{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41050938", "kind": "science-record", "revision": 4, "content_hash": "sha256:8441734e39aad38ee7a2fbac81845116f247c020b1759484cd945d90eb1ae228", "created_at": "2026-11-01T20:31:06Z", "updated_at": "2026-11-01T22:57:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated analysis of stem cell-related genes shared between type 2 diabetes mellitus and sepsis.", "doi": "10.3389/fchem.2025.1666651", "pmid": "41050938", "authors": ["Yubo Wang", "Xinhai Jiang", "Xiaohan Song", "Zhijie Ma", "Yan Wang"], "journal": "Frontiers in chemistry", "year": 2025, "abstract": "Background: Diabetes-induced immune impairment and insulin resistance increase infection risk, which may progress to sepsis that further deteriorates diabetic status. Stem cell-based interventions show therapeutic potential for both diseases. This study sought to uncover common stem cell-related genes (SCRGs) between T2DM and sepsis.\nMethods: The GSE15932 dataset for T2DM and GSE65682 dataset for sepsis from the Gene Expression Omnibus (GEO) were utilized to locate common differentially expressed genes (DEGs), which were then intersected with SCRGs to derive shared differentially expressed SCRGs (DE-SCRGs). The stem-cell-related biomarkers were discovered through combining functional similarity analysis, machine learning algorithms, and receiver operating characteristic (ROC) curves. Subsequently, functional enrichment analysis, immune infiltration, and single-cell analyses were conducted to investigate the potential pathways by which biomarkers regulate T2DM and sepsis. Finally, the expression of biomarkers was further verified at both transcriptional and protein levels through the establishment of an in vitro model of T2DM-sepsis.\nResults: Through a comprehensive analysis, CAPG and DDAH2 were found and those were significantly highly expressed in both T2DM and sepsis. Analysis of functional enrichment demonstrated they were implicated in \"FC gamma R-mediated phagocytosis\" and \"Ribosome\". Immune infiltration indicated a considerable disparity in the quantity of CD8 T cells and monocytes when comparing T2DM versus control groups, as well as sepsis versus control groups. At the cellular level, notable differences in CARG expression among alpha cells, beta cells, delta cells, and pancreatic stellate cells (PSCs) were observed in the two groups being compared. At transcription and protein levels, CAPG and DDAH2 were significantly more highly expressed in the T2DM-sepsis model than in the controls. The results corroborated the bioinformatics analysis conclusions, reinforcing the study's validity.\nConclusion: Two common stem cell-related biomarkers (CAPG and DDAH2) and their common pathways between T2DM and sepsis were discovered, providing new insights for further molecular mechanism studies.", "claims": [{"id": "claim-method", "statement": "The “limma” R package (version 3.54.2) was utilized to investigate differentially expressed genes (DEGs) between T2DM and control groups in GSE15932 with |log fold change| (|logFC|) > 0.5 and P-value <0.05 as screening thresholds (Ritchie et al., 2015).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41050938", "locator": "sections[4] \"Differential expression analysis\" paragraph 2", "quote": "The “limma” R package (version 3.54.2) was utilized to investigate differentially expressed genes (DEGs) between T2DM and control groups in GSE15932 with |log fold change| (|logFC|) > 0.5 and P-value <0.05 as screening thresholds (Ritchie et al., 2015)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets (GSE15932, GSE20966, GSE65682, GSE95233, and GSE195986) analyzed in this study were collected from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41050938", "locator": "sections[31] \"Data availability statement\" paragraph 2", "quote": "The datasets (GSE15932, GSE20966, GSE65682, GSE95233, and GSE195986) analyzed in this study were collected from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified two shared stem cell-related biomarkers, CAPG and DDAH2, for T2DM and sepsis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41050938", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Two common stem cell-related biomarkers (CAPG and DDAH2) and their common pathways between T2DM and sepsis were discovered, providing new insights for further molecular mechanism studies."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified two shared stem cell-related biomarkers, CAPG and DDAH2, for T2DM and sepsis.", "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:41050938"], "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:GSE15932"], "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:GSE15932"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41050938", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fchem.2025.1666651", "sha256": 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"2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE15932 not downloaded", "asset:data:geo:GSE15932 licence not read", "asset:data:geo:GSE195986 not downloaded", "asset:data:geo:GSE195986 licence not read", "asset:data:geo:GSE20966 not downloaded", "asset:data:geo:GSE20966 licence not read", "asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE95233 not downloaded", "asset:data:geo:GSE95233 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The “limma” R package (version 3.54.2) was utilized to investigate differentially expressed genes (DEGs) between T2DM and control groups in GSE15932 with |log fold change| (|logFC|) > 0.5 and P-value <0.05 as screening thresholds (Ritchie et al., 2015)."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {"sample_size": "via the Wilcoxon test (n = 2) and Student’s t-test"}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", 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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": ["GSE15932", "GSE20966", "GSE65682", "GSE95233", "GSE195986"], "resolved_accessions": ["GSE15932", "GSE20966", "GSE65682", "GSE95233", "GSE195986"], "statements": ["The datasets (GSE15932, GSE20966, GSE65682, GSE95233, and GSE195986) analyzed in this study were collected from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo)."], "basis": "The paper names GSE15932, GSE20966, GSE65682, GSE95233, GSE195986 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:41050938", "data:geo:GSE15932"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15932"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:02:25Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13251, "completion_tokens": 1545, "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:41050938", "type": "paper", "label": "pmid:41050938"}, {"id": "source:pmid:41050938", "type": "manuscript", "label": "PMID 41050938 full text"}, {"id": "data:geo:GSE15932", "type": "dataset", "label": "GEO GSE15932"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41050938", "type": "paper", "label": "pmid:41050938"}, {"id": "source:pmid:41050938", "type": "manuscript", "label": "PMID 41050938 full text"}, {"id": "data:geo:GSE15932", "type": "dataset", "label": "GEO GSE15932"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41050938", "type": "extraction", "used": ["source:pmid:41050938"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15932", "type": "accession_resolution", "used": ["data:geo:GSE15932"], "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:41050938", "parent_hash": "sha256:2e887f30faee0bc0d9adc95790023955b2a8d35819b6de74dc5b23a1d600d4ef", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE15932 licence not read", "asset:data:geo:GSE15932 not downloaded", "asset:data:geo:GSE195986 licence not read", "asset:data:geo:GSE195986 not downloaded", "asset:data:geo:GSE20966 licence not read", "asset:data:geo:GSE20966 not downloaded", "asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE95233 licence not read", "asset:data:geo:GSE95233 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s (Figure 7D). DDAH2 was not detected in the scRNA-seq dataset due to the absence of information fo", "(Supplementary Table S7). As no blood-based scRNA-seq datasets with case–control design were avail"], "order_basis": "paper_text_order:4992", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["(E) The volcano plot showing the DEGs of the RNA-seq dataset (F) The expression of each biomarker"], "order_basis": "paper_text_order:5686", "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 “limma” R package (version 3.54.2) was utilized to investigate differentially expressed genes (DEGs) between T2DM and control groups in GSE15932 with |log fold change| (|logFC|) > 0.5 and P-value <0.05 as screening thresholds (Ritchie et al., 2015)."], "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":"2026-11-04T00:43:58+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}}}