{"id":"W2314506682","doi":"10.3389/fmicb.2016.00426","title":"The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis","year":2016,"lang":"en","type":"article","venue":"Frontiers in Microbiology","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":56,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary; University of Manitoba","funders":"","keywords":"Biology; Mycobacterium avium subspecies paratuberculosis; Paratuberculosis; Dysbiosis; Akkermansia; Microbiology; Microbiome; Feces; Bacteroides; Gut flora; Eubacterium; Lachnospiraceae; Mycobacterium; Immunology; Bacteria; 16S ribosomal RNA; Genetics; Firmicutes","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":[],"consensus_categories":[],"category_scores_codex":[0.0003129837,0.000201673,0.0004737329,0.0002807816,0.00008468015,0.00002320546,0.0001046482,0.0002591415,0.00001797156],"category_scores_gemma":[0.0002220701,0.0001115578,0.00006751099,0.0002874,0.0005826878,0.00009625092,0.00008766101,0.0002967325,0.00000304557],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000218746,"about_ca_system_score_gemma":0.00007687679,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005461433,"about_ca_topic_score_gemma":0.001558356,"domain_scores_codex":[0.9984474,0.0002688813,0.0003257994,0.0003456112,0.00005964514,0.0005526841],"domain_scores_gemma":[0.9992743,0.0002033532,0.0001133882,0.0002308648,0.00008805095,0.00009004593],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0008624641,0.00007001702,0.5493825,0.00003708476,0.0000710992,0.00001399172,0.0001638057,8.517252e-8,0.4471245,0.000008261037,0.001955726,0.0003104866],"study_design_scores_gemma":[0.002718793,0.000429561,0.9375138,0.0002651949,0.00003009923,0.00008542829,0.0001021068,4.165874e-7,0.0578804,0.00002494598,0.0008152964,0.0001339851],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9969053,0.001143151,0.00001101011,0.001055221,0.0003243039,0.0003825561,0.0000801185,0.00002019995,0.00007812206],"genre_scores_gemma":[0.9970798,0.002215126,0.0001846348,0.00004708235,0.00005692684,0.00003800295,0.00003714741,0.00001931093,0.0003219167],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3892441,"threshold_uncertainty_score":0.4549196,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005042381388188166,"score_gpt":0.2195326308174317,"score_spread":0.2144902494292436,"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."}}