{"id":"W4410822545","doi":"10.21203/rs.3.rs-5776739/v1","title":"4000-year-old Mycobacterium lepromatosis genomes from Chile reveal long-establishment of Hansen’s Disease in the Americas","year":2025,"lang":"en","type":"preprint","venue":"Research Square","topic":"Leprosy Research and Treatment","field":"Medicine","cited_by":0,"is_retracted":false,"has_abstract":false,"ca_institutions":"Simon Fraser University","funders":"Social Sciences and Humanities Research Council of Canada; Agencia Nacional de Investigación y Desarrollo; Max-Planck-Gesellschaft; Deutscher Akademischer Austauschdienst","keywords":"Disease; Genome; Genealogy; Biology; Mycobacterium; Evolutionary biology; Genetics; Geography; Medicine; History; Pathology; Gene; Bacteria","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.001785767,0.0004553944,0.0009627299,0.0008537055,0.0001738357,0.0002203073,0.0009430553,0.0002721493,0.0005505224],"category_scores_gemma":[0.0008379795,0.0003094342,0.000442707,0.001025359,0.000451619,0.00008964512,0.001687466,0.002231438,0.000100125],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008771138,"about_ca_system_score_gemma":0.002231467,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0115519,"about_ca_topic_score_gemma":0.0003089994,"domain_scores_codex":[0.9927896,0.001266761,0.0006961867,0.001215256,0.002877519,0.001154708],"domain_scores_gemma":[0.99503,0.0009202001,0.0001557864,0.002612357,0.0006607665,0.0006208654],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.002541772,0.003180788,0.9697452,0.005205251,0.0006439329,0.002336641,0.00275158,0.00002844277,0.0002534969,0.0001448269,0.006135732,0.007032345],"study_design_scores_gemma":[0.002437077,0.0007605381,0.9857236,0.004449615,0.0001791505,0.000006025713,0.001156728,0.00009593,0.001223877,0.001143679,0.002529171,0.0002946216],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9715659,0.008558674,0.00001051746,0.007800296,0.0001445355,0.005540119,0.002830132,0.00005984823,0.003490001],"genre_scores_gemma":[0.9870459,0.004064749,0.0002453716,0.0001203856,0.0003486494,0.001919333,0.00208886,0.00004596021,0.004120778],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01597839,"threshold_uncertainty_score":0.9999357,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04584145188955467,"score_gpt":0.3797275198378077,"score_spread":0.333886067948253,"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."}}