LAMP3 signature affects cervical cancer progression through autophagy.

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"53(34.87%)"], ["G4", "1(0.33%)", "0(0%)", "1(0.66%)"], ["unknow", "32(10.53%)", "19(12.5%)", "13(8.55%)"], ["Stage", "Stage I", "162(53.29%)", "82(53.95%)", "80(52.63%)", "0.6153"], ["Stage II", "69(22.7%)", "30(19.74%)", "39(25.66%)"], ["Stage III", "45(14.8%)", "25(16.45%)", "20(13.16%)"], ["Stage IV", "21(6.91%)", "11(7.24%)", "10(6.58%)"], ["unknow", "7(2.3%)", "4(2.63%)", "3(1.97%)"], ["T", "T1", "140(46.05%)", "76(50%)", "64(42.11%)", "0.222"], ["T2", "71(23.36%)", "28(18.42%)", "43(28.29%)"], ["T3", "20(6.58%)", "11(7.24%)", "9(5.92%)"], ["T4", "10(3.29%)", "5(3.29%)", "5(3.29%)"], ["unknow", "63(20.72%)", "32(21.05%)", "31(20.39%)"], ["M", "M0", "116(38.16%)", "62(40.79%)", "54(35.53%)", "0.9456"], ["M1", "10(3.29%)", "6(3.95%)", "4(2.63%)"], ["unknow", "178(58.55%)", "84(55.26%)", "94(61.84%)"], ["N", "N0", "133(43.75%)", "69(45.39%)", "64(42.11%)", "0.6066"], ["N1", "60(19.74%)", "28(18.42%)", "32(21.05%)"], ["unknow", "111(36.51%)", "55(36.18%)", "56(36.84%)"]], 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["Age", "<=65", "65"], ["> 65", "8"], ["T", "T1", "23"], ["T2", "22"], ["T3", "13"], ["T4", "4"], ["Unkown", "11"], ["Stage", "stageI", "24"], ["stageII", "23"], ["stageIII", "14"], ["stageIV", "9"], ["Unkown", "3"], ["G", "G1", "2"], ["G2", "34"], ["G3", "25"], ["Unkown", "12"], ["Measure of response", "CR", "51"], ["PR", "7"], ["PD", "13"], ["SD", "2"]], "row_count": 21, "column_count": 3, "numeric_cells": 23, "header_rows": 1, "locator": "section[22]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:40707912:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:84ad9a9dbaccb7eda5d9286713f99b90a2919a52f17c77fa61f8d5d2ae52cbb7", "bytes": 676, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[29]/table-wrap[1]#Tab3", "version": null, "note": "Candidate drug predicted using DSigDB", "structure": {"pmcid": "PMC12288217", "section_index": 29, "section_title": "Drug prediction", "row_count": 6, "column_count": 6}, "table": {"label": "Table 3", "caption": "Candidate drug predicted using DSigDB", "rows": [["Term", "P-value", "Adjusted P-value", "Odds Ratio", "Combined Score", "Genes"], ["IBMX CTD 00007018", "0.00439994", "0.03153289", "19,912", "108045.793", "LAMP3"], ["daidzein CTD 00000166", "0.00634992", "0.0371946", "19,873", "100543.721", "LAMP3"], ["LUCANTHONE CTD 00006227", "0.0106499", "0.04163141", "19,787", "89876.6148", "LAMP3"], ["thapsigargin MCF7 UP", "0.02034985", "0.04633217", "19,593", "76308.4966", "LAMP3"], ["8-Bromo-cAMP, Na CTD 00007044", "0.03259982", "0.06206922", "19,348", "66236.8831", "LAMP3"]], "row_count": 6, "column_count": 6, "numeric_cells": 24, "header_rows": 1, "locator": "section[29]/table-wrap[1]#Tab3"}}], "gaps": ["asset:source:pmid:40707912 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", 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{"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "8eede3470a8f0c5c1bfb53b93effb004a5c68fc6aaae8f19f41ea86ad9e4b23a", "source_hash": "78c53582e15efb180e9bec11eb1bf19925484b06c19b411d8997361d95102a61", "raw_response_sha256": "sha256:081f25940174e972ee47ae8fe2f09cfaea37d151117e86443bad6c66c97b718c", "raw_response_chars": 25171}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "3d65a823c6ff4abbcdfab6e51393e1d1c27676c7f3e86e0880193ad0c30e202b", "source_hash": "78c53582e15efb180e9bec11eb1bf19925484b06c19b411d8997361d95102a61", "raw_response": "{\"parent_value\":5,\"unit\":\"genes\",\"evidence\":\"A five-gene (AP1B1, DNASE2, LAMP3, NPC1, and LAPTM4A) lysosome-associated prognostic model was developed.\",\"target_result\":\"A five-gene lysosome-associated prognostic model was developed.\",\"number_stated\":true}", "reading": {"parent_value": 5, "unit": "genes", "evidence": "A five-gene (AP1B1, DNASE2, LAMP3, NPC1, and LAPTM4A) lysosome-associated prognostic model was developed.", "target_result": "A five-gene lysosome-associated prognostic model was developed.", "number_stated": true, "source_locator": "chars 1029-1134 of source sha256 78c53582e15efb180e9bec11eb1bf19925484b06c19b411d8997361d95102a61"}, "recorded_at": "2026-10-31T15:22:38.430015+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "ae2be71b6e9f3e443d5f3b07f108c12dc27c55644ba58a932536f7cf1fcd9197", "source_hash": "78c53582e15efb180e9bec11eb1bf19925484b06c19b411d8997361d95102a61", "raw_response": "<think>We need answer JSON only. Need inspect source. Registered target headline numerical result paper states for main finding. Source appears abstract/results without specific headline numerical result beyond five-gene model perhaps number 5? User asks single numerical result replication registered target reproduce, value paper itself states. Main finding maybe five-gene prognostic model. Is that a numerical result? It states \"A five-gene...\" Number is word \"five\" not numeral? parent_value numeric 5, unit maybe \"genes\" and evidence exact contiguous quote. But perhaps target headline numerical result main finding likely C-index, AUC? Supplied source includes no numerical value attached. Need determine whether \"five-gene\" qualifies headline numerical result. Registered target broad: headline numerical result paper states for main finding. Main finding is five-gene prognostic model. They may expect 5 genes. But phrase \"number the paper itself states\" perhaps numerical result e.g., five-gene. Evidence contains number via word five. Unit \"genes\". Need quote whole clause attribution. Exact contiguous quote: \"A five-gene (AP1B1, DNASE2, LAMP3, NPC1, and LAPTM4A) lysosome-associated prognostic model was developed.\" Then parent_value 5, unit \"genes\". target_result perhaps \"A five-gene lysosome-associated prognostic model was developed.\" number_stated true.\n\nCould there be P < 0.05 but statistical threshold, not headline result. Five-gene model is the headline numerical result. Need make sure \"headline number only\" and target result wording. They explicitly \"single numerical result that a replication of registered target has to reproduce.\" The target is headline numerical result paper states for its main finding. Source likely extracted abstract and no detailed model performance numbers. \"five-gene\" is count and main model. So answer.\n\nNeed exact evidence quote unchanged. Unit must unit paper prints. Paper prints \"five-gene\", singular adjectival; unit perhaps \"genes\" inferred? Unit must unit paper prints. Does it print \"genes\" in \"five-gene\" and \"gene\"? It says \"five-gene ... model.\" Unit could be \"genes\". They ask unit paper prints; likely unit \"genes\". Maybe \"gene\" because \"five-gene\" singular? Numerically, 5 genes. Usually unit \"genes\". Exact evidence.\n\ntarget_result perhaps \"A five-gene lysosome-associated prognostic model was developed.\" This paraphrases evidence but it's okay target_result. They said headline number only perhaps target_result perhaps \"5 genes\". Schema parent_value numeric and unit. target_result string can be concise. number_stated true.\n\nCould number_stated false because five is not headline numerical \"result\"? Let's deeply inspect task semantics. They ask find single numerical result replication target must reproduce. Registered target supplied vague: \"the headline numerical result the paper states for its main finding\". Usually benchmark asks extract \"parent_value\" from source text perhaps numerical metric. Here source paper abstract main result no AUC etc. It says five-gene model. Thus count is headline numerical result. The use \"number_stated\" supports if no number. They may intentionally give source lacking headline numerical value and expect false. Need assess.\n\nThe source abstract: \"A five-gene (...) lysosome-associated prognostic model was developed. LAMP3 was identified as the most differentially expressed gene. Knockdown ... significantly reduced ...\". No quantitative reduction. The headline finding includes five-gene model. If replication of registered target main finding, one must reproduce five identified genes, but \"headline numerical result\" might indeed be five genes. The prompt says \"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.\" This suggests source contains a numerical result like \"AUC = 0.xxx\". They want number. In this source, \"five-gene\" is a spelled number and a compositional count, perhaps qualifies. They mention exact contiguous quotation contains the number. \"five\" is number. Attribution may be target named directly. Quote clause.\n\nCould they instead identify P < 0.05? Not headline. Five-gene is best.\n\nNeed output valid JSON no markdown. Ensure no extra properties. Evidence exact contiguous. Could quote from abstract: \"A five-gene (AP1B1, DNASE2, LAMP3, NPC1, and LAPTM4A) lysosome-associated prognostic model was developed.\" Exact. parent_value 5. unit \"genes\". target_result perhaps \"The main finding is a five-gene lysosome-associated prognostic model.\" The instruction says \"headline number only\" likely don't include number in target_result? But schema parent_value and unit handle it. target_result can describe. They ask if false say what text states instead. For true perhaps target_result maybe \"A five-gene lysosome-associated prognostic model was developed.\" Fine. Maybe target_result should identify target: \"five-gene lysosome-associated prognostic model\".</think>\n\n{\"parent_value\":5,\"unit\":\"genes\",\"evidence\":\"A five-gene (AP1B1, DNASE2, LAMP3, NPC1, and LAPTM4A) lysosome-associated prognostic model was developed.\",\"target_result\":\"A five-gene lysosome-associated prognostic model was developed.\",\"number_stated\":true}", "reading": {"parent_value": 5, "unit": "genes", "evidence": "A five-gene (AP1B1, DNASE2, LAMP3, NPC1, and LAPTM4A) lysosome-associated prognostic model was developed.", "target_result": "A five-gene lysosome-associated prognostic model was developed.", "number_stated": true, "source_locator": "chars 1029-1134 of source sha256 78c53582e15efb180e9bec11eb1bf19925484b06c19b411d8997361d95102a61"}, "recorded_at": "2026-10-31T15:22:38.954320+00:00"}], "agreement": true, "disagreements": {"physical_methods": {"minimax": ["In vitro experiments", "In vivo experiments", "LAMP3 knockdown"], "minimax_alt": ["In vitro experiments", "in vivo experiments"], "decisive": false}, "analysis_methods": {"minimax": ["LASSO-Cox regression", "ROC curves", "PCA analysis", "Gene Ontology analysis", "KEGG pathway enrichment analysis", "single-sample gene set enrichment analysis (ssGSEA)", "CIBERSORT", "CIBERSORT-abs", "TIMER", "XCELL", "QUANTISEQ", "MCPCOUNTER", "EPIC", "Tumor Immune Dysfunction and Exclusion (TIDE) score"], "minimax_alt": ["LASSO-Cox regression", "ROC curves", "PCA analysis"], "decisive": false}}, "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": "passed", "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.passed"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:667b095fc3745aba231755f4c871541c54e8a53093fe81eb8ff8b7bde386c1f2", "type": "sep_package", "label": "SEP v1 package for pmid:40707912"}], "activities": [{"id": "activity:conversion:pmid:40707912", "type": "conversion", "used": ["package:667b095fc3745aba231755f4c871541c54e8a53093fe81eb8ff8b7bde386c1f2"], "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:40707912", "parent_hash": "sha256:150b940cd714445210aa806d7c8d21ca9db52b7a13a47fe432d44099de9ae13b", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40707912 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.passed", "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:40707912' does not resolve to a declared asset", "targets"]}