{"id":"W2344906993","doi":"10.1101/051037","title":"Origin of modern syphilis and emergence of a contemporary pandemic cluster","year":2016,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Syphilis Diagnosis and Treatment","field":"Medicine","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Social Sciences and Humanities Research Council of Canada; Universität Zürich","keywords":"Treponema; Pandemic; Biology; Syphilis; Phylogenetic tree; Ancestor; Most recent common ancestor; Whole genome sequencing; Population; Genome; Evolutionary biology; Virology; Genetics; Disease; Coronavirus disease 2019 (COVID-19); Geography; Gene; Infectious disease (medical specialty); Demography; Medicine","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004069725,0.00014713,0.0002210435,0.0008036447,0.0009173917,0.0007844107,0.0002465648,0.000526079,0.00289375],"category_scores_gemma":[0.0006902197,0.0001375701,0.0001548168,0.0007755932,0.0008093143,0.0004596429,0.0008315215,0.0007728857,0.0002974269],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007220932,"about_ca_system_score_gemma":0.000416073,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002238814,"about_ca_topic_score_gemma":0.002007323,"domain_scores_codex":[0.999733,0.00004642902,0.00001214428,0.00009139797,0.00005061956,0.00006629285],"domain_scores_gemma":[0.9996048,0.00004710657,0.0001339116,0.00004041442,0.00007936959,0.00009444104],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001350579,0.0002351599,0.8175097,0.0001837796,0.0001609537,0.002367855,0.011034,0.0007328488,0.08217873,0.01054782,0.002496911,0.07120176],"study_design_scores_gemma":[0.00003243479,0.0003751207,0.9666654,0.00007159189,0.00004713221,0.004269176,0.004326331,0.001481077,0.005745744,0.004570804,0.01236107,0.00005417125],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9961489,0.0004625867,0.0007106486,0.0002549671,0.00001761746,0.00001242254,0.000129944,0.00001690009,0.002246067],"genre_scores_gemma":[0.9985209,0.0002197568,0.0006563886,0.00007652172,0.0000315109,0.000003660942,0.0001559198,0.000006740673,0.0003286881],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00289375,"threshold_uncertainty_score":0.009680569,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03649047539250167,"score_gpt":0.2679194184829484,"score_spread":0.2314289430904468,"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."}}