{"id":"W2146862880","doi":"10.1128/jb.186.2.400-410.2004","title":"Complete Sequence and Evolutionary Genomic Analysis of the <i>Pseudomonas aeruginosa</i> Transposable Bacteriophage D3112","year":2003,"lang":"en","type":"article","venue":"Journal of Bacteriology","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":75,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"","keywords":"Biology; Prophage; Genetics; Transposable element; Bacteriophage; Genome; Lysogenic cycle; Phylogenetic tree; Gene; Horizontal gene transfer; Temperateness; Escherichia coli","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":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0002570818,0.0001401158,0.0004305195,0.0001017513,0.0001204328,0.00001581401,0.0002728196,0.00008238106,0.002168255],"category_scores_gemma":[0.00003041468,0.0000998102,0.0002821113,0.0003762284,0.0004262685,0.0002429269,0.00006987282,0.0002343934,0.00001543708],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001202406,"about_ca_system_score_gemma":0.00003756441,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001061081,"about_ca_topic_score_gemma":0.0001092356,"domain_scores_codex":[0.9987224,0.0002327354,0.0005612805,0.0001699241,0.0001008418,0.0002128354],"domain_scores_gemma":[0.9990631,0.00009068341,0.0005083509,0.0002191343,0.00003254871,0.00008622489],"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":[0.00004082514,0.00004874043,0.04302619,0.000004971442,0.0002187763,0.000008530446,0.0001746984,0.0004220615,0.9556441,0.00004712697,0.000122418,0.0002415123],"study_design_scores_gemma":[0.0003387332,0.000138731,0.9622155,0.00001587146,0.0004767278,0.0006735571,0.00005245405,0.00008288246,0.00473396,0.00009430946,0.03105659,0.0001206372],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9981981,0.000156931,0.0001398465,0.0002497891,0.000355111,0.00008231182,0.00008671535,0.000003393824,0.0007277935],"genre_scores_gemma":[0.9978705,0.0001621747,0.001488474,0.0002669622,0.0000237062,0.000001386951,0.000005178188,0.000008634146,0.0001729759],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9509102,"threshold_uncertainty_score":0.9987439,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01469724160568025,"score_gpt":0.2282592643532333,"score_spread":0.213562022747553,"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."}}