Comprehensive analysis of lactylation-related gene and immune microenvironment in atrial fibrillation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40329965", "kind": "science-record", "revision": 4, "content_hash": "sha256:efdae728384b30a3947de35b6c0e5e56c0216cf588a45cd31b236ca4c4e69d3b", "created_at": "2026-11-01T20:30:29Z", "updated_at": "2026-11-01T22:56:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis of lactylation-related gene and immune microenvironment in atrial fibrillation.", "doi": "10.3389/fcvm.2025.1567310", "pmid": "40329965", "authors": ["Yazhe Ma", "Youcheng Wang", "Yuanjia Ke", "Qingyan Zhao", "Jie Fan", "Yang Chen"], "journal": "Frontiers in cardiovascular medicine", "year": 2025, "abstract": "Background: Atrial fibrillation (AF) is a common arrhythmia associated with an increased risk of stroke, heart failure, and mortality. Immune infiltration plays a crucial role in AF pathogenesis, yet its mechanisms remain unclear. Lactylation, a novel post-translational modification, has been implicated in immune regulation, but its association with AF remains unexplored. This study aims to elucidate the relationship between lactylation and immune infiltration in AF and identify potential diagnostic biomarkers.\nMethods: Gene expression data from left atrial tissue samples of AF and sinus rhythm (SR) patients were obtained from the Gene Expression Omnibus (GEO) database (GSE41177, GSE79768, GSE115574, GSE2240, GSE14975, and GSE128188). Differentially expressed genes (DEGs) between AF and SR samples were identified, followed by pathway enrichment and immune infiltration analysis. Correlation analysis and WGCNA were performed to assess interactions between lactylation-related genes and immune-associated DEGs. Machine learning models, including Random Forest and Support Vector Machine (SVM), were applied to select potential AF-related diagnostic biomarkers, and validated in the animal model (beagles; n = 6).\nResults: A total of 5,648 DEGs were identified, including six lactylation-related genes (DDX39A, ARID3A, TKT, NUP50, G6PD, and VCAN). Co-expression and WGCNA analyses identified lactylation- and immune-associated gene modules in AF. Functional enrichment analysis highlighted immune-related pathways such as T cell activation and neutrophil degranulation. A five-gene diagnostic model (FOXK1, JAM3, LOC100288798, MCM4, and RCAN1) achieved high predictive accuracy (AUC = 0.969 in training, 0.907 in self-test, and 0.950, 0.760, 0.890 in independent datasets). Experimental validation confirmed the upregulated expression of these biomarkers in AF.\nConclusion: This study reveals a strong association between lactylation-related genes and immune infiltration in AF, suggesting their involvement in immune remodeling. The identified five-gene signature serves as a potential diagnostic biomarker set, offering novel insights into AF pathogenesis and contributing to improved diagnosis and targeted therapeutic strategies. Future studies integrating proteomic and single-cell analyses will further clarify the role of lactylation in AF.", "claims": [{"id": "claim-method", "statement": "Machine learning models, including Random Forest and Support Vector Machine (SVM), were applied to select potential AF-related diagnostic biomarkers, and validated in the animal model (beagles; n = 6).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40329965", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Machine learning models, including Random Forest and Support Vector Machine (SVM), were applied to select potential AF-related diagnostic biomarkers, and validated in the animal model (beagles; n = 6)."}], "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:40329965", "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": "A five-gene diagnostic model (FOXK1, JAM3, LOC100288798, MCM4, and RCAN1) achieved high predictive accuracy (AUC = 0.969 in training, 0.907 in self-test, and 0.950, 0.760, 0.890 in independent datasets).", "kind": "quantitative", "target": {"value": 0.969, "unit": "auc", "tolerance": null, "source": "A five-gene diagnostic model (FOXK1, JAM3, LOC100288798, MCM4, and RCAN1) achieved high predictive accuracy (AUC = 0.969 in training, 0.907 in self-test, and 0.950, 0.760, 0.890 in independent datasets)."}, "evidence": [{"asset": "source:pmid:40329965", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A five-gene diagnostic model (FOXK1, JAM3, LOC100288798, MCM4, and RCAN1) achieved high predictive accuracy (AUC = 0.969 in training, 0.907 in self-test, and 0.950, 0.760, 0.890 in independent datasets)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A five-gene diagnostic model (FOXK1, JAM3, LOC100288798, MCM4, and RCAN1) achieved high predictive accuracy (AUC = 0.969 in training, 0.907 in self-test, and 0.950, 0.760, 0.890 in independent datasets).", "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:40329965"], "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:GSE115574"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:machine_learning_random_forest", "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:GSE115574"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:machine_learning_random_forest"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40329965", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcvm.2025.1567310", "sha256": "sha256:9673ad7097b0a6b5aba18fbccecff948bc18feb8686ff3c4df46b527c7924304", "bytes": 34719, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcvm.2025.1567310", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12053079", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE115574", "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=GSE115574", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE115574", "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": ["GSM3182680", "GSM3182681", "GSM3182682", "GSM3182683", "GSM3182684", "GSM3182685", "GSM3182686", "GSM3182687", "GSM3182688", "GSM3182689", "GSM3182690", "GSM3182691", "GSM3182692", "GSM3182693", "GSM3182694", "GSM3182695", "GSM3182696", "GSM3182697", "GSM3182698", "GSM3182699", "GSM3182700", "GSM3182701", "GSM3182702", "GSM3182703", "GSM3182704", "GSM3182705", "GSM3182706", "GSM3182707", "GSM3182708", "GSM3182709", "GSM3182710", "GSM3182711", "GSM3182712", "GSM3182713", "GSM3182714", "GSM3182715", "GSM3182716", "GSM3182717", "GSM3182718", "GSM3182719", "GSM3182720", "GSM3182721", "GSM3182722", "GSM3182723", "GSM3182724", "GSM3182725", "GSM3182726", "GSM3182727", "GSM3182728", "GSM3182729", "GSM3182730", "GSM3182731", "GSM3182732", "GSM3182733", "GSM3182734", "GSM3182735", "GSM3182736", "GSM3182737", "GSM3182738"], "sample_count": 59, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data from human left and right atrial tissues in patients with degenerative MR in SR and AFib.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE128188", "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=GSE128188", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE128188", "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": ["GSM3666571", "GSM3666572", "GSM3666573", "GSM3666574", "GSM3666575", "GSM3666576", "GSM3666577", "GSM3666578", "GSM3666579", "GSM3666580", "GSM3666581", "GSM3666582", "GSM3666583", "GSM3666584", "GSM3666585", "GSM3666586", "GSM3666587", "GSM3666588", "GSM3666589", "GSM3666590"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Differentially Expressed Genes for Atrial Fibrillation Identified using RNA Sequencing from Paired Human Left and Right Atrial Appendages.", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE14975", "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=GSE14975", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14975", "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": ["GSM373956", "GSM373957", "GSM373958", "GSM373959", "GSM373960", "GSM373961", "GSM373962", "GSM373963", "GSM373964", "GSM373965"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Rac1-Induced Connective Tissue Growth Factor regulates Connexin 43 and N-Cadherin Expression in Atrial Fibrillation", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE2240", "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=GSE2240", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2240", "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": ["GSM40980", "GSM40981", "GSM40982", "GSM40983", "GSM40984", "GSM40985", "GSM40986", "GSM40987", "GSM40988", "GSM40989", "GSM40990", "GSM40991", "GSM40992", "GSM40993", "GSM40994", "GSM40995", "GSM40996", "GSM40997", "GSM40998", "GSM40999", "GSM41000", "GSM41001", "GSM41002", "GSM41003", "GSM41004", "GSM41005", "GSM41006", "GSM41007", "GSM41008", "GSM41009", "GSM41010", "GSM41011", "GSM41012", "GSM41013", "GSM41014", "GSM41085", "GSM41086", "GSM41087", "GSM41088", "GSM41089", "GSM41090", "GSM41091", "GSM41092", "GSM41093", "GSM41094", "GSM41095", "GSM41096", "GSM41097", "GSM41098", "GSM41099", "GSM41100", "GSM41101", "GSM41102", "GSM41103", "GSM41104", "GSM41105", "GSM41106", "GSM41107", "GSM41108", "GSM41109", "GSM41110", "GSM41111", "GSM41112", "GSM41113", "GSM41114", "GSM41115", "GSM41116", "GSM41117", "GSM41118", "GSM41119"], "sample_count": 70, "group_sizes": null, "group_sizes_basis": null, "platform": "96;97", "taxon": "Homo sapiens", "title": "Comparison of atrial tissue of patients with atrial fibrillation and sinus rhythm with ventricular gene expression", "resolution_checked_at": "2026-11-01T15:14:33Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE41177", "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=GSE41177", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41177", "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": ["GSM1005418", "GSM1005419", "GSM1005420", "GSM1005421", "GSM1005422", "GSM1005423", "GSM1005424", "GSM1005425", "GSM1005426", "GSM1005427", "GSM1005428", "GSM1005429", "GSM1005430", "GSM1005431", "GSM1005432", "GSM1005433", "GSM1005434", "GSM1005435", "GSM1005436", "GSM1005437", "GSM1005438", "GSM1005439", "GSM1005440", "GSM1005441", "GSM1005442", "GSM1005443", "GSM1005444", "GSM1005445", "GSM1006245", "GSM1006246", "GSM1006247", "GSM1006248", "GSM1006249", "GSM1006250", "GSM1006251", "GSM1006252", "GSM1006253", "GSM1006254"], "sample_count": 38, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Region-specific gene expression profiles in left atria of patients with valvular atrial fibrillation", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE79768", "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=GSE79768", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE79768", "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": ["GSM2102184", "GSM2102185", "GSM2102186", "GSM2102187", "GSM2102188", "GSM2102189", "GSM2102190", "GSM2102191", "GSM2102192", "GSM2102193", "GSM2102194", "GSM2102195", "GSM2102196", "GSM2102197", "GSM2102198", "GSM2102199", "GSM2102200", "GSM2102201", "GSM2102202", "GSM2102203", "GSM2102204", "GSM2102205", "GSM2102206", "GSM2102207", "GSM2102208", "GSM2102209"], "sample_count": 26, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Atrial fibrillation is associated with altered left-to-right atria gene expression ratio: implications for arrhythmogenesis and thrombogenesis", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE115574 not downloaded", "asset:data:geo:GSE115574 licence not read", "asset:data:geo:GSE128188 not downloaded", "asset:data:geo:GSE128188 licence not read", "asset:data:geo:GSE14975 not downloaded", "asset:data:geo:GSE14975 licence not read", "asset:data:geo:GSE2240 not downloaded", "asset:data:geo:GSE2240 licence not read", "asset:data:geo:GSE41177 not downloaded", "asset:data:geo:GSE41177 licence not read", "asset:data:geo:GSE79768 not downloaded", "asset:data:geo:GSE79768 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Machine learning models, including Random Forest and Support Vector Machine (SVM), were applied to select potential AF-related diagnostic biomarkers, and validated in the animal model (beagles; n = 6)."}}, {"id": "method-2", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Support Vector Machine"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "cross_validate", "expected_value": 0.969, "unit": "auc", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.machine_learning_random_forest"]}, "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": false, "required_operations": [], "missing_operations": ["machine_learning_random_forest"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: random_forest."}, "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": ["GSE41177", "GSE79768", "GSE115574", "GSE2240", "GSE14975", "GSE128188"], "resolved_accessions": ["GSE41177", "GSE79768", "GSE115574", "GSE2240", "GSE14975", "GSE128188"], "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 GSE41177, GSE79768, GSE115574, GSE2240, GSE14975, GSE128188 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": [], "assets": ["source:pmid:40329965", "data:geo:GSE115574"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "machine_learning_random_forest", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE115574"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:51:59Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10150, "completion_tokens": 2123, "cached_tokens": 128}}, "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:40329965", "type": "paper", "label": "pmid:40329965"}, {"id": "source:pmid:40329965", "type": "manuscript", "label": "PMID 40329965 full text"}, {"id": "data:geo:GSE115574", "type": "dataset", "label": "GEO GSE115574"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40329965", "type": "paper", "label": "pmid:40329965"}, {"id": "source:pmid:40329965", "type": "manuscript", "label": "PMID 40329965 full text"}, {"id": "data:geo:GSE115574", "type": "dataset", "label": "GEO GSE115574"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40329965", "type": "extraction", "used": ["source:pmid:40329965"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE115574", "type": "accession_resolution", "used": ["data:geo:GSE115574"], "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:40329965", "parent_hash": "sha256:7c6d25b1cfaa55a0afe0e28924cfea77d371d02932ce8e1674c9d376334665ca", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE115574 licence not read", "asset:data:geo:GSE115574 not downloaded", "asset:data:geo:GSE128188 licence not read", "asset:data:geo:GSE128188 not downloaded", "asset:data:geo:GSE14975 licence not read", "asset:data:geo:GSE14975 not downloaded", "asset:data:geo:GSE2240 licence not read", "asset:data:geo:GSE2240 not downloaded", "asset:data:geo:GSE41177 licence not read", "asset:data:geo:GSE41177 not downloaded", "asset:data:geo:GSE79768 licence not read", "asset:data:geo:GSE79768 not downloaded", "execution.not_run", "method.machine_learning_random_forest", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:machine_learning_random_forest"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["quickly removed from the heart then perfumed qPCR. Statistical analysis Statistical analyses w"], "order_basis": "paper_text_order:3580", "id": "assay:1"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Machine learning models, including Random Forest and Support Vector Machine (SVM), were applied to select potential AF-related diagnostic biomarkers, and validated in the animal model (beagles; n = 6)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}