Comprehensive analysis based on the ubiquitination- and deubiquitylation-related genes reveals the function of NEURL3 in esophageal squamous cell carcinoma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40918133", "kind": "science-record", "revision": 2, "content_hash": "sha256:16290cdc8ff8c5938b61c18a2ffed2af9b2ac59b8331d4082abc8a84be88cd5b", "created_at": "2026-11-01T10:25:53Z", "updated_at": "2026-11-01T14:01:47Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Comprehensive analysis based on the ubiquitination- and deubiquitylation-related genes reveals the function of NEURL3 in esophageal squamous cell carcinoma.", "doi": "10.3389/fimmu.2025.1632090", "pmid": "40918133", "authors": null, "journal": "Frontiers in immunology", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 11.0, "unit": "genes", "tolerance": null, "source": "chars 1341-1470 of source sha256 326a3168b5767c30cab61b3cc17c94ff1d439a311c6fbd5eee06421a52c48127"}, "evidence": [{"asset": "source:pmid:40918133", "locator": "chars 1341-1470 of source sha256 326a3168b5767c30cab61b3cc17c94ff1d439a311c6fbd5eee06421a52c48127", "quote": "The URGs and DRGs prognostic signature consisted of 11 genes and exhibited high accuracy in predicting prognosis of ESCC patient."}]}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40918133"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:40918133", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40918133' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40918133", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1632090", "sha256": "sha256:326a3168b5767c30cab61b3cc17c94ff1d439a311c6fbd5eee06421a52c48127", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1632090", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40918133:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:472cde3c9e86c0e5daf4e12afb1f54a220584fdd28eeddfbe540718a97a74fee", "bytes": 1410, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[1]#T1", "version": null, "note": "Univariate and multivariate Cox regression analysis of various prognostic factors in ESCC patients.", "structure": {"pmcid": "PMC12408286", "section_index": 23, "section_title": "Construction and validation of a nomogram for ESCC patients", "row_count": 16, "column_count": 7}, "table": {"label": "Table 1", "caption": "Univariate and multivariate Cox regression analysis of various prognostic factors in ESCC patients.", "rows": [["Patient characteristics", "Univariate analysis", "Multivariate analysis"], ["HR", "95%CI", "P", "HR", "95%CI", "P"], ["Gender (Female vs. Male)", "1.210", "0.685-2.138", "0.511", "", "", ""], ["Age (≥66 vs. <66; y)", "2.033", "1.231-3.357", "0.006", "2.079", "1.131-3.818", "0.018"], ["Drinking (Yes vs. No)", "1.053", "0.656-1.689", "0.831", "", "", ""], ["Smoking (Yes vs. No)", "0.859", "0.532-1.387", "0.534", "", "", ""], ["TNM stage (III-IV vs. I-II)", "2.188", "1.338-3.579", "0.002", "1.915", "1.065-3.443", "0.030"], ["Tumor location (Middle vs. Lower)", "0.724", "0.350-1.497", "0.384", "", "", ""], ["Tumor location (Upper vs. Lower)", "0.643", "0.329-1.255", "0.196", "", "", ""], ["Tumor grade (Moderately vs. Well)", "0.734", "0.377-1.428", "0.362", "", "", ""], ["Tumor grade (Poorly vs. Well)", "0.632", "0.374-1.067", "0.086", "", "", ""], ["Arrhythrnia (Yes vs. No)", "1.388", "0.829-2.322", "0.212", "", "", ""], ["Pneumonia (Yes vs. No)", "1.807", "0.865-3.773", "0.115", "", "", ""], ["Anastomotic leak (Yes vs. No)", "1.513", "0.693-3.301", "0.298", "", "", ""], ["Adjuvant therapy (Yes vs. No)", "2.133", "1.043-4.362", "0.038", "", "", ""], ["Risk score (High vs. Low)", "5.147", "3.015-8.787", "<0.001", "5.563", "2.871-10.780", "<0.001"]], "row_count": 16, "column_count": 7, "numeric_cells": 54, "header_rows": 2, "locator": "section[23]/table-wrap[1]#T1"}}], "gaps": ["asset:source:pmid:40918133 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40918133", "asset:table:pmid:40918133:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40918133"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "passed", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "dd98846aa6ba823ff7ada3f094e62103e9026e40a6987fcb7171045964053788", "source_hash": "326a3168b5767c30cab61b3cc17c94ff1d439a311c6fbd5eee06421a52c48127", "raw_response_sha256": "sha256:fa05343c57a4fbd8914498524891475aec4aacf6011b1064e17d93cc6b564998", "raw_response_chars": 5670}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "f86b3113b1ceb9dfc26d553603e55ac816dca419fc67d970d4218de410bad4d4", "source_hash": "326a3168b5767c30cab61b3cc17c94ff1d439a311c6fbd5eee06421a52c48127", "raw_response_sha256": "sha256:f875d14e0fa25915b75b42374fc031c2a2ef5cac60a5c4c8153e95ff24e7ddf4", "raw_response_chars": 31651}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "ec1b7187c798c3f3c8ee44e033c43a00786d3324f91030506236b1c799bff2f9", "source_hash": "326a3168b5767c30cab61b3cc17c94ff1d439a311c6fbd5eee06421a52c48127", "raw_response": "{\"parent_value\":11,\"unit\":\"genes\",\"evidence\":\"The URGs and DRGs prognostic signature consisted of 11 genes and exhibited high accuracy in predicting prognosis of ESCC patient.\",\"target_result\":\"The URGs and DRGs prognostic signature consisted of 11 genes.\",\"number_stated\":true}", "reading": {"parent_value": 11, "unit": "genes", "evidence": "The URGs and DRGs prognostic signature consisted of 11 genes and exhibited high accuracy in predicting prognosis of ESCC patient.", "target_result": "The URGs and DRGs prognostic signature consisted of 11 genes.", "number_stated": true, "source_locator": "chars 1341-1470 of source sha256 326a3168b5767c30cab61b3cc17c94ff1d439a311c6fbd5eee06421a52c48127"}, "recorded_at": "2026-10-31T15:33:57.968671+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "7b0ce2167eb09f83bde54ee115ef796c1d8abd699673d02b00b56d83bf7ce630", "source_hash": "326a3168b5767c30cab61b3cc17c94ff1d439a311c6fbd5eee06421a52c48127", "raw_response": "<think>We need answer JSON only. Need identify single numerical result replication registered target headline numerical result paper main finding. Source supplied appears abstract + methods snippets, results snippets, no detailed numeric performance (AUC etc). Need infer what qualifies headline numerical result. Registered target generic \"headline numerical result the paper states for its main finding.\" Could be 11 genes? The paper's main finding prognostic signature consisted of 11 genes, two molecular subtypes, etc. Need determine expected extraction likely asks numerical result from source. We need report headline number only, exact contiguous quote containing number, attribution via wording. Which number is \"headline numerical result\" perhaps 11 genes. Let's parse.\n\nPaper title comprehensive analysis ... main finding nomogram based on 11 URG/DRG signature. Abstract says \"The URGs and DRGs prognostic signature consisted of 11 genes and exhibited high accuracy...\" This is prominent headline numerical result. It may be target. User asks \"find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed.\" Registered target is \"the headline numerical result the paper states for its main finding.\" So likely 11 genes. Need quote exact clause. Evidence perhaps \"The URGs and DRGs prognostic signature consisted of 11 genes and exhibited high accuracy in predicting prognosis of ESCC patient.\" Unit \"genes\". parent_value 11. target_result likely \"The prognostic signature consisted of 11 genes.\" number_stated true.\n\nBut maybe headline numerical result is number of immune cell types 28? Main finding perhaps 28 immune cell types? Yet article abstract headline has no metric except 11 genes. The \"registered target\" perhaps hidden context asks one numerical result. We need only source. Could be C2 subtype survival, but no numerical value in supplied text. Thus 11 is only headline result. Need ensure exact quote contiguous and whole clause for attribution. JSON string.\n\nCould answer:\n{\n\"parent_value\":11,\n\"unit\":\"genes\",\n\"evidence\":\"The URGs and DRGs prognostic signature consisted of 11 genes and exhibited high accuracy in predicting prognosis of ESCC patient.\",\n\"target_result\":\"The URGs and DRGs prognostic signature consisted of 11 genes.\",\n\"number_stated\":true\n}\nNeed no extra. Is unit perhaps \"genes\" as paper prints. It prints \"11 genes\", yes.\n\nLet's ensure \"headline number only\" means parent_value and unit, evidence still whole clause. target_result perhaps concise. Fine.</think>\n\n{\"parent_value\":11,\"unit\":\"genes\",\"evidence\":\"The URGs and DRGs prognostic signature consisted of 11 genes and exhibited high accuracy in predicting prognosis of ESCC patient.\",\"target_result\":\"The URGs and DRGs prognostic signature consisted of 11 genes.\",\"number_stated\":true}", "reading": {"parent_value": 11, "unit": "genes", "evidence": "The URGs and DRGs prognostic signature consisted of 11 genes and exhibited high accuracy in predicting prognosis of ESCC patient.", "target_result": "The URGs and DRGs prognostic signature consisted of 11 genes.", "number_stated": true, "source_locator": "chars 1341-1470 of source sha256 326a3168b5767c30cab61b3cc17c94ff1d439a311c6fbd5eee06421a52c48127"}, "recorded_at": "2026-10-31T15:34:01.406184+00:00"}], "agreement": true, "disagreements": {"physical_methods": {"minimax": ["Loss-of-function studies", "In vitro ESCC cell proliferation assay", "In vitro ESCC cell motility assay"], "minimax_alt": ["Loss-of-function studies", "NEURL3 knockdown in ESCC cells"], "decisive": false}, "analysis_methods": {"minimax": ["Differential expression analysis", "Prognostic gene analysis", "Prognostic signature construction", "Unsupervised clustering analysis", "Gene Ontology enrichment analysis", "Disease Ontology enrichment analysis", "KEGG pathway enrichment analysis", "Single-sample gene set enrichment analysis (ssGSEA)", "Spearman correlation analysis", "TIMER analysis", "CIBERSORT-ABS analysis", "QUANTISEQ analysis", "EPIC analysis", "MCPCOUNTER analysis", "CIBERSORT analysis", "XCELL analysis", "oncoPredict drug-sensitivity analysis", "Molecular docking using AMDock", "Nomogram construction"], "minimax_alt": ["Unsupervised clustering analysis", "Gene Ontology (GO) functional enrichment analysis", "Disease Ontology (DO) and KEGG analysis using the BioEnricher R package", "Single-sample gene set enrichment analysis (ssGSEA)", "Spearman correlation analysis", "TIMER, CIBERSORT-ABS, QUANTISEQ, EPIC, MCPCOUNTER, CIBERSORT, and XCELL algorithms using the IOBR R package", "oncoPredict R package for drug-sensitivity assessment", "Molecular docking using AMDock software", "Nomogram construction combining the URGs and DRGs prognostic signature with clinical characteristics"], "decisive": false}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "passed", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:7f0e48fd3c0aa9598e84be8fb21485fb570fbab731df716ed9cefd16441e97c7", "type": "sep_package", "label": "SEP v1 package for pmid:40918133"}], "activities": [{"id": "activity:conversion:pmid:40918133", "type": "conversion", "used": ["package:7f0e48fd3c0aa9598e84be8fb21485fb570fbab731df716ed9cefd16441e97c7"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40918133", "parent_hash": "sha256:f3abf5caa441a82db1e2d1c7216a7811a8ce6d2b828e4267aa47c7ba2187d19d", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40918133 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.passed", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40918133' does not resolve to a declared asset", "targets"]}