{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40330909", "kind": "science-record", "revision": 4, "content_hash": "sha256:27e50493bdfd47aa011ab73c911a988e788b5ed69bb88375ea9f9d0658092e87", "created_at": "2026-11-01T20:30:29Z", "updated_at": "2026-11-01T22:56:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Ferroptosis -Related Genes in MAFLD/MASH and HQHF Validation.", "doi": "10.2147/HMER.S509778", "pmid": "40330909", "authors": ["Sutong Liu", "Lihui Zhang", "Junjiao Xu", "Qing Zhao", "Dongfang Shang", "Xiaoyan Liu", "Qiang Zhang", "Minghao Liu", "Wenxia Zhao"], "journal": "Hepatic medicine : evidence and research", "year": 2025, "abstract": "Purpose: Metabolic associated fatty liver disease (MAFLD) and its progressive form, Metabolic Dysfunction-Associated Steatohepatitis(MASH), are prevalent liver disorders with significant health implications. This study aims to identify differentially expressed genes (DEGs) associated with MAFLD/MASH and explore their potential link to ferroptosis, a form of regulated cell death.\nMethods: We conducted differential expression analysis using two datasets from the GEO database. Genes related to ferroptosis were identified from the Genecards and FerrDb databases, and the intersection genes were obtained by intersecting the DEGs with ferroptosis-related genes. Functional enrichment was performed using GO and KEGG pathways. The clinical diagnostic value of the intersection genes was evaluated through ROC analysis. Finally, the research findings were validated using a high-fat diet (HFD) mouse model, observing the improvement in gene expression with HQHF treatment.\nResults: We utilized two datasets, GSE89632 and GSE63067, from the GEO database, comprising 39 samples, including 24 healthy controls. Differential expression analysis revealed significant gene expression changes in NAFLD and NASH compared to healthy controls. These DEGs were visualized using volcano plots. Ferroptosis-related genes were identified from Genecards and FerrDb databases, resulting in 1937 unique genes. Venn analysis revealed intersections between DEGs and ferroptosis genes, highlighting potential regulatory roles. Functional enrichment analysis using GO and KEGG pathways indicated significant involvement in cellular components and signaling pathways, such as PPAR and HIF-1. The clinical diagnostic value of intersecting genes was assessed using ROC analysis, demonstrating promising diagnostic potential. In addition, a high-fat diet (HFD) mouse model was used to validate the research findings, showing that HQHF treatment can alleviate lipid deposition and inflammation in the liver. Transmission electron microscopy results indicated that HQHF prevented mitochondrial damage and significantly reduced the content of Fe2+ in the liver, alleviating iron deposition. We verified the reliable genes with diagnostic value through qPCR, and the results suggested that HQHF can lower the transcription levels of P4HA1, NR4A1, and EFEMP1, while increasing the transcription levels of ENo3, GRIA3, ME1, and FADS2, confirming our ROC results.\nConclusion: This study provides insights into the molecular mechanisms underlying MAFLD/MASH and suggests ferroptosis-related genes as potential diagnostic biomarkers and therapeutic targets. Further research is warranted to explore these findings in clinical settings.", "claims": [{"id": "claim-method", "statement": "The normalizeBetweenArrays function from the limma package was used to normalize the data and perform differential analysis, with the results visualized using the ggplot2 package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40330909", "locator": "sections[5] \"Differential Expression Analysis\" paragraph 2", "quote": "The normalizeBetweenArrays function from the limma package was used to normalize the data and perform differential analysis, with the results visualized using the ggplot2 package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The disease dataset used in this article was downloaded from the GEO database, and the phenotypic genes were obtained from the Genecards (https://www.genecards.org/) database, http://www.zhounan.org/ferrdb/current/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40330909", "locator": "sections[30] \"Data Sharing Statement\" paragraph 2", "quote": "The disease dataset used in this article was downloaded from the GEO database, and the phenotypic genes were obtained from the Genecards (https://www.genecards.org/) database, http://www.zhounan.org/ferrdb/current/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential-expression analysis of the GEO datasets identified 4 upregulated and 1 downregulated NAFLD genes overlapping with ferroptosis genes, and 3 upregulated and 3 downregulated NASH genes overlapping with ferroptosis genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40330909", "locator": "sections[19] \"Identification of Differential Genes in NAFLD/NASH\" paragraph 2", "quote": "The results showed that there were 3 overlapping genes between NASH’s upregulated genes and ferroptosis genes, and 3 overlapping genes among the downregulated genes; for NAFLD, there were 4 overlapping genes in the upregulated genes and 1 overlapping gene among the downregulated genes (Figure 1E–H)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential-expression analysis of the GEO datasets identified 4 upregulated and 1 downregulated NAFLD genes overlapping with ferroptosis genes, and 3 upregulated and 3 downregulated NASH genes overlapping with ferroptosis 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:40330909"], "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:GSE63067"], "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:GSE63067"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40330909", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/HMER.S509778", "sha256": 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:40330909", "data:geo:GSE63067"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE63067"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:52:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10764, "completion_tokens": 1499, "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:40330909", "type": "paper", "label": "pmid:40330909"}, {"id": "source:pmid:40330909", "type": "manuscript", "label": "PMID 40330909 full text"}, {"id": "data:geo:GSE63067", "type": "dataset", "label": "GEO GSE63067"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40330909", "type": "paper", "label": "pmid:40330909"}, {"id": "source:pmid:40330909", "type": "manuscript", "label": "PMID 40330909 full text"}, {"id": "data:geo:GSE63067", "type": "dataset", "label": "GEO GSE63067"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40330909", "type": "extraction", "used": ["source:pmid:40330909"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE63067", "type": "accession_resolution", "used": ["data:geo:GSE63067"], "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:40330909", "parent_hash": "sha256:5df8cd374d8b2cd7fab5e94e113b9614e24593dd3e130b480adba947b9a8f2ff", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE63067 licence not read", "asset:data:geo:GSE63067 not downloaded", "asset:data:geo:GSE89632 licence not read", "asset:data:geo:GSE89632 not downloaded", "execution.not_run", "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": 0.99, "evidence": ["s were validated using a high-fat diet (HFD) mouse model, observing the improvement in gene expressio", "otential. In addition, a high-fat diet (HFD) mouse model was used to validate the research findings,", "s were validated using a high-fat diet (HFD) mouse model, observing the improvement in gene exp", "otential. In addition, a high-fat diet (HFD) mouse model was used to validate the research find"], "order_basis": "paper_text_order:928", "id": "assay:1"}, {"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": ["reliable genes with diagnostic value through qPCR, and the results suggested that HQHF can low"], "order_basis": "paper_text_order:2258", "id": "assay:2"}, {"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": ["The normalizeBetweenArrays function from the limma package was used to normalize the data and perform differential analysis, with the results visualized using the ggplot2 package."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"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":"2026-11-04T00:47:30+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}}}