{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002577608,0.0003055947,0.0002017294,0.0004587355,0.0002411799,0.0003916622,0.0002351358,0.0004065669,0.002047912],"category_scores_gemma":[0.0001443362,0.0001805862,0.0001729325,0.0002194787,0.0002758263,0.0003658428,0.0002166347,0.0008739362,0.0007274176],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001771636,"about_ca_system_score_gemma":0.0001119302,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000180991,"about_ca_topic_score_gemma":0.0002748716,"domain_scores_codex":[0.9998592,0.00001383627,0.000009598247,0.0000506219,0.0000289135,0.00003763123],"domain_scores_gemma":[0.9998152,0.00007063544,0.00003556064,0.00002583184,0.00002145218,0.00003142534],"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":[0.00001631376,0.000009620568,0.00005589102,0.00001106095,6.4218e-7,0.00001749073,0.00001112948,0.00001548844,0.9994326,0.00007211477,0.000006422807,0.0003512377],"study_design_scores_gemma":[0.00001048777,0.00008103756,0.006592317,0.000006106372,0.000007614418,0.0002483583,0.00004097524,0.001752005,0.9895505,0.0001260577,0.001579675,0.000004794675],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.8921033,0.0009562718,0.101714,0.0001306425,0.00005739376,0.0002242756,0.001010143,0.0003530632,0.003450844],"genre_scores_gemma":[0.9103745,0.001162784,0.08092769,0.000133473,0.0000479718,0.0006012925,0.001575718,0.0001496742,0.005026853],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.002047912,"threshold_uncertainty_score":0.006851017,"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."}}