{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41113402", "kind": "science-record", "revision": 3, "content_hash": "sha256:7aabcb6a8695cbf9c48244f649f303b5771d5a4637a4e6a992a7903c6b6a86b6", "created_at": "2026-11-01T20:31:09Z", "updated_at": "2026-11-01T22:14:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "[Shared Therapeutic Targets of Obesity and Type 2 Diabetes Mellitus and the Intervention Mechanisms of Chinese Herbal Components].", "doi": "10.12182/20250760104", "pmid": "41113402", "authors": ["Ruli Li", "Rongrong Wang", "Lianxin Li", "Chuchu Wang", "Tianlan Liao", "Boxun Zhang", "Rensong Yue"], "journal": "Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition", "year": 2025, "abstract": "Objective: To explore the shared potential targets and molecular mechanisms of obesity and type 2 diabetes mellitus (T2DM) using bioinformatics methods, to validate the expression of core targets through animal experiments, and to analyze the intervention potential of active components of traditional Chinese medicine (TCM).\nMethods: The obese population datasets (GSE151839 and GSE162653) were obtained from the Gene Expression Omnibus (GEO) database to screen for differentially expressed genes, which were then intersected with T2DM-related targets from the GeneCards database to identify shared targets. A protein-protein interaction (PPI) network was constructed using the STRING database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to identify enriched biological processes and signaling pathways. The expression of core targets in adipose tissue from patients with obesity and T2DM was validated using the GEO database. A total of 12 specific-pathogen-free (SPF) male Sprague-Dawley (SD) rats, aged 8 weeks and weighing between 180 and 200 g, were randomly assigned to a control group and a model group (n = 6 each). A T2DM rat model was established, and the mRNA and protein expression levels of core targets in adipose tissue were measured. Molecular docking and molecular dynamics simulations were performed to assess the binding ability of TCM active components to core targets.\nResults: A total of 460 and 796 obesity-related differentially expressed genes were identified in the GSE151839 and GSE162653 datasets, respectively, and 109 shared targets were obtained by intersection with T2DM-related targets. According to PPI network analysis, PTPRC, MMP9, ITGB2, CD86, CCR5, and CCR2 were identified as the core targets. GO and KEGG analysis showed that these targets are mainly enriched in biological processes such as inflammatory response, immune regulation, and cell adhesion. Animal experiments confirmed that the mRNA and protein expression of core targets, including PTPRC, ITGAX, MMP9, ITGB2, CCR2, and CXCL1, were significantly upregulated in the adipose tissue of T2DM rats (P < 0.05). Molecular docking and molecular dynamics simulations revealed that berberine and puerarin had good binding ability with PTPRC, MMP9, and ITGB2.\nConclusion: This study reveals the shared molecular mechanisms between obesity and T2DM and shows that core targets, such as PTPRC and MMP9, may promote disease progression by regulating the inflammation-immune network. These findings provide a theoretical basis for the development of targeted therapeutic strategies based on TCM active ingredients.", "claims": [{"id": "claim-method", "statement": "变量首先通过F检验评估方差齐性，正态分布数据以\\begin{document}$\\bar x\\pm s $\\end{document}表示，两组数据采用非配对t检验（two-tailed）进行组间比较，P<0.05为差异有统计学意义。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41113402", "locator": "sections[19] \"统计学方法\" paragraph 2", "quote": "变量首先通过F检验评估方差齐性，正态分布数据以\\begin{document}$\\bar x\\pm s $\\end{document}表示，两组数据采用非配对t检验（two-tailed）进行组间比较，P<0.05为差异有统计学意义。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "从GSE151839数据集获得10名肥胖〔体质量指数（body mass index, BMI）35～50 kg/m2〕和10名健康正常体质量（BMI 18.5～26.9 kg/m2）女性（按年龄和种族配对）脂肪中的基因表达情况。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41113402", "locator": "sections[5] \"肥胖差异基因及T2DM疾病靶点的获取\" paragraph 2", "quote": "从GSE151839数据集获得10名肥胖〔体质量指数（body mass index, BMI）35～50 kg/m2〕和10名健康正常体质量（BMI 18.5～26.9 kg/m2）女性（按年龄和种族配对）脂肪中的基因表达情况。"}], "state": "complete"}, {"id": "claim-target-result", "statement": "本研究揭示了肥胖与T2DM的共同分子机制，发现PTPRC、MMP9等核心靶点可能通过调控炎症-免疫网络促进疾病进展，为开发基于中药活性成分的靶向治疗策略提供了理论依据。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41113402", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "本研究揭示了肥胖与T2DM的共同分子机制，发现PTPRC、MMP9等核心靶点可能通过调控炎症-免疫网络促进疾病进展，为开发基于中药活性成分的靶向治疗策略提供了理论依据。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "本研究揭示了肥胖与T2DM的共同分子机制，发现PTPRC、MMP9等核心靶点可能通过调控炎症-免疫网络促进疾病进展，为开发基于中药活性成分的靶向治疗策略提供了理论依据。", "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:41113402"], "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": ["GSE151839", "GSE162653", "GSE205668", "GSE29231"], "resolved_accessions": ["GSE151839", "GSE162653", "GSE205668", "GSE29231"], "statements": ["从GSE151839数据集获得10名肥胖〔体质量指数（body mass index, BMI）35～50 kg/m2〕和10名健康正常体质量（BMI 18.5～26.9 kg/m2）女性（按年龄和种族配对）脂肪中的基因表达情况。"], "basis": "The paper names GSE151839, GSE162653, GSE205668, GSE29231 in GEO数据库 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:41113402", "data:geo:GSE151839"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE151839"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:03:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 10227, "completion_tokens": 2081, "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:41113402", "type": "paper", "label": "pmid:41113402"}, {"id": "source:pmid:41113402", "type": "manuscript", "label": "PMID 41113402 full text"}, {"id": "data:geo:GSE151839", "type": "dataset", "label": "GEO GSE151839"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41113402", "type": "paper", "label": "pmid:41113402"}, {"id": "source:pmid:41113402", "type": "manuscript", "label": "PMID 41113402 full text"}, {"id": "data:geo:GSE151839", "type": "dataset", "label": "GEO GSE151839"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41113402", "type": "extraction", "used": ["source:pmid:41113402"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE151839", "type": "accession_resolution", "used": ["data:geo:GSE151839"], "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:41113402", "parent_hash": "sha256:c56f62e28756e4a53737a01f90b9a66ea37fb1d3711e203184f64d3fa88ad0a2", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE151839 licence not read", "asset:data:geo:GSE151839 not downloaded", "asset:data:geo:GSE162653 licence not read", "asset:data:geo:GSE162653 not downloaded", "asset:data:geo:GSE205668 licence not read", "asset:data:geo:GSE205668 not downloaded", "asset:data:geo:GSE29231 licence not read", "asset:data:geo:GSE29231 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": 0.99, "evidence": ["pathogen-free (SPF) male Sprague-Dawley (SD) rats, aged 8 weeks and weighing between 180 and 2", "group and a model group (n = 6 each). A T2DM rat model was established, and the mRNA and prot", "ly upregulated in the adipose tissue of T2DM rats (P < 0.05). Molecular docking and molecular"], "order_basis": "paper_text_order:1133", "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": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T00:25:30+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}}}