{"id":"W3011808998","doi":"10.21769/bioprotoc.3562","title":"Characterization of Immunological Niches within Peyer’s Patches by ex vivo Photoactivation and Flow Cytometry Analysis","year":2020,"lang":"en","type":"article","venue":"BIO-PROTOCOL","topic":"T-cell and B-cell Immunology","field":"Immunology and Microbiology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Benoziyo Endowment Fund for the Advancement of Science; Azrieli Foundation; Rising Tide Foundation; Gerald O. Mann Charitable Foundation; European Molecular Biology Organization","keywords":"Germinal center; Flow cytometry; Ex vivo; Biology; Affinity maturation; Cell biology; Population; Peyer's patch; Follicular dendritic cells; T cell; Niche; B cell; Immunology; Antibody; Molecular biology; Immune system; In vivo; Antigen-presenting cell; Genetics; Biochemistry","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001881654,0.0002747883,0.0005719148,0.000200453,0.0001392433,0.00002392668,0.0002487804,0.0005119505,0.001311642],"category_scores_gemma":[0.0001031684,0.0002221662,0.000145018,0.0007397581,0.0003599938,0.0001528957,0.0001498625,0.0003067124,0.0000656371],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002672307,"about_ca_system_score_gemma":0.00004171606,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006828646,"about_ca_topic_score_gemma":0.00000396885,"domain_scores_codex":[0.998296,0.000267941,0.0005926662,0.0004961943,0.00005973714,0.0002875056],"domain_scores_gemma":[0.9990565,0.00009073161,0.000450944,0.0002745237,0.000092474,0.0000347932],"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":[0.0009094639,0.000236499,0.008101648,0.00006437687,0.0006471406,0.000001610024,0.0005202004,0.000001331609,0.9872441,0.00003412838,0.0002866689,0.001952843],"study_design_scores_gemma":[0.001992122,0.0006139214,0.00614205,0.00001384963,0.00014523,0.000005624412,0.0002107322,0.00009241496,0.9673595,0.0000156767,0.02316633,0.0002425808],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.891214,0.00004830783,0.001060845,0.0004126611,0.00009000671,0.106719,0.0001542412,0.0001369572,0.0001640883],"genre_scores_gemma":[0.8608823,0.000009841322,0.0001707886,0.0002622178,0.00002964501,0.1375988,0.000364849,0.00002018872,0.0006613201],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03087986,"threshold_uncertainty_score":0.9996013,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01959044737200719,"score_gpt":0.25055794042706,"score_spread":0.2309674930550528,"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."}}