Identification of RAD51AP1 as a key gene in hepatitis B virus-associated hepatocellular carcinoma.

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generative AI and AI-assisted technologies in the writing process", "row_count": 35, "column_count": 2}, "table": {"label": null, "caption": "Abbreviation", "rows": [["Abbreviation", "Meaning"], ["HCC", "Hepatocellular carcinoma"], ["HBV", "Hepatitis B virus"], ["WGCNA", "Weighted gene co-expression network analysis"], ["OS", "Overall survival"], ["TCGA", "The Cancer Genome Atlas"], ["GEO", "Gene Expression Omnibus"], ["DEG", "Differentially expressed genes"], ["PPI", "Protein-protein interaction"], ["DFI", "Disease-free interval"], ["ICGC", "International Cancer Genome Consortium"], ["DMEM", "Dulbecco's modified Eagle's medium"], ["MEM", "Minimum essential medium"], ["FBS", "Fetal bovine serum"], ["SDS-PAGE", "Sodium dodecyl sulfate-polyacrylamide gel electrophoresis"], ["PVDF", "Polyvinylidene difluoride"], ["CCK-8", "Cell counting kit-8"], ["PBS", "Phosphate buffer solution"], ["EdU", "5-ethynyl-2-deoxyuridine"], ["PI", "Propidium Iodide"], ["ANOVA", "Analysis of variance"], ["DElncRNA", "Differentially expressed lncRNA"], ["HR", "Hazard ratio"], ["cccDNA", "Covalently closed circular DNA"], ["pgRNA", "Pregenomic RNA"], ["ORF", "Open reading frame"], ["CC", "Chronic carriers"], ["AVR-CC", "Active viral replication chronic carriers"], ["PFS", "Progression-free survival"], ["ESCC", "Esophageal squamous cell carcinoma"], ["CCND1", "Cell cycle proteins D1"], ["GSK-3β", "Glycogen synthase kinase 3 beta"], ["NC", "Negative control"], ["Tet", "Tetracycline"], ["GSEA", "Gene set enrichment analysis"]], "row_count": 35, "column_count": 2, "numeric_cells": 5, "header_rows": 1, "locator": "section[29]/table-wrap[1]#undtbl1"}}], "gaps": ["asset:source:pmid:39850418 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:39850418", "asset:table:pmid:39850418:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39850418"]}, "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": "f89235a2f6566c9b6bd37b8e2e28f7a40d4490a32d974c43768ce87e8369c465", "source_hash": "78b5cce6adf0356402a5d768f076e6ea6b4b600786873849fcdfb37e5f113127", "raw_response_sha256": "sha256:f27afca3aac0d9c851521dbba84a0c617c4cc4b30911a08dacbb645690a26a27", "raw_response_chars": 6911}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "cd6db9f7ce8059d9b5135645e5868f83ee661a18a89d669dd6a8384a77a985b3", "source_hash": "78b5cce6adf0356402a5d768f076e6ea6b4b600786873849fcdfb37e5f113127", "raw_response_sha256": "sha256:759425c8f0fb027b08317ce192cad1bbcf0c61e494c82d355a96dca69213ab74", "raw_response_chars": 48902}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "fe0155dbc3ade4850d7df97daa2e107fcc754379a70de6a0324754843ff68ffc", "source_hash": "78b5cce6adf0356402a5d768f076e6ea6b4b600786873849fcdfb37e5f113127", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"RAD51AP1 was identified as a specific key gene linked to the progression of HBV-associated HCC; high expression was associated with worse overall survival in patients with HBV-associated HCC, and the LINC01419/miR-8070/RAD51AP1 axis promotes HBV-associated HCC progression through an HBV-boosted positive feedback loop and Wnt/β-catenin signaling.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "RAD51AP1 was identified as a specific key gene linked to the progression of HBV-associated HCC; high expression was associated with worse overall survival in patients with HBV-associated HCC, and the LINC01419/miR-8070/RAD51AP1 axis promotes HBV-associated HCC progression through an HBV-boosted positive feedback loop and Wnt/β-catenin signaling.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:22:12.076408+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "a5176d084d57b9e47c2075aed4f7cf7780b4435f2324b6969c25fac20c5644e0", "source_hash": "78b5cce6adf0356402a5d768f076e6ea6b4b600786873849fcdfb37e5f113127", "raw_response": "<think>We need answer JSON only. Need inspect source for headline numerical result registered target main finding. Text contains no headline numerical result, mostly qualitative. There are methodological numbers: 75% ethanol, etc; SPSS 23, etc, p < .05, replicated 3 times. But target is \"headline numerical result the paper states for its main finding\". No quantitative main finding. Need number_stated false, parent_value 0, unit empty, evidence empty, target_result state what text does state instead. Need exact schema. Could target_result summarize no numerical result; qualitative: RAD51AP1 identified as key gene; high expression associated with worse OS; axis etc. Must not invent source. Output valid JSON.\n\nQuestion subtle: \"single numerical result that a replication of the registered target has to reproduce.\" Registered target is headline numerical result. Source excerpt lacks result section details, perhaps article abstract where key gene with maybe AUC 0.?? omitted? Given source text explicitly no headline numeric. We should false.\n\nNeed ensure target_result wording perhaps: \"The text states qualitatively that RAD51AP1 was identified as a key gene linked to HBV-associated HCC, that high RAD51AP1 expression was associated with worse overall survival in HBV-associated HCC, and that the LINC01419/miR-8070/RAD51AP1 axis promotes HBV-associated HCC progression through an HBV-boosted positive feedback loop and Wnt/β-catenin signaling; it gives no numerical result for the main finding.\" This is okay. JSON only.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states qualitatively that RAD51AP1 was identified as a key gene linked to HBV-associated hepatocellular carcinoma and that the LINC01419/miR-8070/RAD51AP1 axis promotes HBV-associated HCC progression through an HBV-boosted positive feedback loop and Wnt/β-catenin signaling; it states no headline numerical result for the main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states qualitatively that RAD51AP1 was identified as a key gene linked to HBV-associated hepatocellular carcinoma and that the LINC01419/miR-8070/RAD51AP1 axis promotes HBV-associated HCC progression through an HBV-boosted positive feedback loop and Wnt/β-catenin signaling; it states no headline numerical result for the main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:22:11.573254+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "High expression of RAD51AP1 was associated with worse overall survival (OS) in patients with HBV-associated HCC, but not in patients with non-HBV-associated HCC.", "minimax_alt": "unclear", "decisive": false}, "physical_methods": {"minimax": ["CCK-8 assay", "wound healing assay", "Transwell assay", "cell cycle analysis", "flow cytometry"], "minimax_alt": ["CCK-8 assay", "wound healing assay", "Transwell assay", "flow cytometric cell cycle analysis"], "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:4c19e9fe67b9e7322d8134e8538b17d200d432a8c851865f596b914e9db11c18", "type": "sep_package", "label": "SEP v1 package for pmid:39850418"}], "activities": [{"id": "activity:conversion:pmid:39850418", "type": "conversion", "used": ["package:4c19e9fe67b9e7322d8134e8538b17d200d432a8c851865f596b914e9db11c18"], "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:39850418", "parent_hash": "sha256:4ab3f34d8d8367bbcee8c0aa81f1d356ed74589ef24afdf3b8b11d8590d96f08", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39850418 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:39850418' does not resolve to a declared asset", "targets"]}