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pmid:40149517
The Impact of Tertiary Lymphoid Structures on Tumor Prognosis and the Immune Microenvironment in Colorectal Cancer.
Biomedicines · 2025 doi:10.3390/biomedicines13030539
Paper
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Experiment
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Data
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Analysis
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Execution
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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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Complete file
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["source:pmid:40149517"]}, "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": "7d08cf1024eb84b040363e7bbb64b42a910d8ab18e6318d709f4a5f1b2ff3a38", "source_hash": "d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1", "raw_response_sha256": "sha256:74c0effad3ff054525063fd775f0b3cde0826baea85146b02e3df547c1bfeb61", "raw_response_chars": 4501}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "44398bbab2834c294c6c5afaaa17d2e09b4a9ea5158379bd2c32a363199d4213", "source_hash": "d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1", "raw_response_sha256": "sha256:3fabded801f45d39c65d47cdbddcdda7613f5b01b553b792e46287ce7c744a21", "raw_response_chars": 58121}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "06150ff5d84966465ce8954ff558ddb075b24e8f8860155d7457d9c6ee47534b", "source_hash": "d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1", "raw_response": "{\"parent_value\":13,\"unit\":\"genes\",\"evidence\":\"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.\",\"target_result\":\"13-gene TLS-associated prognostic model for colorectal cancer\",\"number_stated\":true}", "reading": {"parent_value": 13, "unit": "genes", "evidence": "A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.", "target_result": "13-gene TLS-associated prognostic model for colorectal cancer", "number_stated": true, "source_locator": "chars 1132-1231 of source sha256 d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1"}, "recorded_at": "2026-10-31T15:36:21.523094+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "424568f4073ab4871d293859b9624bd2bedd8310dcd5e420ed28d7de3d03cb90", "source_hash": "d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1", "raw_response": "<think>We need answer JSON only. Need interpret task. Need find single numerical result replication registered target headline numerical result paper states for main finding, value stated not calculated. Target is main finding. Source abstract says \"A 13-gene TLS-associated prognostic model for CRC was developed\" likely headline numerical result 13 genes. But elsewhere says 11 genes, conclusions 10 genes. Need determine registered target headline numerical result paper states for main finding. Asked \"headline numerical result the paper states for its main finding\". Likely value 13, unit genes, evidence exact contiguous quote containing number, perhaps whole clause. We need report headline number only. Number stated true. Evidence exact contiguous quote. Maybe \"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.\" Unit \"genes\". parent_value 13. target_result maybe perhaps \"A 13-gene TLS-associated prognostic model for CRC was developed.\" But instruction \"Report the headline number only\" perhaps target_result should be concise. JSON schema includes target_result. We need populate likely \"13-gene TLS-associated prognostic model for CRC\" or numerical result statement. Evidence quote whole clause. Exact quote: \"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.\" This is contiguous and directly target. Unit paper prints? It prints \"13-gene\", unit genes. Could use \"genes\". Need make sure \"registered target\" perhaps asks headline numerical result, singular. Could it instead be 582 sample cohort? The \"main finding\" is prognostic model, headline result likely 13-gene model. Abstract results starts exact. The paper inconsistent (11 genes in section, 10 conclusion), but registered target wants headline number, likely abstract's 13. We should not calculate. Output valid JSON.\n\nCould target_result be \"13-gene TLS-associated prognostic model for CRC\" but headline number only might mean value only and unit separately. target_result perhaps \"The paper states a 13-gene TLS-associated prognostic model for CRC.\" Evidence. Let's formulate no extra. Ensure evidence exact punctuation. JSON escaping not issue.</think>\n\n{\"parent_value\":13,\"unit\":\"genes\",\"evidence\":\"A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.\",\"target_result\":\"A 13-gene TLS-associated prognostic model for CRC was developed.\",\"number_stated\":true}", "reading": {"parent_value": 13, "unit": "genes", "evidence": "A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes.", "target_result": "A 13-gene TLS-associated prognostic model for CRC was developed.", "number_stated": true, "source_locator": "chars 1132-1231 of source sha256 d1d092e0bcde1b7be25ba9a182969d0427020ef7a800fbae6ebb02b0d7044db1"}, "recorded_at": "2026-10-31T15:36:16.347912+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "A 13-gene TLS-associated prognostic model for colorectal cancer was developed, and the TLS-high group exhibited significantly better outcomes than the TLS-low group.", "minimax_alt": "A 13-gene TLS-associated prognostic model for CRC was developed, emphasizing immune response genes. Survival analysis indicated significantly better outcomes for the TLS-high group.", "decisive": false}, "analysis_methods": {"minimax": ["Cox regression analysis", "Kaplan-Meier survival analysis", "single-sample gene set enrichment analysis (ssGSEA)"], "minimax_alt": ["single-sample gene set enrichment analysis (ssGSEA)", "Cox regression", "Kaplan-Meier survival analysis"], "decisive": false}, "statistical_method": {"minimax": "Cox regression and Kaplan-Meier survival analyses", "minimax_alt": "Cox and Kaplan-Meier analyses", "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:61a7b5db963b96dfe378742e6447f007949bfadcbd68be0f3c0e831be1155cb4", "type": "sep_package", "label": "SEP v1 package for pmid:40149517"}], "activities": [{"id": "activity:conversion:pmid:40149517", "type": "conversion", "used": ["package:61a7b5db963b96dfe378742e6447f007949bfadcbd68be0f3c0e831be1155cb4"], "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:40149517", "parent_hash": "sha256:3f48f0e0381d4e1fb5faf949800838eb36bdc4b9cf3cfbb6bd86144d98cae654", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40149517 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:40149517' does not resolve to a declared asset", "targets"]}