{"id":"W4415673178","doi":"10.3390/microorganisms13112473","title":"Genomic Drivers of Biofilm Formation in Salmonella Enteritidis and S. Kentucky from Poultry Production","year":2025,"lang":"en","type":"article","venue":"Microorganisms","topic":"Bacterial biofilms and quorum sensing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Agriculture and Agri-Food Canada; Public Health Agency of Canada; University of Manitoba","funders":"Agriculture and Agri-Food Canada; Mitacs; Canadian Poultry Research Council","keywords":"Biofilm; Gene; Phylogenetic tree; Phenotype; Salmonella enteritidis; Nonsynonymous substitution; Strain (injury)","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":[0.00005198888,0.00008158985,0.0001018244,0.00005191819,0.00002992331,0.00001352726,0.00004929583,0.0001012037,0.000006444764],"category_scores_gemma":[0.00001489977,0.00008586374,0.00002328383,0.00006568494,0.00004495712,0.00000567145,0.00006651801,0.00003919,0.000001990158],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001675757,"about_ca_system_score_gemma":0.00001707478,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001243466,"about_ca_topic_score_gemma":0.00004983915,"domain_scores_codex":[0.9994743,0.00002476151,0.000172999,0.0002003048,0.0000265833,0.000101053],"domain_scores_gemma":[0.9997649,0.000002549978,0.00005585301,0.0001355567,0.00002467798,0.00001652713],"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":[0.00004910932,0.00002079441,0.01020652,0.00001770144,0.00001248539,6.937336e-7,0.0001053261,9.867326e-7,0.9878037,0.00001099257,0.0002794699,0.0014922],"study_design_scores_gemma":[0.0003217464,0.00003458934,0.03346552,0.00003521629,0.000009763493,0.0000056091,0.0003018957,0.000002726828,0.9640365,0.00003112006,0.00167941,0.00007586226],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9988728,0.0003610693,0.00007355586,0.0002113584,0.00022212,0.0001107549,0.0000272271,0.000005349456,0.0001158321],"genre_scores_gemma":[0.9982498,0.0002999946,0.001037329,0.00008003141,0.00005208002,0.000001065508,0.0001596823,0.000007361422,0.000112651],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02376718,"threshold_uncertainty_score":0.3501422,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004087697036246526,"score_gpt":0.1985714821832376,"score_spread":0.1944837851469911,"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."}}