{"id":"W2136134669","doi":"10.1128/jb.187.10.3311-3318.2005","title":"Mosaic Prophages with Horizontally Acquired Genes Account for the Emergence and Diversification of the Globally Disseminated M1T1 Clone of <i>Streptococcus pyogenes</i>","year":2005,"lang":"en","type":"article","venue":"Journal of Bacteriology","topic":"Streptococcal Infections and Treatments","field":"Medicine","cited_by":124,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Mount Sinai Hospital","funders":"National Institutes of Health; National Institute of Allergy and Infectious Diseases; U.S. Department of Veterans Affairs","keywords":"Biology; Prophage; Streptococcus pyogenes; clone (Java method); Gene; Genetics; Diversification (marketing strategy); Streptococcus pneumoniae; Virology; Microbiology; Bacteriophage; Bacteria; Staphylococcus aureus; Escherichia coli","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":[0.0001331875,0.0001007293,0.0002785274,0.00004010183,0.00007609334,0.000005372388,0.00011881,0.00006198319,0.00002778999],"category_scores_gemma":[0.00004272045,0.00004592336,0.0001027683,0.0001250934,0.0002060012,0.00007179766,0.00003333966,0.0000513545,3.068304e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003341492,"about_ca_system_score_gemma":0.00009663848,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003196484,"about_ca_topic_score_gemma":0.00002033719,"domain_scores_codex":[0.9992869,0.00003325538,0.0003669966,0.00009834066,0.0001089453,0.0001055867],"domain_scores_gemma":[0.9987938,0.00008575174,0.0005632644,0.0001733891,0.000344405,0.00003934104],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0009498897,0.0002851287,0.3576145,0.00004970606,0.0005041287,0.000003143077,0.0001371102,0.00005671539,0.6162351,0.00003960573,0.0002103922,0.02391455],"study_design_scores_gemma":[0.001587625,0.00197489,0.8988101,0.00009370344,0.0004812036,0.0002510754,0.0001960337,0.00003806639,0.09540229,0.00001262259,0.001101282,0.0000510655],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9970375,0.00105983,0.0001915804,0.0009482061,0.0001249632,0.0005786077,0.00003222657,0.000003392544,0.0000236986],"genre_scores_gemma":[0.998821,0.0004952832,0.0004677951,0.00003452785,0.00008753455,0.00002308859,0.000005062702,0.0000069345,0.00005874018],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5411957,"threshold_uncertainty_score":0.18727,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01363052781820529,"score_gpt":0.2690178834476356,"score_spread":0.2553873556294303,"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."}}