{"id":"W3182860789","doi":"10.1101/2021.03.25.21250180","title":"Contemporary syphilis is characterised by rapid global spread of pandemic <i>Treponema pallidum</i> lineages","year":2021,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Syphilis Diagnosis and Treatment","field":"Medicine","cited_by":0,"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; National Health and Medical Research Council; National Institutes of Health; Wellcome Trust; Sahlgrenska Universitetssjukhuset; Centers for Disease Control and Prevention; Queensland Government; Public Health England; National Institute for Health and Care Research; Instituut voor Tropische Geneeskunde; UK Research and Innovation; Medical Research Council; Alberta Precision Laboratories","keywords":"Treponema; Biology; Syphilis; Population; Genome; Subspecies; Virology; Phylogenetic tree; Pandemic; Evolutionary biology; Genetics; Zoology; Demography; Coronavirus disease 2019 (COVID-19); Gene; Infectious disease (medical specialty)","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":[0.0002623929,0.0001511004,0.0002192708,0.0005654317,0.0003615683,0.0007572013,0.000174067,0.000245786,0.00176701],"category_scores_gemma":[0.0007008764,0.0001179757,0.0002034681,0.0009775027,0.0003873565,0.0003567583,0.0004096325,0.000380734,0.0002412293],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004458971,"about_ca_system_score_gemma":0.0002522428,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005040976,"about_ca_topic_score_gemma":0.006458011,"domain_scores_codex":[0.9997941,0.00003796179,0.0000111072,0.00007862431,0.00003414348,0.00004415538],"domain_scores_gemma":[0.9995282,0.00005900889,0.0002535767,0.00003896814,0.0000800667,0.00004024179],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.000357348,0.00003179169,0.9155637,0.000113051,0.0001765554,0.0003244491,0.001275703,0.00158725,0.05010833,0.0007602448,0.0008467191,0.02885487],"study_design_scores_gemma":[0.000004628143,0.00007725837,0.9943645,0.00002085102,0.00002891663,0.0003777971,0.0006043703,0.0008781986,0.00157103,0.0003638774,0.00169765,0.00001086755],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975761,0.0002593862,0.0006674988,0.00006978909,0.00000447509,0.000005261191,0.0003607972,0.00002236988,0.001034425],"genre_scores_gemma":[0.9987887,0.0001669672,0.0004808904,0.00002652327,0.000008516453,0.000003678192,0.0004067976,0.0000053388,0.0001126733],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005040976,"threshold_uncertainty_score":0.01002324,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04752332932731112,"score_gpt":0.3059552430862368,"score_spread":0.2584319137589257,"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."}}