FGF2 as a Potential Tumor Suppressor in Lung Adenocarcinoma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41594226", "kind": "science-record", "revision": 1, "content_hash": "sha256:38e7964e28f2c08610355cec08443bb1cc84cf6e2689ad085e8ea0eb40076fd4", "created_at": "2026-11-01T10:25:54Z", "updated_at": "2026-11-01T10:25:54Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "FGF2 as a Potential Tumor Suppressor in Lung Adenocarcinoma.", "doi": "10.3390/diagnostics16020250", "pmid": "41594226", "authors": null, "journal": "Diagnostics (Basel, Switzerland)", "year": 2026, "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:41594226"], "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": 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"format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/diagnostics16020250", "sha256": "sha256:58c85e07c03ba6930610eeb89afa541d1df8a710d589b8a06b2a3e5e9dfb68b5", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/diagnostics16020250", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:41594226 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:41594226"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41594226"]}, "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": "fe5227e0563d261803f9c2b1641226347196216d7ace56a7688253ef8b664c08", "source_hash": "58c85e07c03ba6930610eeb89afa541d1df8a710d589b8a06b2a3e5e9dfb68b5", "raw_response_sha256": "sha256:1c633c1012a3b5c6eb53ac2886b3a0f91d5533fc8e282ada2e60c587604a8162", "raw_response_chars": 4623}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "90d167a9b2591636faa0e560a9651723c09e91321012488caa70d25da972ce4f", "source_hash": "58c85e07c03ba6930610eeb89afa541d1df8a710d589b8a06b2a3e5e9dfb68b5", "raw_response_sha256": "sha256:02c82627ddaff0f644376c98fdebf8737f54d215597adc49120319ca7a52e2f8", "raw_response_chars": 69257}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "69b9b004abff3a81ffc4b1bddcc261ef255eeae9a8869f724cccdf388e107064", "source_hash": "58c85e07c03ba6930610eeb89afa541d1df8a710d589b8a06b2a3e5e9dfb68b5", "raw_response": "{\"parent_value\":949,\"unit\":\"differentially expressed genes (DEGs)\",\"evidence\":\"A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets, with enrichment in cell adhesion and metastasis-related pathways.\",\"target_result\":\"A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets.\",\"number_stated\":true}", "reading": {"parent_value": 949, "unit": "differentially expressed genes (DEGs)", "evidence": "A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets, with enrichment in cell adhesion and metastasis-related pathways.", "target_result": "A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets.", "number_stated": true, "source_locator": "chars 1136-1296 of source sha256 58c85e07c03ba6930610eeb89afa541d1df8a710d589b8a06b2a3e5e9dfb68b5"}, "recorded_at": "2026-10-31T15:17:36.339387+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "3f3f275e0634b4813a70153b21553adc58388aead49c073e8f771de62249d944", "source_hash": "58c85e07c03ba6930610eeb89afa541d1df8a710d589b8a06b2a3e5e9dfb68b5", "raw_response": "<think>We need answer JSON only. Need interpret task carefully. Need find single numerical result replication of registered target: \"the headline numerical result the paper states for its main finding\". Source abstract/results. Candidate 949 DEGs commonly identified; among 11 hub genes FGF2 downregulated. Headline numerical result perhaps 949 differentially expressed genes. But target wording \"headline numerical result the paper states for its main finding\" likely expects 949? Need determine unit printed. Number maybe 949 DEGs. There is 11 hub genes. Which is headline number for main finding? They ask \"single numerical result that a replication of the registered target has to reproduce.\" Registered target main finding. Main finding FGF2 downregulated etc. Abstract Results starts \"A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets...\" This is likely headline numerical result. Could be 11 hub genes identified, FGF2 among. But \"headline numerical result\" perhaps total 949 DEGs is headline. Need evidence exact contiguous quote containing number, and attribution via wording. Quote whole clause. Need unit as printed: \"DEGs\" likely. parent_value 949, unit \"DEGs\" (paper prints DEGs). Evidence exact quote: \"A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets, with enrichment in cell adhesion and metastasis-related pathways.\" This exact contiguous clause/sentence. target_result perhaps \"949 differentially expressed genes (DEGs) were commonly identified across datasets.\" Need perhaps state main finding numerical result.\n\nBut let's inspect wording. User wants \"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.\" We should only number and unit. JSON has target_result required. Could say \"949 DEGs\". Evidence exact quote. number_stated true.\n\nQuestion: Does \"headline numerical result the paper states for its main finding\" refer registered target generic, not target FGF2. Maybe paper's headline result is in abstract. Numbers: 3 datasets, 949 DEGs, 11 hub genes. Main finding is FGF2 as tumor suppressor. If replication, numerical result might be 11 robust hub genes. Which is \"headline numerical result\"? The first result number perhaps 949. They call \"headline numerical result\" often extraction task asks exact numerical result attached to a target. REGISTERED TARGET is \"the headline numerical result the paper states for its main finding\". Could be ambiguously target itself. We need infer expected from source. Abstract's Results: \"A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets... Among the 11 hub genes identified, FGF2 was consistently downregulated...\" Main headline count likely 949 DEGs. The paper's title and conclusion main finding doesn't have a specific effect size. The standout number is 949. Also section details numerous method params, MCODE score, etc., clearly distractors. Need choose 949.\n\nUnit: \"differentially expressed genes (DEGs)\" perhaps unit string \"DEGs\". Evidence quote exact full sentence. target_result could be \"949 differentially expressed genes (DEGs)\". Headline number only in parent_value/unit/evidence. They demand JSON object no extra prose. Ensure valid JSON and Unicode okay. Could unit be \"DEGs\" exactly printed. Evidence exact contiguous quotation no ellipsis. Quote perhaps sentence exactly:\n\"A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets, with enrichment in cell adhesion and metastasis-related pathways.\"\nYes.\n\nShould target_result state what? Since number stated true, likely describe result. \"949 differentially expressed genes (DEGs) were commonly identified across datasets.\" It duplicates. Could say \"Headline numerical result: 949 DEGs.\" But \"headline number only\" perhaps target_result should be \"949 DEGs\". JSON parent_value number 949 unit \"DEGs\", evidence. Let's deliver.</think>\n\n{\"parent_value\":949,\"unit\":\"DEGs\",\"evidence\":\"A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets, with enrichment in cell adhesion and metastasis-related pathways.\",\"target_result\":\"949 differentially expressed genes (DEGs)\",\"number_stated\":true}", "reading": {"parent_value": 949, "unit": "DEGs", "evidence": "A total of 949 differentially expressed genes (DEGs) were commonly identified across datasets, with enrichment in cell adhesion and metastasis-related pathways.", "target_result": "949 differentially expressed genes (DEGs)", "number_stated": true, "source_locator": "chars 1136-1296 of source sha256 58c85e07c03ba6930610eeb89afa541d1df8a710d589b8a06b2a3e5e9dfb68b5"}, "recorded_at": "2026-10-31T15:17:35.836311+00:00"}], "agreement": false, "disagreements": {"physical_methods": {"minimax": ["Transwell migration assay", "Wound healing assay"], "minimax_alt": ["Transwell migration assay", "Wound healing assay", "Exogenous FGF2 treatment of LUAD cell lines"], "decisive": false}, "analysis_methods": {"minimax": ["Gene Expression Omnibus (GEO) differential-expression analysis", "Gene Ontology (GO) enrichment analysis", "KEGG pathway enrichment analysis", "Cancer hallmark enrichment analysis", "STRING protein–protein interaction network construction", "MCODE (Molecular Complex Detection) clustering", "CytoHubba hub-gene prioritization using Degree, Closeness, and Maximum Neighborhood Component (MNC) algorithms", "Kaplan–Meier Plotter survival analysis"], "minimax_alt": ["Analysis of three independent GEO datasets to identify consistently dysregulated genes in LUAD", "Gene Ontology (GO), KEGG, and cancer hallmark enrichment analysis", "Protein–protein interaction (PPI) network construction using STRING (version 12.0)", "MCODE (Molecular Complex Detection) clustering", "CytoHubba hub-gene prioritization using Degree, Closeness, and Maximum Neighborhood Component (MNC)", "Kaplan–Meier Plotter survival analysis", "Expression validation across TCGA, CPTAC, TNMplot, LCE, and the Human Protein Atlas"], "decisive": false}, "unit": {"minimax": "differentially expressed genes (DEGs)", "minimax_alt": "DEGs", "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:5dd150bbe1363fb544b562a33156c64e3453206c70a1d92d3c1691b1fd5a7ddd", "type": "sep_package", "label": "SEP v1 package for pmid:41594226"}], "activities": [{"id": "activity:conversion:pmid:41594226", "type": "conversion", "used": ["package:5dd150bbe1363fb544b562a33156c64e3453206c70a1d92d3c1691b1fd5a7ddd"], "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": "6c1ec35e-fd2b-497b-b874-010e452ea0e9", "parent_hash": "5dd150bbe1363fb544b562a33156c64e3453206c70a1d92d3c1691b1fd5a7ddd", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:41594226 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:41594226' does not resolve to a declared asset", "targets"]}