Stratification of Hepatocellular Carcinoma Using N6-Methyladenosine.

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RNA"], ["TCGA", "The Cancer Genome Atlas"], ["TIDE", "Tumor immune dysfunction and exclusion"], ["TIGIT", "T cell immunoreceptor with Ig and ITIM domains"], ["TIM-3", "T cell immunoglobulin and mucin-domain containing-3"], ["TMB", "Tumor mutation burden"], ["TPM", "Transcripts per million kilobase"], ["UMAP", "Uniform Manifold Approximation and Projection"], ["VIRMA", "Vir-Like m6A Methyltransferase Associated protein"], ["WTAP", "Wilms tumor 1-associating protein"], ["YTH", "YT521-B homology"], ["ZC3H13", "Zinc finger CCCH-type containing 13"]], "row_count": 41, "column_count": 2, "numeric_cells": 17, "header_rows": 0, "locator": "section[27]/table-wrap[1]#array1"}}], "gaps": ["asset:source:pmid:40647517 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:40647517", "asset:table:pmid:40647517:1", "asset:table:pmid:40647517:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40647517"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "534e7237c05162882c88d29a2340f41c3d1f1b20a71ea79fc7c953f379bbc681", "source_hash": "89c4ce9ba45756c1a2fc08adc805c6b3261c310b39f7412dc5ca47398b377fce", "raw_response_sha256": "sha256:1df773b70ceaab30f4530fe3865b500721b2ff23f43047f500d39c43bffa1b3a", "raw_response_chars": 4123}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "96e668253720e08d0873e7cf5aad8e71e910f68fb25a48f138a8ee1b06dd851b", "source_hash": "89c4ce9ba45756c1a2fc08adc805c6b3261c310b39f7412dc5ca47398b377fce", "raw_response_sha256": "sha256:dad7f10807f17f02f20602b6943d04967ecd00a901244d320864aba2027c5789", "raw_response_chars": 57386}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "e0c28c8be21e36076add9fe73785e0cdb910801ffb3674378e74ab2ff09d2d59", "source_hash": "89c4ce9ba45756c1a2fc08adc805c6b3261c310b39f7412dc5ca47398b377fce", "raw_response": "{\"parent_value\":0.75,\"unit\":\"AUC\",\"evidence\":\"achieving area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.\",\"target_result\":\"AUC values greater than 0.75 across both internal and external cohorts\",\"number_stated\":true}", "reading": {"parent_value": 0.75, "unit": "AUC", "evidence": "achieving area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.", "target_result": "AUC values greater than 0.75 across both internal and external cohorts", "number_stated": true, "source_locator": "chars 503-611 of source sha256 89c4ce9ba45756c1a2fc08adc805c6b3261c310b39f7412dc5ca47398b377fce"}, "recorded_at": "2026-10-31T15:26:53.755468+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "7a5cb748e8915141093abbb7cd0b7794c2bf995e98e31b0b275ffeaf75286402", "source_hash": "89c4ce9ba45756c1a2fc08adc805c6b3261c310b39f7412dc5ca47398b377fce", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline main finding. Source abstract: identified validated 8-gene risk score, achieving AUC values greater than 0.75 across internal/external cohorts. Registered target headline numerical result main finding. Likely 0.75 AUC? Need report headline number only, paper stated value, unit printed. Evidence exact contiguous quote containing number and attribution. \"achieving area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.\" Is headline numerical result likely AUC &gt; 0.75. Parent_value number needs 0.75. Unit perhaps \"AUC\" or \"area under the ROC curve (AUC)\"? They ask unit must be unit paper prints. AUC is dimensionless metric, text prints \"area under the ROC curve (AUC) values greater than 0.75\". Could unit be \"AUC\"? Need output target_result perhaps \"AUC greater than 0.75\" or \"area under the ROC curve (AUC) values greater than 0.75\". Headline number only means value 0.75, not 8 perhaps. Main finding: risk score performance AUC &gt; 0.75. The title and abstract. Could \"8-gene risk score\" be main numerical headline? But registered target asks \"headline numerical result the paper states for its main finding.\" Likely extraction benchmark expects a number. Abstract says \"identified and validated an 8-gene risk score ... achieving AUC values greater than 0.75\". Which is the headline result? The \"8-gene\" is signature architecture, while numerical predictive performance is AUC &gt; 0.75. They emphasize \"headline number.\" likely 0.75.\n\nNeed exact contiguous evidence quote. Could quote whole sentence: \"In this study, we identified and validated an 8-gene risk score that robustly predicts prognosis in HCC patients, achieving area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.\" This contains 8 as well and number. They say evidence exact contiguous quotation containing number; attribution. \"headline number only\" likely evidence can have 8 but parent_value should 0.75. Could quote narrower clause: \"achieving area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.\" This is exact contiguous and directly attributes. It doesn't include \"In this study, we identified...\" but enough. Unit paper prints perhaps \"area under the ROC curve (AUC)\". Since no conventional unit. Schema unit string. Should unit be \"AUC\" likely. target_result maybe \"AUC values greater than 0.75 across both internal and external cohorts\". number_stated true.\n\nCould interpret greater-than relation means parent_value 0.75 and unit \"AUC\". target_result should state \"AUC values greater than 0.75\". They request \"Report the headline number only: the value the paper itself states\". JSON parent_value 0.75. Evidence exact quote. Good.\n\nNeed valid JSON no markdown. Ensure no unsupported claims. \"area under the ROC curve (AUC)\" as unit perhaps paper prints. They explicitly say unit must be unit paper prints. If dimensionless, use \"AUC\". Let's formulate:\n{\n \"parent_value\":0.75,\n \"unit\":\"area under the ROC curve (AUC)\",\n \"evidence\":\"achieving area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.\",\n \"target_result\":\"AUC values greater than 0.75 across both internal and external cohorts\",\n \"number_stated\":true\n}\nQuestion: \"single numerical result that a replication ... has to reproduce. Report the headline number only\" Could they expect \"8\" because headline numerical result is 8-gene risk score? But replication needs reproduce AUC &gt;0.75; headline result. Let's deeply assess task conventions.\n\nPrompt: \"REGISTERED TARGET: the headline numerical result the paper states for its main finding\". Need find number. They give source abstract, methods, conclusions. Abstract opening contains main findings. Numerical values:\n- 8-gene risk score\n- AUC &gt;0.75\nOther methods irrelevant.\nWhich is \"headline numerical result\"? Usually scientific paper headline numeric result could be sample size/effect. Here main finding predictive signature, headline metric AUC &gt; 0.75. The 8-gene signature is also central. They specifically likely want \"0.75\" because abstract phrase \"achieving ... AUC values greater than 0.75\". Their framing \"value the paper itself states ... not calculated, converted...\" and \"Attribution may be carried by ... respectively...\" Generic extraction instructions. Need choose.\n\n\"single numerical result that a replication of the registered target has to reproduce.\" A replication of headline result: AUC values &gt;0.75. 8-gene risk score also must reproduce. But target_result likely 0.75 AUC. \"headline number only\" perhaps not multiple values. Unit AUC.</think>\n\n{\"parent_value\":0.75,\"unit\":\"area under the ROC curve (AUC)\",\"evidence\":\"achieving area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.\",\"target_result\":\"AUC values greater than 0.75 across both internal and external cohorts\",\"number_stated\":true}", "reading": {"parent_value": 0.75, "unit": "area under the ROC curve (AUC)", "evidence": "achieving area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.", "target_result": "AUC values greater than 0.75 across both internal and external cohorts", "number_stated": true, "source_locator": "chars 503-611 of source sha256 89c4ce9ba45756c1a2fc08adc805c6b3261c310b39f7412dc5ca47398b377fce"}, "recorded_at": "2026-10-31T15:26:59.310307+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "An 8-gene risk score predicted HCC prognosis with area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.", "minimax_alt": "In this study, we identified and validated an 8-gene risk score that robustly predicts prognosis in HCC patients, achieving area under the ROC curve (AUC) values greater than 0.75 across both internal and external cohorts.", "decisive": false}, "physical_methods": {"minimax": ["in vitro experiments", "immunohistochemical staining", "quantitative reverse transcriptase PCR", "Western blot analysis"], "minimax_alt": ["in vitro experiments", "quantitative real-time PCR (qRT-PCR)", "Western blotting", "Bradford assay", "immunohistochemical staining"], "decisive": false}, "analysis_methods": {"minimax": ["receiver operating characteristic (ROC) curve analysis", "Kaplan–Meier survival analysis", "log-rank test", "principal component analysis", "UMAP", "single-cell RNA sequencing analysis", "pseudotime analysis using monocle2", "unpaired two-tailed Student's t-test", "one-way ANOVA", "Tukey's post hoc test", "2−ΔΔCt method"], "minimax_alt": ["area under the ROC curve (AUC) assessment", "Kaplan–Meier survival analysis", "log-rank test", "Tumor immune dysfunction and exclusion (TIDE) and immunophenotype score (IPS) assessment", "Seurat filtering and normalization", "principal component analysis (PCA) dimensionality reduction", "UMAP clustering", "SingleR and celldex cell-type annotation", "monocle2 pseudotime analysis", "2−ΔΔCt relative-expression calculation", "unpaired two-tailed Student’s t-test", "one-way ANOVA with Tukey’s post hoc test"], "decisive": false}, "statistical_method": {"minimax": "receiver operating characteristic (ROC) curve analysis", "minimax_alt": "area under the ROC curve (AUC)", "decisive": true}, "unit": {"minimax": "AUC", "minimax_alt": "area under the ROC curve (AUC)", "decisive": true}}, "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": "blocked", "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.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:6700b6b02e61e5c5bf1d212313647bfdc860d15984fc19b78ed11435816d4ac9", "type": "sep_package", "label": "SEP v1 package for pmid:40647517"}], "activities": [{"id": "activity:conversion:pmid:40647517", "type": "conversion", "used": ["package:6700b6b02e61e5c5bf1d212313647bfdc860d15984fc19b78ed11435816d4ac9"], "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:40647517", "parent_hash": "sha256:4de76ac7882bd374d3c32429da5c2b32f67719d088e5340634cf14d589b17325", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40647517 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "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:40647517' does not resolve to a declared asset", "targets"]}