{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002103487,0.0003462218,0.0002810701,0.0004619785,0.0001920758,0.0003831362,0.0001819257,0.0002214565,0.0009792723],"category_scores_gemma":[0.0003122235,0.0001515515,0.0002445203,0.0003942664,0.0001679667,0.0002746177,0.0002793627,0.0003517354,0.0003048207],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000192483,"about_ca_system_score_gemma":0.0001540987,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008590004,"about_ca_topic_score_gemma":0.0008698467,"domain_scores_codex":[0.9998272,0.00002396271,0.00001401148,0.00005065369,0.00005311328,0.00003102351],"domain_scores_gemma":[0.999869,0.00002973582,0.00003148196,0.00001549873,0.00003495796,0.00001940861],"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":[0.00003781731,0.000005009122,0.0005028492,0.00003680673,0.000006126919,0.00002439949,0.000022845,0.00003922875,0.9984282,0.00001732706,0.00003005734,0.0008493754],"study_design_scores_gemma":[0.000004022788,0.0001102639,0.04226126,0.000013937,0.00004471248,0.0005585424,0.00009232377,0.001336957,0.9532208,0.00005439778,0.00229253,0.00001033429],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9871836,0.001032343,0.007086458,0.0000725974,0.00001864859,0.00002179468,0.003078365,0.000128857,0.001377494],"genre_scores_gemma":[0.9750097,0.001694768,0.01540393,0.00009694519,0.00002050494,0.00006404204,0.005940839,0.0001015678,0.001667815],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009792723,"threshold_uncertainty_score":0.00327599,"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."}}