Prognostic biomarker PSMD14 facilitates bladder cancer tumorigenesis and progression by regulating Nucleolin-YAP1 axis.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40121994", "kind": "science-record", "revision": 1, "content_hash": "sha256:add0f1f2b21e1b195720090083663a1c4da8c9ddcc003c2c7ecc5ae0b44930e0", "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": "Prognostic biomarker PSMD14 facilitates bladder cancer tumorigenesis and progression by regulating Nucleolin-YAP1 axis.", "doi": "10.1016/j.tranon.2025.102370", "pmid": "40121994", "authors": null, "journal": "Translational oncology", "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:40121994"], "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:accession_absent", "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:40121994", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent", "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:40121994' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40121994", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.tranon.2025.102370", "sha256": "sha256:0e30d4a6bcc27acfc6f51e9e3cf9380fa9bfb1f23e86d4da344ced28cbb93e68", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.tranon.2025.102370", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40121994 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:40121994"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40121994"]}, "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": "9b6d8bb5a4dc4b2db3029f2a1ffdc5ac670838f176bfd954b16e7f5f731de85c", "source_hash": "0e30d4a6bcc27acfc6f51e9e3cf9380fa9bfb1f23e86d4da344ced28cbb93e68", "raw_response_sha256": "sha256:232d128d95b9ce7289dd9c6187a3275f9f3a86401d7a261a855c49bdbeaabb84", "raw_response_chars": 2437}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "fbcb3df746d030740a76696894279c8aa5521c42ee656d14fb13a470ed90bf43", "source_hash": "0e30d4a6bcc27acfc6f51e9e3cf9380fa9bfb1f23e86d4da344ced28cbb93e68", "raw_response_sha256": "sha256:9a11877a96c04996fad5a1f0b59af1bf0fe753b42c0255e6f53883911be67416", "raw_response_chars": 23290}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "0160d9b47c9fe0b544b6777b746279f87a6e7b1a2f0dd1115cf8d2c2600ee880", "source_hash": "0e30d4a6bcc27acfc6f51e9e3cf9380fa9bfb1f23e86d4da344ced28cbb93e68", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The source text states no numerical result for the registered target; it only lists qualitative findings and statistical-analysis methods.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The source text states no numerical result for the registered target; it only lists qualitative findings and statistical-analysis methods.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:34:34.520273+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "94979f35385c586bb5b49a9433ee309a9659f851880826140f900a2e7aae5c40", "source_hash": "0e30d4a6bcc27acfc6f51e9e3cf9380fa9bfb1f23e86d4da344ced28cbb93e68", "raw_response": "<think>We need answer JSON only. Need inspect source. Registered target headline numerical result paper states main finding. Source only abstract bullet conclusions and stats. No numerical result for main finding. Need number_stated false, parent 0, unit/evidence empty, target_result say text does state instead. Need perhaps describe findings rather than numerical. Exact schema. Ensure no invention. target_result perhaps \"The text states that PSMD14 was overexpressed in bladder cancer and drove malignancy; via deubiquitinating NCL, it increased NCL protein stability and facilitated bladder cancer growth, progression, and cisplatin resistance; upregulated NCL was involved in malignant behaviors; and via NCL, PSMD14 improved YAP1 mRNA stability to facilitate growth, progression, and cisplatin resistance. It reports no headline numerical result for the main finding.\" Evidence empty per instructions. Since no exact number. JSON valid.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states that PSMD14 was overexpressed in bladder cancer and drove malignancy; PSMD14 deubiquitinated NCL, increased NCL protein stability, and facilitated bladder cancer growth, progression, and cisplatin resistance; upregulated NCL was involved in malignant behaviors; and PSMD14 improved YAP1 mRNA stability through NCL. No headline numerical result for the main finding is stated.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states that PSMD14 was overexpressed in bladder cancer and drove malignancy; PSMD14 deubiquitinated NCL, increased NCL protein stability, and facilitated bladder cancer growth, progression, and cisplatin resistance; upregulated NCL was involved in malignant behaviors; and PSMD14 improved YAP1 mRNA stability through NCL. No headline numerical result for the main finding is stated.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:34:34.082175+00:00"}], "agreement": false, "disagreements": {"work_type": {"minimax": "analysis_plus_physical_validation", "minimax_alt": "physical_data_generation", "decisive": true}, "physical_methods": {"minimax": ["three independent experiments"], "minimax_alt": [], "decisive": false}, "statistical_method": {"minimax": "Paired or unpaired Student's t-tests were performed to analyze the differences between two groups. Pearson's correlation test was used to determine the association between two groups.", "minimax_alt": "Paired or unpaired Student's t-tests", "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:0299e624f70705f517a13832ccb170d7dc22a2af17a64a7ce472d25e8aad6102", "type": "sep_package", "label": "SEP v1 package for pmid:40121994"}], "activities": [{"id": "activity:conversion:pmid:40121994", "type": "conversion", "used": ["package:0299e624f70705f517a13832ccb170d7dc22a2af17a64a7ce472d25e8aad6102"], "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": "d12fda34-83ae-430a-adbb-fe83a7bd04ad", "parent_hash": "0299e624f70705f517a13832ccb170d7dc22a2af17a64a7ce472d25e8aad6102", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40121994 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:accession_absent", "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:40121994' does not resolve to a declared asset", "targets"]}