{"id":"W4402900072","doi":"10.1093/ismeco/ycae115","title":"Amplicon sequencing with internal standards yields accurate picocyanobacteria cell abundances as validated with flow cytometry","year":2024,"lang":"en","type":"article","venue":"ISME Communications","topic":"Microbial Community Ecology and Physiology","field":"Environmental Science","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"St. Francis Xavier University","funders":"Simons Foundation","keywords":"Prochlorococcus; Amplicon; Biology; Pyrosequencing; Synechococcus; Relative species abundance; Abundance (ecology); Ecology; Genetics; Gene; Polymerase chain reaction; Cyanobacteria; Bacteria","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":[0.0003243918,0.0001752838,0.0001808022,0.00006690212,0.0005019588,0.0001374556,0.001222256,0.0001033375,0.004886939],"category_scores_gemma":[0.00001941004,0.0001358887,0.00003787879,0.0004577232,0.0006549385,0.0003392332,0.000670487,0.00063477,0.0004428332],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003123154,"about_ca_system_score_gemma":0.000150114,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009431439,"about_ca_topic_score_gemma":0.004783149,"domain_scores_codex":[0.9988532,0.0003065047,0.0002017439,0.0002421877,0.0001401891,0.0002561823],"domain_scores_gemma":[0.9982448,0.0002959606,0.00007778335,0.001270023,0.00003412862,0.00007727477],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0006883738,0.0005812988,0.01733376,0.0001722834,0.0004770151,0.00008017162,0.01508829,0.005238414,0.9292607,0.003001946,0.01760382,0.01047391],"study_design_scores_gemma":[0.002569499,0.003952476,0.03673168,0.001280344,0.0004635318,0.0008889145,0.004003785,0.01943387,0.0921705,0.006417455,0.8294748,0.002613137],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9523208,0.0001778319,0.004278887,0.001177509,0.0001141328,0.0002190641,0.0001261923,0.0001720375,0.04141353],"genre_scores_gemma":[0.9940928,0.0002165298,0.004378593,0.0003907319,0.00001804789,0.00003308071,0.0001511451,0.0000221303,0.0006969356],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8370902,"threshold_uncertainty_score":0.9960227,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02049995492091949,"score_gpt":0.2857146465092663,"score_spread":0.2652146915883468,"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."}}