A tumor-infiltrating B lymphocytes -related index based on machine-learning predicts prognosis and immunotherapy response in lung adenocarcinoma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40196113", "kind": "science-record", "revision": 1, "content_hash": "sha256:8a517a4b06618a212bd7d6dc5586f72460626b1054616a7687f69e0fdf7a58b9", "created_at": "2026-11-01T10:25:50Z", "updated_at": "2026-11-01T10:25:50Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "A tumor-infiltrating B lymphocytes -related index based on machine-learning predicts prognosis and immunotherapy response in lung adenocarcinoma.", "doi": "10.3389/fimmu.2025.1524120", "pmid": "40196113", "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", "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:40196113"], "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:40196113", "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:40196113' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40196113", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1524120", "sha256": "sha256:633c178f7006495c14136802cb684b2035459c2366e0f6ff2de2ddbf057de6a6", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1524120", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40196113 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:40196113"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40196113"]}, "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": "4d18e4b996f8cc7459c30372b880d4e4724244a4eab13615c68104ab4566d09b", "source_hash": "633c178f7006495c14136802cb684b2035459c2366e0f6ff2de2ddbf057de6a6", "raw_response_sha256": "sha256:a14b2f31aee2c3b393835b462b4529172badfb3f48646eb8654621e95dbfabba", "raw_response_chars": 6439}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "1f98bcd7cf162e137d91b69b95b94b0b9597a7d4e399e47d1423c0873edac8cf", "source_hash": "633c178f7006495c14136802cb684b2035459c2366e0f6ff2de2ddbf057de6a6", "raw_response_sha256": "sha256:a0617ec57593c833388d62aa15592c23d4333681120447aae58f82fd7f2e48fb", "raw_response_chars": 49629}], "target_providers": [], "agreement": false, "disagreements": {"target_result": {"minimax": "BRI was inversely correlated with cytotoxic CD8+ T-cell infiltration (r = -0.43, p < 0.001) and positively correlated with regulatory T cells (r = 0.31, p = 0.008).", "minimax_alt": "Notably, BRI was found to inversely correlate with cytotoxic CD8+ T-cell infiltration (r = -0.43, p < 0.001) and positively correlate with regulatory T cells (r = 0.31, p = 0.008).", "decisive": false}, "analysis_methods": {"minimax": ["single-cell RNA sequencing", "Seurat", "LogNormalize", "principal component analysis", "UMAP", "SingleR", "FindAllMarkers", "Weighted Gene Co-expression Network Analysis (WGCNA)", "dynamic tree-cutting", "Non-negative Matrix Factorization (NMF)", "univariate Cox regression analysis", "Random Survival Forest (RSF)", "Elastic Network (Enet)", "Lasso", "Ridge", "Stepwise Cox", "CoxBoost", "Partial Least Squares Regression for Cox (plsRcox)", "Supervised Principal Components (SuperPC)", "Generalized Boosted Regression Modeling (GBM)", "Survival Support Vector Machine (survival-SVM)", "Harrell concordance index (C-index)", "Pearson’s rank correlation analysis", "bi-directional log-rank test"], "minimax_alt": ["single-cell RNA sequencing (scRNA-seq) using the Seurat R package", "principal component analysis (PCA)", "UMAP", "SingleR cell-type annotation", "Weighted Gene Co-expression Network Analysis (WGCNA)", "Non-negative Matrix Factorization (NMF) clustering", "univariate Cox regression analysis", "Random Survival Forest (RSF)", "Elastic Network (Enet)", "Lasso", "Ridge", "Stepwise Cox", "CoxBoost", "Partial Least Squares Regression for Cox (plsRcox)", "Supervised Principal Components (SuperPC)", "Generalized Boosted Regression Modeling (GBM)", "Survival Support Vector Machine (survival-SVM)", "Harrell concordance index (C-index)", "Pearson’s rank correlation analysis", "χ2 test", "Wilcoxon rank-sum test", "T test", "Kaplan-Meier survival analysis", "bi-directional 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": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"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:27d198abf398407202894a4bd536805831c368eee014c3516d9191545e5cf930", "type": "sep_package", "label": "SEP v1 package for pmid:40196113"}], "activities": [{"id": "activity:conversion:pmid:40196113", "type": "conversion", "used": ["package:27d198abf398407202894a4bd536805831c368eee014c3516d9191545e5cf930"], "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": "79ec72ce-2f6a-40c0-9cf7-b8573f350f5d", "parent_hash": "27d198abf398407202894a4bd536805831c368eee014c3516d9191545e5cf930", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40196113 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:40196113' does not resolve to a declared asset", "targets"]}