Unique Biological Characteristics of Patients with High Gleason Score and Localized/Locally Advanced Prostate Cancer Using an In Silico Translational Approach.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40710219", "kind": "science-record", "revision": 2, "content_hash": "sha256:79e73b478ba22d3e94de4d544f0fee065588b882fa4b79707e91065cc1dff577", "created_at": "2026-11-01T10:25:52Z", "updated_at": "2026-11-01T14:01:44Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Unique Biological Characteristics of Patients with High Gleason Score and Localized/Locally Advanced Prostate Cancer Using an In Silico Translational Approach.", "doi": "10.3390/curroncol32070409", "pmid": "40710219", "authors": null, "journal": "Current oncology (Toronto, Ont.)", "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", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40710219"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:40710219", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["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:40710219' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40710219", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/curroncol32070409", "sha256": "sha256:4b8065c421a696d99e615cd5bf33fe21c74793cd8596e35cc94784bfc196aaf9", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/curroncol32070409", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:40710219:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:24acc9a820e5f6a349592ecfedd41c6c2e593a0193d57329a8b2a443a8f31ae8", "bytes": 843, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#curroncol-32-00409-t001", "version": null, "note": "Descriptive characteristics of patients with localized/locally advanced prostate cancer in TCGA (n = 493, radical prostatectomy cohort) and GSE116918 (n = 248, radiation therapy cohort).", "structure": {"pmcid": "PMC12294092", "section_index": 9, "section_title": "3.1. Patients Characteristics", "row_count": 12, "column_count": 3}, "table": {"label": "Table 1", "caption": "Descriptive characteristics of patients with localized/locally advanced prostate cancer in TCGA (n = 493, radical prostatectomy cohort) and GSE116918 (n = 248, radiation therapy cohort).", "rows": [["Cohort", "TCGA", "GSE116918"], ["Treatment", "Radical prostatectomy", "Radiation therapy"], ["Number of patients", "493", "248"], ["Median age (range) years at surgery", "61 (41–78)", "68 (48–79)"], ["Clinical T stage at diagnosis (%)", "", ""], ["cT1/T2/T3/T4/Unknown", "175/172/52/2/92 (35.5/35/10/0.5/19)", "51/76/92/4/25 (21/31/37/1/10)"], ["Biopsy GS (%)", "", ""], ["6", "45 (9)", "42 (17)"], ["7", "245 (50)", "99 (40)"], ["8", "62 (12)", "52 (21)"], ["9", "137 (28)", "54 (21.5)"], ["10", "4 (1)", "1 (0.5)"]], "row_count": 12, "column_count": 3, "numeric_cells": 22, "header_rows": 1, "locator": "section[9]/table-wrap[1]#curroncol-32-00409-t001"}}, {"id": "asset:table:pmid:40710219:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5609dd3a0f0434e8cedacba38b343f4d1953f124d181fdff38e42418d687cf69", "bytes": 632, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#array1", "version": null, "note": null, "structure": {"pmcid": "PMC12294092", "section_index": 18, "section_title": "Abbreviations", "row_count": 16, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["GS", "Gleason score"], ["PCa", "prostate cancer"], ["TME", "tumor microenvironment"], ["BCR-FS", "biochemical recurrence-free survival"], ["OS", "overall survival"], ["MFS", "metastasis-free survival"], ["RP", "radical prostatectomy"], ["IL2", "interleukin 2"], ["IL6", "interleukin 6"], ["NK", "natural killer"], ["Th1", "T helper type 1"], ["DC", "dendritic cell"], ["Tregs", "regulatory T cells"], ["Th2", "T helper type 2"], ["HRD", "homologous recombination defect"], ["SNV", "single-nucleotide variation"]], "row_count": 16, "column_count": 2, "numeric_cells": 4, "header_rows": 0, "locator": "section[18]/table-wrap[1]#array1"}}], "gaps": ["asset:source:pmid:40710219 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:40710219", "asset:table:pmid:40710219:1", "asset:table:pmid:40710219:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40710219"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "passed", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "b1c5212b2078d9bda5be4e44973db79d90b4b1f62c7d66e169a9ce9ec1bf7275", "source_hash": "4b8065c421a696d99e615cd5bf33fe21c74793cd8596e35cc94784bfc196aaf9", "raw_response_sha256": "sha256:773731606fd7ebccf1234ee447f8edb8fb140268fadc12e19d498d0914b53dd0", "raw_response_chars": 4226}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "c6aca92f686437c03f36f1724f5e08c2712210e61c52b0a635e79697b2a02ecb", "source_hash": "4b8065c421a696d99e615cd5bf33fe21c74793cd8596e35cc94784bfc196aaf9", "raw_response_sha256": "sha256:c4dfcd032e86bfb63e9c38d58c7edb6b719563be6d1229bde9fca56b0eb17185", "raw_response_chars": 54485}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "90401a4be463145cca61b8116aeaa1b6f8ca6571d53e154aaaf1356d65cb45d7", "source_hash": "4b8065c421a696d99e615cd5bf33fe21c74793cd8596e35cc94784bfc196aaf9", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that Gleason score was positively correlated with HRD mutations, intratumor heterogeneity, fractional mutations, SNV neoantigens, silent mutation rate, and non-silent mutation rate, but it gives no numerical value for this main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that Gleason score was positively correlated with HRD mutations, intratumor heterogeneity, fractional mutations, SNV neoantigens, silent mutation rate, and non-silent mutation rate, but it gives no numerical value for this main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:22:45.788705+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "4152c886e972a2ca8cb4b96a6eafa857ba3b6c5062c9a94ee99c35e507583545", "source_hash": "4b8065c421a696d99e615cd5bf33fe21c74793cd8596e35cc94784bfc196aaf9", "raw_response": "<think>We need answer JSON only. Need determine no headline numerical result stated. Source has numbers: GS? version 4.1.0, 1.5 times IQR, p &lt;0.05, dates/accessions, GSE, section nums. Registered target headline numerical result main finding. Text states correlations qualitatively, no coefficient/sample size/etc. Need number_stated false, parent_value 0, unit \"\", evidence \"\", target_result what text states instead. Need perhaps quote/explain no numerical result, main finding is positive correlations with listed metrics and first report. Exact quote? Evidence must be empty per instruction if no number. target_result likely sentence paraphrase. Ensure valid JSON. No extra properties. Could target_result quote source perhaps: \"To our knowledge, this is the first report showing...\" Since asks say what text does state instead. Could quote exact clause, but no need? Better exact source wording. Need make sure single numerical result absent. Output:\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that GS was positively correlated with HRD mutations, intratumor heterogeneity, fractional mutations, SNV neoantigens, silent mutation rate, and non-silent mutation rate, but gives no numerical value for this main finding.\",\"number_stated\":false}\n\nDoes target_result itself need source exact? It can say. No issue. JSON only.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that GS was positively correlated with HRD mutations, intratumor heterogeneity, fractional mutations, SNV neoantigens, silent mutation rate, and non-silent mutation rate, but provides no numerical value for this main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states that GS was positively correlated with HRD mutations, intratumor heterogeneity, fractional mutations, SNV neoantigens, silent mutation rate, and non-silent mutation rate, but provides no numerical value for this main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:22:47.126898+00:00"}], "agreement": true, "disagreements": {"target_result": {"minimax": "unclear", "minimax_alt": "Unclear: the supplied source text states a qualitative main finding but no headline numerical result for the registered target.", "decisive": false}, "analysis_methods": {"minimax": ["GSVA", "Kruskal–Wallis test", "Kaplan–Meier method", "log-rank test"], "minimax_alt": ["mRNA expression analysis", "GSVA algorithm", "Tukey-style boxplots", "Kruskal–Wallis test", "Kaplan–Meier method", "log-rank test"], "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:cee46c449abf7345ca3c1900cab5c7b684fe5ed4578adeedf8b07e4469c44f4e", "type": "sep_package", "label": "SEP v1 package for pmid:40710219"}], "activities": [{"id": "activity:conversion:pmid:40710219", "type": "conversion", "used": ["package:cee46c449abf7345ca3c1900cab5c7b684fe5ed4578adeedf8b07e4469c44f4e"], "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:40710219", "parent_hash": "sha256:ff8bf8664b0e0fe8841d2fa45f49bf1915847ad6e9580023ad320011aebe6e88", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40710219 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:40710219' does not resolve to a declared asset", "targets"]}