{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39318238", "kind": "science-record", "revision": 4, "content_hash": "sha256:32642cf99dc04120c8294af7e7c18a43bff01a197fd34a70c5c7c5d4d51001b4", "created_at": "2026-11-01T20:29:30Z", "updated_at": "2026-11-01T22:55:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of dilated cardiomyopathy-linked key genes by bioinformatics methods and evaluating the impact of tannic acid and monosodium glutamate in rats.", "doi": "10.1002/bab.2670", "pmid": "39318238", "authors": ["Habibe Karadas", "Hilal Tosun", "Hamid Ceylan"], "journal": "Biotechnology and applied biochemistry", "year": 2025, "abstract": "Dilated cardiomyopathy (DCM) is the most common type of myocardial dysfunction, affecting mostly young adults, but its therapeutic diagnosis and biomarkers for prognosis are lacking. This study aimed to investigate the possible effect of the common food additive monosodium glutamate (MSG) and tannic acid (TA), a phenolic compound, on the key molecular actors responsible for DCM. DCM-related publicly available microarray datasets (GSE120895, GSE17800, and GSE19303) were downloaded from the comprehensive Gene Expression Omnibus (GEO) database, and analyzed to identify differentially expressed genes (DEGs). By integrating DEGs and gene-disease validity curation results, overlapping genes were screened and identified as hub genes. Protein-protein interaction (PPI) network and ontology analysis were performed to make sense of the identified biological data. Finally, mRNA expression changes of identified hub genes in the heart tissues of rats treated with MSG and TA were measured by the qPCR method. Six upregulated (IGF1, TTN, ACTB, LMNA, EDN1, and NPPB) DEGs were identified between the DCM and healthy control samples as the hub genes. qPCR results revealed that the mRNA levels of these genes involved in DCM development increased significantly in rat heart tissues exposed to MSG. In contrast, this increase was remarkably alleviated by TA treatment. Our results provide new insights into critical molecular mechanisms that should be focused on in future DCM studies. Moreover, MSG may play a critical role in DCM formation, and TA may be used as a promising therapeutic agent in DCM.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) between EMBs of DCM patients and healthy individuals’ samples were screened and analyzed using GEO2R (http://www.ncbi.nlm.gov/geo2r).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39318238", "locator": "sections[5] \"Data pre‐processing and screening for DEGs\" paragraph 2", "quote": "Differentially expressed genes (DEGs) between EMBs of DCM patients and healthy individuals’ samples were screened and analyzed using GEO2R (http://www.ncbi.nlm.gov/geo2r)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used and analyzed during the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39318238", "locator": "sections[25] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The data used and analyzed during the current study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Six upregulated DEGs—IGF1, TTN, ACTB, LMNA, EDN1, and NPPB—were identified as DCM hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39318238", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Six upregulated (IGF1, TTN, ACTB, LMNA, EDN1, and NPPB) DEGs were identified between the DCM and healthy control samples as the hub genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Six upregulated DEGs—IGF1, TTN, ACTB, LMNA, EDN1, and NPPB—were identified as DCM hub 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:39318238"], "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. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE120895", "GSE17800", "GSE19303"], "resolved_accessions": ["GSE120895", "GSE17800", "GSE19303"], "statements": ["The data used and analyzed during the current study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE120895, GSE17800, GSE19303 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:39318238", "data:geo:GSE120895"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE120895"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:32:40Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 7562, "completion_tokens": 1801, "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:39318238", "type": "paper", "label": "pmid:39318238"}, {"id": "source:pmid:39318238", "type": "manuscript", "label": "PMID 39318238 full text"}, {"id": "data:geo:GSE120895", "type": "dataset", "label": "GEO GSE120895"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39318238", "type": "paper", "label": "pmid:39318238"}, {"id": "source:pmid:39318238", "type": "manuscript", "label": "PMID 39318238 full text"}, {"id": "data:geo:GSE120895", "type": "dataset", "label": "GEO GSE120895"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39318238", "type": "extraction", "used": ["source:pmid:39318238"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE120895", "type": "accession_resolution", "used": ["data:geo:GSE120895"], "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:39318238", "parent_hash": "sha256:f195a906818afac9fa23ee730f0279b2739cffc40740b895fb6b212da531a6ba", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE120895 licence not read", "asset:data:geo:GSE120895 not downloaded", "asset:data:geo:GSE17800 licence not read", "asset:data:geo:GSE17800 not downloaded", "asset:data:geo:GSE19303 licence not read", "asset:data:geo:GSE19303 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": ["pact of tannic acid and monosodium glutamate in rats.", "t of tannic acid and monosodium glutamate in rats.", "identified hub genes in the heart tissues of rats treated with MSG and TA were measured by the", "n DCM development increased significantly in rat heart tissues exposed to MSG. In contrast, t"], "order_basis": "paper_text_order:105", "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": 0.99, "evidence": ["treated with MSG and TA were measured by the qPCR method. Six upregulated (IGF1, TTN, ACTB, LM", "nd healthy control samples as the hub genes. qPCR results revealed that the mRNA levels of the"], "order_basis": "paper_text_order:1110", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) between EMBs of DCM patients and healthy individuals’ samples were screened and analyzed using GEO2R (http://www.ncbi.nlm.gov/geo2r)."], "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. 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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. 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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}}}