{"id":"W2106578715","doi":"10.1038/srep04245","title":"Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array","year":2014,"lang":"en","type":"article","venue":"Scientific Reports","topic":"Yersinia bacterium, plague, ectoparasites research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":60,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"Government of Canada; Genome Canada; Ontario Genomics; Natural Sciences and Engineering Research Council of Canada; McMaster University; Ontario Genomics Institute","keywords":"Ancient DNA; Metagenomics; Vibrio cholerae; Biology; DNA sequencing; Yersinia pestis; DNA microarray; Computational biology; Shotgun sequencing; Evolutionary biology; DNA; Genetics; Gene; Bacteria; Medicine","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":[],"consensus_categories":[],"category_scores_codex":[0.001291139,0.0001659289,0.0001715561,0.0001803867,0.0001677219,0.0001042873,0.0001694314,0.0001458628,0.00003297423],"category_scores_gemma":[0.0004554834,0.0001350481,0.0000652928,0.0004129432,0.0004427979,0.000007872764,0.0001159996,0.0001463451,0.00001321123],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004431478,"about_ca_system_score_gemma":0.0001368328,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000043039,"about_ca_topic_score_gemma":0.00155665,"domain_scores_codex":[0.9977022,0.0001709557,0.0003238265,0.000971254,0.0003279363,0.0005038531],"domain_scores_gemma":[0.9988121,0.00002021574,0.0001392614,0.0007207478,0.0001652002,0.0001424306],"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":[0.0001085246,0.00005834758,0.0444817,0.00001020438,0.000007627328,0.00007130595,0.00006943999,0.00004033408,0.9536954,9.653738e-7,0.0001179233,0.00133825],"study_design_scores_gemma":[0.0002407525,0.0002808636,0.09005312,0.00001452588,0.000004853437,0.0005148397,0.00002139747,0.00003784917,0.8855474,0.00008312067,0.0230178,0.0001834947],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9946601,0.00004173874,0.003999129,0.00004035722,0.0007145024,0.0003192609,0.000005565845,0.00002433894,0.0001949395],"genre_scores_gemma":[0.9979653,0.000002282494,0.001382661,0.00003010137,0.0001019753,0.00003620476,0.0001788869,0.00001689813,0.000285638],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06814799,"threshold_uncertainty_score":0.5507101,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01109118267578093,"score_gpt":0.23910107498359,"score_spread":0.2280098923078091,"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."}}