{"id":"W4389882912","doi":"10.1101/2023.12.16.23300077","title":"Strain-level characterization of health-associated bacterial consortia that colonize the human gut during infancy","year":2023,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"National Institute of Allergy and Infectious Diseases; National Institutes of Health; Fred Hutchinson Cancer Research Center","keywords":"Metagenomics; Microbiome; Cohort; Biology; Gut microbiome; Cohort study; Cystic fibrosis; Strain (injury); Human microbiome; Gut flora; Genetics; Gene; Medicine; Immunology; Internal medicine","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006382531,0.0003010621,0.0004661599,0.001062955,0.0002819166,0.0007233725,0.0002006889,0.0003611672,0.0008039526],"category_scores_gemma":[0.001251664,0.0001965176,0.0004118944,0.001050067,0.0002268423,0.000320323,0.0007293966,0.0003678616,0.0003599785],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001363852,"about_ca_system_score_gemma":0.0002377676,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001250495,"about_ca_topic_score_gemma":0.001252896,"domain_scores_codex":[0.9995195,0.00008796902,0.00004177956,0.0001850432,0.0000926033,0.00007312569],"domain_scores_gemma":[0.9994171,0.0001192667,0.0002013202,0.00006630812,0.0001168117,0.00007929961],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0007545889,0.00009376767,0.5904697,0.0003656474,0.0003090395,0.0002574714,0.0006137233,0.000684731,0.385392,0.000239687,0.000658869,0.02016083],"study_design_scores_gemma":[0.00001387669,0.0002662182,0.9696522,0.00005805682,0.0001494752,0.0006451232,0.0005027915,0.00161476,0.02390459,0.0003014453,0.002866017,0.00002549157],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9920236,0.001944518,0.00141869,0.00006863502,0.0000130368,0.00001679143,0.004142318,0.00002415915,0.0003482969],"genre_scores_gemma":[0.9892113,0.0008735217,0.003525886,0.00007211236,0.00002086983,0.00004920976,0.005881683,0.00002468979,0.0003406852],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001250495,"threshold_uncertainty_score":0.003375411,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06234482107486843,"score_gpt":0.3096987188006159,"score_spread":0.2473538977257475,"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."}}