{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001402159,0.00007918361,0.0001662154,0.00008497986,0.000007780787,0.000004575779,0.00006033573,0.0002009849,0.0001029132],"category_scores_gemma":[0.00004472057,0.00004353625,0.00009621977,0.0001915362,0.00003995847,0.00001677665,0.00001150071,0.000577468,0.00001456302],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003187794,"about_ca_system_score_gemma":0.0001047131,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002803656,"about_ca_topic_score_gemma":0.00004524067,"domain_scores_codex":[0.9993367,0.00002808216,0.0001314883,0.0001645003,0.0002281811,0.0001110711],"domain_scores_gemma":[0.999599,0.0001059398,0.00002611536,0.0002139335,0.00002486692,0.0000301147],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0002124499,0.002677205,0.1736197,0.0008792892,0.0005016442,0.005038613,0.03328624,0.00001144561,0.00436122,0.005248075,0.5724348,0.2017294],"study_design_scores_gemma":[0.0004604327,0.0002519896,0.3370897,0.0001811785,0.0001176788,0.00009088722,0.0003841094,0.00007015061,0.0002199262,0.00008265596,0.6609852,0.00006610146],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6721946,0.3112729,0.000001625045,0.006812161,0.0005214426,0.0003076235,0.000008671434,0.00002788778,0.008853105],"genre_scores_gemma":[0.9954984,0.0005143805,0.0001452266,0.002682483,0.0001208249,0.00003918888,0.00001328617,0.000009059457,0.0009772037],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3233038,"threshold_uncertainty_score":0.2508843,"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."}}