{"id":"W2793794831","doi":"10.1101/261586","title":"Whole genome sequencing reveals the emergence of a <i>Pseudomonas aeruginosa</i> shared strain sub-lineage among patients treated within a single cystic fibrosis centre","year":2018,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Plant Pathogenic Bacteria Studies","field":"Agricultural and Biological Sciences","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Health and Medical Research Council; Medical Research Council; Children's Health Foundation; Australian Cystic Fibrosis Research Trust; Cystic Fibrosis in Australia; Queensland Health; Prince Charles Hospital Foundation; Cystic Fibrosis Foundation","keywords":"Biology; Genome; Lineage (genetic); Monophyly; Genetics; Context (archaeology); Whole genome sequencing; Pseudomonas aeruginosa; Phylogenetics; Phylogenetic tree; Strain (injury); Gene; Clade; Bacteria","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002021984,0.0001664976,0.000381118,0.0004354079,0.0005110496,0.0006228141,0.0002711443,0.0006272864,0.001148528],"category_scores_gemma":[0.0008606607,0.0001484716,0.0004416411,0.0009718446,0.0003360395,0.0002014305,0.00045086,0.0005774216,0.000285282],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000329873,"about_ca_system_score_gemma":0.0003217566,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.008316785,"about_ca_topic_score_gemma":0.009993047,"domain_scores_codex":[0.9995908,0.00007262557,0.00002706172,0.0001448358,0.00006497646,0.00009979693],"domain_scores_gemma":[0.9993141,0.0001529005,0.0002616816,0.00004500671,0.00008232213,0.0001439793],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0003115507,0.00004962244,0.9422148,0.00006182725,0.0001644449,0.001159341,0.001346987,0.0002737122,0.04697547,0.00009052569,0.0005575773,0.006794165],"study_design_scores_gemma":[0.000005201698,0.00007921502,0.9964581,0.00001234193,0.00003720864,0.0009589831,0.0006952913,0.000474768,0.0007032942,0.00003973248,0.0005296785,0.000006101594],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9993747,0.0000900597,0.00009876654,0.00004427712,0.000001767782,0.000003263917,0.0002506636,0.000004391481,0.0001321711],"genre_scores_gemma":[0.9990221,0.00004570358,0.0002673549,0.00006768836,0.000003719616,0.00000370136,0.0005151369,0.000005667412,0.00006898239],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.008316785,"threshold_uncertainty_score":0.01653677,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01827127867811966,"score_gpt":0.185933609792663,"score_spread":0.1676623311145434,"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."}}