{"id":"W4415647114","doi":"10.3390/bacteria4040055","title":"Genomic Mapping of Brazilian Escherichia coli: Characterizing Shiga Toxin-Producing, Enteropathogenic, and Diffusely Adherent Strains Using an In Silico Approach","year":2025,"lang":"en","type":"article","venue":"Bacteria","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Lethbridge","funders":"Fundação de Amparo à Pesquisa do Estado de Mato Grosso; Conselho Nacional de Desenvolvimento Científico e Tecnológico; Mitacs; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; Results Driven Agriculture Research","keywords":"In silico; Genome; Context (archaeology); Resistome; Phylogenetic tree; Clade; Escherichia coli; Multilocus sequence typing","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":[0.0003575796,0.0002389273,0.0003461319,0.0001262073,0.00009156855,0.00005959055,0.0002518983,0.0001300218,0.000008601474],"category_scores_gemma":[0.00008056887,0.000248582,0.000062525,0.0001936137,0.0001328554,0.0000158599,0.0004259173,0.0001535159,4.671213e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005499538,"about_ca_system_score_gemma":0.0001588528,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008539098,"about_ca_topic_score_gemma":0.0001220807,"domain_scores_codex":[0.9983407,0.0001618578,0.0003892918,0.0006134317,0.0001018509,0.0003928827],"domain_scores_gemma":[0.99927,0.000007592596,0.0001293817,0.0004417545,0.00006156524,0.00008974677],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00007391099,0.0002122138,0.06442395,0.0001574195,0.00006858024,0.000002378367,0.0005284605,0.0000052743,0.9335722,0.00002111983,0.000009395425,0.0009250394],"study_design_scores_gemma":[0.0008326981,0.0001613662,0.8103345,0.00009248406,0.00001835606,0.000004516243,0.00062885,0.0004141796,0.1865363,0.00000966604,0.0007203167,0.00024678],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9984413,0.0004781215,0.0002021583,0.00003689801,0.0001129907,0.0004599371,0.00004211368,0.00001287872,0.0002136493],"genre_scores_gemma":[0.995407,0.0002133692,0.003918083,0.0001185876,0.00009907062,0.00004571076,0.00006943628,0.00002794588,0.0001008384],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.747036,"threshold_uncertainty_score":0.9999967,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02831089683505343,"score_gpt":0.2837528553893318,"score_spread":0.2554419585542783,"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."}}