{"id":"W4415204255","doi":"10.3390/genes16101218","title":"Genomic Relationship Between Brochothrix campestris and Its Phages: A Cross-Replicon and Interspecies Perspective","year":2025,"lang":"en","type":"article","venue":"Genes","topic":"Insect and Arachnid Ecology and Behavior","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval; Ministère de l'Agriculture, des Pêcheries et de l'Alimentation","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Genome; Plasmid; Gene; Nanopore sequencing; Genomics; Strain (injury); Horizontal gene transfer; Bacteriocin; Genome evolution","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":[0.00007377611,0.0001010008,0.0001030784,0.00004982336,0.0002077526,0.00003426335,0.00006392226,0.0001491254,0.00001151922],"category_scores_gemma":[0.0000577907,0.00009679612,0.00003204151,0.00004565948,0.0001146423,0.000005563751,0.00008731445,0.00007557847,0.000004668423],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001319442,"about_ca_system_score_gemma":0.00003411005,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001619601,"about_ca_topic_score_gemma":0.00004370252,"domain_scores_codex":[0.9994432,0.00002718349,0.0001058843,0.0002691395,0.00002334459,0.0001312618],"domain_scores_gemma":[0.9997454,0.00003040155,0.00003259538,0.0001086877,0.00005090921,0.00003195961],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00003251197,0.00001330061,0.7187054,0.00001226389,0.00002948035,0.000001239844,0.0001957619,7.71379e-7,0.2792144,0.0009532166,0.0001448856,0.0006967349],"study_design_scores_gemma":[0.0003855551,0.00009284828,0.8396828,0.000007204493,0.00004238899,0.000008030681,0.0004936767,0.000001961853,0.1573667,0.000457921,0.001344938,0.0001160266],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.990881,0.008130924,0.00007118871,0.0002079509,0.00008196411,0.0001227856,0.00002014248,0.00001128017,0.0004727819],"genre_scores_gemma":[0.9957253,0.0003305672,0.00006108263,0.0001052254,0.0001263555,0.00001771551,0.0000241069,0.000006333956,0.003603315],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1218477,"threshold_uncertainty_score":0.3947231,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02011176094504181,"score_gpt":0.3139289189233307,"score_spread":0.2938171579782889,"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."}}