{"id":"W4394907364","doi":"10.1021/acs.jproteome.3c00891","title":"In-Depth Proteome Coverage of In Vitro-Cultured <i>Treponema pallidum</i> and Quantitative Comparison Analyses with In Vivo-Grown Treponemes","year":2024,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"Syphilis Diagnosis and Treatment","field":"Medicine","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Victoria","funders":"NHLBI Division of Intramural Research; Social Sciences and Humanities Research Council of Canada; Canadian Institutes of Health Research; National Institutes of Health; Open Philanthropy Project; National Institute of Allergy and Infectious Diseases; Natural Sciences and Engineering Research Council of Canada; Division of Intramural Research, National Institute of Allergy and Infectious Diseases","keywords":"Treponema; Proteome; Proteomics; Biology; In vivo; In vitro; Microbiology; Computational biology; Molecular biology; Syphilis; Immunology; Biochemistry; Genetics; Gene","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":[0.00218994,0.0001951057,0.0009495793,0.001740752,0.00003659025,0.00007336495,0.0001152535,0.0001088348,0.0000558245],"category_scores_gemma":[0.0004745834,0.0001195278,0.0001116905,0.001673207,0.0001932108,0.0003146724,0.0000561506,0.0009398585,0.000002673973],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003676677,"about_ca_system_score_gemma":0.0004460284,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006286164,"about_ca_topic_score_gemma":0.0008662911,"domain_scores_codex":[0.9967485,0.0004419736,0.0009729305,0.0003125918,0.001134693,0.0003893315],"domain_scores_gemma":[0.9984953,0.0005570146,0.0002263252,0.0001854306,0.0003784602,0.0001574301],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.006613979,0.003063055,0.2587853,0.001441667,0.0005009199,0.008539362,0.006710393,0.0001165135,0.7117907,0.0001250581,0.0002933984,0.002019596],"study_design_scores_gemma":[0.008547002,0.007063229,0.3038737,0.006152496,0.0001108171,0.0005228539,0.00341961,0.0006856535,0.6681381,0.0008461581,0.0004069914,0.0002333303],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9872476,0.007903489,0.00001911725,0.002915079,0.00002633266,0.001472045,0.00001276798,0.000005327447,0.0003982211],"genre_scores_gemma":[0.9963059,0.001071836,0.002239037,0.0000166711,0.00005343473,0.0001574021,0.000002551505,0.00002358662,0.0001296196],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04508841,"threshold_uncertainty_score":0.4874201,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1537214175096505,"score_gpt":0.4723945262398264,"score_spread":0.3186731087301758,"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."}}