{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28508029", "kind": "science-record", "revision": 6, "content_hash": "sha256:ede402e04761ba16651b476f3b56b9120bf46910fe7a16e209ea54057ae51f59", "created_at": "2026-11-01T15:40:25Z", "updated_at": "2026-11-01T21:20:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A B-Cell Gene Signature Correlates With the Extent of Gluten-Induced Intestinal Injury in Celiac Disease.", "doi": "10.1016/j.jcmgh.2017.01.011", "pmid": "28508029", "authors": ["Mitchell E Garber", "Alok Saldanha", "Joel S Parker", "Wendell D Jones", "Katri Kaukinen", "Kaija Laurila", "Marja-Leena Lähdeaho", "Purvesh Khatri", "Chaitan Khosla", "Daniel C Adelman", "Markku Mäki"], "journal": "Cellular and molecular gastroenterology and hepatology", "year": 2017, "abstract": "BACKGROUND & AIMS: Celiac disease (CeD) provides an opportunity to study autoimmunity and the transition in immune cells as dietary gluten induces small intestinal lesions.\nMETHODS: Seventy-three celiac disease patients on a long-term, gluten-free diet ingested a known amount of gluten daily for 6 weeks. A peripheral blood sample and intestinal biopsy specimens were taken before and 6 weeks after initiating the gluten challenge. Biopsy results were reported on a continuous numeric scale that measured the villus-height-to-crypt-depth ratio to quantify gluten-induced intestinal injury. Pooled B and T cells were isolated from whole blood, and RNA was analyzed by DNA microarray looking for changes in peripheral B- and T-cell gene expression that correlated with changes in villus height to crypt depth, as patients maintained a relatively healthy intestinal mucosa or deteriorated in the face of a gluten challenge.\nRESULTS: Gluten-dependent intestinal damage from baseline to 6 weeks varied widely across all patients, ranging from no change to extensive damage. Genes differentially expressed in B cells correlated strongly with the extent of intestinal damage. A relative increase in B-cell gene expression correlated with a lack of sensitivity to gluten whereas their relative decrease correlated with gluten-induced mucosal injury. A core B-cell gene module, representing a subset of B-cell genes analyzed, accounted for the correlation with intestinal injury.\nCONCLUSIONS: Genes comprising the core B-cell module showed a net increase in expression from baseline to 6 weeks in patients with little to no intestinal damage, suggesting that these individuals may have mounted a B-cell immune response to maintain mucosal homeostasis and circumvent inflammation. DNA microarray data were deposited at the GEO repository (accession number: GSE87629; available: https://www.ncbi.nlm.nih.gov/geo/).", "claims": [{"id": "claim-method", "statement": "The chi-square test was used to determine whether the number of patients who segregated above and below baseline for the 2 groups differed from expected values distributed randomly.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28508029", "locator": "sections[24] \"Immune Response in Patients With Little to No Gluten-Induced Intestinal Injury\" paragraph 2", "quote": "The chi-square test was used to determine whether the number of patients who segregated above and below baseline for the 2 groups differed from expected values distributed randomly."}], "state": "complete"}, {"id": "claim-data-access", "statement": "DNA microarray data were deposited at the GEO repository (accession number: GSE87629; available: https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28508029", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "DNA microarray data were deposited at the GEO repository (accession number: GSE87629; available: https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28508029"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE3982"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE3982"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28508029", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.jcmgh.2017.01.011", "sha256": "sha256:ab989c3f62ff2e5c3cf7762cb2600b26b488cd8516e5caff7e883c5dbf79d35f", "bytes": 62810, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.jcmgh.2017.01.011", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5413199", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE3982", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3982", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE3982", "version": null, "note": "DNA microarray data were deposited at the GEO repository (accession number: GSE87629; available: https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "DNA microarray data were deposited at the GEO repository (accession number: GSE87629; available: https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM90660", "GSM90661", "GSM90662", "GSM90663", "GSM90664", "GSM90665", "GSM90666", "GSM90836", "GSM90837", "GSM90838", "GSM90839", "GSM90840", "GSM90841", "GSM90842", "GSM90843", "GSM90844", "GSM90845", "GSM90846", "GSM90847", "GSM90848", "GSM90849", "GSM90850", "GSM90851", "GSM90852", "GSM90853", "GSM90854", "GSM90855", "GSM90856", "GSM90857", "GSM90858", "GSM90859", "GSM92194"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Human immune cell transcriptome", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE87629", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87629", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87629", "version": null, "note": "DNA microarray data were deposited at the GEO repository (accession number: GSE87629; available: https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "DNA microarray data were deposited at the GEO repository (accession number: GSE87629; available: https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2335776", "GSM2335777", "GSM2335778", "GSM2335779", "GSM2335780", "GSM2335781", "GSM2335782", "GSM2335783", "GSM2335784", "GSM2335785", "GSM2335786", "GSM2335787", "GSM2335788", "GSM2335789", "GSM2335790", "GSM2335791", "GSM2335792", "GSM2335793", "GSM2335794", "GSM2335795", "GSM2335796", "GSM2335797", "GSM2335798", "GSM2335799", "GSM2335800", "GSM2335801", "GSM2335802", "GSM2335803", "GSM2335804", "GSM2335805", "GSM2335806", "GSM2335807", "GSM2335808", "GSM2335809", "GSM2335810", "GSM2335811", "GSM2335812", "GSM2335813", "GSM2335814", "GSM2335815", "GSM2335816", "GSM2335817", "GSM2335818", "GSM2335819", "GSM2335820", "GSM2335821", "GSM2335822", "GSM2335823", "GSM2335824", "GSM2335825", "GSM2335826", "GSM2335827", "GSM2335828", "GSM2335829", "GSM2335830", "GSM2335831", "GSM2335832", "GSM2335833", "GSM2335834", "GSM2335835", "GSM2335836", "GSM2335837", "GSM2335838", "GSM2335839", "GSM2335840", "GSM2335841", "GSM2335842", "GSM2335843", "GSM2335844", "GSM2335845", "GSM2335846", "GSM2335847", "GSM2335848", "GSM2335849", "GSM2335850", "GSM2335851", "GSM2335852", "GSM2335853", "GSM2335854", "GSM2335855", "GSM2335856", "GSM2335857", "GSM2335858", "GSM2335859", "GSM2335860", "GSM2335861", "GSM2335862", "GSM2335863", "GSM2335864", "GSM2335865", "GSM2335866", "GSM2335867", "GSM2335868", "GSM2335869", "GSM2335870", "GSM2335871", "GSM2335872", "GSM2335873", "GSM2335874", "GSM2335875", "GSM2335876", "GSM2335877", "GSM2335878", "GSM2335879", "GSM2335880", "GSM2335881", "GSM2335882", "GSM2335883", "GSM2335884", "GSM2335885", "GSM2335886", "GSM2335887", "GSM2335888", "GSM2335889", "GSM2335890", "GSM2335891", "GSM2335892", "GSM2335893", "GSM2335894", "GSM2335895", "GSM2335896", "GSM2335897", "GSM2335898", "GSM2335899", "GSM2335900", "GSM2335901", "GSM2335902", "GSM2335903", "GSM2335904", "GSM2335905", "GSM2335906", "GSM2335907", "GSM2335908", "GSM2335909", "GSM2335910", "GSM2335911", "GSM2335912", "GSM2335913", "GSM2335914", "GSM2335915", "GSM2335916", "GSM2335917", "GSM2335918", "GSM2335919", "GSM2335920", "GSM2335921"], "sample_count": 146, "group_sizes": null, "group_sizes_basis": null, "platform": "6947;10558", "taxon": "Homo sapiens", "title": "Genome-wide analysis of B and T cell gene expression during a six-week gluten challenge in patients with celiac disease", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:28508029:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:10313d30dce9ed7da99eeac7f3b322c8ffbd4e6e16a4fbb3ba0f405581248d81", "bytes": 5098, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#tbl1", "version": null, "note": "Patient Data", "structure": {"pmcid": "PMC5413199", "section_index": 18, "section_title": "Gluten-Dependent Intestinal Damage", "row_count": 74, "column_count": 11}, "table": {"label": "Table 1", "caption": "Patient Data", "rows": [["Patient ID", "Vh:Cd (time, 0 days)", "Vh:Cd (time, 42 days)", "ΔVh:Cd (time 0 - time 42)", "Gluten challenge, g/day", "Age range, y", "Sex", "Anti–TG2-IgA (time, 0 days)", "Anti–TG2-IgA (time, 42 days)", "Anti–TG2-IgA fold change", "Anti–TG2-IgA positivity"], ["Z", "3.1", "0.2", "2.9", "6", "41–50", "F", "7", "216", "31", "Pos"], ["X", "3.1", "0.2", "2.9", "6", "51–60", "F", "6", "8", "-", "Neg"], ["AV", "3.1", "0.2", "2.9", "3", "61–70", "F", "17", "183", "11", "Pos"], ["O", "3.5", "0.7", "2.8", "6", "51–60", "F", "8", "146", "18", "Pos"], ["P", "2.7", "0.2", "2.5", "6", "41–50", "F", "11", "227", "21", "Pos"], ["AS", "3.2", "0.7", "2.5", "3", "51–60", "M", "11", "8", "-", "Neg"], ["M", "2.9", "0.5", "2.4", "6", "61–70", "M", "12", "19", "-", "Neg"], ["Y", "2.8", "0.4", "2.4", "6", "51–60", "F", "10", "10", "-", "Neg"], ["G", "2.6", "0.3", "2.3", "6", "31–40", "M", "6", "240", "40", "Pos"], ["W", "2.6", "0.3", "2.3", "6", "41–50", "F", "6", "53", "9", "Pos"], ["AF", "2.7", "0.4", "2.3", "3", "41–50", "M", "23", "40", "-", "Baseline pos"], ["R", "3", "0.8", "2.2", "6", "61–70", "F", "7", "10", "-", "Neg"], ["AW", "2.8", "0.6", "2.2", "3", "41–50", "F", "15", "85", "6", "Pos"], ["K", "2.4", "0.3", "2.1", "6", "41–50", "F", "15", "282", "19", "Pos"], ["CM", "2.8", "0.7", "2.1", "1.5", "41–50", "F", "10", "72", "7", "Pos"], ["AQ", "2.4", "0.4", "2", "3", "61–70", "F", "10", "22", "2", "Pos"], ["AY", "2.6", "0.6", "2", "3", "61–70", "M", "12", "36", "3", "Pos"], ["AC", "2.3", "0.3", "2", "3", "61–70", "M", "7", "11", "-", "Neg"], ["V", "2.6", "0.7", "1.9", "6", "61–70", "F", "10", "133", "13", "Pos"], ["CX", "2.6", "0.7", "1.9", "1.5", "61–70", "F", "12", "34", "3", "Pos"], ["AP", "3", "1.1", "1.9", "3", "51–60", "F", "8", "88", "11", "Pos"], ["CS", "2.5", "0.6", "1.9", "1.5", "61–70", "F", "9", "8", "-", "Neg"], ["AH", "2.7", "0.9", "1.8", "3", "41–50", "F", "10", "114", "11", "Pos"], ["H", "2", "0.4", "1.6", "6", "51–60", "F", "109", "365", "-", "Baseline pos"], ["AA", "2.5", "0.9", "1.6", "3", "51–60", "F", "25", "59", "-", "Baseline pos"], ["AG", "2.5", "0.9", "1.6", "3", "51–60", "M", "11", "23", "2", "Pos"], ["BK", "2.6", "1", "1.6", "3", "41–50", "M", "14", "24", "2", "Pos"], ["S", "2.8", "1.2", "1.6", "6", "61–70", "F", "11", "14", "-", "Neg"], ["AN", "2.9", "1.3", "1.6", "3", "41–50", "F", "16", "5", "-", "Neg"], ["AU", "1.7", "0.2", "1.5", "3", "61–70", "M", "22", "21", "-", "Baseline pos"], ["DK", "3", "1.5", "1.5", "1.5", "61–70", "F", "9", "8", "-", "Neg"], ["AL", "2.7", "1.3", "1.4", "3", "51–60", "M", "11", "52", "5", "Pos"], ["AI", "2.5", "1.2", "1.3", "3", "51–60", "F", "8", "95", "12", "Pos"], ["AK", "2.9", "1.6", "1.3", "3", "61–70", "F", "15", "7", "-", "Neg"], ["AE", "2.4", "1.1", "1.3", "3", "71–80", "M", "8", "67", "8", "Pos"], ["T", "2.9", "1.7", "1.2", "6", "61–70", "M", "7", "15", "-", "Neg"], ["AD", "2.3", "1.1", "1.2", "3", "51–60", "F", "50", "41", "-", "Baseline pos"], ["DF", "2.6", "1.5", "1.1", "1.5", "51–60", "M", "6", "4", "-", "Neg"], ["L", "1.4", "0.3", "1.1", "6", "61–70", "M", "23", "209", "-", "Baseline pos"], ["AM", "3.3", "2.2", "1.1", "3", "51–60", "F", "6", "6", "-", "Neg"], ["CE", "1.3", "0.4", "0.9", "1.5", "61–70", "M", "10", "21", "2", "Pos"], ["DC", "2.9", "2", "0.9", "1.5", "51–60", "F", "7", "5", "-", "Neg"], ["CA", "3.6", "2.8", "0.8", "1.5", "31–40", "F", "8", "7", "-", "Neg"], ["DZ", "3.2", "2.4", "0.8", "1.5", "61–70", "F", "6", "5", "-", "Neg"], ["CG", "2", "1.3", "0.7", "1.5", "61–70", "F", "6", "8", "-", "Neg"], ["DQ", "2.9", "2.2", "0.7", "1.5", "61–70", "F", "4", "3", "-", "Neg"], ["DY", "3", "2.3", "0.7", "1.5", "61–70", "F", "7", "5", "-", "Neg"], ["DB", "2.9", "2.2", "0.7", "1.5", "41–50", "M", "9", "6", "-", "Neg"], ["C", "1.1", "0.5", "0.6", "6", "21–30", "F", "74", "239", "-", "Baseline pos"], ["CN", "3.1", "2.5", "0.6", "1.5", "71–80", "F", "14", "11", "-", "Neg"], ["AT", "2.3", "1.7", "0.6", "3", "41–50", "M", "25", "70", "-", "Baseline pos"], ["DG", "2.9", "2.5", "0.4", "1.5", "61–70", "F", "3", "3", "-", "Neg"], ["U", "2.5", "2.1", "0.4", "6", "51–60", "F", "15", "32", "2", "Pos"], ["DH", "3.3", "3", "0.3", "1.5", "61–70", "F", "6", "4", "-", "Neg"], ["DW", "2.6", "2.3", "0.3", "1.5", "61–70", "M", "8", "6", "-", "Neg"], ["A", "2.9", "2.6", "0.3", "6", "41–50", "F", "47", "43", "-", "Baseline pos"], ["CB", "3", "2.7", "0.3", "1.5", "31–40", "F", "17", "32", "2", "Pos"], ["CJ", "3", "2.8", "0.2", "1.5", "61–70", "F", "8", "7", "-", "Neg"], ["DR", "2.9", "2.7", "0.2", "1.5", "61–70", "F", "8", "6", "-", "Neg"], ["AO", "2.9", "2.8", "0.1", "3", "51–60", "M", "14", "16", "-", "Neg"], ["DJ", "2.7", "2.6", "0.1", "1.5", "61–70", "F", "16", "11", "-", "Neg"], ["Q", "2.8", "2.7", "0.1", "6", "61–70", "M", "13", "32", "2", "Pos"], ["N", "2.7", "2.7", "0", "6", "51–60", "M", "8", "10", "-", "Neg"], ["DN", "2.3", "2.3", "0", "1.5", "61–70", "M", "14", "12", "-", "Neg"], ["DP", "2.8", "2.8", "0", "1.5", "51–60", "M", "7", "6", "-", "Neg"], ["DM", "1.3", "1.4", "-0.1", "1.5", "41–50", "F", "13", "12", "-", "Neg"], ["AJ", "2.5", "2.6", "-0.1", "3", "51–60", "F", "13", "16", "-", "Neg"], ["DX", "2.9", "3.1", "-0.2", "1.5", "61–70", "F", "10", "6", "-", "Neg"], ["CT", "2.8", "3", "-0.2", "1.5", "71–80", "M", "15", "23", "2", "Pos"], ["AR", "2.3", "2.6", "-0.3", "3", "51–60", "M", "13", "22", "2", "Pos"], ["DA", "2.4", "2.8", "-0.4", "1.5", "51–60", "F", "36", "22", "-", "Baseline pos"], ["AX", "2.8", "3.3", "-0.5", "3", "51–60", "M", "20", "19", "-", "Baseline pos"], ["AB", "2.3", "3.4", "-1.1", "3", "41–50", "M", "9", "9", "-", "Neg"]], "row_count": 74, "column_count": 11, "numeric_cells": 542, "header_rows": 1, "locator": "section[18]/table-wrap[1]#tbl1"}}, {"id": "asset:table:pmid:28508029:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8d3247a0528538e948cf4f310385d768583a1cf978a57ef7c4f4f08ee690092b", "bytes": 3054, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#tbl2", "version": null, "note": "Gene Symbols and the Corresponding Illumina Microarray Probe IDs Representing the Core B-Cell Gene Module, Non-correlating B-Cell Gene List, and the Extended Core B-Cell Gene Module", "structure": {"pmcid": "PMC5413199", "section_index": 22, "section_title": "A Subset of B-Cell Genes Drives Correlation to ΔVh:Cd", "row_count": 38, "column_count": 7}, "table": {"label": "Table 2", "caption": "Gene Symbols and the Corresponding Illumina Microarray Probe IDs Representing the Core B-Cell Gene Module, Non-correlating B-Cell Gene List, and the Extended Core B-Cell Gene Module", "rows": [["Core B-cell gene module", "Non-correlating B-cell gene list", "Extended core B-cell gene module"], ["Gene", "Probe ID", "Gene", "Probe ID", "Gene", "Probe ID", "B-cell expression"], ["", "", "", "", "All probes from core B-cell gene module plus the following"], ["ADAM28", "ILMN_1664631", "ABCB4", "ILMN_1767349", "AFF3", "ILMN_1775235", "1"], ["ALOX5", "ILMN_1680996", "BACH2", "ILMN_1670695", "ALS2CR13", "ILMN_1739942", "ND"], ["BACH2", "ILMN_2058468", "BLNK", "ILMN_2142935", "BASP1", "ILMN_1651826", "3"], ["BANK1", "ILMN_1661646", "CCR9", "ILMN_2337386", "BTK", "ILMN_1662026", "4"], ["BCL11A", "ILMN_1659800", "CCR9", "ILMN_1664316", "C22ORF13", "ILMN_1764410", "ND"], ["BCL11A", "ILMN_1752899", "CD180", "ILMN_1665647", "C4ORF34", "ILMN_2224907", "ND"], ["BCL11A", "ILMN_2255133", "CD1C", "ILMN_1654210", "CD24", "ILMN_2060413", "4"], ["BCL11A", "ILMN_2342271", "CD40", "ILMN_2367818", "CD74", "ILMN_1736567", "3"], ["BLK", "ILMN_1668277", "CD79B", "ILMN_1710017", "CD74", "ILMN_2379644", "3"], ["BLR1", "ILMN_2337928", "CD79B", "ILMN_1785439", "CD79A", "ILMN_1734878", "4"], ["CD19", "ILMN_1782704", "CD79B", "ILMN_2366212", "CNTNAP2", "ILMN_1690223", "1"], ["CD22", "ILMN_1792075", "COCH", "ILMN_1711514", "CXXC5", "ILMN_1745256", "ND"], ["CD37", "ILMN_1786176", "CR2", "ILMN_1684724", "CYBASC3", "ILMN_2129505", "ND"], ["CD37", "ILMN_2375825", "CR2", "ILMN_2369666", "FAIM3", "ILMN_1775542", "2"], ["CD40", "ILMN_1779257", "EAF2", "ILMN_1708798", "FCRLA", "ILMN_1691071", "ND"], ["CD72", "ILMN_1723004", "FCGR2B", "ILMN_1804174", "GGA2", "ILMN_1686152", "3"], ["CD79A", "ILMN_1659227", "FCGR2B", "ILMN_2382403", "HLA-DQB1", "ILMN_1661266", "2"], ["FCER2", "ILMN_1662451", "FCGR2B", "ILMN_1660027", "HLA-DRB4", "ILMN_1752592", "5"], ["GNG7", "ILMN_1728107", "FCRL2", "ILMN_1665152", "KIAA0746", "ILMN_1797822", "3"], ["HHEX", "ILMN_1762712", "FCRL2", "ILMN_1791329", "LYN", "ILMN_1781155", "3"], ["HLA-DOB", "ILMN_1700428", "KIAA0125", "ILMN_1707491", "MARCKS", "ILMN_1807042", "2"], ["HLA-DQA1", "ILMN_1808405", "LOC653980", "ILMN_1659943", "MDS028", "ILMN_1701244", "2"], ["OSBPL10", "ILMN_1669497", "LOC91353", "ILMN_2083066", "NAPSB", "ILMN_2109416", "ND"], ["PNOC", "ILMN_1676003", "MEF2C", "ILMN_1742544", "PLCG2", "ILMN_1815719", "3"], ["RASGRP3", "ILMN_1727045", "MS4A1", "ILMN_2401714", "PTPN6", "ILMN_1738675", "3"], ["SPIB", "ILMN_2143314", "MS4A1", "ILMN_1776939", "SEMA4B", "ILMN_1672589", "ND"], ["TCL1A", "ILMN_1788841", "P2RX5", "ILMN_1677793", "SIDT2", "ILMN_1791912", "2"], ["VPREB3", "ILMN_1700147", "P2RY14", "ILMN_2258409", "SNX2", "ILMN_1691575", "3"], ["", "", "P2RY14", "ILMN_2342835", "SWAP70", "ILMN_1785175", "4"], ["", "", "RALGPS2", "ILMN_1654692", "SYK", "ILMN_2059549", "4"], ["", "", "RALGPS2", "ILMN_2276290", "TLR10", "ILMN_2414762", "ND"], ["", "", "RALGPS2", "ILMN_1813703", "", "", ""], ["", "", "RNASE6", "ILMN_1780533", "", "", ""], ["", "", "SCN3A", "ILMN_2387395", "", "", ""], ["", "", "TNFRSF17", "ILMN_1768016", "", "", ""]], "row_count": 38, "column_count": 7, "numeric_cells": 151, "header_rows": 1, "locator": "section[22]/table-wrap[1]#tbl2"}}, {"id": "asset:table:pmid:28508029:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9c0dd3f1c560ab0416d550a5629ee7415c175d278a89ed9234ad94126b644bab", "bytes": 707, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[2]#tbl3", "version": null, "note": "Spearman Correlation of B- and T-Cell Gene Lists With ΔVh:Cd", "structure": {"pmcid": "PMC5413199", "section_index": 22, "section_title": "A Subset of B-Cell Genes Drives Correlation to ΔVh:Cd", "row_count": 10, "column_count": 3}, "table": {"label": "Table 3", "caption": "Spearman Correlation of B- and T-Cell Gene Lists With ΔVh:Cd", "rows": [["Gene list", "Correlation", "P value"], ["All B-cell genes Bindea et al33", "-0.54", "8.74E-07"], ["All B-cell genes Newman et al34", "-0.52", "1.90E-06"], ["Core B-cell gene module", "-0.59", "3.30E-08"], ["Non-correlating B-cell gene list", "-0.24", "3.80E-02"], ["Single-gene SPIB", "-0.56", "2.50E-07"], ["Extended core B-cell gene module", "-0.60", "2.65E-08"], ["Th1 genes Bindea et al33", "0.34", "2.58E-03"], ["Th2 genes Bindea et al33", "0.31", "7.21E-03"], ["All T-cell genes Newman et al34", "0.10", "3.92E-01"]], "row_count": 10, "column_count": 3, "numeric_cells": 23, "header_rows": 1, "locator": "section[22]/table-wrap[2]#tbl3"}}], "gaps": ["asset:data:geo:GSE3982 not downloaded", "asset:data:geo:GSE3982 licence not read", "asset:data:geo:GSE87629 not downloaded", "asset:data:geo:GSE87629 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The chi-square test was used to determine whether the number of patients who segregated above and below baseline for the 2 groups differed from expected values distributed randomly."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["chi_square_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: chi_square."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE87629", "GSE3982"], "resolved_accessions": ["GSE87629", "GSE3982"], "statements": ["DNA microarray data were deposited at the GEO repository (accession number: GSE87629; available: https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE87629, GSE3982 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["chi_square_test"], "assets": ["source:pmid:28508029", "data:geo:GSE3982", "asset:table:pmid:28508029:1", "asset:table:pmid:28508029:2", "asset:table:pmid:28508029:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE3982"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:09:36Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 47490, "completion_tokens": 1581, "cached_tokens": 15872}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:28508029", "type": "paper", "label": "pmid:28508029"}, {"id": "source:pmid:28508029", "type": "manuscript", "label": "PMID 28508029 full text"}, {"id": "data:geo:GSE3982", "type": "dataset", "label": "GEO GSE3982"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28508029", "type": "paper", "label": "pmid:28508029"}, {"id": "source:pmid:28508029", "type": "manuscript", "label": "PMID 28508029 full text"}, {"id": "data:geo:GSE3982", "type": "dataset", "label": "GEO GSE3982"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28508029", "type": "extraction", "used": ["source:pmid:28508029"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE3982", "type": "accession_resolution", "used": ["data:geo:GSE3982"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:28508029", "parent_hash": "sha256:8a80bb88dc556a9ec21bb0c2692618b8e460041659fa7e5402029b463ba8f650", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE3982 licence not read", "asset:data:geo:GSE3982 not downloaded", "asset:data:geo:GSE87629 licence not read", "asset:data:geo:GSE87629 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rom whole blood, and RNA was analyzed by DNA microarray looking for changes in peripheral B- and T-c", "homeostasis and circumvent inflammation. DNA microarray data were deposited at the GEO repository (a", "se two possibilities, we compared uncentered microarray data from both baseline and 6-week time poin"], "order_basis": "paper_text_order:733", "id": "assay:1"}, {"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The chi-square test was used to determine whether the number of patients who segregated above and below baseline for the 2 groups differed from expected values distributed randomly."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:36:46+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}