{"id":"W4291178371","doi":"10.1186/s42523-022-00197-6","title":"Does swab type matter? Comparing methods for Mannheimia haemolytica recovery and upper respiratory microbiome characterization in feedlot cattle","year":2022,"lang":"en","type":"article","venue":"Animal Microbiome","topic":"Microbial infections and disease research","field":"Immunology and Microbiology","cited_by":20,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"Texas A and M University","keywords":"Bovine respiratory disease; Biology; Veterinary medicine; McNemar's test; Microbiology; 16S ribosomal RNA; Concordance; Microbiome; Medicine; Bacteria; Bioinformatics","routes":{"ca_aff":true,"ca_fund":false,"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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0006916983,0.0002538199,0.000417905,0.0006016432,0.0005496768,0.0000893262,0.0002397344,0.0001649881,0.002097149],"category_scores_gemma":[0.00003626086,0.0002212698,0.0001138285,0.0005197776,0.0001971047,0.0001782934,0.000458626,0.0003544041,0.0002371653],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002099534,"about_ca_system_score_gemma":0.0001285067,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001536178,"about_ca_topic_score_gemma":0.00002168553,"domain_scores_codex":[0.9978825,0.0004615646,0.0004452371,0.0005929189,0.00002608465,0.0005916279],"domain_scores_gemma":[0.9992906,0.0001539146,0.0001268255,0.0002874764,0.00009189484,0.00004923558],"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":[0.0008362462,0.0002415684,0.009142387,0.00008680839,0.00009762541,0.000002370284,0.0001446322,0.000003740311,0.9844167,0.000111448,0.003178231,0.001738242],"study_design_scores_gemma":[0.003444978,0.001034266,0.1264491,0.00007913538,0.0001045088,0.0002474064,0.0003229009,0.00001993137,0.4946326,0.000156049,0.372638,0.0008711358],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9953522,0.001399676,0.0003135795,0.0004368586,0.0008940082,0.0007634324,0.0006153045,0.00006126133,0.0001636746],"genre_scores_gemma":[0.992905,0.00005857956,0.0009033849,0.0008958533,0.00006174305,0.0001967428,0.001552142,0.00007285357,0.003353659],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4897841,"threshold_uncertainty_score":0.9988151,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03133093191217245,"score_gpt":0.3330294989150029,"score_spread":0.3016985670028305,"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."}}