Integrated spatial and single-cell transcriptomics reveals RPL8 as a prognostic biomarker and therapeutic target in hepatocellular carcinoma.

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"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:41496405' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41496405", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.tranon.2025.102663", "sha256": "sha256:1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.tranon.2025.102663", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:41496405 not verified"]}, "analysis": {"state": "absent", "methods": [], 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"minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "f372affa765397d57a6d94c1b28107a613798a7cd1ca1c0bc9cf64bcc0acd061", "source_hash": "1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "raw_response_sha256": "sha256:edff96497d4f11d05e8d51845935b7419efb242c1bd06ac35a5140bf76667560", "raw_response_chars": 68999}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "fc37cf343621b7911fcf143bb5101ab1f049c160957c2fe842c4ba65ba5a8e83", "source_hash": "1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "raw_response": "{\"parent_value\":0.95,\"unit\":\"AUC\",\"evidence\":\"Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.\",\"target_result\":\"RPL8 was identified as a highly specific diagnostic biomarker for hepatocellular carcinoma.\",\"number_stated\":true}", "reading": {"parent_value": 0.95, "unit": "AUC", "evidence": "Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.", "target_result": "RPL8 was identified as a highly specific diagnostic biomarker for hepatocellular carcinoma.", "number_stated": true, "source_locator": "chars 142-253 of source sha256 1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365"}, "recorded_at": "2026-10-31T15:27:41.752946+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "e18e8e7c70fef8547ab68a76a981dcf7e8ec1db1c99cbda90f01b09592c86ccf", "source_hash": "1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline main finding. Paper title/main finding RPL8 biomarker/target HCC. Headline result likely AUC=0.95 diagnostic performance. Need report headline number only, value paper states for registered target, unit paper prints. Need exact contiguous quote containing number, attribution via wording, quote whole clause. Need determine target_result perhaps \"AUC = 0.95\" and unit likely \"AUC\" perhaps no unit. Parent_value 0.95. Evidence exact quote e.g. \"Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.\" Unit maybe \"AUC\" (dimensionless). User says headline number only, unit must be unit paper prints. Could use unit \"AUC\" because printed metric. Or empty unit? They expect number and unit. \"AUC=0.95\" no physical unit; unit could be \"AUC\". Usually extraction task unit as \"AUC\". Need target_result describe. Exact contiguous quotation. Ensure no spaces altered? Source: \"Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.\" We can quote exact. target_result maybe \"Diagnostic AUC for RPL8 in HCC: 0.95\" but \"headline number only\" perhaps target_result should state number and unit? Schema includes target_result. number_stated true. Parent_value 0.95. unit \"AUC\". Evidence exact full clause. Could target_result be \"AUC = 0.95\" only. They ask \"Report headline number only\". likely output target_result concise. Let's understand perhaps benchmark expects parent_value, unit, evidence. Main finding could instead be IC50 decrease from 75.1 to 52.16 µM, but that's later functional result, not headline. Abstract highlights AUC 0.95 prominently. \"single numerical result that a replication of the registered target has to reproduce\" likely they registered target as headline numerical result. Need infer extraction from paper. Main finding headline numerical result likely AUC 0.95 in bullet \"highly specific diagnostic (AUC=0.95).\" Prognostic HRs 1.42 and 1.35 also numerical, but headline bullet singular AUC. The registered target wording generic. Use AUC.\n\nCould unit be \"\" because AUC is unitless, but requirement says unit must be unit paper prints. Paper prints \"AUC=0.95\", so \"AUC\" as unit/metric. JSON valid.</think>\n\n{\"parent_value\":0.95,\"unit\":\"AUC\",\"evidence\":\"Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.\",\"target_result\":\"AUC = 0.95\",\"number_stated\":true}", "reading": {"parent_value": 0.95, "unit": "AUC", "evidence": "Integrated analysis identifies RPL8 as a highly specific diagnostic (AUC=0.95) and prognostic biomarker in HCC.", "target_result": "AUC = 0.95", "number_stated": true, "source_locator": "chars 142-253 of source sha256 1a841691a262a5f598bb3b37320f9890fe4d952f3347345c8576b6b97241a365"}, "recorded_at": "2026-10-31T15:27:44.365097+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "RPL8 mRNA/protein were markedly elevated (p < 0.001) with AUC 0.95 for diagnosis.", "minimax_alt": "AUC=0.95 for diagnosis of HCC using RPL8.", "decisive": false}, "work_type": {"minimax": "analysis_only_for_target", "minimax_alt": "analysis_plus_physical_validation", "decisive": true}, "physical_methods": {"minimax": [], "minimax_alt": ["RPL8 knockdown in HUH7 cells", "Proliferation and migration assays", "Drug-sensitivity screens and sirolimus dose-response assays", "Quantitative real-time PCR", "Western blotting", "Flow-cytometric cell-cycle analysis"], "decisive": false}, "analysis_methods": {"minimax": ["Differential gene expression analysis using the limma package with empirical Bayes moderation"], "minimax_alt": ["Multistage survival analysis with survminer-determined optimal cutoffs", "Kaplan-Meier survival analysis with log-rank test", "Univariate Cox proportional hazards regression", "Multivariable Cox regression adjusted for age, gender, and TNM stage", "Random-effects meta-analysis with I² heterogeneity assessment", "limma differential expression analysis with empirical Bayes moderation", "Gene set enrichment analysis with Benjamini-Hochberg FDR correction", "GSVA with z-score transformation", "CancerSEA functional-state assessment using Lee et al.'s algorithm", "Pearson correlation analysis", "Spearman correlation analysis", "Wilcoxon rank-sum test", "UMAP dimensionality reduction", "One-way analysis of variance and t-tests"], "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": "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:4f383d8f2b2e262d31d349d65792f091b3c803e59c55765aa75f9ed9a846f6b4", "type": "sep_package", "label": "SEP v1 package for pmid:41496405"}], "activities": [{"id": "activity:conversion:pmid:41496405", "type": "conversion", "used": ["package:4f383d8f2b2e262d31d349d65792f091b3c803e59c55765aa75f9ed9a846f6b4"], "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": "e8c5452e-07db-4e48-a87b-5e8c70083264", "parent_hash": "4f383d8f2b2e262d31d349d65792f091b3c803e59c55765aa75f9ed9a846f6b4", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:41496405 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:41496405' does not resolve to a declared asset", "targets"]}