The correlation between LAG-3 expression and the efficacy of chemoimmunotherapy in advanced biliary tract cancer.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39751894", "kind": "science-record", "revision": 2, "content_hash": "sha256:3f4ec524d9d46a571f9ab71ab55a859d9b58b23f6c9759ec51aa132e025eace9", "created_at": "2026-11-01T10:25:48Z", "updated_at": "2026-11-01T14:01:32Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "The correlation between LAG-3 expression and the efficacy of chemoimmunotherapy in advanced biliary tract cancer.", "doi": "10.1007/s00262-024-03878-0", "pmid": "39751894", "authors": null, "journal": "Cancer immunology, immunotherapy : CII", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 70.6, "unit": "percent", "tolerance": null, "source": "chars 1132-1275 of source sha256 c2cc7c034d43a161cbee6bf48b1df2ed9484287c0028b97b855f75c3c6d71774"}, "evidence": [{"asset": "source:pmid:39751894", "locator": "chars 1132-1275 of source sha256 c2cc7c034d43a161cbee6bf48b1df2ed9484287c0028b97b855f75c3c6d71774", "quote": "The objective response rate (ORR) was significantly higher in LAG-3-positive tumors than in LAG-3-negative tumors (70.6% vs. 33.3%, P = 0.029)."}]}], "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:39751894"], "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:39751894", "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:39751894' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39751894", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s00262-024-03878-0", "sha256": "sha256:c2cc7c034d43a161cbee6bf48b1df2ed9484287c0028b97b855f75c3c6d71774", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s00262-024-03878-0", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:39751894:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:effbc6714246de9e2ed13d14ecf64d0e237c36acd6b6b2eb601827dd9cb20893", "bytes": 1043, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab1", "version": null, "note": "Demographic difference between LAG-3-positive and LAG-3-negative subgroup", "structure": {"pmcid": "PMC11699023", "section_index": 10, "section_title": "Patient characteristics", "row_count": 20, "column_count": 5}, "table": {"label": "Table 1", "caption": "Demographic difference between LAG-3-positive and LAG-3-negative subgroup", "rows": [["Characteristic", "All (N = 44)", "LAG-3-positive (N = 17)", "LAG-3-negative (N = 27)", "P value"], ["Age"], ["Median (range), year", "67 (30–80)", "67 (30–80)", "68(35–80)", "0.407"], ["Sex (%)"], ["Male", "20 (45)", "8 (47)", "12 (44)", "> 0.99"], ["Female", "24 (55)", "9 (53)", "15 (56)"], ["Stage (%)"], ["II", "1 (2)", "0 (0)", "1 (4)", "NA"], ["III", "2 (5)", "0 (0)", "2 (7)"], ["IIIB", "4 (9)", "2 (12)", "2 (7)"], ["IVA", "7 (16)", "3 (18)", "4 (15)"], ["IVB", "30 (68)", "12 (70)", "18 (67)"], ["Primary tumor site (%)"], ["Intrahepatic bile duct", "26 (59)", "9 (53)", "17 (63)", "NA"], ["Extrahepatic bile duct", "11 (25)", "5 (29)", "6 (22)"], ["Gallbladder", "5 (11)", "1 (6)", "4 (15)"], ["Ampulla of vater", "2 (5)", "2 (12)", "0 (0)"], ["PD-L1 expression (%)"], ["CPS ≥ 1", "18 (41)", "14 (82)", "4 (15)", "< 0.001"], ["CPS < 1", "26 (59)", "3 (18)", "23 (85)"]], "row_count": 20, "column_count": 5, "numeric_cells": 50, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:39751894:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fb8d2de8e853ca70f330eff0ba3e6f3aa90c0bef0fecf58f1108458d72f61791", "bytes": 492, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#Tab2", "version": null, "note": "Response rate in this study", "structure": {"pmcid": "PMC11699023", "section_index": 10, "section_title": "Patient characteristics", "row_count": 9, "column_count": 2}, "table": {"label": "Table 2", "caption": "Response rate in this study", "rows": [["Best overall response", "N = 44 (%)"], ["Complete response", "0 (0)"], ["Partial response", "21 (47.7)"], ["Stable disease", "4 (9.1)"], ["Stable disease ≥ 12 weeks", "13 (29.5)"], ["Progressive disease", "5 (11.4)"], ["Not evaluated", "1 (2.3)"], ["Objective response", "21 (47.4)"], ["Long-term disease control", "34 (77.3)"]], "row_count": 9, "column_count": 2, "numeric_cells": 10, "header_rows": 1, "locator": "section[10]/table-wrap[2]#Tab2"}}], "gaps": ["asset:source:pmid:39751894 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:39751894", "asset:table:pmid:39751894:1", "asset:table:pmid:39751894:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39751894"]}, "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": "637d93870f423ad621f21057f8469d3ac69911136bc30089459152336b7c4520", "source_hash": "c2cc7c034d43a161cbee6bf48b1df2ed9484287c0028b97b855f75c3c6d71774", "raw_response_sha256": "sha256:2cb5d11e2729bb16dcac93ba5ac55da949c184fbf4bd17f681df4cab54cc776c", "raw_response_chars": 2471}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "3eeb2a7da4363c87b0de6dbea1909601a20252d9a4cd48dbe9f84e8c3564a799", "source_hash": "c2cc7c034d43a161cbee6bf48b1df2ed9484287c0028b97b855f75c3c6d71774", "raw_response_sha256": "sha256:12979860c58f21e78c7bfb6487cb9c4d74a5d96fc0371c99a2ad7a0e12398f46", "raw_response_chars": 34464}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "a54f7c24df0f409c0799bd6d6b9d26c6e69e94c2c0bf387788ab7f6cac589f94", "source_hash": "c2cc7c034d43a161cbee6bf48b1df2ed9484287c0028b97b855f75c3c6d71774", "raw_response": "{\"parent_value\":70.6,\"unit\":\"%\",\"evidence\":\"The objective response rate (ORR) was significantly higher in LAG-3-positive tumors than in LAG-3-negative tumors (70.6% vs. 33.3%, P = 0.029).\",\"target_result\":\"The objective response rate was 70.6% in LAG-3-positive tumors, compared with 33.3% in LAG-3-negative tumors.\",\"number_stated\":true}", "reading": {"parent_value": 70.6, "unit": "%", "evidence": "The objective response rate (ORR) was significantly higher in LAG-3-positive tumors than in LAG-3-negative tumors (70.6% vs. 33.3%, P = 0.029).", "target_result": "The objective response rate was 70.6% in LAG-3-positive tumors, compared with 33.3% in LAG-3-negative tumors.", "number_stated": true, "source_locator": "chars 1132-1275 of source sha256 c2cc7c034d43a161cbee6bf48b1df2ed9484287c0028b97b855f75c3c6d71774"}, "recorded_at": "2026-10-31T15:26:22.006161+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "ff02a4c17d4788b9600fbae36de818f0a8154a1312c26fbecb23b8334cb09519", "source_hash": "c2cc7c034d43a161cbee6bf48b1df2ed9484287c0028b97b855f75c3c6d71774", "raw_response": "<think>We need answer JSON only. Need interpret request: single numerical result replication registered target main finding. Need headline number only, paper stated, unit printed. Target broad \"headline numerical result paper states for main finding\". Need determine likely main headline number from abstract. Could be ORR 70.6% vs 33.3%, P=.029. \"headline numerical result\" likely 70.6%? Main finding LAG-3 positivity predicts efficacy, objective response rate. Need exact contiguous quotation contains number, whole clause for attribution. Need parent_value number likely 70.6, unit \"%\". Evidence exact sentence: \"The objective response rate (ORR) was significantly higher in LAG-3-positive tumors than in LAG-3-negative tumors (70.6% vs. 33.3%, P = 0.029).\" That contains both. But asks \"single numerical result\" headline number only, value paper states for registered target. They expect one number. Could headline result be 38.6% LAG-3 positivity? Yet main finding as efficacy likely ORR 70.6 vs 33.3. Registered target intentionally generic. Need output one number and unit. Evidence must quote whole clause. target_result likely \"70.6%\" maybe. number_stated true. parent_value 70.6. Need ensure exact quotation and no shortening. \"The objective response rate (ORR) was significantly higher...\" Whole clause/sentence. Evidence contains multiple numerical values, but headline number only in parent_value. Is that okay? They insist evidence exact contiguous quote contains number. likely.\n\nCould potentially headline numerical result be deeper therapeutic response, 20.1%, 38.6%, 57.6%. But main headline abstract results usually first ORR. Let's parse wording: \"find the single numerical result that a replication of the registered target has to reproduce. REGISTERED TARGET: the headline numerical result the paper states for its main finding.\" This likely benchmark where target description vague and extract headline. Main finding could be \"LAG-3 expression may serve as biomarker\", headline numerical result ORR significantly higher: 70.6% vs 33.3%. Single result perhaps 70.6% (the positive group's ORR), comparison 33.3. Need perhaps evidence entire clause \"The objective response rate (ORR) was significantly higher in LAG-3-positive tumors than in LAG-3-negative tumors (70.6% vs. 33.3%, P = 0.029).\" Good.\n\nCould unit be \"%\" exactly printed. parent_value 70.6. target_result maybe \"The objective response rate was 70.6% in LAG-3-positive tumors.\" But should only headline number? They request target_result perhaps state result. We can put \"70.6%\" only. Need valid JSON escaping? Evidence exact Unicode en dash etc not issue. We must not invent source. Use exact source. Ensure exact quotation punctuation. Sentence from source exactly. Let's deliver JSON.</think>\n\n{\"parent_value\":70.6,\"unit\":\"%\",\"evidence\":\"The objective response rate (ORR) was significantly higher in LAG-3-positive tumors than in LAG-3-negative tumors (70.6% vs. 33.3%, P = 0.029).\",\"target_result\":\"70.6%\",\"number_stated\":true}", "reading": {"parent_value": 70.6, "unit": "%", "evidence": "The objective response rate (ORR) was significantly higher in LAG-3-positive tumors than in LAG-3-negative tumors (70.6% vs. 33.3%, P = 0.029).", "target_result": "70.6%", "number_stated": true, "source_locator": "chars 1132-1275 of source sha256 c2cc7c034d43a161cbee6bf48b1df2ed9484287c0028b97b855f75c3c6d71774"}, "recorded_at": "2026-10-31T15:26:24.676693+00:00"}], "agreement": false, "disagreements": {"work_type": {"minimax": "analysis_only_for_target", "minimax_alt": "analysis_plus_physical_validation", "decisive": true}, "physical_methods": {"minimax": [], "minimax_alt": ["Immunohistochemical staining for PD-L1 and LAG-3", "Digital spatial profiling in selected regions of interest"], "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": []}}, {"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:a94bd79521587ecd419c41ef62d31d37e481058471cbbe303177b8ba842f4598", "type": "sep_package", "label": "SEP v1 package for pmid:39751894"}], "activities": [{"id": "activity:conversion:pmid:39751894", "type": "conversion", "used": ["package:a94bd79521587ecd419c41ef62d31d37e481058471cbbe303177b8ba842f4598"], "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:39751894", "parent_hash": "sha256:76e1e916099b32ef94c4bcac886994e1cbcad605fcfca561b20d4ad009cac3bb", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39751894 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:39751894' does not resolve to a declared asset", "targets"]}