A comprehensive prognostic and immunological implications of Gremlin 1 in lung adenocarcinoma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40066442", "kind": "science-record", "revision": 1, "content_hash": "sha256:1cafc551d4d413b7cfe7a1ef49c134c81cdc2ccfa0a19b661e6f83a92089b9cf", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T10:25:49Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "A comprehensive prognostic and immunological implications of Gremlin 1 in lung adenocarcinoma.", "doi": "10.3389/fimmu.2025.1529195", "pmid": "40066442", "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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"capabilities": [], "data_gaps": ["source:pmid:40066442"]}, "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": "8f36b44e7de5717ce167aa66b97100f086a0ee75b3fbbbc8e7310a480bb20d09", "source_hash": "9ce79c1c9a6a2083c1b46534d73c4551cab4352f4bacfe288cc33ace5ba3438c", "raw_response_sha256": "sha256:bd4b025aab2c0aef5067a26d3d51a9984dbf56b7ae5676894a8e62d08d0a70d4", "raw_response_chars": 5307}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "7013c76b09cee57902880a1f5ee97d24cbf48f7adb48da0cbe69ee04c732633f", "source_hash": "9ce79c1c9a6a2083c1b46534d73c4551cab4352f4bacfe288cc33ace5ba3438c", "raw_response_sha256": "sha256:010c8ee6a8d1fa4a08af312ae4f0a5f6a9decc1ae451cb1d32f0e094dd7d0b31", "raw_response_chars": 31970}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "4e645e8be7606da86c3069ea0c99c1dbb395fd28c333769cb6b1c89604f738b4", "source_hash": "9ce79c1c9a6a2083c1b46534d73c4551cab4352f4bacfe288cc33ace5ba3438c", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that GREM1 was significantly upregulated in tumor tissues and correlated with poor prognosis; 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 GREM1 was significantly upregulated in tumor tissues and correlated with poor prognosis; it does not state a headline numerical result for the main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:32:51.796338+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "a78f0697217e2cfb41e3080e93014aa06b7740af130dcc7ef8b63fcb21e71ab6", "source_hash": "9ce79c1c9a6a2083c1b46534d73c4551cab4352f4bacfe288cc33ace5ba3438c", "raw_response": "<think>We need answer JSON only. Need inspect source for headline numerical result for main finding registered target. Text appears no actual numerical result except methods thresholds, versions, 22 cell subtypes, antibody dilutions, p&lt;0.050, maybe target no numerical result. Must set false parent 0 unit/evidence empty and target_result says text states qualitative association: GREM1 upregulated tumor tissues and correlated poor prognosis etc. Need exact wording perhaps evidence empty mandated. Need ensure \"single numerical result\" no number attached main finding. There is no numerical outcome. \"22 infiltrating immune cell subtypes\", \"10%\", etc irrelevant. \"Statistical significance ... P &lt;0.050\" is methodological threshold, not headline result. Thus false.\n\nNeed output valid JSON. target_result string perhaps \"The text states that GREM1 was significantly upregulated in tumor tissues and correlated with poor prognosis, but it reports no numerical value for this main finding.\" This is paraphrase okay target_result. They require evidence empty. parent_value 0. unit \"\". number false. Ensure no prose outside.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that GREM1 was significantly upregulated in tumor tissues and correlated with poor prognosis, but it reports no numerical value for this main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states that GREM1 was significantly upregulated in tumor tissues and correlated with poor prognosis, but it reports no numerical value for this main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:32:52.393467+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "No headline numerical result is stated; the paper reports qualitatively that GREM1 was significantly upregulated in tumor tissues and correlated with poor prognosis.", "minimax_alt": "unclear — the supplied text gives no headline numerical result for the main finding; it only states that GREM1 was significantly upregulated in tumor tissues and correlated with poor prognosis.", "decisive": false}, "analysis_methods": {"minimax": ["Weighted Gene Co-expression Network Analysis (WGCNA)", "GO enrichment analysis", "KEGG enrichment analysis", "Kaplan-Meier survival analysis", "log-rank test", "univariate Cox regression", "multivariate Cox regression", "ESTIMATE algorithm", "TIMER 2.0", "CIBERSORT", "Spearman correlation analysis", "Pearson correlation analysis", "Benjamini-Hochberg False Discovery Rate correction"], "minimax_alt": ["Weighted Gene Co-expression Network Analysis (WGCNA)", "GO enrichment analysis", "KEGG enrichment analysis", "Kaplan-Meier survival analysis", "log-rank test", "univariate Cox regression", "multivariate Cox regression", "ESTIMATE algorithm", "TIMER 2.0", "CIBERSORT", "Pearson correlation analysis", "Spearman correlation analysis", "Wilcoxon test", "Benjamini-Hochberg False Discovery Rate (FDR) correction", "TMB and MSI calculation using maftools"], "decisive": false}, "statistical_method": {"minimax": "Kaplan-Meier survival analysis with the log-rank test, together with univariate and multivariate Cox regression analyses", "minimax_alt": "Kaplan-Meier survival analysis with the log-rank test, together with univariate and multivariate Cox regression calculating hazard ratios and 95% confidence intervals.", "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:ff5585bd25953b76950f1414563595a8528057f00c3dad9d882ff3ef2c26473b", "type": "sep_package", "label": "SEP v1 package for pmid:40066442"}], "activities": [{"id": "activity:conversion:pmid:40066442", "type": "conversion", "used": ["package:ff5585bd25953b76950f1414563595a8528057f00c3dad9d882ff3ef2c26473b"], "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": "f6b32a1a-7e84-43d0-ace1-7cc8ebd01932", "parent_hash": "ff5585bd25953b76950f1414563595a8528057f00c3dad9d882ff3ef2c26473b", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40066442 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:40066442' does not resolve to a declared asset", "targets"]}