Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:40735323

Lactylation prognostic signature identifies DHCR7 as a modulator of chemoresistance and immunotherapy efficacy in bladder cancer.

Frontiers in immunology · 2025 doi:10.3389/fimmu.2025.1585727

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
id
pmid:40735323
kind
science-record
content_hash
sha256:ea5b7a673852f9e2859df72a54abd85a07e37e0a204fe0f34e312069f7425443
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:52Z
updated_at
2026-11-01T10:25:52Z
generator object · 3 fields
name
corpus-assay-engine
converter
sep_to_sci_v1
source_package_schema
urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
Lactylation prognostic signature identifies DHCR7 as a modulator of chemoresistance and immunotherapy efficacy in bladder cancer.
doi
10.3389/fimmu.2025.1585727
pmid
40735323
authors
null
journal
Frontiers in immunology
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
id
claim-1
statement
the headline numerical result the paper states for its main finding
kind
qualitative
state
blocked
target object · 4 fields
value
null
unit
null
tolerance
null
source
null
evidence array · 0 items
gaps array · 2 items
[0]
abstract
[1]
authors
experiment object · 8 fields
state
partial
objective
the headline numerical result the paper states for its main finding
steps array · 3 items
[0] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:40735323
outputs array · 1 item
[0]
the published estimate, its unit and its interval
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
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.
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the source data with its provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
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:40735323
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the registered result
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
[0]
step:obtain_source_data blocked on data:not_downloaded
[1]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[2]
step:run_analysis input 'materials:the source data behind the published result in pmid:40735323' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 1 item
[0] object · 15 fields
id
source:pmid:40735323
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3389/fimmu.2025.1585727
sha256
sha256:34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3389/fimmu.2025.1585727
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
gaps array · 1 item
[0]
asset:source:pmid:40735323 not verified
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
targets
capability object · 3 fields
state
absent
requirements array · 0 items
gaps array · 1 item
[0]
capability
readiness object · 8 fields
state
partial
tier
null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 1 item
[0]
source:pmid:40735323
steps array · 1 item
[0]
read_published_estimate
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
[0]
xml
capabilities array · 0 items
data_gaps array · 1 item
[0]
source:pmid:40735323
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 2 items
[0] object · 7 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
full-text-reading-v1
prompt_hash
dfea8f3272c67f8ec25035dc814b880dc76a3c1fdf726f0441ce89d100074bf1
source_hash
34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0
raw_response_sha256
sha256:156230b25a4d7ce407ecd74ec355595125f553fd3b4ecce2074b806140f09239
raw_response_chars
7158
[1] object · 7 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
full-text-reading-v1
prompt_hash
d63dcc570cae7e5627b599644a8cad3b3fd3aa24af9acfe575ba438d92be64a4
source_hash
34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0
raw_response_sha256
sha256:12aaa927aa2feffeff425009e788131c02aadd99d80cadef47ef4d459b90de59
raw_response_chars
68291
target_providers array · 2 items
[0] object · 8 fields
provider
minimax
model
MiniMax-M3.1-Flash
prompt_version
replication-target-v2
prompt_hash
a6f73910a475c3ee29686575ecba4a97d40cae255b39ecaf1102c42ab7a75336
source_hash
34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0
raw_response
{"parent_value":9,"unit":"genes","evidence":"DHCR7 emerged as a pivotal prognostic gene from the nine gene model, prompting subsequent focused analyses.","target_result":"The lactylation prognostic signature was based on a nine-gene model, with DHCR7 identified as a pivotal prognostic gene.","number_stated":true}
reading object · 6 fields
parent_value
9
unit
genes
evidence
DHCR7 emerged as a pivotal prognostic gene from the nine gene model, prompting subsequent focused analyses.
target_result
The lactylation prognostic signature was based on a nine-gene model, with DHCR7 identified as a pivotal prognostic gene.
number_stated
true
source_locator
chars 1686-1793 of source sha256 34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0
recorded_at
2026-10-31T15:23:35.595331+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
prompt_version
replication-target-v2
prompt_hash
b4c93deff8b4b2803eb42a23d8003e1d85272771ae348f2b3e1a14b4dd1e9cce
source_hash
34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0
raw_response
<think>We need answer JSON only. Need infer registered target "headline numerical result the paper states for its main finding". Source text seems no headline numerical result. It has 10th most common, 22 genes, two clusters, nine gene model, etc. User asks single numerical result replication target has to reproduce. Likely no headline number in supplied source. Need set false, parent 0, unit evidence empty, target_result say what text states instead. Need exact JSON. Need carefully identify perhaps key finding DHCR7 enhances cisplatin and immunotherapy, no number. The text does not state effect sizes, AUC, survival etc. So number_stated false. target_result perhaps "The text states that knockdown of DHCR7 enhances the efficacy of both cisplatin chemotherapy and immunotherapy in bladder cancer." They ask if no number, say what text does state instead. Could include 10th most common? But target is headline numerical result paper states main finding. The headline finding is DHCR7, no numerical result. So target_result concise. Need ensure unit empty and evidence "". parent_value 0. JSON valid.</think> {"parent_value":0,"unit":"","evidence":"","target_result":"Knockdown of DHCR7 enhances the efficacy of both cisplatin chemotherapy and immunotherapy in bladder cancer; no numerical result for this main finding is stated.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
Knockdown of DHCR7 enhances the efficacy of both cisplatin chemotherapy and immunotherapy in bladder cancer; no numerical result for this main finding is stated.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:23:35.403903+00:00
agreement
false
disagreements object · 5 fields
target_result object · 3 fields
minimax
A nine-gene lactylation risk prediction model for forecasting bladder cancer prognosis, with DHCR7 identified as a pivotal biomarker involved in cisplatin resistance and influencing immunotherapy efficacy in bladder cancer.
minimax_alt
unknown
decisive
false
physical_methods object · 3 fields
minimax array · 5 items
[0]
in vivo experiments
[1]
in vitro experiments
[2]
DHCR7 knockdown
[3]
cisplatin chemotherapy
[4]
immunotherapy efficacy experiments
minimax_alt array · 5 items
[0]
in vivo experiments
[1]
in vitro experiments
[2]
DHCR7 knockdown
[3]
cisplatin chemotherapy
[4]
immunotherapy
decisive
false
analysis_methods object · 3 fields
minimax array · 15 items
[0]
unsupervised clustering analysis
[1]
survival analysis using Kaplan-Meier curves with log-rank tests
[2]
ROC curve analysis using the timeROC R package
[3]
CIBERSORT
[4]
single-sample gene set enrichment analysis (ssGSEA)
[5]
Gene Set Enrichment Analysis (GSEA)
[6]
Gene Set Variance Analysis (GSVA)
[7]
WGCNA
[8]
Spearman correlation analysis
[9]
two-tailed Wilcoxon test
[10]
Student’s two-tailed t-test
[11]
single-cell RNA sequencing analysis using Seurat
[12]
Harmony batch-effect integration
[13]
CellCall intercellular communication analysis
[14]
tumor mutational burden analysis using maftools
minimax_alt array · 24 items
[0]
unsupervised clustering analysis
[1]
Kaplan-Meier survival analysis
[2]
log-rank test
[3]
ROC analysis using the timeROC R package
[4]
CIBERSORT
[5]
single-sample Gene Set Enrichment Analysis (ssGSEA)
[6]
ESTIMATE
[7]
single-cell RNA-seq analysis using the Seurat R package
[8]
Harmony data integration
[9]
AUCell
[10]
UCell
[11]
singscore
[12]
ssgsea
[13]
AddModuleScore
[14]
CellCall
[15]
functional enrichment analysis using clusterProfiler
[16]
Gene Ontology (GO) enrichment analysis
[17]
Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis
[18]
GSVA
[19]
GSEA
[20]
WGCNA
[21]
two-tailed Wilcoxon test
[22]
Student’s two-tailed t-test
[23]
Spearman correlation analysis
decisive
false
statistical_method object · 3 fields
minimax
Survival differences were assessed using K-M survival curves with log-rank tests.
minimax_alt
decisive
true
number_stated object · 3 fields
minimax
true
minimax_alt
false
decisive
true
agreement_basis object · 2 fields
policy
decisive_fields
decisive_fields array · 4 items
[0]
work_type
[1]
number_stated
[2]
parent_value
[3]
unit
blinded
true
human_critique object · 5 fields
status
not_run
reviewer
null
signed_at
null
conflict_checked
false
commentary
null
stages array · 7 items
[0] object · 4 fields
key
target_materials
status
pending
reason
null
evidence
null
[1] object · 4 fields
key
independent_readings
status
blocked
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 0 items
[2] object · 4 fields
key
source_resolution
status
pending
reason
null
evidence
null
[3] object · 4 fields
key
protocol_reconstruction
status
pending
reason
null
evidence
null
[4] object · 4 fields
key
control_execution
status
pending
reason
null
evidence
null
[5] object · 4 fields
key
control_comparison
status
pending
reason
null
evidence
null
[6] object · 4 fields
key
publication
status
pending
reason
null
evidence
null
gaps array · 2 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 1 item
[0] object · 3 fields
id
package:4bb2378f984506ca44293c2d6f7990fdf7865c2c8a28c7aa41e9d8af077402a6
type
sep_package
label
SEP v1 package for pmid:40735323
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:40735323
type
conversion
used array · 1 item
[0]
package:4bb2378f984506ca44293c2d6f7990fdf7865c2c8a28c7aa41e9d8af077402a6
agent
agent:corpus-assay-engine
agents array · 3 items
[0] object · 3 fields
id
agent:minimax
type
model
label
minimax
[1] object · 3 fields
id
agent:minimax_alt
type
model
label
minimax_alt
[2] object · 3 fields
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 object · 4 fields
parent_id
324c76b7-aa61-4ca1-a677-57c5693c4457
parent_hash
4bb2378f984506ca44293c2d6f7990fdf7865c2c8a28c7aa41e9d8af077402a6
fork_of
null
gaps array · 13 items
[0]
abstract
[1]
asset:source:pmid:40735323 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.blocked
[9]
step:obtain_source_data blocked on data:not_downloaded
[10]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[11]
step:run_analysis input 'materials:the source data behind the published result in pmid:40735323' does not resolve to a declared asset
[12]
targets
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40735323", "kind": "science-record", "revision": 1, "content_hash": "sha256:ea5b7a673852f9e2859df72a54abd85a07e37e0a204fe0f34e312069f7425443", "created_at": "2026-11-01T10:25:52Z", "updated_at": "2026-11-01T10:25:52Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Lactylation prognostic signature identifies DHCR7 as a modulator of chemoresistance and immunotherapy efficacy in bladder cancer.", "doi": "10.3389/fimmu.2025.1585727", "pmid": "40735323", "authors": null, "journal": "Frontiers in immunology", "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:40735323"], "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:40735323", "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:40735323' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40735323", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2025.1585727", "sha256": "sha256:34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2025.1585727", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}], "gaps": ["asset:source:pmid:40735323 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:40735323"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40735323"]}, "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": "dfea8f3272c67f8ec25035dc814b880dc76a3c1fdf726f0441ce89d100074bf1", "source_hash": "34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0", "raw_response_sha256": "sha256:156230b25a4d7ce407ecd74ec355595125f553fd3b4ecce2074b806140f09239", "raw_response_chars": 7158}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "d63dcc570cae7e5627b599644a8cad3b3fd3aa24af9acfe575ba438d92be64a4", "source_hash": "34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0", "raw_response_sha256": "sha256:12aaa927aa2feffeff425009e788131c02aadd99d80cadef47ef4d459b90de59", "raw_response_chars": 68291}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "a6f73910a475c3ee29686575ecba4a97d40cae255b39ecaf1102c42ab7a75336", "source_hash": "34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0", "raw_response": "{\"parent_value\":9,\"unit\":\"genes\",\"evidence\":\"DHCR7 emerged as a pivotal prognostic gene from the nine gene model, prompting subsequent focused analyses.\",\"target_result\":\"The lactylation prognostic signature was based on a nine-gene model, with DHCR7 identified as a pivotal prognostic gene.\",\"number_stated\":true}", "reading": {"parent_value": 9, "unit": "genes", "evidence": "DHCR7 emerged as a pivotal prognostic gene from the nine gene model, prompting subsequent focused analyses.", "target_result": "The lactylation prognostic signature was based on a nine-gene model, with DHCR7 identified as a pivotal prognostic gene.", "number_stated": true, "source_locator": "chars 1686-1793 of source sha256 34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0"}, "recorded_at": "2026-10-31T15:23:35.595331+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "b4c93deff8b4b2803eb42a23d8003e1d85272771ae348f2b3e1a14b4dd1e9cce", "source_hash": "34568557d3d0155d08144ee5cbe9e571bdb09c92dc86135bdb00fd22f71c9ee0", "raw_response": "<think>We need answer JSON only. Need infer registered target \"headline numerical result the paper states for its main finding\". Source text seems no headline numerical result. It has 10th most common, 22 genes, two clusters, nine gene model, etc. User asks single numerical result replication target has to reproduce. Likely no headline number in supplied source. Need set false, parent 0, unit evidence empty, target_result say what text states instead. Need exact JSON. Need carefully identify perhaps key finding DHCR7 enhances cisplatin and immunotherapy, no number. The text does not state effect sizes, AUC, survival etc. So number_stated false. target_result perhaps \"The text states that knockdown of DHCR7 enhances the efficacy of both cisplatin chemotherapy and immunotherapy in bladder cancer.\" They ask if no number, say what text does state instead. Could include 10th most common? But target is headline numerical result paper states main finding. The headline finding is DHCR7, no numerical result. So target_result concise.\n\nNeed ensure unit empty and evidence \"\". parent_value 0. JSON valid.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"Knockdown of DHCR7 enhances the efficacy of both cisplatin chemotherapy and immunotherapy in bladder cancer; no numerical result for this main finding is stated.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "Knockdown of DHCR7 enhances the efficacy of both cisplatin chemotherapy and immunotherapy in bladder cancer; no numerical result for this main finding is stated.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:23:35.403903+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "A nine-gene lactylation risk prediction model for forecasting bladder cancer prognosis, with DHCR7 identified as a pivotal biomarker involved in cisplatin resistance and influencing immunotherapy efficacy in bladder cancer.", "minimax_alt": "unknown", "decisive": false}, "physical_methods": {"minimax": ["in vivo experiments", "in vitro experiments", "DHCR7 knockdown", "cisplatin chemotherapy", "immunotherapy efficacy experiments"], "minimax_alt": ["in vivo experiments", "in vitro experiments", "DHCR7 knockdown", "cisplatin chemotherapy", "immunotherapy"], "decisive": false}, "analysis_methods": {"minimax": ["unsupervised clustering analysis", "survival analysis using Kaplan-Meier curves with log-rank tests", "ROC curve analysis using the timeROC R package", "CIBERSORT", "single-sample gene set enrichment analysis (ssGSEA)", "Gene Set Enrichment Analysis (GSEA)", "Gene Set Variance Analysis (GSVA)", "WGCNA", "Spearman correlation analysis", "two-tailed Wilcoxon test", "Student’s two-tailed t-test", "single-cell RNA sequencing analysis using Seurat", "Harmony batch-effect integration", "CellCall intercellular communication analysis", "tumor mutational burden analysis using maftools"], "minimax_alt": ["unsupervised clustering analysis", "Kaplan-Meier survival analysis", "log-rank test", "ROC analysis using the timeROC R package", "CIBERSORT", "single-sample Gene Set Enrichment Analysis (ssGSEA)", "ESTIMATE", "single-cell RNA-seq analysis using the Seurat R package", "Harmony data integration", "AUCell", "UCell", "singscore", "ssgsea", "AddModuleScore", "CellCall", "functional enrichment analysis using clusterProfiler", "Gene Ontology (GO) enrichment analysis", "Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis", "GSVA", "GSEA", "WGCNA", "two-tailed Wilcoxon test", "Student’s two-tailed t-test", "Spearman correlation analysis"], "decisive": false}, "statistical_method": {"minimax": "Survival differences were assessed using K-M survival curves with log-rank tests.", "minimax_alt": "", "decisive": true}, "number_stated": {"minimax": true, "minimax_alt": false, "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:4bb2378f984506ca44293c2d6f7990fdf7865c2c8a28c7aa41e9d8af077402a6", "type": "sep_package", "label": "SEP v1 package for pmid:40735323"}], "activities": [{"id": "activity:conversion:pmid:40735323", "type": "conversion", "used": ["package:4bb2378f984506ca44293c2d6f7990fdf7865c2c8a28c7aa41e9d8af077402a6"], "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": "324c76b7-aa61-4ca1-a677-57c5693c4457", "parent_hash": "4bb2378f984506ca44293c2d6f7990fdf7865c2c8a28c7aa41e9d8af077402a6", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:40735323 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:40735323' does not resolve to a declared asset", "targets"]}