{"id":"W2999460683","doi":"10.1101/2020.01.16.908186","title":"A comparative ‘omics approach to candidate pathogenicity factor discovery in the brain-eating amoeba <i>Naegleria fowleri</i>","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Legionella and Acanthamoeba research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University; University of Alberta","funders":"Alberta Heritage Foundation for Medical Research; Grantová Agentura České Republiky; Commonwealth Scientific and Industrial Research Organisation","keywords":"Naegleria fowleri; Biology; Pathogenicity island; Pathogenicity; Genome; Microbiology; Transcriptome; Genetics; Virology; Gene; Meningoencephalitis","routes":{"ca_aff":true,"ca_fund":true,"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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0005633165,0.0006341187,0.0006746312,0.0001346443,0.0002011927,0.0004612338,0.001318896,0.0004975782,0.000003678365],"category_scores_gemma":[0.0003197399,0.0005386329,0.0002305629,0.0005557715,0.000157244,0.00002116091,0.001316197,0.001006377,0.00001944521],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001371666,"about_ca_system_score_gemma":0.0008297657,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002102778,"about_ca_topic_score_gemma":0.00002503702,"domain_scores_codex":[0.9963021,0.0004908699,0.000543776,0.00143498,0.0004673864,0.0007609226],"domain_scores_gemma":[0.9978539,0.00007499181,0.0002635688,0.001301879,0.0002072465,0.0002983756],"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":[0.0001547281,0.0002336992,0.005785617,0.000175233,0.0001287414,0.00002712266,0.0001752772,0.000210985,0.9913828,0.0001695275,0.001555056,0.000001257219],"study_design_scores_gemma":[0.001332033,0.0004003152,0.1090436,0.0002376058,0.00006302584,1.489655e-7,0.0001446467,0.00115435,0.8750566,0.000004549004,0.0108159,0.001747175],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.991669,0.0005700555,0.004251441,0.0006851892,0.0002904551,0.001555418,0.0008505811,0.0000484663,0.00007941991],"genre_scores_gemma":[0.9949904,0.0001291592,0.001691975,0.00189891,0.0007524141,0.0004224945,0.00001220033,0.00009403596,0.000008392384],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1163261,"threshold_uncertainty_score":0.9997065,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02935494447558638,"score_gpt":0.2643060183861409,"score_spread":0.2349510739105545,"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."}}