{"id":"W4407143766","doi":"10.1186/s40168-025-02039-4","title":"Quantitative profiling of the vaginal microbiota improves resolution of the microbiota-immune axis","year":2025,"lang":"en","type":"article","venue":"Microbiome","topic":"Reproductive tract infections research","field":"Immunology and Microbiology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"Toronto General Hospital; McMaster University; University of Toronto; University Health Network","funders":"Canadian Institutes of Health Research","keywords":"Bacterial vaginosis; Biology; Immunology; Proinflammatory cytokine; Lactobacillus; Lactobacillus crispatus; Sex organ; Immune system; Cohort; Medical microbiology; Metagenomics; Microbiology; Bacteria; Internal medicine; Medicine; Inflammation","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":[0.0007975623,0.0002547278,0.0004313451,0.0003375004,0.0004482586,0.00001854729,0.0009793122,0.0002785749,0.00009197773],"category_scores_gemma":[0.00039824,0.0001600446,0.0003719348,0.001584453,0.00194844,0.0001038706,0.0006353337,0.0006699894,0.00006727907],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001644177,"about_ca_system_score_gemma":0.0003800276,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005172628,"about_ca_topic_score_gemma":0.00003435848,"domain_scores_codex":[0.9976275,0.0006578116,0.0007108817,0.0004959914,0.00005513629,0.000452683],"domain_scores_gemma":[0.9975663,0.000226375,0.000420271,0.001240339,0.000537003,0.000009747593],"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":[0.000203155,0.0003285577,0.001964095,0.0001700026,0.0003925018,1.816555e-7,0.0003011876,0.00001305226,0.9920051,0.002279584,0.001905095,0.0004374883],"study_design_scores_gemma":[0.000724471,0.0001172756,0.04959198,0.000216557,0.00007834339,0.00004144184,0.0002662247,0.000002287081,0.939974,0.0001369031,0.008716226,0.0001342797],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9887752,0.005237876,0.0001944171,0.001396653,0.001782194,0.001156258,0.0002366709,0.00003352733,0.001187236],"genre_scores_gemma":[0.9902551,0.00003803872,0.0005904009,0.00004765659,0.00001276332,0.00002724786,0.00003678127,0.00002033325,0.00897174],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05203109,"threshold_uncertainty_score":0.717911,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01439025357474154,"score_gpt":0.2894393909719969,"score_spread":0.2750491373972553,"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."}}