{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31343435", "kind": "science-record", "revision": 5, "content_hash": "sha256:97fe88a30fc07c2288fe57caa3e24cb35ea857373cb7b39a4feb3fa5585b467c", "created_at": "2026-11-01T15:40:47Z", "updated_at": "2026-11-01T21:22:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the long noncoding RNAs-based biomarkers and pathogenesis of malignant transformation from dysplasia to oral squamous cell carcinoma by bioinformatics method.", "doi": "10.1097/CEJ.0000000000000527", "pmid": "31343435", "authors": ["Hongcheng Jia", "Xuan Wang", "Zheng Sun"], "journal": "European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP)", "year": 2020, "abstract": "Long noncoding RNAs (lncRNAs) play an important role in many biological processes and carcinogenesis. We aimed to explore lncRNA-based pathogenesis, diagnostic biomarkers, and predictive factors of malignant transformation from dysplasia to oral squamous cell carcinoma (OSCC). Microarray data of GSE30784 consisting of 167 OSCC, 17 dysplasia, and 45 normal oral tissues were downloaded from the GEO database. The differentially expressed genes (DEGs) and lncRNAs between the three samples were identified using R, followed by lncRNA-mRNA coexpression and coregulation network analysis for the prediction of lncRNA target genes. Gene Ontology and Kyoto encydopedia of gene and genomes pathway analysis were performed to further characterize potential interactions. A total of 4462 DEGs and 76 differentially expressed lncRNAs were screened between the three groups, and 200 DEGs and only double homeobox A pseudogene 10 (DUXAP10) were screened among the three groups. A total of 1662 interactions of 46 lncRNAs and their coexpressed target genes were predicted, and 38 pairs of lncRNA-lncRNA coregulated 843 target genes. The coregulated target genes significantly enriched in antigen adaptive immune response, activation of phagocytosis receptor signaling, mast granule NF-κB inflammation, etc. Overall, lncRNAs were differentially expressed in OSCC and dysplasia. The target genes might play an important role in the carcinogenesis and development of OSCC. These results improve our understanding regarding the lncRNA-based pathogenesis and identify some potential targets for early diagnosis of malignant transformation from dysplasia to OSCC.", "claims": [{"id": "claim-method", "statement": "Functional enrichment analysis of coregulated genes was done by Maere et al. (2005). Functional enrichment analysis of coexpressed genes was done by Huang et al. (2009).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31343435", "locator": "sections[7] \"Functional analysis of target genes regulated by long noncoding RNAs\" paragraph 2", "quote": "Functional enrichment analysis of coregulated genes was done by Maere et al. (2005). Functional enrichment analysis of coexpressed genes was done by Huang et al. (2009)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data (GSE30784) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The gene chip data were completed and submitted to GEO by Chen et al. (2008) from the Fred Hutchinson Cancer Research Center, which included 167 cases of OSCC, 17 cases of atypical hyperplasia, and 45 cases of normal control. The platform is GPL570, namely, the Affymetrix U133 2 Plus GeneChip arrays. GEOquery package in R language was used to obtain the gene chip expression data whose accession number is GSE30784, and its acquisition address is https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30784/matrix/GSE30784_series_matrix.txt.gz. The dataset contains 229 samples and expression information of 54 675 probes. At the same time, the annotation information of the probes, such as the associated gene symbols, Entrez Gene ID and gene name, and the clinical annotation information of the sample, such as age, gender, and disease status (cancer, dysplasia and control), were also obtained.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31343435", "locator": "sections[3] \"Affymetrix microarray data\" paragraph 2", "quote": "The data (GSE30784) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/)."}, {"asset": "source:pmid:31343435", "locator": "sections[3] \"Affymetrix microarray data\" paragraph 2", "quote": "The gene chip data were completed and submitted to GEO by Chen et al."}, {"asset": "source:pmid:31343435", "locator": "sections[3] \"Affymetrix microarray data\" paragraph 2", "quote": "(2008) from the Fred Hutchinson Cancer Research Center, which included 167 cases of OSCC, 17 cases of atypical hyperplasia, and 45 cases of normal control."}, {"asset": "source:pmid:31343435", "locator": "sections[3] \"Affymetrix microarray data\" paragraph 2", "quote": "The platform is GPL570, namely, the Affymetrix U133 2 Plus GeneChip arrays."}, {"asset": "source:pmid:31343435", "locator": "sections[4] \"Data preprocessing\" paragraph 2", "quote": "GEOquery package in R language was used to obtain the gene chip expression data whose accession number is GSE30784, and its acquisition address is https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30784/matrix/GSE30784_series_matrix.txt.gz."}, {"asset": "source:pmid:31343435", "locator": "sections[4] \"Data preprocessing\" paragraph 2", "quote": "The dataset contains 229 samples and expression information of 54 675 probes."}, {"asset": "source:pmid:31343435", "locator": "sections[4] \"Data preprocessing\" paragraph 2", "quote": "At the same time, the annotation information of the probes, such as the associated gene symbols, Entrez Gene ID and gene name, and the clinical annotation information of the sample, such as age, gender, and disease status (cancer, dysplasia and control), were also obtained."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31343435"], "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:GSE30784"], "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:GSE30784"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31343435", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/CEJ.0000000000000527", "sha256": "sha256:588ecb6b2df1bd8fb265b590cff214b9da3c09b8b6e4650e30152972009e0780", "bytes": 21900, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/CEJ.0000000000000527", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7012364", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30784", "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=GSE30784", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30784", "version": null, "note": "The data (GSE30784) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). 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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": ["GSE30784"], "resolved_accessions": ["GSE30784"], "statements": ["The data (GSE30784) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The gene chip data were completed and submitted to GEO by Chen et al. (2008) from the Fred Hutchinson Cancer Research Center, which included 167 cases of OSCC, 17 cases of atypical hyperplasia, and 45 cases of normal control. The platform is GPL570, namely, the Affymetrix U133 2 Plus GeneChip arrays. GEOquery package in R language was used to obtain the gene chip expression data whose accession number is GSE30784, and its acquisition address is https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30784/matrix/GSE30784_series_matrix.txt.gz. The dataset contains 229 samples and expression information of 54 675 probes. At the same time, the annotation information of the probes, such as the associated gene symbols, Entrez Gene ID and gene name, and the clinical annotation information of the sample, such as age, gender, and disease status (cancer, dysplasia and control), were also obtained."], "basis": "The paper names GSE30784 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31343435", "data:geo:GSE30784", "asset:table:pmid:31343435:1", "asset:table:pmid:31343435:2", "asset:table:pmid:31343435:3", "asset:table:pmid:31343435:4", "asset:table:pmid:31343435:5", "asset:table:pmid:31343435:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE30784"]}, "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": "2026-10-31T18:15:42Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 16167, "completion_tokens": 1551, "cached_tokens": 776}}, "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:31343435", "type": "paper", "label": "pmid:31343435"}, {"id": "source:pmid:31343435", "type": "manuscript", "label": "PMID 31343435 full text"}, {"id": "data:geo:GSE30784", "type": "dataset", "label": "GEO GSE30784"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31343435", "type": "paper", "label": "pmid:31343435"}, {"id": "source:pmid:31343435", "type": "manuscript", "label": "PMID 31343435 full text"}, {"id": "data:geo:GSE30784", "type": "dataset", "label": "GEO GSE30784"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31343435", "type": "extraction", "used": ["source:pmid:31343435"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE30784", "type": "accession_resolution", "used": ["data:geo:GSE30784"], "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:31343435", "parent_hash": "sha256:f348fa36cb8c67c7aeb191075f5c377c6484003596b6640449f129eb462f276e", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE30784 licence not read", "asset:data:geo:GSE30784 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["asia to oral squamous cell carcinoma (OSCC). Microarray data of GSE30784 consisting of 167 OSCC, 17"], "order_basis": "paper_text_order:402", "id": "assay:1"}]},"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":"2026-11-04T03:35:42+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}}}