Identification of kidney renal clear cell carcinoma prognosis based on gene expression and clinical information.

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"target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "dc1992711e83dc7b3d2fca3fe67d8d545be692a4e3c4ca597b956e4efdbabdd4", "source_hash": "6648dcac8a92cacb631ca93b16ca4ebcf4443bcab6323a424d5ed145a3991cde", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that a KIRC risk stratification model and clinical nomogram were developed by integrating molecular risk scores with key clinicopathological parameters, using four genes (BASP1, CCL8, FCGR1B, FKBP11); it does not state a headline numerical result for the main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that a KIRC risk stratification model and clinical nomogram were developed by integrating molecular risk scores with key clinicopathological parameters, using four genes (BASP1, CCL8, FCGR1B, FKBP11); it does not state a headline numerical result for the main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:34:32.173391+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "68f9990835c20f21c219881e0f5263bb1bc1f9fd82a0636fbecaf05290e50946", "source_hash": "6648dcac8a92cacb631ca93b16ca4ebcf4443bcab6323a424d5ed145a3991cde", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline for main finding / registered target. Source has numbers: 29 immune gene sets, four genes, version 4.5.1, p&lt;0.05. Headline numerical result paper states main finding likely \"four genes (BASP1, CCL8, FCGR1B, FKBP11)\" risk stratification. Need determine what they expect parent_value. Prompt: \"single numerical result that a replication of registered target has to reproduce. Report headline number only: value paper itself states for registered target, not calculated... unit paper prints. Evidence exact contiguous quote containing number... attribution...\" Registered target: headline numerical result paper states for its main finding. Main finding says \"find four genes ... for determining risk stratification\". So number = 4, unit perhaps \"genes\". Evidence exact clause containing number, perhaps whole sentence. target_result describe four genes. Need quote exact contiguous source text. Could use \"At the same time, we combined TCGA and GEO to find four genes (BASP1, CCL8, FCGR1B, FKBP11) for determining the risk stratification of KIRC, and constructed a model for clinicians to assess KIRC prognosis based on gene expression and clinical information.\" This is exact. Unit \"genes\". target_result maybe \"The study found four genes (BASP1, CCL8, FCGR1B, and FKBP11) for determining KIRC risk stratification.\" number_stated true. Ensure headline number only in parent_value but target_result can explain? Request says \"Report headline number only\" likely parent_value 4 and target_result maybe phrase. Schema requires target_result. Could state result. Evidence includes other numerals? GEO, TCGA no numbers. Fine.\n\nCould there be concern 29 immune gene sets as main methodological finding? Main finding headline four genes. \"headline numerical result\" clearly four genes. Need JSON valid.</think>\n\n{\"parent_value\":4,\"unit\":\"genes\",\"evidence\":\"At the same time, we combined TCGA and GEO to find four genes (BASP1, CCL8, FCGR1B, FKBP11) for determining the risk stratification of KIRC, and constructed a model for clinicians to assess KIRC prognosis based on gene expression and clinical information.\",\"target_result\":\"Four genes (BASP1, CCL8, FCGR1B, and FKBP11) were identified for determining KIRC risk stratification.\",\"number_stated\":true}", "reading": {"parent_value": 4, "unit": "genes", "evidence": "At the same time, we combined TCGA and GEO to find four genes (BASP1, CCL8, FCGR1B, FKBP11) for determining the risk stratification of KIRC, and constructed a model for clinicians to assess KIRC prognosis based on gene expression and clinical information.", "target_result": "Four genes (BASP1, CCL8, FCGR1B, and FKBP11) were identified for determining KIRC risk stratification.", "number_stated": true, "source_locator": "chars 1302-1557 of source sha256 6648dcac8a92cacb631ca93b16ca4ebcf4443bcab6323a424d5ed145a3991cde"}, "recorded_at": "2026-10-31T15:34:33.341341+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "four genes (BASP1, CCL8, FCGR1B, FKBP11) for determining the risk stratification of KIRC", "minimax_alt": "At the same time, we combined TCGA and GEO to find four genes (BASP1, CCL8, FCGR1B, FKBP11) for determining the risk stratification of KIRC, and constructed a model for clinicians to assess KIRC prognosis based on gene expression and clinical information.", "decisive": false}, "physical_methods": {"minimax": ["Quantitative real-time PCR (qPCR)"], "minimax_alt": ["Quantitative real-time PCR (qPCR) performed on KIRC and paired adjacent normal tissues"], "decisive": false}, "analysis_methods": {"minimax": ["Immunological grouping based on 29 immune gene sets through R language", "Joint processing of TCGA RNA sequencing data, clinical information, and tumor mutation data", "Combined TCGA and GEO analysis", "KIRC risk stratification model based on gene expression and clinical information", "Clinical nomogram integrating molecular risk scores with clinicopathological parameters"], "minimax_alt": ["Immunological grouping of GSE40435 and GSE46699 KIRC data based on 29 immune gene sets through R language", "Joint processing of TCGA KIRC RNA-sequencing, clinical, and tumor-mutation data", "Integration of TCGA and GEO data to identify four genes and construct a KIRC risk-stratification model", "Clinical nomogram integrating molecular risk scores with key clinicopathological parameters", "Chi-square test (chisq.test) for categorical-variable comparisons", "Mann-Whitney-Wilcoxon test (wilcox.test) for two-group continuous-variable comparisons", "Kruskal–Wallis H test (kruskal.test) for multi-group continuous-variable comparisons"], "decisive": false}, "statistical_method": {"minimax": "chi-square test for categorical-variable comparisons, Mann-Whitney-Wilcoxon test for two-group continuous-variable comparisons, and Kruskal–Wallis H test for multi-group continuous-variable comparisons, with p-value <0.05 considered statistically significant", "minimax_alt": "R software (version 4.5.1), with the chi-square test (chisq.test) for categorical variables, the Mann-Whitney-Wilcoxon test (wilcox.test) for two-group continuous-variable comparisons, and the Kruskal–Wallis H test (kruskal.test) for multi-group continuous-variable comparisons; a p-value <0.05 was considered statistically significant.", "decisive": true}, "number_stated": {"minimax": false, "minimax_alt": true, "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:9a2a9e9b5d6ef81fa6633b06576a8e56322d7e744abc2a938b631053161f5f38", "type": "sep_package", "label": "SEP v1 package for pmid:40909125"}], "activities": [{"id": "activity:conversion:pmid:40909125", "type": "conversion", "used": ["package:9a2a9e9b5d6ef81fa6633b06576a8e56322d7e744abc2a938b631053161f5f38"], "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": "6c7291a2-eaaa-410a-bc8f-cbe85eeac3c2", "parent_hash": "9a2a9e9b5d6ef81fa6633b06576a8e56322d7e744abc2a938b631053161f5f38", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40909125 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:40909125' does not resolve to a declared asset", "targets"]}