Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39915534", "kind": "science-record", "revision": 1, "content_hash": "sha256:614a2f9952a4a055e0f7c51608f82273c945c0169ff8e52d20bb6dfe2c85d865", "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": "Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma.", "doi": "10.1038/s41598-025-88120-2", "pmid": "39915534", "authors": null, "journal": "Scientific reports", "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": 18.0, "unit": "microbial genera", "tolerance": null, "source": "chars 779-867 of source sha256 3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458"}, "evidence": [{"asset": "source:pmid:39915534", "locator": "chars 779-867 of source sha256 3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "quote": "18 microbial genera were found to be significantly associated with RFS in LUSC patients."}]}], "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:39915534"], "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:39915534", "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:39915534' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39915534", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-88120-2", "sha256": "sha256:3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-88120-2", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:39915534 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, 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"prompt_version": "full-text-reading-v1", "prompt_hash": "794f7960016dea602082eadfac06bec410d4211c864bf81c89453f643991a0e0", "source_hash": "3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "raw_response_sha256": "sha256:36aefab4b8208eaf32a1cb022883b893aadb335adfe1ae265286824c0e4b43b8", "raw_response_chars": 44171}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "8719c88a18edad84f5bcb5e7eec78055daef7fee8e35a74ad94359792d70c484", "source_hash": "3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "raw_response": "{\"parent_value\":18,\"unit\":\"microbial genera\",\"evidence\":\"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\",\"target_result\":\"The paper states that 18 microbial genera were significantly associated with recurrence-free survival (RFS) in LUSC patients.\",\"number_stated\":true}", "reading": {"parent_value": 18, "unit": "microbial genera", "evidence": "18 microbial genera were found to be significantly associated with RFS in LUSC patients.", "target_result": "The paper states that 18 microbial genera were significantly associated with recurrence-free survival (RFS) in LUSC patients.", "number_stated": true, "source_locator": "chars 779-867 of source sha256 3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458"}, "recorded_at": "2026-10-31T15:29:26.675986+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "e73fb191414a2d3476f6aefde418bddbe714bd915ec1219a60c1d36f7d436b52", "source_hash": "3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458", "raw_response": "<think>We need answer JSON only. Need inspect supplied text. Asked single numerical result headline for main finding. Source only abstract + methods, no results section except abstract: \"18 microbial genera were found significantly associated...\" \"four mRNA...\" Is headline numerical result perhaps 18 microbial genera? Registered target vague \"headline numerical result the paper states for its main finding\". Need identify number stated for main finding. Likely 18 microbial genera? Could be four mRNA. Need determine perhaps paper title, main finding is microbial and genetic markers; abstract highlights \"18 microbial genera were found to be significantly associated with RFS...\" and \"finally identifying four mRNA...\" Which single numerical result replication target? They ask headline number only, value paper itself states for registered target. The source text likely omitted Results due truncated? We can only extract. Registered target defined generically. Need perhaps answer 18 microbial genera because first/headline count, main finding. Need quote exact contiguous clause containing number and attribution. Evidence exact quote. Unit \"microbial genera\" perhaps unit. parent_value 18. target_result could say \"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\" number_stated true. Evidence same exact quote. But perhaps headline numerical result is four mRNA? Let's carefully parse.\n\nPrompt probably benchmark asks identify \"single numerical result that a replication of the registered target has to reproduce.\" Registered target is \"the headline numerical result the paper states for its main finding\". In source, abstract likely has key numbers, and methods. The paper's title exploring prognostic role. Main finding could involve risk score model with 18 microbial genera and 4 mRNAs. Which is headline? Maybe the benchmark expects article's key finding metric (e.g., AUC) but supplied source lacks result values. Yet abstract says counts. They want single numerical result, likely \"18 microbial genera\". Let's reason wording: \"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.\" This task generated with target maybe specific claim hidden in source. Registered target description generic, and source may contain exact number. Need output.\n\nCould select 18 microbial genera as headline because sentence \"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\" This is main finding and a count. Unit perhaps \"microbial genera\" (not a physical unit). JSON unit must string. Evidence exact contiguous quote. target_result perhaps concise. Ensure exact punctuation. Source has:\n\"18 microbial genera were found to be significantly associated with RFS in LUSC patients. The microbial signature built with these microbial genera, exhibited robust predictive accuracy in both the training and validation datasets. Furthermore, hub mRNA between high- and low-risk groups were selected by XGBOOST and intersect with mRNAs screened by univariate Cox regression analysis, finally identifying four mRNA significantly associated with LUSC prognosis.\"\n\nCould evidence quote whole clause/sentence. They request headline number only perhaps target_result could be \"18 microbial genera\". Need no extra prose outside JSON.\n\nBut maybe main headline is four mRNA because final main finding. Which one would replication need reproduce? Let's inspect title and abstract ordering. Main finding: microbiome risk score based on 18 genera. Abstract says 18 microbial genera associated; microbial signature predictive. Then four mRNA. If asked \"single numerical result\" perhaps likely number in paper's title? No title no number. They may expect first/most headline number = 18. \"the headline numerical result the paper states for its main finding\" and evidence must attribution. The abstract's central finding is risk score model from 18 genera, likely count.\n\nCould unit be \"microbial genera\" exactly. The number is count. parent_value 18. target_result perhaps \"18 microbial genera were significantly associated with recurrence-free survival (RFS) in LUSC patients.\" But exact source calls RFS; don't expand unless target result no evidence constraint? Better mirror.\n\nNeed valid JSON, escaped perhaps no issue.</think>\n\n{\"parent_value\":18,\"unit\":\"microbial genera\",\"evidence\":\"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\",\"target_result\":\"18 microbial genera were found to be significantly associated with RFS in LUSC patients.\",\"number_stated\":true}", "reading": {"parent_value": 18, "unit": "microbial genera", "evidence": "18 microbial genera were found to be significantly associated with RFS in LUSC patients.", "target_result": "18 microbial genera were found to be significantly associated with RFS in LUSC patients.", "number_stated": true, "source_locator": "chars 779-867 of source sha256 3b47c26a959031762d2646144588cff641f10eada2703cc5e9f86d1064ea2458"}, "recorded_at": "2026-10-31T15:29:30.240024+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "18 microbial genera were significantly associated with recurrence-free survival (RFS) in LUSC patients.", "minimax_alt": "18 microbial genera were found to be significantly associated with RFS in LUSC patients.", "decisive": false}, "analysis_methods": {"minimax": ["univariate Cox proportional hazards analysis", "least absolute shrinkage and selection operator (LASSO) regression", "10-fold cross-validation", "multivariate Cox regression analysis"], "minimax_alt": ["univariate Cox proportional hazards analysis", "LASSO regression", "10-fold cross-validation", "multivariate Cox regression analysis"], "decisive": false}, "statistical_method": {"minimax": "univariate Cox regression analysis combined with the least absolute contraction and selection operator (LASSO) regression", "minimax_alt": "Univariate Cox proportional hazards analysis combined with LASSO regression, with the LASSO regularization parameter selected by 10-fold cross-validation", "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:151e519206a3fff4f44a32f5e10f09db321b5bd8832ab8ef095bd0faa01b0de8", "type": "sep_package", "label": "SEP v1 package for pmid:39915534"}], "activities": [{"id": "activity:conversion:pmid:39915534", "type": "conversion", "used": ["package:151e519206a3fff4f44a32f5e10f09db321b5bd8832ab8ef095bd0faa01b0de8"], "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": "e9423780-c4b4-4514-8965-efa167158bd1", "parent_hash": "151e519206a3fff4f44a32f5e10f09db321b5bd8832ab8ef095bd0faa01b0de8", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:39915534 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:39915534' does not resolve to a declared asset", "targets"]}