Ribosome Biogenesis Underpins Tumor Progression: A Comprehensive Signature for Survival and Immunotherapy Response Prediction.

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"Abbreviations", "row_count": 26, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["FDR", "False discovery rate"], ["GEO", "Gene Expression Omnibus"], ["HER2", "Human epidermal growth factor receptor 2"], ["HR", "Hazard ratio"], ["ICI", "Immune checkpoint inhibitor"], ["KEGG", "Kyoto Encyclopedia of Genes and Genomes"], ["KIRC", "Kidney renal clear cell carcinoma"], ["KM", "Kaplan–Meier"], ["LASSO", "Least absolute shrinkage and selection operator"], ["LIHC", "Liver hepatocellular carcinoma"], ["LUAD", "Lung adenocarcinoma"], ["mTOR", "mammalian target of rapamycin"], ["MSI", "Microsatellite instability"], ["OMIM", "Online Mendelian Inheritance in Man"], ["OS", "Overall survival"], ["TP53", "Tumor protein p53"], ["PD-1", "Programmed cell death protein 1"], ["PD-L1", "Programmed cell death-ligand 1"], ["PPI", "Protein–protein interaction"], ["RiBi", "RiBi"], ["R2", "Coefficient of determination"], ["RNAss", "RNA expression–based stemness"], ["TCGA", "The Cancer Genome Atlas"], ["T-cell", "T lymphocyte"], ["TIDE", "Tumor Immune Dysfunction and Exclusion"], ["Xena", "UCSC Xena browser"]], "row_count": 26, "column_count": 2, "numeric_cells": 6, "header_rows": 0, "locator": "section[28]/table-wrap[1]#array1"}}], "gaps": ["asset:source:pmid:40805273 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:40805273", "asset:table:pmid:40805273:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40805273"]}, "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": "83136ca3724100b9ed25f8d960fd9736971142d35e010bbb1ace5703c8f09e91", "source_hash": "cb0ebb3294043f08ba791a2421f8e654889b7741cfe63a8c8669a035d7151774", "raw_response_sha256": "sha256:c45b1533cb7dea9419f7824d36ccb41ccaa373c2dca2e079516364a84ec46740", "raw_response_chars": 3948}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "be500bbbba439d2edb9c8f358d754330e3cfd31e54ed662fd1e03c9928c8190b", "source_hash": "cb0ebb3294043f08ba791a2421f8e654889b7741cfe63a8c8669a035d7151774", "raw_response_sha256": "sha256:ccf32a81e0e8ccaaa92f69d9c8ad73d3ce7aa0d48531419661ba37c1148ea83a", "raw_response_chars": 64935}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "edb561c1f63449dd2280f7d19a10f7a759558fcdf8c5d44d08433dd72a472ca5", "source_hash": "cb0ebb3294043f08ba791a2421f8e654889b7741cfe63a8c8669a035d7151774", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that higher RiBi scores were linked to worse outcomes and that the OncoRibo-68 signature showed robust prognostic power across multiple cohorts, most notably in breast cancer, but it does not state a headline numerical result for the main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states that higher RiBi scores were linked to worse outcomes and that the OncoRibo-68 signature showed robust prognostic power across multiple cohorts, most notably in breast cancer, but it does not state a headline numerical result for the main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:30:08.533594+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "3ebe2d6b27631d9dc7b0389fbf50177a15b5ce2998f09abf32bfa0f67d92a835", "source_hash": "cb0ebb3294043f08ba791a2421f8e654889b7741cfe63a8c8669a035d7151774", "raw_response": "<think>We need answer JSON only. Need inspect source. Registered target headline numerical result paper states for main finding. Source includes scores PanRibo-515 and OncoRibo-68, but these are named signatures, numerical result? Need determine requested single numerical result replication registered target. The supplied excerpt has no performance metric/headline number, only 68/515 in score names, 2.5 section, cohorts/year citations perhaps. Need perhaps target is headline numerical result paper states for main finding. They say if no number for registered target, number_stated false, parent 0 unit/evidence empty, target_result say what text states instead. We must be careful: exact quote evidence only if number stated. Is OncoRibo-68 a numerical result? It's a gene-set size/name, perhaps headline number? The \"registered target: the headline numerical result the paper states for its main finding.\" Main finding is OncoRibo-68 signature and perhaps numbers 68, but not outcome value. Replication must reproduce headline numerical result. No AUC etc supplied. Thus false.\n\nNeed target_result concise what text states instead. Could say \"The text reports an OncoRibo-68 signature associated with prognostic and immunotherapy-response relevance, but it states no headline numerical result value.\" Since no evidence required? Empty. Need valid JSON. parent_value 0, unit \"\", evidence \"\", number_stated false. Ensure no unsupported wording perhaps it says higher scores linked worse outcomes, elevated often better survival ICI. \"The text describes higher RiBi scores as linked to worse outcomes and elevated OncoRibo-68 expression as often associated with better survival in immune-checkpoint inhibitor-treated cohorts, but it gives no numerical result for the main finding.\" This states accurately. But is target_result expected what text states instead, perhaps quote? They only demand exact quote evidence where number. Could quote full relevant clause. We can say \"The source states the qualitative findings but no headline numerical result for the registered target.\" Yet target_result should state what text does state instead. Let's craft.\n\nNeed determine whether unit should maybe \"genes\" and parent_value 68? Let's investigate task design. They want find single numerical result replication of registered target has to reproduce, value paper itself states. Registered target generic: headline numerical result paper states for main finding. Source likely abstract and excerpts. Could infer title main finding signature \"OncoRibo-68\"; perhaps headline numerical result might be 68? But \"replication of registered target\" likely benchmark asks extract reported main result metric. They distinguish parent_value. Source contains OncoRibo-68 repeatedly. Could be regarded as number attached directly to target (\"OncoRibo-68\"), and paper prints number 68. But is it a numerical result? Need deeply parse wording.\n\n\"Read the supplied paper text and 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. The unit must be the unit the paper prints. ... Attribution may be carried by the text's own wording: a number may be attached to the target by a parenthetical list, by the word 'respectively', or by words that name the target directly. When that is how the text links them, quote the whole clause so a reader can check the attribution for themselves. If the text states no number for the registered target, set number_stated to false, leave parent_value at 0, leave unit and evidence empty, and say in target_result what the text does state instead.\"\n\nThis seems generated extraction task where target maybe specific claim but registered target here is \"the headline numerical result the paper states for its main finding.\" We need find one numeric result. Source provided perhaps only portions (abstract plus selected sections) and might have no main performance number. They intentionally test false due incomplete text. Number in title of signature may not be a \"result\" and no unit. Likely false.\n\nCould target be 68? OncoRibo-68 is main signature, and 68 presumably number of genes. The source does not explicitly say \"68 genes\" exactly? It says \"PanRibo-515 and OncoRibo-68\" and \"OncoRibo-68 gene set\". Could quote clause. Unit could \"genes\" perhaps inferred from \"gene set\" but not explicit that 68 is count. Yet replication of main finding could need reproduce AUC or HR, not number of signature genes. User says \"single numerical result\", \"headline number\" implies effect metric. So no.\n\nNeed perhaps evidence exact contiguous quote containing number. If false, evidence empty mandated. target_result can mention only qualitative. Let's answer JSON.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that higher RiBi scores were linked to worse outcomes and that elevated OncoRibo-68 expression often correlated with better survival in immune-checkpoint inhibitor-treated cohorts, but it provides no headline numerical result for the main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states that higher RiBi scores were linked to worse outcomes and that elevated OncoRibo-68 expression often correlated with better survival in immune-checkpoint inhibitor-treated cohorts, but it provides no headline numerical result for the main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:30:17.427269+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "No headline numerical result is stated in the supplied text; the main finding is that higher RiBi scores, represented by PanRibo-515 and OncoRibo-68, were linked to worse outcomes.", "minimax_alt": "unclear—the source text states no headline numerical result. It reports qualitative associations: higher PanRibo-515/OncoRibo-68 scores were linked to worse outcomes, while elevated OncoRibo-68 expression was often associated with better survival in the named immune checkpoint inhibitor cohorts.", "decisive": false}, "analysis_methods": {"minimax": ["TIDE biomarker comparison using receiver operating characteristic (ROC) curves and area under the curve (AUC) values", "Kaplan–Meier analyses", "log-rank test comparisons"], "minimax_alt": ["LASSO regression", "TIDE (Tumor Immune Dysfunction and Exclusion) web-tool analysis", "receiver operating characteristic (ROC) curve analysis", "area under the curve (AUC) analysis", "Kaplan–Meier analysis", "log-rank test"], "decisive": false}, "statistical_method": {"minimax": "unclear", "minimax_alt": "Kaplan–Meier survival analysis with log-rank test comparisons for the ICI survival finding", "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:6f0b2e401e35fac775bb1a8b7db6d8d31357ba7100a94ae1c96f364b3f67d8f0", "type": "sep_package", "label": "SEP v1 package for pmid:40805273"}], "activities": [{"id": "activity:conversion:pmid:40805273", "type": "conversion", "used": ["package:6f0b2e401e35fac775bb1a8b7db6d8d31357ba7100a94ae1c96f364b3f67d8f0"], "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:40805273", "parent_hash": "sha256:e2a9e819c91627deafc55979519122eb219d34ee003592c1fa42f78c0fae64c0", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40805273 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:accession_absent", "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:40805273' does not resolve to a declared asset", "targets"]}