{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32225123", "kind": "science-record", "revision": 7, "content_hash": "sha256:f0c0304aff5d9bed5078909a5c3bd9aafb8e704412eb7d879ccb7e4b06bdd0d2", "created_at": "2026-11-01T15:40:58Z", "updated_at": "2026-11-01T21:23:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Galectin-1 Overexpression Activates the FAK/PI3K/AKT/mTOR Pathway and Is Correlated with Upper Urinary Urothelial Carcinoma Progression and Survival.", "doi": "10.3390/cells9040806", "pmid": "32225123", "authors": ["Yu-Li Su", "Hao-Lun Luo", "Chun-Chieh Huang", "Ting-Ting Liu", "Eng-Yen Huang", "Ming-Tse Sung", "Jen-Jie Lin", "Po-Hui Chiang", "Yen-Ta Chen", "Chih-Hsiung Kang", "Yuan-Tso Cheng"], "journal": "Cells", "year": 2020, "abstract": "Galectin-1 (GAL1) is a β-galactoside-binding protein involved in multiple aspects of tumorigenesis. However, the biological role of GAL1 in upper tract urothelial carcinoma (UTUC) has not been entirely understood. Herein, we investigated the oncological effects of GAL1 expression in tumor specimens and identified related gene alterations through molecular analysis of GAL1. Clinical parameter data and tumor specimens were collected from 86 patients with pT3N0M0 UTUC who had undergone radical nephroureterectomy. We analyzed the difference in survival by using Kaplan-Meier analyses and Cox proportional regression models and in GAL1 expression by using immunohistochemical (IHC) methods. Public genomic data from the Cancer Genome Atlas (TCGA) and GSE32894 data sets were analyzed for comparison. Using four urothelial carcinoma (UC) cell lines (BFTC-909, T24, RT4, and J82) as in vitro models, we evaluated the functions of GAL1 in UC cell growth, invasiveness, and migration and its role in downstream signaling pathways. The study population was classified into two groups, GAL1-high (n = 35) and GAL1-low (GAL1 n = 51), according to IHC interpretation. Univariate analysis revealed that high GAL1 expression was significantly associated with poor recurrence-free survival (RFS; p = 0.028) and low cancer-specific survival (CSS; p = 0.025). Multivariate analysis revealed that GAL1-high was an independent predictive factor for RFS (hazard ratio (HR) 2.43; 95% confidence interval (CI) 1.17-5.05, p = 0.018) and CSS (HR 4.04; 95% CI 1.25-13.03, p = 0.019). In vitro studies revealed that GAL1 knockdown significantly reduced migration and invasiveness in UTUC (BFTC-909) and bladder cancer cells (T24). GAL1 knockdown significantly reduced protein levels of matrix metalloproteinase-2 (MMP-2) and MMP-9, which increased tissue inhibitor of metalloproteinase-1 (TIMP-1) and promoted epithelial-mesenchymal transition (EMT). Through gene expression microarray analysis of GAL1 vector and GAL1-KD cells, we identified multiple significant signaling pathways including p53, Forkhead box O (FOXO), and phosphoinositide 3-kinase/protein kinase B (PI3K/AKT). We validated microarray results through immunoblotting, thus proving that downregulation of GAL1 reduced focal adhesion kinase (FAK), p-PI3K, p-AKT, and p-mTOR expression. We concluded that GAL1 expression was highly related to oncological survival in patients with locally advanced UTUC. GAL1 promoted UC invasion and metastasis by activating the FAK/PI3K/AKT/mTOR pathway.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier analyses and Cox proportional regression models were used for univariate and multivariate survival analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32225123", "locator": "sections[14] \"2.12. Statistical Analysis\" paragraph 2", "quote": "Kaplan–Meier analyses and Cox proportional regression models were used for univariate and multivariate survival analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We analyzed comprehensive TCGA cancer genome expression data by using UALCAN platform (http://ualcan.path.uab.edu/index.html).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32225123", "locator": "sections[13] \"2.11. Bioinformatics Analysis\" paragraph 2", "quote": "We analyzed comprehensive TCGA cancer genome expression data by using UALCAN platform (http://ualcan.path.uab.edu/index.html)."}], "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:32225123"], "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:GSE32894"], "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:GSE32894"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32225123", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cells9040806", "sha256": "sha256:6e01640ca0b329a9380c87ac0efde3ca904f3c66844242c2cb268ffc2564046e", "bytes": 46843, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cells9040806", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7226470", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE32894", "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=GSE32894", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32894", "version": null, "note": "We analyzed comprehensive TCGA cancer genome expression data by using UALCAN platform (http://ualcan.path.uab.edu/index.html).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We analyzed comprehensive TCGA cancer genome expression data by using UALCAN platform (http://ualcan.path.uab.edu/index.html).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM814052", "GSM814053", "GSM814054", "GSM814055", "GSM814056", "GSM814057", "GSM814058", "GSM814059", "GSM814060", "GSM814061", "GSM814062", "GSM814063", "GSM814064", "GSM814065", "GSM814066", "GSM814067", "GSM814068", "GSM814069", "GSM814070", "GSM814071", "GSM814072", "GSM814073", "GSM814074", "GSM814075", "GSM814076", "GSM814077", "GSM814078", "GSM814079", "GSM814080", "GSM814081", "GSM814082", "GSM814083", "GSM814084", "GSM814085", "GSM814086", "GSM814087", "GSM814088", "GSM814089", "GSM814090", "GSM814091", "GSM814092", "GSM814093", "GSM814094", "GSM814095", "GSM814096", "GSM814097", "GSM814098", "GSM814099", "GSM814100", "GSM814101", "GSM814102", "GSM814103", "GSM814104", "GSM814105", "GSM814106", "GSM814107", "GSM814108", "GSM814109", "GSM814110", "GSM814111", "GSM814112", "GSM814113", "GSM814114", "GSM814115", "GSM814116", "GSM814117", "GSM814118", "GSM814119", "GSM814120", "GSM814121", "GSM814122", "GSM814123", "GSM814124", "GSM814125", "GSM814126", "GSM814127", "GSM814128", "GSM814129", "GSM814130", "GSM814131", "GSM814132", "GSM814133", "GSM814134", "GSM814135", "GSM814136", "GSM814137", "GSM814138", "GSM814139", "GSM814140", "GSM814141", "GSM814142", "GSM814143", "GSM814144", "GSM814145", "GSM814146", "GSM814147", "GSM814148", "GSM814149", "GSM814150", "GSM814151", "GSM814152", "GSM814153", "GSM814154", "GSM814155", "GSM814156", "GSM814157", "GSM814158", "GSM814159", "GSM814160", "GSM814161", "GSM814162", "GSM814163", "GSM814164", "GSM814165", "GSM814166", "GSM814167", "GSM814168", "GSM814169", "GSM814170", "GSM814171", "GSM814172", "GSM814173", "GSM814174", "GSM814175", "GSM814176", "GSM814177", "GSM814178", "GSM814179", "GSM814180", "GSM814181", "GSM814182", "GSM814183", "GSM814184", "GSM814185", "GSM814186", "GSM814187", "GSM814188", "GSM814189", "GSM814190", "GSM814191", "GSM814192", "GSM814193", "GSM814194", "GSM814195", "GSM814196", "GSM814197", "GSM814198", "GSM814199", "GSM814200", "GSM814201", "GSM814202", "GSM814203", "GSM814204", "GSM814205", "GSM814206", "GSM814207", "GSM814208", "GSM814209", "GSM814210", "GSM814211", "GSM814212", "GSM814213", "GSM814214", "GSM814215", "GSM814216", "GSM814217", "GSM814218", "GSM814219", "GSM814220", "GSM814221", "GSM814222", "GSM814223", "GSM814224", "GSM814225", "GSM814226", "GSM814227", "GSM814228", "GSM814229", "GSM814230", "GSM814231", "GSM814232", "GSM814233", "GSM814234", "GSM814235", "GSM814236", "GSM814237", "GSM814238", "GSM814239", "GSM814240", "GSM814241", "GSM814242", "GSM814243", "GSM814244", "GSM814245", "GSM814246", "GSM814247", "GSM814248", "GSM814249", "GSM814250", "GSM814251", "GSM814252", "GSM814253", "GSM814254", "GSM814255", "GSM814256", "GSM814257", "GSM814258", "GSM814259", "GSM814260", "GSM814261", "GSM814262", "GSM814263", "GSM814264", "GSM814265", "GSM814266", "GSM814267", "GSM814268", "GSM814269", "GSM814270", "GSM814271", "GSM814272", "GSM814273", "GSM814274", "GSM814275", "GSM814276", "GSM814277", "GSM814278", "GSM814279", "GSM814280", "GSM814281", "GSM814282", "GSM814283", "GSM814284", "GSM814285", "GSM814286", "GSM814287", "GSM814288", "GSM814289", "GSM814290", "GSM814291", "GSM814292", "GSM814293", "GSM814294", "GSM814295", "GSM814296", "GSM814297", "GSM814298", "GSM814299", "GSM814300", "GSM814301", "GSM814302", "GSM814303", "GSM814304", "GSM814305", "GSM814306", "GSM814307", "GSM814308", "GSM814309", "GSM814310", "GSM814311", "GSM814312", "GSM814313", "GSM814314", "GSM814315", "GSM814316", "GSM814317", "GSM814318", "GSM814319", "GSM814320", "GSM814321", "GSM814322", "GSM814323", "GSM814324", "GSM814325", "GSM814326", "GSM814327", "GSM814328", "GSM814329", "GSM814330", "GSM814331", "GSM814332", "GSM814333", "GSM814334", "GSM814335", "GSM814336", "GSM814337", "GSM814338", "GSM814339", "GSM814340", "GSM814341", "GSM814342", "GSM814343", "GSM814344", "GSM814345", "GSM814346", "GSM814347", "GSM814348", "GSM814349", "GSM814350", "GSM814351", "GSM814352", "GSM814353", "GSM814354", "GSM814355", "GSM814356", "GSM814357", "GSM814358", "GSM814359"], "sample_count": 308, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "A Molecular Taxonomy of Urothelial Carcinoma", "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:32225123:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f9c0d78b453303d5c62a112d9ab6af7fea850be09e461b02cb584f637c8a468f", "bytes": 1449, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#cells-09-00806-t001", "version": null, "note": "Clinicopathological features of 86 patients with pT3 upper tract UC stratified by GAL1 expression.", "structure": {"pmcid": "PMC7226470", "section_index": 17, "section_title": "3.2. High Expression of GAL1 is Associated with Poor Disease Recurrence and CSS", "row_count": 34, "column_count": 4}, "table": {"label": "Table 1", "caption": "Clinicopathological features of 86 patients with pT3 upper tract UC stratified by GAL1 expression.", "rows": [["", "GAL1-Low", "GAL1-High", "p-Value"], ["", "(N = 51, %)", "(N = 35, %)", ""], ["Age (years)", "70.5 ± 10.8", "68.0 ± 9.8", "0.27"], ["Gender", "", "", ""], ["Female", "31 (60.8)", "18 (51.4)", "0.39"], ["Male", "20 (39.2)", "17 (48.6)", ""], ["Smoking", "", "", ""], ["Yes", "8 (15.7)", "4 (11.4)", "0.75"], ["No", "43 (84.3)", "31 (88.6)", ""], ["Primary site", "", "", ""], ["Renal pelvis", "26 (51.0)", "26 (74.3)", "0.09"], ["Ureter", "19 (37.3)", "7 (20.1)", ""], ["Both", "6 (11.8)", "2 (5.7)", ""], ["Grade", "", "", ""], ["Low", "0 (0)", "1 (2.9)", "0.41"], ["High", "51 (100)", "34 (97.1)", ""], ["Histopathologic variant", "", "", ""], ["Presence", "20 (39.2)", "14 (40)", "0.94"], ["Absence", "31 (60.8)", "21 (60)", ""], ["CIS", "", "", ""], ["Presence", "17 (33.3)", "13 (37.1)", "0.72"], ["Absence", "34 (66.7)", "22 (62.9)", ""], ["LVI", "", "", ""], ["Presence", "20 (39.2)", "14 (40)", "0.94"], ["Absence", "31 (60.8)", "21 (60)", ""], ["Tumor necrosis", "", "", ""], ["Presence", "18 (35.3)", "16 (45.7)", "0.33"], ["Absence", "33 (64.7)", "19 (54.3)", ""], ["Multicentricity", "", "", ""], ["Yes", "12 (23.5)", "5 (14.3)", "0.29"], ["No", "39 (76.5)", "30 (85.7)", ""], ["Papillary feature", "", "", ""], ["Presence", "31 (60.8)", "15 (42.9)", "0.10"], ["Absence", "20 (39.2)", "20 (57.1)", ""]], "row_count": 34, "column_count": 4, "numeric_cells": 57, "header_rows": 2, "locator": "section[17]/table-wrap[1]#cells-09-00806-t001"}}, {"id": "asset:table:pmid:32225123:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1becf135f09cfd4d6336668115a8974911aacdda930ac9851ab61d214680925d", "bytes": 1410, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[2]#cells-09-00806-t002", "version": null, "note": "Univariate and multivariate analyses of RFS and CSS.", "structure": {"pmcid": "PMC7226470", "section_index": 17, "section_title": "3.2. High Expression of GAL1 is Associated with Poor Disease Recurrence and CSS", "row_count": 25, "column_count": 7}, "table": {"label": "Table 2", "caption": "Univariate and multivariate analyses of RFS and CSS.", "rows": [["Characteristics", "RFS", "CSS"], ["Univariate", "Multivariate", "Univariate", "Multivariate"], ["p-Value", "HR (95% CI)", "p-Value", "p-Value", "HR (95% CI)", "p-Value"], ["Age", "", "", "", "", "", ""], ["≥65 vs. <65", "0.99", "", "", "0.67", "", ""], ["Gender", "", "", "", "", "", ""], ["Male vs. female", "0.17", "", "", "0.41", "", ""], ["Smoking history", "", "", "", "", "", ""], ["Yes vs. no", "0.16", "", "", "0.08", "", ""], ["Primary site", "", "", "", "", "", ""], ["Kidney vs. ureter", "0.24", "2.03 (0.96–4.28)", "0.06", "0.23", "", ""], ["Histological variant", "", "", "", "", "", ""], ["Presence vs. absence", "0.74", "", "", "0.26", "3.65 (1.20–11.12)", "0.023"], ["LVI", "", "", "", "", "", ""], ["Presence vs. absence", "0.043", "2.41 (1.15–5.05)", "0.02", "0.18", "3.56 (1.06–11.88)", "0.039"], ["Tumor necrosis", "", "", "", "", "", ""], ["Presence vs. absence", "0.25", "", "", "0.35", "", ""], ["CIS", "", "", "", "", "", ""], ["Presence vs. absence", "0.97", "", "", "0.96", "", ""], ["Papillary feature", "", "", "", "", "", ""], ["Presence vs. absence", "0.039", "", "", "0.62", "", ""], ["Multicentricity", "", "", "", "", "", ""], ["Yes vs. no", "0.74", "", "", "0.82", "", ""], ["Galectin-1", "", "", "", "", "", ""], ["High vs. low", "0.028", "2.43 (1.17–5.05)", "0.018", "0.025", "4.04 (1.25–13.03)", "0.019"]], "row_count": 25, "column_count": 7, "numeric_cells": 38, "header_rows": 3, "locator": "section[17]/table-wrap[2]#cells-09-00806-t002"}}, {"id": "asset:table:pmid:32225123:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2aa5c99b39866a3cf285e50ffaf7228a2bfb7743e36bc3ced764b7715fc831c4", "bytes": 902, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[26]/table-wrap[1]#array1", "version": null, "note": null, "structure": {"pmcid": "PMC7226470", "section_index": 26, "section_title": "Abbreviations", "row_count": 20, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["CIS:", "carcinoma in situ;"], ["CSS:", "cancer-specific survival;"], ["ECM:", "extracellular matrix;"], ["EMT:", "epithelial-mesenchymal transition;"], ["FAK:", "focal adhesion kinase;"], ["GAL1:", "galectin-1;"], ["HR:", "hazard ratio;"], ["IHC:", "immunohistochemical;"], ["IQR:", "interquartile range;"], ["LVI:", "lymphovascular invasion;"], ["MMP:", "matrix metalloproteinase;"], ["mTOR:", "mammalian target of rapamycin;"], ["PI3K:", "phosphoinositide 3-kinase;"], ["q-PCR:", "quantitative polymerase chain reaction;"], ["RFS:", "recurrence-free survival;"], ["TCGA:", "The Cancer Genome Atlas;"], ["TIMP:", "tissue inhibitors of metalloproteinases;"], ["UC:", "urothelial carcinoma;"], ["UCB:", "urothelial carcinoma of the bladder;"], ["UTUC:", "upper tract urothelial carcinoma."]], "row_count": 20, "column_count": 2, "numeric_cells": 2, "header_rows": 0, "locator": "section[26]/table-wrap[1]#array1"}}], "gaps": ["asset:data:geo:GSE32894 not downloaded", "asset:data:geo:GSE32894 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": null, "specific": null, "label": "Kaplan–Meier analyses and Cox proportional regression models", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Kaplan–Meier analyses and Cox proportional regression models were used for univariate and multivariate survival analyses."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE32894"], "resolved_accessions": ["GSE32894"], "statements": ["We analyzed comprehensive TCGA cancer genome expression data by using UALCAN platform (http://ualcan.path.uab.edu/index.html)."], "basis": "The paper names GSE32894 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": ["survival_km"], "assets": ["source:pmid:32225123", "data:geo:GSE32894", "asset:table:pmid:32225123:1", "asset:table:pmid:32225123:2", "asset:table:pmid:32225123:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE32894"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:02Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 39518, "completion_tokens": 1941, "cached_tokens": 13320}}, "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:32225123", "type": "paper", "label": "pmid:32225123"}, {"id": "source:pmid:32225123", "type": "manuscript", "label": "PMID 32225123 full text"}, {"id": "data:geo:GSE32894", "type": "dataset", "label": "GEO GSE32894"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32225123", "type": "paper", "label": "pmid:32225123"}, {"id": "source:pmid:32225123", "type": "manuscript", "label": "PMID 32225123 full text"}, {"id": "data:geo:GSE32894", "type": "dataset", "label": "GEO GSE32894"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32225123", "type": "extraction", "used": ["source:pmid:32225123"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE32894", "type": "accession_resolution", "used": ["data:geo:GSE32894"], "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:32225123", "parent_hash": "sha256:0930a2af5f037e8d5f7d7485fe37beb47b79c39247e2b223e9c58df976766c8f", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE32894 licence not read", "asset:data:geo:GSE32894 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ssion models and in GAL1 expression by using immunohistochemical (IHC) methods. Public genomic data from the", "AL1 expression by using immunohistochemical (IHC) methods. Public genomic data from the Cance", "35) and GAL1-low (GAL1 n = 51), according to IHC interpretation. Univariate analysis revealed", "emorial Hospital. 2.12. Statistical Analysis IHC staining of tumor specimens was performed us"], "order_basis": "paper_text_order:762", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["0.019). In vitro studies revealed that GAL1 knockdown significantly reduced migration and invasive", "TC-909) and bladder cancer cells (T24). GAL1 knockdown significantly reduced protein levels of matr", "r and GAL1-KD). (D) Western blotting of GAL1 knockdown or overexpression in the FAK/PI3K/AKT/mTOR s"], "order_basis": "paper_text_order:1706", "id": "assay:2"}, {"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": ["al transition (EMT). Through gene expression microarray analysis of GAL1 vector and GAL1-KD cells, w", "se/protein kinase B (PI3K/AKT). We validated microarray results through immunoblotting, thus proving", "high-throughput analysis by using Clariom D microarray to analyze two replicate samples (GAL1 vecto", "AKT/mTOR pathway alteration assessed through microarray and Western blotting analyses: (A) A heatmap"], "order_basis": "paper_text_order:2059", "id": "assay:3"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["KT). We validated microarray results through immunoblotting, thus proving that downregulation of GAL1 re", "y alteration assessed through microarray and Western blotting analyses: (A) A heatmap revealed upregulatio", "BFTC-909 cells (GAL-vector and GAL1-KD). (D) Western blotting of GAL1 knockdown or overexpression in the F"], "order_basis": "paper_text_order:2304", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"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":"2026-11-04T00:38:10+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}}}