A bioinformatics analysis of the correlation between hepatic ischemia-reperfusion injury and postoperative cognitive dysfunction.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40778222", "kind": "science-record", "revision": 3, "content_hash": "sha256:1c8b6ae490013de08bede8273acc99734e3fe1cc5e54dfcbffded57ebf483a63", "created_at": "2026-11-01T20:30:52Z", "updated_at": "2026-11-01T22:14:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A bioinformatics analysis of the correlation between hepatic ischemia-reperfusion injury and postoperative cognitive dysfunction.", "doi": "10.3389/fgene.2025.1607446", "pmid": "40778222", "authors": ["Qing Hu", "Haijie Liu", "Yunfei Bao", "Zhihao Feng", "Hongbo Zhang", "Jianling Li"], "journal": "Frontiers in genetics", "year": 2025, "abstract": "Background: Postoperative cognitive dysfunction (POCD) is a common postoperative complication that is prevalent in elderly people. An increasing number of elderly patients are undergoing surgery. As a result, the number of patients presenting with POCD is increasing. Previous studies have demonstrated that hepatic ischemia-reperfusion injury (HIRI) in mice is associated with postoperative cognitive impairment. Therefore, this study investigated the relationship between POCD and HIRI using bioinformatics research methods.\nMethods: The Gene Expression Omnibus (GEO) database GSE202565 and GeneCards data were selected for correlation analysis using bioinformatics analysis methods. The GSE112713 dataset from the GEO database was chosen for preliminary validation of the screened hub genes.\nResults: We analyzed the dataset GSE202565 for differences in gene expression before and after hepatic post-ischemic reperfusion and obtained a total of 53 genes by identifying POCD-related genes. We also screened these 53 genes again and obtained 10 hub genes, which were analyzed and used for correlation prediction. Finally, these 10 hub genes were partially and preliminarily validated using the dataset GSE112713.\nConclusion: HIRI is closely related to POCD, and reducing the occurrence of HIRI may become one of the ways to avoid or improve postoperative cognitive impairment in the future.", "claims": [{"id": "claim-method", "statement": "We plotted a volcano plot with a p-value < 0.05 and |logFC| ≥ 1 as a condition.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40778222", "locator": "sections[19] \"4.2.1 Differential analysis of HIRI-related genes and mapping of volcanoes\" paragraph 2", "quote": "We plotted a volcano plot with a p-value < 0.05 and |logFC| ≥ 1 as a condition."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40778222", "locator": "sections[32] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Intersection of 2,053 POCD-related genes with 259 HIRI-related differentially expressed genes identified 53 POCD-related HIRI genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40778222", "locator": "sections[4] \"2.2 Identification of POCD-related genes and mapping of Venn\" paragraph 2", "quote": "After intersecting 2,053 POCD-related genes with 259 HIRI-related DEGs, 53 DEGs of POCD-related genes were obtained with HIRI-related amounts (Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Intersection of 2,053 POCD-related genes with 259 HIRI-related differentially expressed genes identified 53 POCD-related HIRI 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:40778222"], "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:GSE112713"], "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:GSE112713"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40778222", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2025.1607446", "sha256": "sha256:852f57b400f5db9a9bc82f65a3ba665b4442b13a6938e499dda880f20299428f", "bytes": 42789, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2025.1607446", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12328142", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE112713", "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=GSE112713", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE112713", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3081877", "GSM3081878", "GSM3081879", "GSM3081880", "GSM3081881", "GSM3081882", "GSM3081883", "GSM3081884", "GSM3081885", "GSM3081886", "GSM3081887", "GSM3081888", "GSM3081889", "GSM3081890", "GSM3081891", "GSM3081892", "GSM3081893", "GSM3081894", "GSM3081895", "GSM3081896", "GSM3081897", "GSM3081898", "GSM3081899", "GSM3081900", "GSM3081901", "GSM3081902", "GSM3081903", "GSM3081904", "GSM3081905", "GSM3081906", "GSM3081907", "GSM3081908", "GSM3081909", "GSM3081910", "GSM3081911", "GSM3081912", "GSM3081913", "GSM3081914", "GSM3081915", "GSM3081916", "GSM3081917", "GSM3081918", "GSM3081919", "GSM3081920", "GSM3081921", "GSM3081922", "GSM3081923", "GSM3081924"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "Normothermic machine perfusion (NMP) inhibits proinflammatory responses in the liver and promotes regeneration", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE202565", "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=GSE202565", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE202565", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM6124517", "GSM6124518", "GSM6124519", "GSM6124520", "GSM6124521", "GSM6124522", "GSM6124523", "GSM6124524", "GSM6124525", "GSM6124526", "GSM6124527", "GSM6124528", "GSM6124529", "GSM6124530", "GSM6124531", "GSM6124532", "GSM6124533", "GSM6124534", "GSM6124535", "GSM6124536", "GSM6124537", "GSM6124538", "GSM6124539", "GSM6124540", "GSM6124541", "GSM6124542", "GSM6124543", "GSM6124544", "GSM6124545", "GSM6124546", "GSM6124547", "GSM6124548"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Pan-caspase inhibition during normothermic machine perfusion of discarded livers mitigates ischemia-reperfusion injury", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE112713 not downloaded", "asset:data:geo:GSE112713 licence not read", "asset:data:geo:GSE202565 not downloaded", "asset:data:geo:GSE202565 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R differential expression analysis using a p-value < 0.05 and |logFC| ≥ 1.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We plotted a volcano plot with a p-value < 0.05 and |logFC| ≥ 1 as a condition."}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE202565", "GSE112713"], "resolved_accessions": ["GSE202565", "GSE112713"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."], "basis": "The paper names GSE202565, GSE112713 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:40778222", "data:geo:GSE112713"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE112713"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:58:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13529, "completion_tokens": 1819, "cached_tokens": 0}}, "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:40778222", "type": "paper", "label": "pmid:40778222"}, {"id": "source:pmid:40778222", "type": "manuscript", "label": "PMID 40778222 full text"}, {"id": "data:geo:GSE112713", "type": "dataset", "label": "GEO GSE112713"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40778222", "type": "paper", "label": "pmid:40778222"}, {"id": "source:pmid:40778222", "type": "manuscript", "label": "PMID 40778222 full text"}, {"id": "data:geo:GSE112713", "type": "dataset", "label": "GEO GSE112713"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40778222", "type": "extraction", "used": ["source:pmid:40778222"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE112713", "type": "accession_resolution", "used": ["data:geo:GSE112713"], "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:40778222", "parent_hash": "sha256:76f5a8dc73ab2f01eb5931bf9561abc8887178717e98e49d261c94ed45e02733", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE112713 licence not read", "asset:data:geo:GSE112713 not downloaded", "asset:data:geo:GSE202565 licence not read", "asset:data:geo:GSE202565 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["t hepatic ischemia-reperfusion injury (HIRI) in mice is associated with postoperative cognitive i"], "order_basis": "paper_text_order:436", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["PPI"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}