{"id":"W4366003044","doi":"10.1101/2023.04.13.536804","title":"Sex biased human thymic architecture guides T cell development through spatially defined niches","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; BC Children's Hospital; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; National Institutes of Health; BC Children's Hospital; Michael Smith Health Research BC; Universities Space Research Association; Genome British Columbia; Canadian Institutes of Health Research; Li Ka Shing Foundation","keywords":"Biology; Niche; Population; Ecological niche; FOXP3; Cell; Immune system; Immunology; Genetics; Ecology; 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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0004696388,0.000886815,0.00067704,0.0001748782,0.0003429385,0.0002069878,0.0009829068,0.001028639,0.00002279273],"category_scores_gemma":[0.0001334254,0.000937278,0.0003018601,0.0002592929,0.0001680495,0.000007797922,0.0006801557,0.0007204656,0.00006626136],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001231278,"about_ca_system_score_gemma":0.001040117,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002053664,"about_ca_topic_score_gemma":0.00009576911,"domain_scores_codex":[0.9962571,0.0001661438,0.0008197088,0.001555014,0.0004151569,0.000786832],"domain_scores_gemma":[0.9975421,0.00003733578,0.0004056,0.001492331,0.0002901204,0.0002324945],"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":[0.00004915885,0.0001872108,0.004879753,0.0004318127,0.0002207444,0.00003248425,0.00004277909,0.0005429541,0.9926034,0.00002752508,0.0009768308,0.000005343652],"study_design_scores_gemma":[0.0007652984,0.0001250012,0.008047253,0.0002129519,0.00009353061,2.693803e-8,0.000003586405,0.0000278536,0.9672755,0.000009152747,0.02231496,0.001124867],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9867495,0.001119897,0.009517193,0.0001434119,0.001105785,0.0007453331,0.0002026887,0.0003637626,0.00005248654],"genre_scores_gemma":[0.9780306,0.0002635605,0.01982866,0.0004127537,0.0008143393,0.0001923677,0.00002235116,0.0003098904,0.0001254913],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02532788,"threshold_uncertainty_score":0.9993078,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02899973212575239,"score_gpt":0.2321732816061262,"score_spread":0.2031735494803738,"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."}}