{"id":"W3041495679","doi":"10.3390/microorganisms8071016","title":"The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance","year":2020,"lang":"en","type":"article","venue":"Microorganisms","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":34,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ste. Anne's Hospital; Wilfrid Laurier University; Public Health Agency of Canada; Université Laval; Université de Montréal; University of Guelph; Fonds de Recherche du Québec – Nature et Technologies; University of Calgary; McGill University; Health Canada","funders":"Genome Canada; Health Canada; Genome British Columbia; Université Laval","keywords":"Salmonella enterica; Nanopore sequencing; Plasmid; Minion; Biology; Salmonella; Genetics; Genome; Whole genome sequencing; Antibiotic resistance; Gene; Serotype; Computational biology; Microbiology; 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":[],"consensus_categories":[],"category_scores_codex":[0.0002159349,0.0001365305,0.0002462165,0.000003755079,0.0002013835,0.00003231183,0.0005432231,0.00008920227,0.0001755343],"category_scores_gemma":[0.0002199819,0.00004552951,0.000101027,0.0003212755,0.0001737022,0.00003441748,0.0001418845,0.000121376,0.0002260195],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001254142,"about_ca_system_score_gemma":0.00001036398,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006213081,"about_ca_topic_score_gemma":0.0001301032,"domain_scores_codex":[0.9987882,0.0001593912,0.0003174868,0.0002973528,0.0001299918,0.000307594],"domain_scores_gemma":[0.9991258,0.0004604694,0.0001537192,0.00009293642,0.00005152806,0.0001154813],"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":[0.0001135399,0.00002187118,0.005608451,0.000007558469,0.00001501758,0.000007079429,0.0001247428,5.597772e-7,0.9865249,0.0003370218,0.006313145,0.0009261005],"study_design_scores_gemma":[0.0003047377,0.0006642953,0.1381946,0.00003523066,0.00002459872,0.00002185539,0.0009417151,0.00001062625,0.5433479,0.00204756,0.3140773,0.0003295153],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9807428,0.0008289674,0.000004170055,0.01615318,0.00009964788,0.0001301827,0.00002525037,0.00005111679,0.001964661],"genre_scores_gemma":[0.997318,0.0002142722,0.00009811037,0.001583104,0.0001590918,0.00000172424,0.00001355726,0.000001840157,0.0006103309],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.443177,"threshold_uncertainty_score":0.2905098,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01843119049776115,"score_gpt":0.2115761140498886,"score_spread":0.1931449235521274,"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."}}