{"id":"W4308298765","doi":"10.1186/s40104-022-00779-z","title":"Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis","year":2022,"lang":"en","type":"article","venue":"Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology","topic":"Milk Quality and Mastitis in Dairy Cows","field":"Agricultural and Biological Sciences","cited_by":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Université Laval; McGill University; Agriculture and Agri-Food Canada","funders":"Agriculture and Agri-Food Canada; China Scholarship Council","keywords":"Streptococcus uberis; DNA methylation; Biology; Methylation; Epigenetics; Genetics; Gene; Bisulfite sequencing; Transcriptome; CpG site; Promoter; Differentially methylated regions; Gene expression; Streptococcus","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":["sts"],"consensus_categories":[],"category_scores_codex":[0.008387802,0.0002261687,0.0007169662,0.0006621949,0.0006577118,0.0001032115,0.001351954,0.0003496966,0.00003424622],"category_scores_gemma":[0.001264735,0.0001165847,0.00008116924,0.002308007,0.007324746,0.001191085,0.001074174,0.0007449128,1.14964e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006831073,"about_ca_system_score_gemma":0.0002759945,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001067595,"about_ca_topic_score_gemma":0.000139565,"domain_scores_codex":[0.9964255,0.0001475687,0.001305574,0.000548645,0.001129674,0.0004430349],"domain_scores_gemma":[0.9971326,0.0001798854,0.00160778,0.0001653811,0.0006980408,0.0002163422],"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":[0.0006254975,0.00009683504,0.001370624,0.00001717764,0.00003104766,0.00003482097,0.0001148629,4.892659e-7,0.902694,0.001648891,0.00005211621,0.09331364],"study_design_scores_gemma":[0.001673498,0.03310036,0.1793068,0.0002457224,0.0002916115,0.005071454,0.01385558,0.0009629677,0.7570405,0.004335056,0.003532605,0.0005838563],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9845092,0.002146172,0.00008088614,0.01276485,0.0001606875,0.000180766,0.0001328806,0.00001342762,0.00001109248],"genre_scores_gemma":[0.9940605,0.004349158,0.001436111,0.00008678705,0.00005986479,0.000001146721,0.000002465968,0.000001922895,0.000002064589],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1779362,"threshold_uncertainty_score":0.9953768,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03350255176201836,"score_gpt":0.2897813553712412,"score_spread":0.2562788036092228,"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."}}