Unveiling ammonia-induced cell death: a new frontier in clear cell renal cell carcinoma prognosis.

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"prompt_version": "full-text-reading-v1", "prompt_hash": "4993bff921667d3772295eb414e12f3076c6060addb0a501805cd3481735d3cd", "source_hash": "e8e203d3622968f0f8f281d9dc5da4ef653082a7d2d344ac5c9b66905f794878", "raw_response_sha256": "sha256:84befa491bbac805fd94299bb4f861d7a8f4b7ca89681a31edd0e1550f4cd352", "raw_response_chars": 47180}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "535daa88fe71c47799ca5ab1de10dd2e0707d3bd9deac431f8bb4168411eeff1", "source_hash": "e8e203d3622968f0f8f281d9dc5da4ef653082a7d2d344ac5c9b66905f794878", "raw_response": "{\"parent_value\":-6.8,\"unit\":\"kcal/mol\",\"evidence\":\"Molecular docking revealed Emodinanthrone as a high-affinity ligand for ATP1A1 (−6.8 kcal/mol).\",\"target_result\":\"Emodinanthrone was identified as a high-affinity ligand for ATP1A1 with a binding energy of −6.8 kcal/mol.\",\"number_stated\":true}", "reading": {"parent_value": -6.8, "unit": "kcal/mol", "evidence": "Molecular docking revealed Emodinanthrone as a high-affinity ligand for ATP1A1 (−6.8 kcal/mol).", "target_result": "Emodinanthrone was identified as a high-affinity ligand for ATP1A1 with a binding energy of −6.8 kcal/mol.", "number_stated": true, "source_locator": "chars 1949-2044 of source sha256 e8e203d3622968f0f8f281d9dc5da4ef653082a7d2d344ac5c9b66905f794878"}, "recorded_at": "2026-10-31T15:30:51.217347+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "bcc95c75d9d8eeb0e7a6bf6124bd9a6d730befbf382d539eeac23813145f5b3c", "source_hash": "e8e203d3622968f0f8f281d9dc5da4ef653082a7d2d344ac5c9b66905f794878", "raw_response": "<think>We need answer JSON only. Need parse target: \"headline numerical result the paper states for its main finding\". Need single numerical result replication of registered target reproduce. Source abstract main finding perhaps molecular docking Emodinanthrone high-affinity ligand ATP1A1 (−6.8 kcal/mol). Need value paper itself states. Evidence exact contiguous quote containing number, whole clause attribution. Could choose abstract sentence: \"Molecular docking revealed Emodinanthrone as a high-affinity ligand for ATP1A1 (−6.8 kcal/mol).\" This is headline numerical result main finding. Parent -6.8, unit kcal/mol, evidence exact. target_result concise. number_stated true.\n\nNeed consider perhaps \"five AICD-related genes\" main finding, headline numerical result? User asks registered target \"the headline numerical result the paper states for its main finding\". Could be target benchmark design, likely expected number from abstract. There are two numerical results: five genes and -6.8 kcal/mol. \"headline numerical result\" likely -6.8. Need understand task framing: \"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 intentionally generic \"the headline numerical result the paper states for its main finding\". The abstract highlights docking score −6.8 kcal/mol. It explicitly states headline. We should quote exact sentence. JSON valid Unicode minus perhaps. parent_value number -6.8. Unit \"kcal/mol\". target_result maybe \"The paper reports a docking binding energy of −6.8 kcal/mol for Emodinanthrone with ATP1A1.\" They say headline number only perhaps target_result could simply \"−6.8 kcal/mol\". Evidence exact. Ensure no extra prose.</think>\n\n{\"parent_value\":-6.8,\"unit\":\"kcal/mol\",\"evidence\":\"Molecular docking revealed Emodinanthrone as a high-affinity ligand for ATP1A1 (−6.8 kcal/mol).\",\"target_result\":\"−6.8 kcal/mol\",\"number_stated\":true}", "reading": {"parent_value": -6.8, "unit": "kcal/mol", "evidence": "Molecular docking revealed Emodinanthrone as a high-affinity ligand for ATP1A1 (−6.8 kcal/mol).", "target_result": "−6.8 kcal/mol", "number_stated": true, "source_locator": "chars 1949-2044 of source sha256 e8e203d3622968f0f8f281d9dc5da4ef653082a7d2d344ac5c9b66905f794878"}, "recorded_at": "2026-10-31T15:30:53.217421+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "Five AICD-related genes (FOXM1, ANK3, ATP1A1, HADH, and PLG) were identified and selected to construct a risk score model.", "minimax_alt": "Molecular docking revealed Emodinanthrone as a high-affinity ligand for ATP1A1 (−6.8 kcal/mol).", "decisive": false}, "physical_methods": {"minimax": ["Cell-based experiments", "In vitro functional assays"], "minimax_alt": ["qRT-PCR measurement of ATP1A1 mRNA expression", "in vitro functional assays of ATP1A1 knockdown in A498 and 786-O renal carcinoma cells"], "decisive": false}, "analysis_methods": {"minimax": ["Differential expression analysis", "Univariate Cox regression", "LASSO", "Random forest", "CoxBoost", "Multivariate Cox regression", "Spatial transcriptomics", "Single-cell transcriptomics", "Molecular docking", "Pan-cancer analysis"], "minimax_alt": ["differential expression analysis", "univariate Cox regression", "LASSO", "random forest", "CoxBoost", "multivariate Cox regression", "spatial transcriptomics", "single-cell transcriptomics", "principal component analysis", "FindAllMarkers differential expression analysis", "ssGSEA gene-set activity quantification", "pan-cancer analysis", "Pearson correlation analysis", "Spearman correlation analysis", "high-throughput virtual screening", "molecular docking analysis"], "decisive": false}, "statistical_method": {"minimax": "Multivariate Cox regression", "minimax_alt": "", "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:cd133db1d4ddd2ab3a17464d68a80f70eafae4b90f9dbbb3edf4ed41de15e5cd", "type": "sep_package", "label": "SEP v1 package for pmid:40821775"}], "activities": [{"id": "activity:conversion:pmid:40821775", "type": "conversion", "used": ["package:cd133db1d4ddd2ab3a17464d68a80f70eafae4b90f9dbbb3edf4ed41de15e5cd"], "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": "e5f8126a-74e4-4d68-bd60-43dc5c207787", "parent_hash": "cd133db1d4ddd2ab3a17464d68a80f70eafae4b90f9dbbb3edf4ed41de15e5cd", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40821775 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:40821775' does not resolve to a declared asset", "targets"]}