{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35464062", "kind": "science-record", "revision": 5, "content_hash": "sha256:f1b9cdc0c89cd6077a4576bb46cf1e620446f508952e527501e6c94bdb70a264", "created_at": "2026-11-01T18:14:19Z", "updated_at": "2026-11-01T22:48:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Endoplasmic Reticulum Stress Mediates Renal Tubular Vacuolation in BK Polyomavirus-Associated Nephropathy.", "doi": "10.3389/fendo.2022.834187", "pmid": "35464062", "authors": ["Guo-Dong Zhao", "Rong Gao", "Xiao-Tao Hou", "Hui Zhang", "Xu-Tao Chen", "Jin-Quan Luo", "Hui-Fei Yang", "Tong Chen", "Xue Shen", "Shi-Cong Yang", "Cheng-Lin Wu", "Gang Huang"], "journal": "Frontiers in endocrinology", "year": 2022, "abstract": "Objective: This study aimed to explore the molecular mechanism of cytoplasmic vacuolation caused by BK polyomavirus (BKPyV) and thus search for potential target for drug repurposing.\nMethods: Morphological features of BK polyomavirus-associated nephropathy (BKPyVAN) were studied under light and electron microscopes. Microarray datasets GSE75693, GSE47199, and GSE72925 were integrated by ComBat, and differentially expressed genes (DEGs) were analyzed using limma. Furthermore, the endoplasmic reticulum (ER)-related genes obtained from GenCLiP 2.0 were intersected with DEGs. GO and KEGG enrichment pathways were performed with intersection genes by R package clusterProfiler. The single-cell RNA sequencing (scRNA-seq) from a BKPyVAN recipient was analyzed with a dataset (GSE140989) downloaded from Gene Expression Omnibus (GEO) as control for gene set variation analysis (GSVA). Immunohistochemistry and electron microscopy of kidney sections from drug-induced ERS mouse models were performed to explore the association of ERS and renal tubular vacuolation. Protein-protein interaction (PPI) network of the intersection genes was constructed to identify hub target. AutoDock was used to screen Food and Drug Administration (FDA)-approved drugs that potentially targeted hub gene.\nResults: Light and electron microscopes exhibited obvious intranuclear inclusions, vacuoles, and virus particles in BKPyV-infected renal tubular cells. Transcriptome analysis revealed 629 DEGs between samples of BKPyVAN and stable transplanted kidneys, of which 16 were ER-associated genes. GO analysis with the intersection genes illustrated that ERS-related pathways were significantly involved, and KEGG analysis showed a prominent enrichment of MAPK, Toll-like receptor, and chemokine signaling pathways. GSVA analysis of the proximal tubule revealed similar pathways enrichment. An electron microscope image of the kidney from ERS mouse models showed an obvious renal tubular vacuolation with prominent activation of ERS markers verified by immunohistochemistry. Furthermore, DDIT3 was identified as the hub gene based on PPI analysis, and ZINCOOOOO1531009 (Risedronate) was indicated to be a potential drug for DDIT3.\nConclusion: ERS was involved in renal tubular cytoplasmic vacuolation in BKPyVAN recipients. Risedronate was screened as a potential drug for BKPyVAN by targeting DDIT3.", "claims": [{"id": "claim-method", "statement": "R package Combat was used to eliminate batch effects. The differentially expressed genes (DEGs) of BKPyVAN and stable transplanted kidneys were analyzed by R package limma. p-Value < 0.05 and | fold change (FC)| > 1.5 were considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35464062", "locator": "sections[6] \"Data of Bulk RNA Sequence\" paragraph 2", "quote": "R package Combat was used to eliminate batch effects. The differentially expressed genes (DEGs) of BKPyVAN and stable transplanted kidneys were analyzed by R package limma. p-Value < 0.05 and | fold change (FC)| > 1.5 were considered statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35464062", "locator": "sections[20] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Transcriptome analysis revealed 629 DEGs between samples of BKPyVAN and stable transplanted kidneys, of which 16 were ER-associated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35464062", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Transcriptome analysis revealed 629 DEGs between samples of BKPyVAN and stable transplanted kidneys, of which 16 were ER-associated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Transcriptome analysis revealed 629 DEGs between samples of BKPyVAN and stable transplanted kidneys, of which 16 were ER-associated genes.", "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:35464062"], "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:GSE140989"], "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:GSE140989"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35464062", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2022.834187", "sha256": "sha256:fe24eb70fe1f32e87c2815cb2184f1873d8556cb987b1ee96210a14584169f6e", "bytes": 44797, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2022.834187", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9027570", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE140989", "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=GSE140989", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE140989", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4191941", "GSM4191942", "GSM4191943", "GSM4191944", "GSM4191945", "GSM4191946", "GSM4191947", "GSM4191948", "GSM4191949", "GSM4191950", "GSM4191951", "GSM4191952", "GSM4191953", "GSM4191954", "GSM4191955", "GSM4191956", "GSM4191957", "GSM4191958", "GSM4191959", "GSM4191960", "GSM4191961", "GSM4191962", "GSM4191963", "GSM4191964", "GSM4191965", "GSM4191966", "GSM4191967", "GSM4191968", "GSM4191969", "GSM4191970", "GSM4191971", "GSM4191972", "GSM4191973", "GSM4191974", "GSM4191975", "GSM4191976", "GSM4191977", "GSM4191978", "GSM4191979", "GSM4191980", "GSM4191981", "GSM4191982", "GSM4191983", "GSM4191984", "GSM4191985", "GSM4191986", "GSM4191987", "GSM4191988", "GSM4191989", "GSM4191990", "GSM4191991", "GSM4191992", "GSM4191993", "GSM4191994", "GSM4191995", "GSM4191996", "GSM4191997", "GSM4191998", "GSM4191999", "GSM4192000", "GSM4192001", "GSM4192002", "GSM4192003", "GSM4192004", "GSM4192005", "GSM4192006", "GSM4192007", "GSM4192008", "GSM4192009", "GSM4192011", "GSM4192012", "GSM4192013", "GSM4192014", "GSM4192015", "GSM4192016", "GSM4192018", "GSM4192020", "GSM4192021", "GSM4192022", "GSM4192023", "GSM4192024", "GSM4192025", "GSM4192026", "GSM4192027", "GSM4192028", "GSM4192029", "GSM4192030", "GSM4192031", "GSM4192033", "GSM4192034", "GSM4192035", "GSM4192038"], "sample_count": 92, "group_sizes": null, "group_sizes_basis": null, "platform": "11154;20301", "taxon": "Homo sapiens", "title": "­Single Cell Transcriptomics  identifies Focal Segmental Glomerulosclerosis Remission  Endothelial Biomarker", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE47199", "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=GSE47199", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE47199", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1146679", "GSM1146680", "GSM1146681", "GSM1146682", "GSM1146683", "GSM1146684", "GSM1146685", "GSM1146686", "GSM1146687", "GSM1146688", "GSM1146689", "GSM1146690", "GSM1146691", "GSM1146692", "GSM1146693", "GSM1146694", "GSM1146695", "GSM1146696", "GSM1146697", "GSM1146698", "GSM1146699", "GSM1146700", "GSM1146701", "GSM1146702", "GSM1146703", "GSM1146704", "GSM1146705", "GSM1146706", "GSM1146707", "GSM1146708", "GSM1146709", "GSM1146710", "GSM1146711", "GSM1146712", "GSM1146713", "GSM1146714", "GSM1146715", "GSM1146716", "GSM1146717", "GSM1146718", "GSM1146719", "GSM1146720", "GSM1146721", "GSM1146722", "GSM1146723", "GSM1146724", "GSM1146725", "GSM1146726", "GSM1146727", "GSM1146728", "GSM1146729", "GSM1146730", "GSM1146731", "GSM1146732", "GSM1146733", "GSM1146734", "GSM1146735"], "sample_count": 57, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression data from blood and biopsies of BKV viremia and nephropathy transplant patients", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE72925", "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=GSE72925", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE72925", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1874730", "GSM1874731", "GSM1874732", "GSM1874733", "GSM1874734", "GSM1874735", "GSM1874736", "GSM1874737", "GSM1874738", "GSM1874739", "GSM1874740", "GSM1874741", "GSM1874742", "GSM1874743", "GSM1874744", "GSM1874745", "GSM1874746", "GSM1874747", "GSM1874748", "GSM1874749", "GSM1874750", "GSM1874751", "GSM1874752", "GSM1874753", "GSM1874754", "GSM1874755", "GSM1874756", "GSM1874757", "GSM1874758", "GSM1874759", "GSM1874760", "GSM1874761", "GSM1874762", "GSM1874763", "GSM1874764", "GSM1874765", "GSM1874766", "GSM1874767", "GSM1874768", "GSM1874769", "GSM1874770", "GSM1874771", "GSM1874772", "GSM1874773", "GSM1874774", "GSM1874775", "GSM1874776", "GSM1874777", "GSM1874778", "GSM1874779", "GSM1874780", "GSM1874781", "GSM1874782", "GSM1874783", "GSM1874784", "GSM1874785", "GSM1874786", "GSM1874787", "GSM1874788", "GSM1874789", "GSM1874790", "GSM1874791", "GSM1874792", "GSM1874793", "GSM1874794", "GSM1874795", "GSM1874796", "GSM1874797", "GSM1874798", "GSM1874799", "GSM1874800", "GSM1874801", "GSM1874802", "GSM1874803", "GSM1874804", "GSM1874805", "GSM1874806", "GSM1874807", "GSM1874808", "GSM1874809", "GSM1874810", "GSM1874811", "GSM1874812", "GSM1874813", "GSM1874814", "GSM1874815", "GSM1874816", "GSM1874817", "GSM1874818", "GSM1874819", "GSM1874820", "GSM1874821", "GSM1874822", "GSM1874823", "GSM1874824", "GSM1874825", "GSM1874826", "GSM1874827", "GSM1874828", "GSM1874829", "GSM1874830", "GSM1874831", "GSM1874832", "GSM1874833", "GSM1874834", "GSM1874835", "GSM1874836", "GSM1874837", "GSM1874838", "GSM1874839", "GSM1874840", "GSM1874841", "GSM1874842", "GSM1874843", "GSM1874844", "GSM1874845", "GSM1874846", "GSM1874847", "GSM1874848", "GSM1874849", "GSM1874850", "GSM1874851", "GSM1874852", "GSM1874853", "GSM1874854", "GSM1874855", "GSM1874856", "GSM1874857", "GSM1874858", "GSM1874859", "GSM1874860", "GSM1874861", "GSM1874862", "GSM1874863", "GSM1874864", "GSM1874865", "GSM1874866", "GSM1874867", "GSM1874868", "GSM1874869", "GSM1874870", "GSM1874871", "GSM1874872", "GSM1874873", "GSM1874874", "GSM1874875", "GSM1874876", "GSM1874877", "GSM1874878", "GSM1874879", "GSM1874880", "GSM1874881", "GSM1874882", "GSM1874883", "GSM1874884", "GSM1874885", "GSM1874886", "GSM1874887", "GSM1874888", "GSM1874889", "GSM1874890", "GSM1874891", "GSM1874892", "GSM1874893", "GSM1874894", "GSM1874895", "GSM1874896", "GSM1874897"], "sample_count": 168, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "INTRAGRAFT ANTI-VIRAL-SPECIFIC GENE EXPRESSION AS A DISTINCTIVE TRANSCRIPTIONAL SIGNATURE FOR POLYOMAVIRUS-ASSOCIATED NEPHROPATHY", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE75693", "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=GSE75693", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75693", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1964039", "GSM1964040", "GSM1964041", "GSM1964042", "GSM1964043", "GSM1964044", "GSM1964045", "GSM1964046", "GSM1964047", "GSM1964048", "GSM1964049", "GSM1964050", "GSM1964051", "GSM1964052", "GSM1964053", "GSM1964054", "GSM1964055", "GSM1964056", "GSM1964057", "GSM1964058", "GSM1964059", "GSM1964060", "GSM1964061", "GSM1964062", "GSM1964063", "GSM1964064", "GSM1964065", "GSM1964066", "GSM1964067", "GSM1964068", "GSM1964069", "GSM1964070", "GSM1964071", "GSM1964072", "GSM1964073", "GSM1964074", "GSM1964075", "GSM1964076", "GSM1964077", "GSM1964078", "GSM1964079", "GSM1964080", "GSM1964081", "GSM1964082", "GSM1964083", "GSM1964084", "GSM1964085", "GSM1964086", "GSM1964087", "GSM1964088", "GSM1964089", "GSM1964090", "GSM1964091", "GSM1964092", "GSM1964093", "GSM1964094", "GSM1964095", "GSM1964096", "GSM1964097", "GSM1964098", "GSM1964099", "GSM1964100", "GSM1964101", "GSM1964102", "GSM1964103", "GSM1964104", "GSM1964105", "GSM1964106", "GSM1964107", "GSM1964108", "GSM1964109", "GSM1964110", "GSM1964111", "GSM1964112", "GSM1964113", "GSM1964114", "GSM1964115", "GSM1964116", "GSM1964117"], "sample_count": 79, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE140989 not downloaded", "asset:data:geo:GSE140989 licence not read", "asset:data:geo:GSE47199 not downloaded", "asset:data:geo:GSE47199 licence not read", "asset:data:geo:GSE72925 not downloaded", "asset:data:geo:GSE72925 licence not read", "asset:data:geo:GSE75693 not downloaded", "asset:data:geo:GSE75693 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "R package Combat was used to eliminate batch effects. The differentially expressed genes (DEGs) of BKPyVAN and stable transplanted kidneys were analyzed by R package limma. p-Value < 0.05 and | fold change (FC)| > 1.5 were considered statistically significant."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Protein-protein interaction"}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE75693", "GSE47199", "GSE72925", "GSE140989"], "resolved_accessions": ["GSE75693", "GSE47199", "GSE72925", "GSE140989"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE75693, GSE47199, GSE72925, GSE140989 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:35464062", "data:geo:GSE140989"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE140989"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:43:27Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13655, "completion_tokens": 1830, "cached_tokens": 264}}, "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:35464062", "type": "paper", "label": "pmid:35464062"}, {"id": "source:pmid:35464062", "type": "manuscript", "label": "PMID 35464062 full text"}, {"id": "data:geo:GSE140989", "type": "dataset", "label": "GEO GSE140989"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35464062", "type": "paper", "label": "pmid:35464062"}, {"id": "source:pmid:35464062", "type": "manuscript", "label": "PMID 35464062 full text"}, {"id": "data:geo:GSE140989", "type": "dataset", "label": "GEO GSE140989"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35464062", "type": "extraction", "used": ["source:pmid:35464062"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE140989", "type": "accession_resolution", "used": ["data:geo:GSE140989"], "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:35464062", "parent_hash": "sha256:b66c57fb43e243b9a95e5e343df2eb1c07092cebdc726fcf9d113fc3ceea99c7", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE140989 licence not read", "asset:data:geo:GSE140989 not downloaded", "asset:data:geo:GSE47199 licence not read", "asset:data:geo:GSE47199 not downloaded", "asset:data:geo:GSE72925 licence not read", "asset:data:geo:GSE72925 not downloaded", "asset:data:geo:GSE75693 licence not read", "asset:data:geo:GSE75693 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": 0.93, "evidence": ["tudied under light and electron microscopes. Microarray datasets GSE75693, GSE47199, and GSE72925 we"], "order_basis": "paper_text_order:380", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tion genes by R package clusterProfiler. The single-cell RNA sequencing (scRNA-seq) from a BKPyVAN recipient was ana", "terProfiler. The single-cell RNA sequencing (scRNA-seq) from a BKPyVAN recipient was analyzed with", "N recipient 5) was processed to generate the single-cell RNA sequencing (scRNA-seq) profile. Detailed information ab", "to generate the single-cell RNA sequencing (scRNA-seq) profile. Detailed information about all sam"], "order_basis": "paper_text_order:746", "id": "assay:2"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["y R package clusterProfiler. The single-cell RNA sequencing (scRNA-seq) from a BKPyVAN recipient was ana", "5) was processed to generate the single-cell RNA sequencing (scRNA-seq) profile. Detailed information ab", "icles in BKPyV-infected renal tubular cells. Transcriptome analysis revealed 629 DEGs between samples o"], "order_basis": "paper_text_order:758", "id": "assay:3"}, {"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": ["trol for gene set variation analysis (GSVA). Immunohistochemistry and electron microscopy of kidney sections f", "minent activation of ERS markers verified by immunohistochemistry. Furthermore, DDIT3 was identified as the hu", "col. Pathological diagnosis was confirmed by immunostaining with antibody against SV40 large T-antigen ("], "order_basis": "paper_text_order:947", "id": "assay:4"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["opy of kidney sections from drug-induced ERS mouse models were performed to explore the associa", "tron microscope image of the kidney from ERS mouse models showed an obvious renal tubular vacuo"], "order_basis": "paper_text_order:1033", "id": "assay:5"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["R package Combat was used to eliminate batch effects. The differentially expressed genes (DEGs) of BKPyVAN and stable transplanted kidneys were analyzed by R package limma. p-Value < 0.05 and | fold change (FC)| > 1.5 were considered statistically significant."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]},"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":"2026-11-04T01:24:45+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}}}