{"id":"W3212315301","doi":"10.1101/2021.11.04.467016","title":"Repeats Mimic Pathogen-Associated Patterns Across a Vast Evolutionary Landscape","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"interferon and immune responses","field":"Immunology and Microbiology","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Princess Margaret Cancer Centre; University Health Network","funders":"Canadian Institutes of Health Research; National Cancer Institute; Pershing Square Sohn Cancer Research Alliance; National Institutes of Health; Agence Nationale de la Recherche; Natural Sciences and Engineering Research Council of Canada; Edward P. Evans Foundation; V Foundation for Cancer Research","keywords":"Biology; Innate immune system; Genome; Mimicry; Genetics; Molecular mimicry; MDA5; Computational biology; Evolutionary biology; RNA; Gene; RNA interference; Immune system; Ecology","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","research_integrity","insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0006160697,0.0006785849,0.0008034115,0.000199051,0.0004107241,0.0001889293,0.0007107264,0.001541413,0.001438983],"category_scores_gemma":[0.0005053781,0.0007511313,0.0004408424,0.000304233,0.0001920295,0.0001370259,0.001156743,0.001494312,0.0005157357],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000268884,"about_ca_system_score_gemma":0.0007471776,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001324365,"about_ca_topic_score_gemma":0.00001402454,"domain_scores_codex":[0.9961652,0.0007465517,0.0007370525,0.001183088,0.0001313896,0.001036739],"domain_scores_gemma":[0.9971792,0.0001489941,0.000519022,0.001469563,0.0005944691,0.00008881203],"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":[0.0002034778,0.00039586,0.01475535,0.0001596702,0.0008830263,0.0002136524,0.00008101804,0.000007922453,0.9800955,0.00004188974,0.003159737,0.000002875467],"study_design_scores_gemma":[0.001573412,0.0001697775,0.4491596,0.001157657,0.0001982025,7.877431e-7,0.00009375299,0.00002859101,0.5396289,4.039437e-7,0.006783526,0.001205365],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9776755,0.01564452,0.0001695112,0.0001291069,0.003697003,0.0003535567,0.001864829,0.0004521422,0.00001381198],"genre_scores_gemma":[0.9981371,0.0007363434,0.0001247084,0.0003780691,0.0001465682,0.0001785337,0.00003118758,0.0001403444,0.0001271041],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4404666,"threshold_uncertainty_score":0.9997548,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01194121849081247,"score_gpt":0.2264573921503767,"score_spread":0.2145161736595642,"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."}}