{"id":"W4405514836","doi":"10.1038/s41586-024-08515-5","title":"Ancient genomes reveal a deep history of Treponema pallidum in the Americas","year":2024,"lang":"en","type":"article","venue":"Nature","topic":"Syphilis Diagnosis and Treatment","field":"Medicine","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University; Simon Fraser University; Western University","funders":"Agencia Nacional de Promoción Científica y Tecnológica; Koneen Säätiö; Max-Planck-Gesellschaft; FP7 International Cooperation; Social Sciences and Humanities Research Council of Canada; Suomen Tiedeseura; Universidad de Chile; Suomen Kulttuurirahasto; Magnus Ehrnroothin Säätiö; Consejo Nacional de Investigaciones Científicas y Técnicas; Helsingin Yliopisto; Deutscher Akademischer Austauschdienst; International Council for Canadian Studies; European Commission; McMaster University","keywords":"Treponema; Syphilis; Biology; Genome; Evolutionary biology; Ancient DNA; Genetics; Virology; Gene; Demography; Population; Sociology; Human immunodeficiency virus (HIV)","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":[0.0002128088,0.0001878825,0.000256918,0.0007166454,0.0003656562,0.0007275323,0.0001668019,0.0004612562,0.00150915],"category_scores_gemma":[0.0004983366,0.0001393469,0.0002884697,0.001068101,0.0003286428,0.0003782248,0.0005727245,0.0006207048,0.0002106068],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002909997,"about_ca_system_score_gemma":0.0002507288,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001843901,"about_ca_topic_score_gemma":0.003509974,"domain_scores_codex":[0.9999009,0.000008787558,0.000004205947,0.0000442285,0.00002049229,0.00002137411],"domain_scores_gemma":[0.9996004,0.0001018752,0.0001482753,0.00002965667,0.00004989293,0.0000699758],"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":[0.00111386,0.0001286786,0.2865046,0.0006888749,0.0004982133,0.001717657,0.003342687,0.001799033,0.6424329,0.002788906,0.002505612,0.05647905],"study_design_scores_gemma":[0.00001857228,0.0001134392,0.9723853,0.00009000523,0.0001396953,0.001446389,0.001172138,0.001409379,0.007019609,0.001425235,0.01476153,0.00001870799],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9906233,0.002738688,0.001441816,0.0003421136,0.00002137363,0.000006476507,0.003351471,0.00006761328,0.001407102],"genre_scores_gemma":[0.9931156,0.0008808855,0.00204383,0.0002073889,0.0000251148,0.000004526701,0.003251681,0.00002410579,0.0004468877],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001843901,"threshold_uncertainty_score":0.005048633,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01978875878522096,"score_gpt":0.2976619432973704,"score_spread":0.2778731845121495,"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."}}