{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40074310", "kind": "science-record", "revision": 2, "content_hash": "sha256:cedfd54dfe8e889a6b34eacf26534a01b64825ed3a6fe338b97d2c9840a5b947", "created_at": "2026-11-01T20:30:17Z", "updated_at": "2026-11-01T21:34:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "ZNF667 alleviates the inflammatory damage in intervertebral disc degeneration via inhibiting NF-κB signaling pathway.", "doi": "10.11817/j.issn.1672-7347.2024.240122", "pmid": "40074310", "authors": ["Hua Zhong", "Lebin Guo", "Yan Yang", "Chenjun Tian", "Fusheng Liu", "Bowen Zheng"], "journal": "Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences", "year": 2024, "abstract": "OBJECTIVES: With the aging population, the incidence of intervertebral disc degeneration (IDD) is increasing every year. The pathogenesis of IDD is complex, and there are currently no effective treatment options. This study aims to investigate the specific function and underlying mechanism of zinc finger protein 667 (ZNF667) in the inflammatory damage of nucleus pulposus cells in IDD.\nMETHODS: Differential expression genes (DEG) associated with IDD were screened from IDD-related datasets in the Gene Expression Omnibus (GEO) (GSE124272 and GSE150408), and ZNF667, which is closely related to gene transcriptional regulation, was selected and analyzed in several IDD-related datasets (GSE124272, GSE150408, GSE56081, GSE147383, GSE23130). Nucleus pulposus tissues were collected from 3 IDD patients and 3 trauma-induced vertebral fracture patients (serving as controls). Hematoxylin and eosin (HE) staining was performed for pathological examination, and immunohistochemistry (IHC) was used to assess ZNF667 expression in the nucleus pulposus tissues. Gene set enrichment analysis (GSEA) was then employed to elucidate the potential mechanisms of ZNF667. For in vitro validation, human primary nucleus pulposus cells were treated with 10 ng/mL of interleukin-1β (IL-1β) to establish an IDD cell model, and subsequently transfected with a ZNF667 overexpression plasmid. Flow cytometry was used to evaluate cell apoptosis, enzyme-linked immunosorbent assay (ELISA) measured the levels of inflammatory factors-cyclooxygenase-2 (COX-2), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) in the cell culture supernatant, real-time polymerase chain reaction (RT-PCR) quantified ZNF667 mRNA expression, and Western blotting assessed protein expression levels of ZNF667, myeloid differentiation factor 88 (MyD88), P65, and phosphorylated P65 (p-P65).\nRESULTS: Analysis of both the GEO datasets and clinical tissue samples revealed that ZNF667 expression is reduced in IDD. In IDD patients, the extracellular matrix and nucleus pulposus cells are significantly diminished, and the arrangement of fibrochondrocytes is disordered. GSEA results showed that ZNF667 may be involved in biological processes such as angiogenesis, epithelial-mesenchymal transition (EMT), oxidative phosphorylation, peroxisome function, steroid biosynthesis, and the NF-κB-mediated TNF-α signaling pathway. In vitro, ZNF667 was expressed at low levels in the IL-1β-induced IDD cell model, and overexpression of ZNF667 reversed the IL-1β-induced increase in cell apoptosis, the upregulation of inflammation factors (COX-2, IL-6, TNF-α), and the increased expression of NF-κB pathway-related proteins (MyD88 and the p-P65/P65 ratio) (all P<0.05).\nCONCLUSIONS: ZNF667 can alleviate nucleus pulposus cell apoptosis and inflammatory responses by inhibiting the NF-κB signaling pathway, thereby exerting a protective effect on intervertebral discs. This finding not only provides new insights into the pathogenesis of IDD but also suggests a potential therapeutic target for its treatment.", "claims": [{"id": "claim-method", "statement": "使用GraphPad Prism 7软件进行数据分析，数据以均数±标准差表示，采用t检验进行2组间的比较，P<0.05为差异有统计学意义。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40074310", "locator": "sections[17] \"统计学处理\" paragraph 2", "quote": "使用GraphPad Prism 7软件进行数据分析，数据以均数±标准差表示，采用t检验进行2组间的比较，P<0.05为差异有统计学意义。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "选取基因表达综合 (gene expression omnibus，GEO)数据库中2个IDD相关基因数据集GSE124272(包括8例IDD患者和8例健康对照者的样本)、GSE150408(包括17例未经过治疗的IDD患者和17例健康对照者的样本)，利用R语言包及limma工具包对2个数据集进行分析，经过交叉筛选得到差异表达基因(differential expression gene，DEG)[log2|差异倍数(fold change，FC)|>0.60，P<0.05]。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40074310", "locator": "sections[7] \"筛选差异表达基因\" paragraph 2", "quote": "选取基因表达综合 (gene expression omnibus，GEO)数据库中2个IDD相关基因数据集GSE124272(包括8例IDD患者和8例健康对照者的样本)、GSE150408(包括17例未经过治疗的IDD患者和17例健康对照者的样本)，利用R语言包及limma工具包对2个数据集进行分析，经过交叉筛选得到差异表达基因(differential expression gene，DEG)[log2|差异倍数(fold change，FC)|>0.60，P<0.05]。"}], "state": "complete"}, {"id": "claim-target-result", "statement": "ZNF667可通过抑制NF-κB信号通路，减轻髓核细胞凋亡和炎症反应，发挥对椎间盘的保护作用。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40074310", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "ZNF667可通过抑制NF-κB信号通路，减轻髓核细胞凋亡和炎症反应，发挥对椎间盘的保护作用。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ZNF667可通过抑制NF-κB信号通路，减轻髓核细胞凋亡和炎症反应，发挥对椎间盘的保护作用。", "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:40074310"], "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:GSE124272"], "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:GSE124272"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40074310", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.11817/j.issn.1672-7347.2024.240122", "sha256": 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"Transcriptome signatures reveal candidate key genes in the whole blood of patients with lumbar disc prolapse", "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:GSE147383", "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=GSE147383", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE147383", "version": null, "note": "选取基因表达综合 (gene expression omnibus，GEO)数据库中2个IDD相关基因数据集GSE124272(包括8例IDD患者和8例健康对照者的样本)、GSE150408(包括17例未经过治疗的IDD患者和17例健康对照者的样本)，利用R语言包及limma工具包对2个数据集进行分析，经过交叉筛选得到差异表达基因(differential expression gene，DEG)[log2|差异倍数(fold change，FC)|>0.60，P<0.05]。", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": 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null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE150408", "version": null, "note": "选取基因表达综合 (gene expression omnibus，GEO)数据库中2个IDD相关基因数据集GSE124272(包括8例IDD患者和8例健康对照者的样本)、GSE150408(包括17例未经过治疗的IDD患者和17例健康对照者的样本)，利用R语言包及limma工具包对2个数据集进行分析，经过交叉筛选得到差异表达基因(differential expression gene，DEG)[log2|差异倍数(fold change，FC)|>0.60，P<0.05]。", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "选取基因表达综合 (gene expression omnibus，GEO)数据库中2个IDD相关基因数据集GSE124272(包括8例IDD患者和8例健康对照者的样本)、GSE150408(包括17例未经过治疗的IDD患者和17例健康对照者的样本)，利用R语言包及limma工具包对2个数据集进行分析，经过交叉筛选得到差异表达基因(differential expression gene，DEG)[log2|差异倍数(fold change，FC)|>0.60，P<0.05]。", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4548691", "GSM4548692", "GSM4548693", "GSM4548694", "GSM4548695", "GSM4548696", "GSM4548697", "GSM4548698", "GSM4548699", "GSM4548700", "GSM4548701", "GSM4548702", "GSM4548703", 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reader quoted the method the paper names (采用t检验进行2组间的比较，P<0.05为差异有统计学意义。), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE124272", "GSE150408", "GSE56081", "GSE147383", "GSE23130"], "resolved_accessions": ["GSE124272", "GSE150408", "GSE56081", "GSE147383", "GSE23130"], "statements": ["选取基因表达综合 (gene expression omnibus，GEO)数据库中2个IDD相关基因数据集GSE124272(包括8例IDD患者和8例健康对照者的样本)、GSE150408(包括17例未经过治疗的IDD患者和17例健康对照者的样本)，利用R语言包及limma工具包对2个数据集进行分析，经过交叉筛选得到差异表达基因(differential expression gene，DEG)[log2|差异倍数(fold change，FC)|>0.60，P<0.05]。"], "basis": "The paper names GSE124272, GSE150408, GSE56081, GSE147383, GSE23130 in 基因表达综合(GEO)数据库 and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40074310", "data:geo:GSE124272"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE124272"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:48:14Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 9790, "completion_tokens": 2283, "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:40074310", "type": "paper", "label": "pmid:40074310"}, {"id": "source:pmid:40074310", "type": "manuscript", "label": "PMID 40074310 full text"}, {"id": "data:geo:GSE124272", "type": "dataset", "label": "GEO GSE124272"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40074310", "type": "paper", "label": "pmid:40074310"}, {"id": "source:pmid:40074310", "type": "manuscript", "label": "PMID 40074310 full text"}, {"id": "data:geo:GSE124272", "type": "dataset", "label": "GEO GSE124272"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40074310", "type": "extraction", "used": ["source:pmid:40074310"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE124272", "type": "accession_resolution", "used": ["data:geo:GSE124272"], "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:40074310", "parent_hash": "sha256:ad6ecbcc4660674b278dc0a40cd3eab59e2f11c2792b871379620cd4e9549b5c", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE124272 licence not read", "asset:data:geo:GSE124272 not downloaded", "asset:data:geo:GSE147383 licence not read", "asset:data:geo:GSE147383 not downloaded", "asset:data:geo:GSE150408 licence not read", "asset:data:geo:GSE150408 not downloaded", "asset:data:geo:GSE23130 licence not read", "asset:data:geo:GSE23130 not downloaded", "asset:data:geo:GSE56081 licence not read", "asset:data:geo:GSE56081 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["performed for pathological examination, and immunohistochemistry (IHC) was used to assess ZNF667 expression i", "gical examination, and immunohistochemistry (IHC) was used to assess ZNF667 expression in the"], "order_basis": "paper_text_order:1033", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["stablish an IDD cell model, and subsequently transfected with a ZNF667 overexpression plasmid. Flow c"], "order_basis": "paper_text_order:1396", "id": "assay:2"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["fected with a ZNF667 overexpression plasmid. Flow cytometry was used to evaluate cell apoptosis, enzyme-"], "order_basis": "paper_text_order:1446", "id": "assay:3"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["id. Flow cytometry was used to evaluate cell apoptosis, enzyme-linked immunosorbent assay (ELISA) m", "reversed the IL-1β-induced increase in cell apoptosis, the upregulation of inflammation factors (C", ": ZNF667 can alleviate nucleus pulposus cell apoptosis and inflammatory responses by inhibiting the"], "order_basis": "paper_text_order:1487", "id": "assay:4"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["poptosis, enzyme-linked immunosorbent assay (ELISA) measured the levels of inflammatory factors", "tometry was used to evaluate cell apoptosis, enzyme-linked immunosorbent assay (ELISA) measured the levels of inflammatory"], "order_basis": "paper_text_order:1498", "id": "assay:5"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["-PCR) quantified ZNF667 mRNA expression, and Western blotting assessed protein expression levels of ZNF667"], "order_basis": "paper_text_order:1785", "id": "assay:6"}]},"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":"2026-11-04T01:59:27+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}}}