{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32306128", "kind": "science-record", "revision": 6, "content_hash": "sha256:f675f932e6d13ba24f92db88f7ac4884bb6d165ef9114da08fb5a38e373b17d7", "created_at": "2026-11-01T15:40:59Z", "updated_at": "2026-11-01T21:23:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High MICB expression as a biomarker for good prognosis of colorectal cancer.", "doi": "10.1007/s00432-020-03159-0", "pmid": "32306128", "authors": ["Qingyang Feng", "Shanchao Yu", "Yihao Mao", "Meiling Ji", "Ye Wei", "Guodong He", "Wenju Chang", "Dexiang Zhu", "Li Ren", "Jianmin Xu"], "journal": "Journal of cancer research and clinical oncology", "year": 2020, "abstract": "INTRODUCTION: Major histocompatibility complex (MHC) plays an important role in colorectal cancer (CRC) immunity. However, the function of MHC class I chain-related B (MICB) molecule is not very clear. In this study, we explored the prognostic effect of MICB in colorectal cancer.\nMATERIAL AND METHODS: From 2008-05 to 2012-11, consecutive CRC patients of Zhongshan Hospital, Fudan University were retrospectively enrolled as primary cohort. The inclusion criteria were as follows: receiving primary radical resection, pathologically confirmed colorectal adenocarcinoma, no treatment before surgery, clinicopathological data available. Another cohort of CRC patients were collected from a public dataset GSE39582 of GEO database from 1987 to 2007 in the same criteria for validation. MICB was detected using immunochemistry and evaluated as prognostic biomarker. The cut-off value of MICB expression was calculated using X-tile software.\nRESULTS: Finally, 863 patients were enrolled in the primary cohort, and 556 patients were enrolled in the validation cohort. MICB expression was significantly associated with tumor size and primary histological type in primary cohort, and with primary tumor location and distant metastases in validation cohort. The survival analysis showed that patients with high MICB expression had significantly better overall survival in both primary (P = 0.002) and validation (P = 0.001) cohorts. The multivariate analysis also confirmed that high MICB expression was a significantly independent protective factor for overall survival in both primary (hazard ratio HR = 0.741, 95% CI 0.594-0.924) and validation (HR = 0.699, 95% CI 0.508-0.961) cohorts.\nCONCLUSION: For stage I-IV CRC patients, MICB was confirmed a novel independent prognostic factor. It could help better stratification of CRC prognosis.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier analysis and Log-rank test were performed to evaluate the relationship between MICB expression and OS.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32306128", "locator": "sections[5] \"Statistical analysis\" paragraph 2", "quote": "Kaplan–Meier analysis and Log-rank test were performed to evaluate the relationship between MICB expression and OS."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32306128", "locator": "sections[19] \"Data availability\" paragraph 2", "quote": "The datasets used and analyzed during the current study are available from the corresponding author on reasonable request."}], "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:32306128"], "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:GSE39582"], "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:GSE39582"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32306128", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s00432-020-03159-0", "sha256": "sha256:765735c41b7b1af72ec7d54e08d46397c2cc014584a12cb7d0ef7a100072731d", "bytes": 18682, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s00432-020-03159-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7230058", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE39582", "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=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "The datasets used and analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1681353", "GSM1681354", "GSM1681355", "GSM1681356", "GSM1681357", "GSM1681358", "GSM1681359", "GSM1681360", "GSM1681361", "GSM1681362", "GSM1681363", "GSM1681364", "GSM1681365", "GSM1681366", "GSM1681367", "GSM1681368", "GSM1681369", "GSM1681370", "GSM1681371", "GSM971957", "GSM971958", "GSM971959", "GSM971960", "GSM971961", "GSM971962", "GSM971963", "GSM971964", "GSM971965", "GSM971966", "GSM971967", "GSM971968", "GSM971969", "GSM971970", "GSM971971", "GSM971972", "GSM971973", "GSM971974", "GSM971975", "GSM971976", "GSM971977", "GSM971978", "GSM971979", "GSM971980", "GSM971981", "GSM971982", "GSM971983", "GSM971984", "GSM971985", "GSM971986", "GSM971987", "GSM971988", "GSM971989", "GSM971990", "GSM971991", "GSM971992", "GSM971993", "GSM971994", "GSM971995", "GSM971996", "GSM971997", "GSM971998", "GSM971999", "GSM972000", "GSM972001", "GSM972002", "GSM972003", "GSM972004", "GSM972005", "GSM972006", "GSM972007", "GSM972008", "GSM972009", "GSM972010", "GSM972011", "GSM972012", "GSM972013", "GSM972014", "GSM972015", "GSM972016", "GSM972017", "GSM972018", "GSM972019", "GSM972020", "GSM972021", "GSM972022", "GSM972023", "GSM972024", "GSM972025", "GSM972026", "GSM972027", "GSM972028", "GSM972029", "GSM972030", "GSM972031", "GSM972032", "GSM972033", "GSM972034", "GSM972035", "GSM972036", "GSM972037", "GSM972038", "GSM972039", "GSM972040", "GSM972041", "GSM972042", "GSM972043", "GSM972044", "GSM972045", "GSM972046", "GSM972047", "GSM972048", "GSM972049", "GSM972050", "GSM972051", "GSM972052", "GSM972053", "GSM972054", "GSM972055", "GSM972056", "GSM972057", "GSM972058", "GSM972059", "GSM972060", "GSM972061", "GSM972062", "GSM972063", "GSM972064", "GSM972065", "GSM972066", "GSM972067", "GSM972068", "GSM972069", "GSM972070", "GSM972071", "GSM972072", "GSM972073", "GSM972074", "GSM972075", "GSM972076", "GSM972077", "GSM972078", "GSM972079", "GSM972080", "GSM972081", "GSM972082", "GSM972083", "GSM972084", "GSM972085", "GSM972086", "GSM972087", "GSM972088", "GSM972089", "GSM972090", "GSM972091", "GSM972092", "GSM972093", "GSM972094", "GSM972095", "GSM972096", "GSM972097", "GSM972098", "GSM972099", "GSM972100", "GSM972101", "GSM972102", "GSM972103", "GSM972104", "GSM972105", "GSM972106", "GSM972107", "GSM972108", "GSM972109", "GSM972110", "GSM972111", "GSM972112", "GSM972113", "GSM972114", "GSM972115", "GSM972116", "GSM972117", "GSM972118", "GSM972119", "GSM972120", "GSM972121", "GSM972122", "GSM972123", "GSM972124", "GSM972125", "GSM972126", "GSM972127", "GSM972128", "GSM972129", "GSM972130", "GSM972131", "GSM972132", "GSM972133", "GSM972134", "GSM972135", "GSM972136", "GSM972137", "GSM972138", "GSM972139", "GSM972140", "GSM972141", "GSM972142", "GSM972143", "GSM972144", "GSM972145", "GSM972146", "GSM972147", "GSM972148", "GSM972149", "GSM972150", "GSM972151", "GSM972152", "GSM972153", "GSM972154", "GSM972155", "GSM972156", "GSM972157", "GSM972158", "GSM972159", "GSM972160", "GSM972161", "GSM972162", "GSM972163", "GSM972164", "GSM972165", "GSM972166", "GSM972167", "GSM972168", "GSM972169", "GSM972170", "GSM972171", "GSM972172", "GSM972173", "GSM972174", "GSM972175", "GSM972176", "GSM972177", "GSM972178", "GSM972179", "GSM972180", "GSM972181", "GSM972182", "GSM972183", "GSM972184", "GSM972185", "GSM972186", "GSM972187", "GSM972188", "GSM972189", "GSM972190", "GSM972191", "GSM972192", "GSM972193", "GSM972194", "GSM972195", "GSM972196", "GSM972197", "GSM972198", "GSM972199", "GSM972200", "GSM972201", "GSM972202", "GSM972203", "GSM972204", "GSM972205", "GSM972206", "GSM972207", "GSM972208", "GSM972209", "GSM972210", "GSM972211", "GSM972212", "GSM972213", "GSM972214", "GSM972215", "GSM972216", "GSM972217", "GSM972218", "GSM972219", "GSM972220", "GSM972221", "GSM972222", "GSM972223", "GSM972224", "GSM972225", "GSM972226", "GSM972227", "GSM972228", "GSM972229", "GSM972230", "GSM972231", "GSM972232", "GSM972233", "GSM972234", "GSM972235", "GSM972236", "GSM972237", "GSM972238", "GSM972239", "GSM972240", "GSM972241", "GSM972242", "GSM972243", "GSM972244", "GSM972245", "GSM972246", "GSM972247", "GSM972248", "GSM972249", "GSM972250", "GSM972251", "GSM972252", "GSM972253", "GSM972254", "GSM972255", "GSM972256", "GSM972257", "GSM972258", "GSM972259", "GSM972260", "GSM972261", "GSM972262", "GSM972263", "GSM972264", "GSM972265", "GSM972266", "GSM972267", "GSM972268", "GSM972269", "GSM972270", "GSM972271", "GSM972272", "GSM972273", "GSM972274", "GSM972275", "GSM972276", "GSM972277", "GSM972278", "GSM972279", "GSM972280", "GSM972281", "GSM972282", "GSM972283", "GSM972284", "GSM972285", "GSM972286", "GSM972287", "GSM972288", "GSM972289", "GSM972290", "GSM972291", "GSM972292", "GSM972293", "GSM972294", "GSM972295", "GSM972296", "GSM972297", "GSM972298", "GSM972299", "GSM972300", "GSM972301", "GSM972302", "GSM972303", "GSM972304", "GSM972305", "GSM972306", "GSM972307", "GSM972308", "GSM972309", "GSM972310", "GSM972311", "GSM972312", "GSM972313", "GSM972314", "GSM972315", "GSM972316", "GSM972317", "GSM972318", "GSM972319", "GSM972320", "GSM972321", "GSM972322", "GSM972323", "GSM972324", "GSM972325", "GSM972326", "GSM972327", "GSM972328", "GSM972329", "GSM972330", "GSM972331", "GSM972332", "GSM972333", "GSM972334", "GSM972335", "GSM972336", "GSM972337", "GSM972338", "GSM972339", "GSM972340", "GSM972341", "GSM972342", "GSM972343", "GSM972344", "GSM972345", "GSM972346", "GSM972347", "GSM972348", "GSM972349", "GSM972350", "GSM972351", "GSM972352", "GSM972353", "GSM972354", "GSM972355", "GSM972356", "GSM972357", "GSM972358", "GSM972359", "GSM972360", "GSM972361", "GSM972362", "GSM972363", "GSM972364", "GSM972365", "GSM972366", "GSM972367", "GSM972368", "GSM972369", "GSM972370", "GSM972371", "GSM972372", "GSM972373", "GSM972374", "GSM972375", "GSM972376", "GSM972377", "GSM972378", "GSM972379", "GSM972380", "GSM972381", "GSM972382", "GSM972383", "GSM972384", "GSM972385", "GSM972386", "GSM972387", "GSM972388", "GSM972389", "GSM972390", "GSM972391", "GSM972392", "GSM972393", "GSM972394", "GSM972395", "GSM972396", "GSM972397", "GSM972398", "GSM972399", "GSM972400", "GSM972401", "GSM972402", "GSM972403", "GSM972404", "GSM972405", "GSM972406", "GSM972407", "GSM972408", "GSM972409", "GSM972410", "GSM972411", "GSM972412", "GSM972413", "GSM972414", "GSM972415", "GSM972416", "GSM972417", "GSM972418", "GSM972419", "GSM972420", "GSM972421", "GSM972422", "GSM972423", "GSM972424", "GSM972425", "GSM972426", "GSM972427", "GSM972428", "GSM972429", "GSM972430", "GSM972431", "GSM972432", "GSM972433", "GSM972434", "GSM972435", "GSM972436", "GSM972437", "GSM972438", "GSM972439", "GSM972440", "GSM972441", "GSM972442", "GSM972443", "GSM972444", "GSM972445", "GSM972446", "GSM972447", "GSM972448", "GSM972449", "GSM972450", "GSM972451", "GSM972452", "GSM972453", "GSM972454", "GSM972455", "GSM972456", "GSM972457", "GSM972458", "GSM972459", "GSM972460", "GSM972461", "GSM972462", "GSM972463", "GSM972464", "GSM972465", "GSM972466", "GSM972467", "GSM972468", "GSM972469", "GSM972470", "GSM972471", "GSM972472", "GSM972473", "GSM972474", "GSM972475", "GSM972476", "GSM972477", "GSM972478", "GSM972479", "GSM972480", "GSM972481", "GSM972482", "GSM972483", "GSM972484", "GSM972485", "GSM972486", "GSM972487", "GSM972488", "GSM972489", "GSM972490", "GSM972491", "GSM972492", "GSM972493", "GSM972494", "GSM972495", "GSM972496", "GSM972497", "GSM972498", "GSM972499", "GSM972500", "GSM972501", "GSM972502", "GSM972503", "GSM972504", "GSM972505", "GSM972506", "GSM972507", "GSM972508", "GSM972509", "GSM972510", "GSM972511", "GSM972512", "GSM972513", "GSM972514", "GSM972515", "GSM972516", "GSM972517", "GSM972518", "GSM972519", "GSM972520", "GSM972521", "GSM972522"], "sample_count": 585, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32306128:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e3aa2ef61e657a4b3ee3d0c60903a7756c16395edfd303d110057c1d4e5a5d8b", "bytes": 2186, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab1", "version": null, "note": "Baseline clinicopathological characteristics of primary and validation cohorts", "structure": {"pmcid": "PMC7230058", "section_index": 7, "section_title": "Patient characteristics", "row_count": 51, "column_count": 7}, "table": {"label": "Table 1", "caption": "Baseline clinicopathological characteristics of primary and validation cohorts", "rows": [["Primary cohort", "Validation cohort", "P"], ["Factors", "No", "%", "Factors", "No", "%"], ["All patients", "863", "100.0", "All patients", "556", "100.0", ""], ["Age (years)", "Age (years)"], ["≤ 60", "415", "48.1", "≤ 60", "157", "28.2", "< 0.001"], ["> 60", "448", "51.9", "> 60", "398", "71.6", ""], ["Unknown", "0", "0", "Unknown", "1", "0.2", ""], ["Gender", "Gender"], ["Male", "505", "58.5", "Male", "306", "55.0", "0.196"], ["Female", "358", "41.5", "Female", "250", "45.0", ""], ["CEA (ng/ml)"], ["≤ 5", "450", "52.1", "", "", "", ""], ["> 5", "413", "47.9", "", "", "", ""], ["Tumor location", "Tumor location"], ["Right-sided colon", "246", "28.5", "Proximal colon", "218", "39.2", "< 0.001"], ["Left-sided colon", "226", "26.2", "Distal colon", "338", "60.8", ""], ["Rectum", "391", "45.3", "", "", "", ""], ["Tumor size (cm)", "", "", "", "", "", ""], ["≤ 4.0", "478", "55.4", "", "", "", ""], ["> 4.0", "385", "44.6", "", "", "", ""], ["Primary histological type"], ["Non-mucinous", "732", "84.8", "", "", "", ""], ["Mucinous", "131", "15.2", "", "", "", ""], ["Primary differentiation"], ["Well/moderate", "584", "67.7", "", "", "", ""], ["Poor/anaplastic", "279", "32.3", "", "", "", ""], ["T stage", "T stage"], ["T1", "29", "3.4", "T1", "11", "2.0", "< 0.001"], ["T2", "120", "13.9", "T2", "44", "7.9", ""], ["T3", "207", "24.0", "T3", "362", "65.1", ""], ["T4", "507", "58.7", "T4", "119", "21.4", ""], ["", "", "", "Unknown", "20", "3.6", ""], ["N stage", "N stage"], ["N0", "457", "53.0", "N0", "294", "52.9", "0.502"], ["N1", "264", "30.6", "N1/N2", "242", "43.5", ""], ["N2", "142", "16.4", "Unknown", "20", "3.6", ""], ["Vascular invasion"], ["No", "761", "88.2", "", "", "", ""], ["Yes", "102", "11.8", "", "", "", ""], ["Nerve invasion"], ["No", "800", "92.7", "", "", "", ""], ["Yes", "63", "7.3", "", "", "", ""], ["M stage", "M stage"], ["M0", "642", "74.4", "M0", "473", "85.1", "< 0.001"], ["M1", "221", "25.6", "M1", "61", "11.0", ""], ["", "", "", "Unknown", "22", "4.0", ""], ["TNM stage", "TNM stage"], ["I", "114", "13.2", "I", "32", "5.8", "< 0.001"], ["II", "282", "32.7", "II", "261", "46.9", ""], ["III", "246", "28.5", "III", "203", "36.5", ""], ["IV", "221", "25.6", "IV", "60", "10.8", ""]], "row_count": 51, "column_count": 7, "numeric_cells": 129, "header_rows": 2, "locator": "section[7]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32306128:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:51ce8bbd54f0e48351947301fcd59786a8230f82e42a51dc738a9ea7ee65ee4f", "bytes": 1724, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab2", "version": null, "note": "Relationship between MICB and clinical characteristics of primary cohort", "structure": {"pmcid": "PMC7230058", "section_index": 10, "section_title": "Association between MICB and clinical characteristics", "row_count": 46, "column_count": 4}, "table": {"label": "Table 2", "caption": "Relationship between MICB and clinical characteristics of primary cohort", "rows": [["Factors", "Primary cohort"], ["MICB expression"], ["Low (%)", "High (%)", "P"], ["All patients", "417", "446", ""], ["Age (years)"], ["≤ 60", "197 (47.2)", "218 (48.9)", "0.631"], ["> 60", "220 (52.8)", "228 (51.1)"], ["Gender", ""], ["Male", "240 (57.6)", "265 (59.4)", "0.579"], ["Female", "177 (42.4)", "181 (40.6)", ""], ["CEA (ng/ml)"], ["≤ 5", "222(53.2)", "228 (51.1)", "0.534"], ["> 5", "195(46.8)", "218 (48.9)"], ["Tumor location"], ["Right-sided colon", "119 (28.5)", "127 (28.5)", "0.937"], ["Left-sided colon", "107 (25.7)", "119 (26.7)"], ["Rectum", "191 (45.8)", "200 (44.8)"], ["Tumor size (cm)"], ["≤ 4.0", "227 (54.4)", "294 (65.9)", "0.001"], ["> 4.0", "190 (45.6)", "152 (34.1)"], ["Primary histological type"], ["Non-mucinous", "329 (78.9)", "403 (90.4)", "< 0.001"], ["Mucinous", "88 (21.1)", "43 (9.6)"], ["Primary differentiation"], ["Well/moderate", "290 (69.5)", "294 (65.9)", "0.255"], ["Poor/anaplastic", "127 (30.5)", "152 (34.1)"], ["T stage"], ["T1/T2", "67 (16.1)", "82 (18.4)", "0.368"], ["T3/T4", "350 (83.9)", "364 (81.6)"], ["N stage"], ["N0", "221 (53.0)", "236 (52.9)", "0.981"], ["N1/N2", "196 (47.0)", "210 (47.1)"], ["Vascular invasion"], ["No", "367 (88.0)", "394 (88.3)", "0.880"], ["Yes", "50 (12.0)", "52 (11.7)"], ["Nerve invasion"], ["No", "388 (93.0)", "412 (92.4)", "0.706"], ["Yes", "29 (7.0)", "34 (7.6)"], ["M stage"], ["M0", "302 (72.4)", "340 (76.2)", "0.200"], ["M1", "115 (27.6)", "106 (23.8)"], ["TNM stage"], ["I", "48 (11.5)", "66 (14.8)", "0.130"], ["II", "145 (34.8)", "137 (30.7)"], ["III", "109 (26.1)", "137 (30.7)"], ["IV", "115 (27.6)", "106 (23.8)"]], "row_count": 46, "column_count": 4, "numeric_cells": 79, "header_rows": 3, "locator": "section[10]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:32306128:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1f009e3876f7ea57acbead9edc95363271c4fb0b20870f4b479027fbb7019a6b", "bytes": 2114, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab3", "version": null, "note": "Cox regression analyses for OS of primary cohort", "structure": {"pmcid": "PMC7230058", "section_index": 11, "section_title": "MICB as prognostic biomarkers", "row_count": 48, "column_count": 5}, "table": {"label": "Table 3", "caption": "Cox regression analyses for OS of primary cohort", "rows": [["Factors", "Overall survival"], ["Univariate analysis", "Multivariate analysis"], ["HR (95% CI)", "P", "HR (95% CI)", "P"], ["Age (years)"], ["≤ 60", "1 (reference)", "0.644", "", ""], ["> 60", "1.053 (0.845–1.312)", ""], ["Gender"], ["Male", "1 (reference)", "0.062", "1 (reference)", "0.339"], ["Female", "0.805 (0.641–1.011)", "0.893 (0.708–1.126)"], ["CEA (ng/ml)"], ["≤ 5", "1 (reference)", "< 0.001", "1 (reference)", "0.003"], ["> 5", "2.540 (2.017–3.197)", "1.441 (1.129–1.840)"], ["Tumor location"], ["Right-sided colon", "1 (reference)", "0.028", "1 (reference)", "0.183"], ["Left-sided colon", "1.000 (0.754–1.326)", "0.854 (0.640–1.139)"], ["Rectum", "0.737 (0.566–0.958)", "0.779 (0.596–1.017)"], ["Tumor size (cm)"], ["≤ 4.0", "1 (reference)", "0.168", "", ""], ["> 4.0", "1.167 (0.937–1.455)", ""], ["Primary histological type"], ["Non-mucinous", "1 (reference)", "0.984", "", ""], ["Mucinous", "0.997 (0.731–1.359)", ""], ["Primary differentiation"], ["Well/moderate", "1 (reference)", "< 0.001", "1 (reference)", "0.098"], ["Poor/anaplastic", "1.628 (1.301–2.038)", "1.213 (0.965–1.525)"], ["T stage"], ["T1/T2", "1 (reference)", "< 0.001", "1 (reference)", "0.062"], ["T3/T4", "3.198 (2.074–4.932)", "1.541 (0.978–2.429)"], ["N stage"], ["N0", "1 (reference)", "< 0.001", "1 (reference)", "< 0.001"], ["N1/N2", "2.775 (2.201–3.499)", "1.752 (1.375–2.232)"], ["M stage"], ["M0", "1 (reference)", "< 0.001", "1 (reference)", "< 0.001"], ["M1", "7.922 (6.318–9.933)", "6.029 (4.718–7.702)"], ["Vascular invasion"], ["No", "1 (reference)", "0.819", "", ""], ["Yes", "1.041 (0.739–1.466)", ""], ["Nerve invasion"], ["No", "1 (reference)", "0.234", "", ""], ["Yes", "0.755 (0.475–1.200)", ""], ["TNM stage"], ["I", "1 (reference)", "< 0.001", "", ""], ["II", "1.771 (0.947–3.315)", ""], ["III", "3.005 (1.632–5.533)", ""], ["IV", "16.535 (9.200–29.718)", ""], ["MICB"], ["Low", "1 (reference)", "0.002", "1 (reference)", "0.008"], ["High", "0.708 (0.568–0.883)", "0.741 (0.594–0.924)"]], "row_count": 48, "column_count": 5, "numeric_cells": 78, "header_rows": 3, "locator": "section[11]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:32306128:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:55ca03d75a4e94c6e785235edcfd2af1fe98e2f33484db26274a86d998cce0f6", "bytes": 1890, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab4", "version": null, "note": "Cox regression analyses for OS of patients with rectal cancer from primary cohort", "structure": {"pmcid": "PMC7230058", "section_index": 12, "section_title": "Stratified analysis of primary cohort", "row_count": 44, "column_count": 5}, "table": {"label": "Table 4", "caption": "Cox regression analyses for OS of patients with rectal cancer from primary cohort", "rows": [["Factors", "Overall survival"], ["Univariate analysis", "Multivariate analysis"], ["HR (95% CI)", "P", "HR (95% CI)", "P"], ["Age (years)"], ["≤ 60", "1 (reference)", "0.623", "", ""], ["> 60", "1.092 (0.769–1.549)", ""], ["Gender"], ["Male", "1 (reference)", "0.453", "", ""], ["Female", "0.871 (0.607–1.250)", ""], ["CEA (ng/ml)"], ["≤ 5", "1 (reference)", "< 0.001", "1 (reference)", "0.003"], ["> 5", "2.346 (1.641–3.354)", "1.747 (1.209–2.526)"], ["Tumor size (cm)"], ["≤ 4.0", "1 (reference)", "0.306", "", ""], ["> 4.0", "1.203 (0.845–1.714)", ""], ["Primary histological type"], ["Non-mucinous", "1 (reference)", "0.701", "", ""], ["Mucinous", "1.111 (0.648–1.906)", ""], ["Primary differentiation"], ["Well/moderate", "1 (reference)", "0.004", "1 (reference)", "0.098"], ["Poor/anaplastic", "1.667 (1.172–2.371)", "1.358 (0.945–1.951)"], ["T stage"], ["T1/T2", "1 (reference)", "< 0.001", "1 (reference)", "0.351"], ["T3/T4", "2.564 (1.538–4.275)", "1.305 (0.746–2.282)"], ["N stage"], ["N0", "1 (reference)", "< 0.001", "1 (reference)", "0.013"], ["N1/N2", "2.371 (1.652–3.404)", "1.606 (1.104–2.336)"], ["M stage"], ["M0", "1 (reference)", "< 0.001", "1 (reference)", "< 0.001"], ["M1", "5.494 (3.856–7.828)", "4.303 (2.976–6.223)"], ["Vascular invasion"], ["No", "1 (reference)", "0.360", "", ""], ["Yes", "1.269 (0.761–2.116)", ""], ["Nerve invasion"], ["No", "1 (reference)", "0.840", "", ""], ["Yes", "0.935 (0.490–1.785)", ""], ["TNM stage"], ["I", "1 (reference)", "< 0.001", "", ""], ["II", "1.595 (0.755–3.368)", ""], ["III", "2.559 (1.272–5.146)", ""], ["IV", "9.924 (5.058–19.473)", ""], ["MICB"], ["Low", "1 (reference)", "< 0.001", "1 (reference)", "< 0.001"], ["High", "0.492 (0.343–0.705)", "0.510 (0.356–0.733)"]], "row_count": 44, "column_count": 5, "numeric_cells": 67, "header_rows": 3, "locator": "section[12]/table-wrap[1]#Tab4"}}], "gaps": ["asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Kaplan–Meier analysis and Log-rank test were performed to evaluate the relationship between MICB expression and OS."}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "cox regression"}}, {"id": "method-3", "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": 0.8, "band": "high", "quote": "Chi-square"}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE39582"], "resolved_accessions": ["GSE39582"], "statements": ["The datasets used and analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE39582 in Gene Expression Omnibus (GEO) repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:32306128", "data:geo:GSE39582", "asset:table:pmid:32306128:1", "asset:table:pmid:32306128:2", "asset:table:pmid:32306128:3", "asset:table:pmid:32306128:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE39582"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 15237, "completion_tokens": 1081, "cached_tokens": 5248}}, "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:32306128", "type": "paper", "label": "pmid:32306128"}, {"id": "source:pmid:32306128", "type": "manuscript", "label": "PMID 32306128 full text"}, {"id": "data:geo:GSE39582", "type": "dataset", "label": "GEO GSE39582"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32306128", "type": "paper", "label": "pmid:32306128"}, {"id": "source:pmid:32306128", "type": "manuscript", "label": "PMID 32306128 full text"}, {"id": "data:geo:GSE39582", "type": "dataset", "label": "GEO GSE39582"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32306128", "type": "extraction", "used": ["source:pmid:32306128"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE39582", "type": "accession_resolution", "used": ["data:geo:GSE39582"], "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:32306128", "parent_hash": "sha256:28a3a69e30aca4da4bd749c4dc2f7d83c51103de312ac14ef071095db8702de0", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan–Meier analysis and Log-rank test were performed to evaluate the relationship between MICB expression and OS."], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T03:13:11+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}}}