0.0004843086,0.0005788736,0.0002236316],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003349303,"about_ca_system_score_gemma":0.000201603,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002678149,"about_ca_topic_score_gemma":0.003524164,"domain_scores_codex":[0.9997975,0.0000450797,0.00001179029,0.0000825958,0.00002050937,0.00004254965],"domain_scores_gemma":[0.9994504,0.0001327731,0.0001771797,0.00006895053,0.00009544099,0.00007525189],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0006698124,0.00005817237,0.8221673,0.0001722429,0.0003562562,0.0003700629,0.003061755,0.005779433,0.1297878,0.0006639721,0.0006071686,0.03630596],"study_design_scores_gemma":[0.00001148345,0.0001076468,0.9914201,0.00002535829,0.0000981407,0.0002943282,0.0004752806,0.00471419,0.001059966,0.00028326,0.001491245,0.00001902269],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9982229,0.0002853838,0.0006944562,0.00003297027,0.000002080054,0.000004332373,0.0002817055,0.00002452697,0.0004517187],"genre_scores_gemma":[0.9976286,0.0002357106,0.001057409,0.00003107982,0.000005802482,0.000004865167,0.0009133528,0.00001645196,0.0001066698],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002678149,"threshold_uncertainty_score":0.005325139,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01815880124741696,"score_gpt":0.2952815600711994,"score_spread":0.2771227588237825,"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."}}