{"id":"W4392804826","doi":"10.1186/s12915-024-01843-y","title":"DNA methylation haplotype block signatures responding to Staphylococcus aureus subclinical mastitis and association with production and health traits","year":2024,"lang":"en","type":"article","venue":"BMC Biology","topic":"Milk Quality and Mastitis in Dairy Cows","field":"Agricultural and Biological Sciences","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Université Laval; Agriculture and Agri-Food Canada","funders":"Agriculture and Agri-Food Canada; China Scholarship Council","keywords":"DNA methylation; Biology; Methylation; Mastitis; Differentially methylated regions; Staphylococcus aureus; Somatic cell count; Gene; Genetics; Subclinical infection; Bisulfite sequencing; Gene expression; Microbiology; Lactation; Virology; 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":[0.001069906,0.0001065883,0.0001745022,0.00005299643,0.0001580865,0.00005832763,0.00005666452,0.0001731283,0.00003231995],"category_scores_gemma":[0.0004204181,0.00004555935,0.00002315654,0.000387154,0.00004868834,0.00007785578,0.00004277467,0.0001621808,0.000006339142],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004759912,"about_ca_system_score_gemma":0.00002571829,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008603762,"about_ca_topic_score_gemma":0.00475542,"domain_scores_codex":[0.9987897,0.0002800092,0.000203136,0.0004182424,0.00009567974,0.0002132407],"domain_scores_gemma":[0.9993258,0.0004397376,0.00006831804,0.00003082142,0.00004174275,0.00009362141],"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":[0.0007238387,0.0001189876,0.1005493,0.0002312939,0.0001301848,0.000008413035,0.00139902,0.0000732446,0.5512363,0.03778426,0.01407608,0.293669],"study_design_scores_gemma":[0.000218398,0.002436058,0.8745529,0.0001838222,0.00003502853,0.0000137556,0.0002518157,0.0001260565,0.002306898,0.003650162,0.115865,0.0003600525],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9843852,0.001769481,0.0001284206,0.01285438,0.0003234131,0.0003106889,0.00005768544,0.0001012493,0.00006949412],"genre_scores_gemma":[0.9976541,0.0001822231,0.0006981688,0.0004008894,0.0004385189,0.00001814124,0.00004002686,0.000001426594,0.0005664865],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7740036,"threshold_uncertainty_score":0.2653636,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05009373789955424,"score_gpt":0.3137460765741713,"score_spread":0.263652338674617,"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."}}