{"id":"W4310045830","doi":"10.1186/s42523-022-00211-x","title":"A longitudinal census of the bacterial community in raw milk correlated with Staphylococcus aureus clinical mastitis infections in dairy cattle","year":2022,"lang":"en","type":"article","venue":"Animal Microbiome","topic":"Milk Quality and Mastitis in Dairy Cows","field":"Agricultural and Biological Sciences","cited_by":17,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; McGill University; Cegep de Saint Hyacinthe","funders":"Natural Sciences and Engineering Research Council of Canada; Dairy Farmers of Canada","keywords":"Mastitis; Staphylococcus aureus; Udder; Microbiome; Biology; Microbiology; Dairy cattle; Staphylococcal infections; Staphylococcus epidermidis; Staphylococcus; Somatic cell count; Veterinary medicine; Lactation; Bacteria; Ice calving; Medicine; Animal science; Pregnancy; Bioinformatics","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":[0.0007119414,0.0001300523,0.0002578471,0.00003408887,0.0003708329,0.00001881243,0.0004438949,0.00008827748,0.0007436186],"category_scores_gemma":[0.00007689179,0.00005737306,0.00009859722,0.0009342284,0.0002868227,0.00006425146,0.000482256,0.0007496857,0.000005075745],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007478012,"about_ca_system_score_gemma":0.00004189725,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.009333877,"about_ca_topic_score_gemma":0.05329188,"domain_scores_codex":[0.9979706,0.0009834105,0.0004506966,0.0002158729,0.0001217172,0.0002576501],"domain_scores_gemma":[0.9992869,0.0003455725,0.0001537963,0.0001312087,0.00003914805,0.00004329628],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0009014854,0.001852875,0.514909,0.00002174724,0.00003163,0.00002626598,0.0005513055,0.0001457734,0.4772795,0.0002384844,0.002481751,0.001560153],"study_design_scores_gemma":[0.0008387344,0.001301548,0.9858883,0.00004192641,0.00001109646,0.00003520429,0.0006245469,0.00001027634,0.0007254275,0.00006316767,0.0103023,0.0001574555],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979683,0.00005490985,5.983716e-7,0.0004744715,0.0003703096,0.0002823382,0.0006350026,0.00002025054,0.0001938053],"genre_scores_gemma":[0.9995591,0.00001218279,0.00001815742,0.0000994929,0.00005559948,0.00002565433,0.0001581451,0.000001584005,0.00007006189],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4765541,"threshold_uncertainty_score":0.9972631,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04339110574913259,"score_gpt":0.267133586358333,"score_spread":0.2237424806092004,"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."}}