{"id":"W3173839943","doi":"10.1038/s41538-021-00097-0","title":"Genomic analysis of Shiga toxin-producing Escherichia coli O157:H7 from cattle and pork-production related environments","year":2021,"lang":"en","type":"article","venue":"npj Science of Food","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Lethbridge; Alberta Ministry of Agriculture and Forestry; Agriculture and Agri-Food Canada","funders":"Agriculture and Agri-Food Canada; Compute Canada; Alberta Innovates; Alberta Innovates Bio Solutions; Alberta Agriculture and Forestry","keywords":"Biology; Outbreak; Escherichia coli; Shiga toxin; Subtyping; Microbiology; Phylogenetic tree; Toxin; Strain (injury); Veterinary medicine; Gene; Genetics; Virology","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004323828,0.0000980519,0.000218761,0.00009944254,0.0001144632,0.00001554212,0.0002057171,0.00005815977,0.00001912319],"category_scores_gemma":[0.0005376234,0.00009700405,0.00006524878,0.0009165018,0.0005247791,0.00001182971,0.0003398402,0.00007544232,0.000001011889],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002796149,"about_ca_system_score_gemma":0.0001647133,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007103632,"about_ca_topic_score_gemma":0.00009289748,"domain_scores_codex":[0.9986198,0.00005174653,0.0002290377,0.0005824356,0.0003064874,0.0002104853],"domain_scores_gemma":[0.9991954,0.00001240221,0.0001362749,0.0004818347,0.0001039968,0.00007007594],"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":[0.00001471887,0.00005985275,0.0146333,0.000007533104,0.0003214727,4.998496e-7,0.0002304208,0.0003800369,0.9838584,0.0000165642,0.00002433224,0.0004528637],"study_design_scores_gemma":[0.0001206912,0.0001267088,0.2598158,0.000006435683,0.0001092446,5.438626e-7,0.0002609517,0.0001150242,0.7392315,0.00004608078,0.00009149325,0.00007557762],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975002,0.001797341,0.00004596812,0.0001760331,0.00009165004,0.0000869865,0.00002624674,0.000003065525,0.0002725394],"genre_scores_gemma":[0.9975517,0.000474132,0.001633854,0.00001865531,0.0000297206,0.000005544991,0.00002686231,0.000006856279,0.0002526663],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2451825,"threshold_uncertainty_score":0.395571,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01337352664042942,"score_gpt":0.2557808569179084,"score_spread":0.242407330277479,"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."}}