{"id":"W2951216710","doi":"10.1101/386078","title":"Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis","year":2018,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Pneumonia and Respiratory Infections","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"NIHR Oxford Biomedical Research Centre; Rijksinstituut voor Volksgezondheid en Milieu; Fonden til Lægevidenskabens Fremme; Wageningen University and Research; Medical Research Council; Ministerie van Economische Zaken, Landbouw en Innovatie; Novo Nordisk Fonden; H. Lundbeck A/S; Lægeforeningen; U.S. Public Health Service; Lundbeckfonden; Nederlandse Zuivel Organisatie; Erasmus Medisch Centrum; March of Dimes Foundation; Dagmar Marshalls Fond; ZonMw; Sundhed og Sygdom, Det Frie Forskningsråd; National Research Foundation; European Commission; Egmont Fonden; A.P. Møller og Hustru Chastine Mc-Kinney Møllers Fond til almene Formaal; Royal Society; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Danmarks Grundforskningsfond; Wellcome Trust; Ministerie van Volksgezondheid, Welzijn en Sport; Augustinus Fonden; Novo Nordisk; National Institute for Health and Care Research","keywords":"Streptococcus pneumoniae; Meningitis; Biology; Pathogen; Serotype; Genetic variation; Human pathogen; Bacteremia; Genome; Pneumococcal disease; Genetics; Microbiology; Gene; Immunology; Virology; Antibiotics; 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":[0.0005840097,0.0003555833,0.0004325323,0.0006635108,0.0003142644,0.0008019086,0.0001699307,0.0005535344,0.001965757],"category_scores_gemma":[0.0008931456,0.0002154246,0.0004700285,0.001071313,0.0001893742,0.0001612343,0.0004969164,0.0007062827,0.0005343739],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002507319,"about_ca_system_score_gemma":0.0004040104,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003026215,"about_ca_topic_score_gemma":0.003984393,"domain_scores_codex":[0.9996755,0.00008722841,0.00001701069,0.0001078536,0.00006942693,0.0000428519],"domain_scores_gemma":[0.999637,0.0001124488,0.00008316027,0.00005155061,0.00003729439,0.00007845409],"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":[0.002691083,0.0003167334,0.3961552,0.0006382221,0.001690125,0.00222527,0.000994017,0.006846657,0.4447038,0.005528838,0.01532382,0.1228862],"study_design_scores_gemma":[0.0001171302,0.0003846747,0.9036134,0.0001446125,0.0005886008,0.001867516,0.0005560198,0.01291633,0.03263747,0.007389164,0.03973073,0.00005432888],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9689062,0.00352453,0.01092931,0.001292924,0.0001514259,0.00002677809,0.01195045,0.0002218556,0.002996431],"genre_scores_gemma":[0.9776881,0.001446146,0.008800199,0.0003847603,0.00009917063,0.00002077501,0.009326233,0.0001063107,0.002128228],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003026215,"threshold_uncertainty_score":0.006576121,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03138233413500618,"score_gpt":0.2558449807210822,"score_spread":0.224462646586076,"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."}}