{"id":"W4383187643","doi":"10.1186/s13073-023-01200-8","title":"Phylogenomic insights into evolutionary trajectories of multidrug resistant S. pneumoniae CC271 over a period of 14 years in China","year":2023,"lang":"en","type":"article","venue":"Genome Medicine","topic":"Pneumonia and Respiratory Infections","field":"Medicine","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"Chinese Academy of Sciences","keywords":"Phylogenetic tree; Biology; Streptococcus pneumoniae; Multiple drug resistance; Genetics; Population; clone (Java method); Multilocus sequence typing; China; Evolutionary biology; Phylogenetics; Gene; Drug resistance; Genotype; Demography; Geography; Antibiotics","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":[0.001060961,0.0004083893,0.0005451459,0.003018505,0.0007596148,0.0005827153,0.0004343986,0.0003364593,0.000733518],"category_scores_gemma":[0.00127922,0.0002041261,0.0007199528,0.004404385,0.0003427663,0.0003728047,0.0006738539,0.0002639939,0.00013493],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001283871,"about_ca_system_score_gemma":0.001206864,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.02756272,"about_ca_topic_score_gemma":0.02538346,"domain_scores_codex":[0.999508,0.0000671792,0.00003232014,0.0001472899,0.0001066125,0.000138532],"domain_scores_gemma":[0.9991081,0.0001303642,0.0002778253,0.00007282299,0.0002402683,0.000170506],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001609335,0.00002310035,0.9742283,0.00007179535,0.0001837715,0.000354409,0.001142817,0.002613894,0.01100089,0.0002207213,0.000260308,0.009739253],"study_design_scores_gemma":[0.000002891559,0.00003029925,0.9962657,0.000006058324,0.00003910689,0.00007163708,0.0002733669,0.002550156,0.0002460444,0.00004901754,0.0004575949,0.000008148457],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9989033,0.0002034731,0.0002051098,0.00002848476,0.00000114039,0.00000585232,0.000463885,0.000004374073,0.0001843104],"genre_scores_gemma":[0.9981914,0.0001452811,0.0002686356,0.00001616319,0.000003064028,0.00001101208,0.001225902,0.000004139747,0.0001343906],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02756272,"threshold_uncertainty_score":0.05480456,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01084803640362364,"score_gpt":0.2617295564075089,"score_spread":0.2508815200038852,"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."}}