{"id":"W3127018168","doi":"10.1099/mgen.0.000511","title":"Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Cystic Fibrosis Research Advances","field":"Medicine","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"National Health and Medical Research Council; Cystic Fibrosis Trust; Cystic Fibrosis Canada","keywords":"Prophage; Biology; Genome; Lineage (genetic); Phylogenetic tree; Population genomics; Genetics; Whole genome sequencing; Clade; Strain (injury); Comparative genomics; Population; Multilocus sequence typing; Genomics; Gene; Genotype; Medicine; Bacteriophage","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002041889,0.0001142617,0.0002512844,0.00005328984,0.00007642299,0.00001455847,0.00009915376,0.0000872425,0.00008495816],"category_scores_gemma":[0.0002120333,0.00008776738,0.0001229773,0.0002180085,0.0002583416,0.00004000388,0.00007272563,0.0002367829,0.000003830983],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004686747,"about_ca_system_score_gemma":0.0003074702,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006086106,"about_ca_topic_score_gemma":0.00006440472,"domain_scores_codex":[0.9989676,0.0001005415,0.0002934575,0.000250959,0.0001668799,0.0002206],"domain_scores_gemma":[0.9992633,0.0001577307,0.0000708461,0.0002506298,0.0001345103,0.0001230198],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.000175064,0.0000672258,0.00141559,0.0001187689,0.00003782976,0.00001260834,0.0004177727,0.00008250876,0.964875,0.0001349296,0.0003344346,0.03232826],"study_design_scores_gemma":[0.004991448,0.0004175219,0.1218341,0.0007357048,0.0003264592,0.0009542881,0.001281976,0.003373936,0.7234074,0.001561079,0.1406738,0.0004422028],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9898607,0.002528598,0.004729492,0.002180114,0.00008466896,0.0003653784,0.0001183404,0.00001525854,0.0001174174],"genre_scores_gemma":[0.9683331,0.001246695,0.02956211,0.0003102597,0.0001011865,0.000005497593,0.00005629079,0.00002235767,0.0003624789],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2414676,"threshold_uncertainty_score":0.357905,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01812040175098389,"score_gpt":0.2624197849440496,"score_spread":0.2442993831930657,"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."}}