Identification of the prognostic effect of mitophagy-related genes in acute myeloid leukemia.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40873580", "kind": "science-record", "revision": 1, "content_hash": "sha256:49f9e47b2d844116fa055cf9e7d8401938a09efbcc01e5ee39df3709710677ea", "created_at": "2026-11-01T10:25:52Z", "updated_at": "2026-11-01T10:25:52Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Identification of the prognostic effect of mitophagy-related genes in acute myeloid leukemia.", "doi": "10.3389/fimmu.2025.1580597", "pmid": "40873580", "authors": null, "journal": "Frontiers in immunology", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", 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"role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1580597", "sha256": "sha256:c3a39adb85eee652e4c8d1145755fecccf7d01e4e041dc6daeff5ae1ac88a398", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1580597", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40873580 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:40873580"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40873580"]}, "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": "d7dcd2ddffcdbbda54223fdca6065927230e1ea86bdbce4b62f8484826596618", "source_hash": "c3a39adb85eee652e4c8d1145755fecccf7d01e4e041dc6daeff5ae1ac88a398", "raw_response_sha256": "sha256:26e80e78afe75c77cb4caf17f87ea6c0431f461417b841b1198e9b8f987ab967", "raw_response_chars": 5960}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "cdc39688c6db38d9291e8209732ed402506be6a4aee9b92eee2deb102112cf26", "source_hash": "c3a39adb85eee652e4c8d1145755fecccf7d01e4e041dc6daeff5ae1ac88a398", "raw_response_sha256": "sha256:796128d08d2c6706c4f4537b60d48b345e1bc3fc039b8e8a1d866c20827e29ca", "raw_response_chars": 64676}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "0e67e6954c6a8c00d7719655d3fccf56655b2b372368b5ebe614bf84b23be25d", "source_hash": "c3a39adb85eee652e4c8d1145755fecccf7d01e4e041dc6daeff5ae1ac88a398", "raw_response": "{\"parent_value\":5,\"unit\":\"genes\",\"evidence\":\"Five MRG-associated genes (ITGB2, VIP, PTK2, FHL2, BAG3) were selected to construct a prognostic model that stratified patients into high- and low-risk groups with significantly different overall survival.\",\"target_result\":\"The paper identifies five mitophagy-related genes as prognostic biomarkers in AML.\",\"number_stated\":true}", "reading": {"parent_value": 5, "unit": "genes", "evidence": "Five MRG-associated genes (ITGB2, VIP, PTK2, FHL2, BAG3) were selected to construct a prognostic model that stratified patients into high- and low-risk groups with significantly different overall survival.", "target_result": "The paper identifies five mitophagy-related genes as prognostic biomarkers in AML.", "number_stated": true, "source_locator": "chars 1204-1409 of source sha256 c3a39adb85eee652e4c8d1145755fecccf7d01e4e041dc6daeff5ae1ac88a398"}, "recorded_at": "2026-10-31T15:32:46.189603+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "286bedbeb4dacd1b09426e0168b44b644b0ee0395b4b1846c2932b414ceb4c33", "source_hash": "c3a39adb85eee652e4c8d1145755fecccf7d01e4e041dc6daeff5ae1ac88a398", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline main finding registered target. Paper text. Main finding: five MRG-associated genes selected prognostic model. Headline numerical result likely 5 genes. Need exact contiguous quote contains number and attribution. \"Five MRG-associated genes (ITGB2, VIP, PTK2, FHL2, BAG3) were selected to construct a prognostic model...\" Number word Five, parent_value numeric 5, unit perhaps \"genes\" or maybe \"MRG-associated genes\". User says unit paper prints. They ask headline number only, value paper itself states, not calculated. Evidence exact contiguous quotation. If textual number \"Five\", parent_value schema number 5. Unit paper prints maybe \"MRG-associated genes\" or \"genes\". Need determine likely expected. Main finding perhaps \"five mitophagy-related genes as prognostic biomarkers\". Registered target \"the headline numerical result the paper states for its main finding\" clearly number five genes. Need quote whole clause. Could use conclusion exact: \"This study identified five mitophagy-related genes as prognostic biomarkers in AML and developed a robust risk model that correlates with survival outcome, immune infiltration, and drug sensitivity.\" This directly attaches five to genes/main finding. Unit \"mitophagy-related genes\" perhaps paper's unit. They say unit must be unit paper prints. Usually JSON tasks numerical result extraction: parent_value, unit. Could set unit \"genes\" because printed noun. Evidence exact sentence. target_result perhaps describe \"Five mitophagy-related genes were identified as prognostic biomarkers in AML.\" But \"Report headline number only\" likely target_result should concise. Must include evidence despite \"headline number only\" schema. number_stated true.\n\nCould unit be \"prognostic biomarkers\" rather than genes? Main result is five genes, unit genes. Exact quote: \"Five prognostic biomarkers—ITGB2, VIP, PTK2, FHL2, and BAG3—were identified and integrated into a novel risk model...\" This says five biomarkers. Better direct headline. Number is word not digit. They say numerical result, paper states \"Five\". parent_value 5 is conversion? They demand not value you calculated, converted. Reporting word Five as numeric 5 is normalization, surely allowed, schema number. Evidence contains word Five. Unit perhaps \"prognostic biomarkers\". They may expect \"genes\" based abstract. Let's parse wording: \"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.\" Target is headline numerical result main finding. Source likely perhaps extraction task where parent_value numerical count. Need output number. \"Five MRG-associated genes ... selected\". Unit likely \"MRG-associated genes\" or simply \"genes\". The source prints \"genes\". We should avoid overcomplication.\n\nEvidence must exact contiguous quotation and not shortened. Could quote sentence exactly. Evidence: \"Five MRG-associated genes (ITGB2, VIP, PTK2, FHL2, BAG3) were selected to construct a prognostic model that stratified patients into high- and low-risk groups with significantly different overall survival.\" This exact contiguous sentence. This directly attributes number to genes. target_result perhaps \"5 MRG-associated genes were selected to construct the prognostic risk model.\" Is that headline number only? They explicitly \"Report the headline number only\" perhaps target_result should just state \"Five MRG-associated genes\". Schema asks target_result, likely concise natural language.\n\nNeed JSON valid. Ensure unit maybe \"MRG-associated genes\". Is unit supposed singular measurement unit? I'd use \"genes\" because numerical unit. But perhaps exact printed phrase needed. The unit paper prints is \"MRG-associated genes\", not merely \"genes\"? It prints the phrase. User says \"The unit must be the unit the paper prints.\" In extraction tasks, if count of genes, unit \"genes\". Let's formulate.\n\nCould main finding instead be \"72 MRGs analyzed\", \"five genes\", \"26 DEGs\", \"731 pathways\", \"84 compounds\". Main conclusion emphasizes five. Registered target broad; likely five genes. Headline numerical result. Answer.\n\nNeed only JSON no markdown.</think>\n\n{\"parent_value\":5,\"unit\":\"MRG-associated genes\",\"evidence\":\"Five MRG-associated genes (ITGB2, VIP, PTK2, FHL2, BAG3) were selected to construct a prognostic model that stratified patients into high- and low-risk groups with significantly different overall survival.\",\"target_result\":\"Five MRG-associated genes were selected to construct the prognostic model.\",\"number_stated\":true}", "reading": {"parent_value": 5, "unit": "MRG-associated genes", "evidence": "Five MRG-associated genes (ITGB2, VIP, PTK2, FHL2, BAG3) were selected to construct a prognostic model that stratified patients into high- and low-risk groups with significantly different overall survival.", "target_result": "Five MRG-associated genes were selected to construct the prognostic model.", "number_stated": true, "source_locator": "chars 1204-1409 of source sha256 c3a39adb85eee652e4c8d1145755fecccf7d01e4e041dc6daeff5ae1ac88a398"}, "recorded_at": "2026-10-31T15:32:51.026787+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "Five MRG-associated genes (ITGB2, VIP, PTK2, FHL2, and BAG3) were selected to construct a prognostic model that stratified AML patients into high- and low-risk groups with significantly different overall survival.", "minimax_alt": "Five MRG-associated genes (ITGB2, VIP, PTK2, FHL2, BAG3) were selected to construct a prognostic model that stratified patients into high- and low-risk groups with significantly different overall survival.", "decisive": false}, "analysis_methods": {"minimax": ["Univariate Cox regression analysis", "Least absolute shrinkage and selection operator (Lasso) regression", "Multivariate Cox regression analysis", "Kaplan-Meier survival analysis", "Nomogram construction and validation", "Time-dependent ROC analysis", "Gene set enrichment analysis", "CIBERSORT immune cell infiltration analysis", "Wilcoxon signed-rank test", "Spearman correlation analysis", "pRRophetic drug sensitivity prediction", "Consensus clustering", "Differential expression analysis"], "minimax_alt": ["consensus clustering based on MRG expression", "differential expression analysis using limma and DESeq2", "univariate Cox regression", "least absolute shrinkage and selection operator (Lasso) regression", "Kaplan-Meier (K-M) survival analysis", "proportional hazards assumption testing", "multivariate Cox regression", "nomogram development", "calibration plots", "time-dependent ROC curves", "chi-square tests"], "decisive": false}, "statistical_method": {"minimax": "Univariate Cox regression and least absolute shrinkage and selection operator (Lasso) regression were used to screen prognostic genes, followed by multivariate Cox regression to identify independent prognostic indicators.", "minimax_alt": "univariate Cox regression and least absolute shrinkage and selection operator (Lasso) regression analyses", "decisive": true}, "unit": {"minimax": "genes", "minimax_alt": "MRG-associated genes", "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; 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