← All .science files
pmid:41510117
Multivesicular body subunit 12B (MVB12B) overexpression represses proliferation and migration in bladder urothelial carcinoma.
Translational cancer research · 2025 doi:10.21037/tcr-2025-1498
Paper
partial
Experiment
partial
Data
partial
Analysis
absent
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
generator object · 3 fields
paper object · 10 fields
claims array · 1 item
gaps array · 2 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 3 items
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 1 field
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 28 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
[17] array · 4 items
[18] array · 4 items
[19] array · 4 items
[20] array · 4 items
[21] array · 4 items
[22] array · 4 items
[23] array · 4 items
[24] array · 4 items
[25] array · 4 items
[26] array · 4 items
[27] array · 4 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 8 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 16 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 3 items
[14] array · 4 items
[15] array · 4 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 11 items
[0] array · 3 items
[1] array · 3 items
[2] array · 3 items
[3] array · 3 items
[4] array · 3 items
[5] array · 3 items
[6] array · 3 items
[7] array · 3 items
[8] array · 3 items
[9] array · 3 items
[10] array · 3 items
gaps array · 1 item
capability object · 3 fields
readiness object · 8 fields
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 5 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 1 item
review object · 5 fields
machine_critique object · 7 fields
providers array · 0 items
target_providers array · 0 items
disagreements array · 0 items
agreement_basis object · 2 fields
decisive_fields array · 4 items
human_critique object · 5 fields
stages array · 7 items
[0] object · 4 fields
[1] object · 4 fields
evidence object · 1 field
provider_errors array · 4 items
[0] object · 4 fields
[1] object · 4 fields
[2] object · 4 fields
[3] object · 4 fields
[2] object · 4 fields
[3] object · 4 fields
[4] object · 4 fields
[5] object · 4 fields
[6] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 1 item
activities array · 1 item
agents array · 1 item
lineage object · 4 fields
gaps array · 14 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41510117", "kind": "science-record", "revision": 2, "content_hash": "sha256:e472e9334104c1b971fd264b6c217b2d79c0220f61c86b352aa1ff02b5a4b43b", "created_at": "2026-11-01T10:25:54Z", "updated_at": "2026-11-01T14:01:53Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Multivesicular body subunit 12B (MVB12B) overexpression represses proliferation and migration in bladder urothelial carcinoma.", "doi": "10.21037/tcr-2025-1498", "pmid": "41510117", "authors": null, "journal": "Translational cancer research", "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:41510117"], "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:41510117", "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:41510117' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41510117", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-2025-1498", "sha256": "sha256:96e9e37f383a3f93f0353b6a8dee59fe72c6785a0fef37fff33543fdbdf9ce4e", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-2025-1498", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:41510117:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6b396ac949a02e94092076aa06a3e7fccc979acc3d71c204fe9cd8112f5b053d", "bytes": 1274, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#t1", "version": null, "note": "Clinicopathological features for BLCA patients in relation to MVB12B expression level", "structure": {"pmcid": "PMC12776198", "section_index": 18, "section_title": "Relationship between MVB12B expression and clinicopathologic characteristics of BLCA", "row_count": 28, "column_count": 4}, "table": {"label": "Table 1", "caption": "Clinicopathological features for BLCA patients in relation to MVB12B expression level", "rows": [["Characteristics", "Low expression of MVB12B", "High expression of MVB12B", "P value"], ["Gender", "", "", ">0.99"], ["Male", "152 (36.9)", "152 (36.9)", ""], ["Female", "54 (13.1)", "54 (13.1)", ""], ["Age", "", "", "0.32"], ["≤70 years", "111 (26.9)", "121 (29.4)", ""], [">70 years", "95 (23.1)", "85 (20.6)", ""], ["Pathologic T stage", "", "", "0.01"], ["T1", "0 (0.0)", "5 (1.3)", ""], ["T2", "55 (14.6)", "63 (16.7)", ""], ["T3", "105 (27.8)", "91 (24.1)", ""], ["T4", "38 (10.1)", "21 (5.6)", ""], ["Pathologic N stage", "", "", "0.003"], ["N0", "107 (29.1)", "131 (35.6)", ""], ["N1", "27 (7.3)", "19 (5.2)", ""], ["N2", "50 (13.6)", "27 (7.3)", ""], ["N3", "6 (1.6)", "1 (0.3)", ""], ["Pathologic M stage", "", "", "0.14"], ["M0", "100 (47.2)", "101 (47.6)", ""], ["M1", "8 (3.8)", "3 (1.4)", ""], ["Pathologic stage", "", "", "<0.001"], ["Stage I", "0 (0.0)", "4 (1.0)", ""], ["Stage II", "51 (12.4)", "78 (19.0)", ""], ["Stage III", "70 (17.1)", "72 (17.6)", ""], ["Stage IV", "85 (20.7)", "50 (12.2)", ""], ["Histologic grade", "", "", "0.003"], ["Low grade", "4 (1.0)", "17 (4.2)", ""], ["High grade", "202 (49.4)", "186 (45.5)", ""]], "row_count": 28, "column_count": 4, "numeric_cells": 51, "header_rows": 1, "locator": "section[18]/table-wrap[1]#t1"}}, {"id": "asset:table:pmid:41510117:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c41d707f046a95fa9d3576f85c8daab05be717ca42557a8f7bcd8b9f3381a699", "bytes": 869, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[2]#t2", "version": null, "note": "MVB12B expression correlates with clinicopathological features in BLCA: a univariate logistic regression analysis", "structure": {"pmcid": "PMC12776198", "section_index": 18, "section_title": "Relationship between MVB12B expression and clinicopathologic characteristics of BLCA", "row_count": 8, "column_count": 4}, "table": {"label": "Table 2", "caption": "MVB12B expression correlates with clinicopathological features in BLCA: a univariate logistic regression analysis", "rows": [["Characteristics", "Total (n)", "OR (95% CI)", "P value"], ["Gender (female vs. male)", "412", "1.000 (0.645–1.551)", ">0.99"], ["Age (>70 vs. ≤70 years)", "412", "0.821 (0.556–1.212)", "0.32"], ["Pathologic T stage (T3 & T4 vs. T1 & T2)", "378", "0.633 (0.411–0.977)", "0.04"], ["Pathologic N stage (N1 & N2 & N3 vs. N0)", "368", "0.463 (0.298–0.718)", "<0.001"], ["Pathologic M stage (M1 vs. M0)", "212", "0.371 (0.096–1.440)", "0.15"], ["Pathologic stage (stage III & IV vs. stage I & II)", "410", "0.490 (0.321–0.747)", "<0.001"], ["Histologic grade (high grade vs. low grade)", "409", "0.217 (0.072–0.656)", "0.007"]], "row_count": 8, "column_count": 4, "numeric_cells": 23, "header_rows": 1, "locator": "section[18]/table-wrap[2]#t2"}}, {"id": "asset:table:pmid:41510117:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a6690e53d144fdb3709d7b39eb3e6dbf0b21917f0a3afb431fea94bc243130ac", "bytes": 825, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#t3", "version": null, "note": "The relationship between the expression of MVB12B and clinical features of BLCA", "structure": {"pmcid": "PMC12776198", "section_index": 20, "section_title": "MVB12B expression is significantly decreased in BLCA cell lines and tissues", "row_count": 16, "column_count": 4}, "table": {"label": "Table 3", "caption": "The relationship between the expression of MVB12B and clinical features of BLCA", "rows": [["Characteristics", "Positive", "Negative", "P value"], ["Gender", "", "", "0.57"], ["Male", "22 (34.9)", "22 (34.9)", ""], ["Female", "11 (17.5)", "8 (12.7)", ""], ["Age", "", "", "0.69"], ["≤70 years", "25 (39.7)", "24 (38.1)", ""], [">70 years", "8 (12.7)", "6 (9.5)", ""], ["Pathologic stage", "", "", "0.28"], ["Stage I & II", "26 (41.3)", "20 (31.7)", ""], ["Stage III & IV", "7 (11.1)", "10 (15.9)", ""], ["Histologic grade", "", "", "0.03"], ["Low grade", "12 (19.0)", "3 (4.8)", ""], ["High grade", "21 (33.3)", "27 (42.9)", ""], ["BLCA vs. non-tumor", "", "0.04"], ["BLCA", "33 (40.7)", "30 (37.0)", ""], ["Non-tumor", "15 (18.5)", "3 (3.7)", ""]], "row_count": 16, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[20]/table-wrap[1]#t3"}}, {"id": "asset:table:pmid:41510117:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1fd4897e0c5f0d76028864501d220b09e53a70197a82bca517d74bc64dc2424b", "bytes": 2729, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#t4", "version": null, "note": "Functions and corresponding scores of MVB12B-interacting proteins", "structure": {"pmcid": "PMC12776198", "section_index": 22, "section_title": "PPI network and GSEA of MVB12B", "row_count": 11, "column_count": 3}, "table": {"label": "Table 4", "caption": "Functions and corresponding scores of MVB12B-interacting proteins", "rows": [["Protein", "Function", "Combined score"], ["TSG101", "Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Binds to ubiquitinated cargo proteins and is required for the sorting of endocytic ubiquitinated cargos into MVBs. May be involved in cell growth and differentiation. Acts as a negative growth regulator", "0.999"], ["VPS25", "Component of the ESCRT-II complex, which is required for MVB formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation", "0.954"], ["VPS37B", "Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for the sorting of endocytic ubiquitinated cargos into MVBs. May be involved in cell growth and differentiation", "0.997"], ["VPS37C", "Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for the sorting of endocytic ubiquitinated cargos into MVBs. May be involved in cell growth and differentiation", "0.978"], ["VPS37A", "Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for the sorting of endocytic ubiquitinated cargos into MVBs. May be involved in cell growth and differentiation", "0.992"], ["VPS37D", "Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for the sorting of endocytic ubiquitinated cargos into MVBs. May be involved in cell growth and differentiation", "0.975"], ["SNF8", "Component of the ESCRT-II, which is required for MVB formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation", "0.954"], ["VPS36", "Component of the ESCRT-II complex, which is required for MVB formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. Its ability to bind ubiquitin probably plays a role in endosomal sorting of ubiquitinated cargo proteins by ESCRT complexes", "0.957"], ["UBAP1", "Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Binds to ubiquitinated cargo proteins and is required for the sorting of endocytic ubiquitinated cargos into MVBs. Plays a role in the proteasomal degradation of ubiquitinated cell-surface proteins, such as EGFR and BST2", "0.966"], ["VPS28", "Component of the ESCRT-I complex, a regulator of vesicular trafficking process", "0.999"]], "row_count": 11, "column_count": 3, "numeric_cells": 18, "header_rows": 1, "locator": "section[22]/table-wrap[1]#t4"}}], "gaps": ["asset:source:pmid:41510117 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:41510117", "asset:table:pmid:41510117:1", "asset:table:pmid:41510117:2", "asset:table:pmid:41510117:3", "asset:table:pmid:41510117:4"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41510117"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "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": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"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", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:ef43a86ed466fbec5f42e12bb2b6c08a6315a94c3cb2ac16de74c267989d0ba0", "type": "sep_package", "label": "SEP v1 package for pmid:41510117"}], "activities": [{"id": "activity:conversion:pmid:41510117", "type": "conversion", "used": ["package:ef43a86ed466fbec5f42e12bb2b6c08a6315a94c3cb2ac16de74c267989d0ba0"], "agent": "agent:corpus-assay-engine"}], "agents": [{"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:41510117", "parent_hash": "sha256:5e8d88c9659425a3f068f59fc06c92cca3905ac0d80c06163d760341b557e334", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:41510117 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "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:41510117' does not resolve to a declared asset", "targets"]}