The Predictive Value of BUB1 in the Prognosis of Oral Squamous Cell Carcinoma.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39147662", "kind": "science-record", "revision": 2, "content_hash": "sha256:130df95b6631e194f65e1a68be57f3e016c1835af6de7ea75cdfb38833f3ee6e", "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 Predictive Value of BUB1 in the Prognosis of Oral Squamous Cell Carcinoma.", "doi": "10.1016/j.identj.2024.07.012", "pmid": "39147662", "authors": null, "journal": "International dental journal", "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:39147662"], "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:39147662", "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:39147662' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39147662", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.identj.2024.07.012", "sha256": "sha256:3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.identj.2024.07.012", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:39147662:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bdcd6d48ad0f3a88eae710f28f6bb4bcb81135a65cda9b627fe8146caa4d8eaa", "bytes": 673, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#tbl0001", "version": null, "note": "Clinicopathologic characteristics of patients with oral squamous cell carcinoma from The Cancer Genome Atlas database.", "structure": {"pmcid": "PMC11976542", "section_index": 3, "section_title": "Data preparation", "row_count": 13, "column_count": 4}, "table": {"label": "Table", "caption": "Clinicopathologic characteristics of patients with oral squamous cell carcinoma from The Cancer Genome Atlas database.", "rows": [["Characteristics", "", "Patients (N = 355)"], ["No.", "%"], ["Age, y", "≤60 (median)", "180", "50.70"], [">60 (median)", "175", "49.30"], ["Pathologic stage", "I", "15", "4.23"], ["II", "82", "23.10"], ["III", "71", "20.00"], ["IV", "177", "49.86"], ["Unknown", "10", "2.82"], ["Survival time", "Long (>5 y)", "33", "9.30"], ["Short (<5 y)", "322", "90.70"], ["Overall survival status", "Deceased", "155", "43.66"], ["Alive", "200", "56.34"]], "row_count": 13, "column_count": 4, "numeric_cells": 27, "header_rows": 2, "locator": "section[3]/table-wrap[1]#tbl0001"}}], "gaps": ["asset:source:pmid:39147662 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:39147662", "asset:table:pmid:39147662:1"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39147662"]}, "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": "f8929209aa6f72b11a7a9ecc932a3e5252c646e9e131c492e74199bf4a9738f2", "source_hash": "3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "raw_response_sha256": "sha256:31802050787780d7f063a903dcb13ecede847602e3e245848dcaffe04218daa6", "raw_response_chars": 4808}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "66619eab0f0c54da87aad21a6cf72ff6fa10a3460b641d821ecab51a72ea6335", "source_hash": "3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "raw_response_sha256": "sha256:8e208a0bed070a4f96154545984b5d3c984e95c055235ecd892aa9bf1a628ca2", "raw_response_chars": 36350}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "90e1ebfcfae12671e43ad46a48b137bacf408ad6e7a73a76fadd48f771fddaa7", "source_hash": "3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that high BUB1 levels may be related to poor prognosis in patients with OSCC and that BUB1 may serve as an independent predictor of prognosis, but it gives no numerical result for this registered target.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states that high BUB1 levels may be related to poor prognosis in patients with OSCC and that BUB1 may serve as an independent predictor of prognosis, but it gives no numerical result for this registered target.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:17:39.533364+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "9c4c9b1aa4b33172f6f9703fff2d2fbc37c05c5a43ee3e912c741ad6b22e85e8", "source_hash": "3532d7f49ce27ce87e8a6c901b4adc807e2ac0c629af80e0910baf221bcc3f41", "raw_response": "<think>We need answer JSON only. Need identify single numerical result replication registered target headline numerical result paper states for main finding. Source supplied perhaps truncated, no survival numerical result. Need decide perhaps headline is elevated BUB1 but no number stated. Registered target \"the headline numerical result the paper states for its main finding\". Need find exact number attached to main finding. Text abstract/results conclusions qualitative. Other numbers are methods and secondary. No headline numeric value for BUB1 expression or prognosis. Thus number_stated false, parent_value 0, unit \"\", evidence \"\", target_result say text states high BUB1 mRNA significantly upregulated in OSCC vs healthy controls and high BUB1 associated poor prognosis, but no numerical value. Need JSON valid, no markdown.\n\nBut carefully: Could target headline numerical result be one of source's numbers, perhaps 62%, 21%, etc? Main finding likely poor prognosis but no KM HR/p value. \"single numerical result that a replication ... has to reproduce.\" The supplied paper text might omit figures with exact survival data, but instruction says source only. We should false.\n\nNeed ensure target_result describes what text does state instead. Exact no evidence required if false. Could mention \"The text states...\" no numbers. JSON:\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that BUB1 mRNA levels were significantly upregulated in OSCC tissues compared with healthy controls and that high BUB1 expression was associated with poor prognosis, but it does not state a numerical result for this headline finding.\",\"number_stated\":false}\nShould evidence maybe exact quotation despite false? User explicitly says leave evidence empty if no number. Yes.\n\nNeed no invented source.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that BUB1 mRNA levels were significantly upregulated in OSCC tissues compared with healthy controls and that high BUB1 expression may be an independent indicator of poor prognosis, but it does not state a numerical value for this headline finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that BUB1 mRNA levels were significantly upregulated in OSCC tissues compared with healthy controls and that high BUB1 expression may be an independent indicator of poor prognosis, but it does not state a numerical value for this headline finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:17:41.950814+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "High BUB1 mRNA levels were associated with poor prognosis in oral squamous cell carcinoma, but the source text does not report a numerical effect estimate for this headline result.", "minimax_alt": "No headline numerical result is stated; the paper's main prognostic finding is that high expression of BUB1 may serve as an independent indicator of poor prognosis in OSCC.", "decisive": false}, "analysis_methods": {"minimax": ["Differential expression analysis using the limma R package", "Kaplan–Meier survival analysis", "Log-rank test", "Gene set enrichment analysis (GSEA)", "Pearson correlation analysis"], "minimax_alt": ["Median-based dichotomisation of BUB1 mRNA expression into high- and low-expression groups", "Differential expression analysis using the limma R package", "Kaplan–Meier survival analysis", "Log-rank test", "Gene set enrichment analysis using MSigDB c2.cp.kegg.v7.0 and GSEA software version 4.0", "Pearson correlation analysis of BUB1 or transcription-factor mRNA levels with drug IC50 values", "Copy-number variation, somatic mutation, and tumour mutation burden analysis", "Disease Ontology functional analysis"], "decisive": false}, "statistical_method": {"minimax": "Kaplan–Meier survival curve with survival differences evaluated by log-rank test", "minimax_alt": "Kaplan–Meier survival analysis with log-rank test", "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:c89937ea59905721c019b71f1e44bdab6759c9365d597de2c4d009d821dc3085", "type": "sep_package", "label": "SEP v1 package for pmid:39147662"}], "activities": [{"id": "activity:conversion:pmid:39147662", "type": "conversion", "used": ["package:c89937ea59905721c019b71f1e44bdab6759c9365d597de2c4d009d821dc3085"], "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:39147662", "parent_hash": "sha256:5f855a47781a08a6f78143c0a60711e6f7341e3ae27f771e524bfc88eacc93de", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39147662 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:39147662' does not resolve to a declared asset", "targets"]}