{"id":"W3175676175","doi":"10.3201/eid2707.204403","title":"Whole-Genome Analysis of <i>Streptococcus pneumoniae</i> Serotype 4 Causing Outbreak of Invasive Pneumococcal Disease, Alberta, Canada","year":2021,"lang":"en","type":"article","venue":"Emerging infectious diseases","topic":"Pneumonia and Respiratory Infections","field":"Medicine","cited_by":34,"is_retracted":false,"has_abstract":true,"ca_institutions":"Calgary Laboratory Services; Public Health Agency of Canada; University of Alberta; University of Calgary","funders":"Alberta Health Services","keywords":"Serotype; Streptococcus pneumoniae; Outbreak; Pneumonia; Lineage (genetic); Biology; Pneumococcal infections; Pneumococcal disease; Clade; Virology; Disease; Medicine; Phylogenetic tree; Microbiology; Genetics; Antibiotics; Gene; Internal medicine","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"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":[0.0003235108,0.0004128229,0.0003113413,0.001337114,0.001362828,0.0007277573,0.0005198878,0.000249029,0.0006228357],"category_scores_gemma":[0.0005653088,0.0001957111,0.0004664108,0.002410278,0.000322383,0.00008058658,0.000349377,0.000422727,0.0001469867],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00972488,"about_ca_system_score_gemma":0.01165587,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.9766501,"about_ca_topic_score_gemma":0.9815415,"domain_scores_codex":[0.9996564,0.00002423417,0.00001406487,0.00005899148,0.0001409126,0.0001054067],"domain_scores_gemma":[0.9995839,0.00003298689,0.00005756704,0.00001282363,0.0002234048,0.00008931102],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0009157786,0.0002110153,0.9150693,0.0001854022,0.0002795536,0.001524332,0.001418505,0.003620895,0.04818629,0.0004337989,0.005114787,0.02304034],"study_design_scores_gemma":[0.000009552919,0.00003533366,0.9959729,0.00001258919,0.00003761489,0.0001232343,0.0006187716,0.0007642618,0.0006000953,0.00002206264,0.001796085,0.000007294246],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9874846,0.0004959688,0.0003641012,0.0001929781,0.00001937974,0.00005946335,0.009094574,0.00002942153,0.002259329],"genre_scores_gemma":[0.9828404,0.0006696928,0.001604698,0.0002368321,0.000009411347,0.00002009212,0.01274646,0.00001436886,0.001858077],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02334988,"threshold_uncertainty_score":0.07055932,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008512249669151742,"score_gpt":0.2468217281447363,"score_spread":0.2383094784755846,"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."}}