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pmid:39979267

HNF4A mitigates sepsis-associated lung injury by upregulating NCOR2/GR/STAB1 axis and promoting macrophage polarization towards M2 phenotype.

Cell death & disease · 2025 doi:10.1038/s41419-025-07452-z

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:39979267
kind
science-record
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sha256:1873a34e2c19cf9458d0033665eef688ddf8b3f8cbed1717e6bc67ca002eaa51
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:49Z
updated_at
2026-11-01T14:01:36Z
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
HNF4A mitigates sepsis-associated lung injury by upregulating NCOR2/GR/STAB1 axis and promoting macrophage polarization towards M2 phenotype.
doi
10.1038/s41419-025-07452-z
pmid
39979267
authors
null
journal
Cell death & disease
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:39979267
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
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[0]
the source data with its provenance
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[2] object · 13 fields
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run_analysis
order
3
name
Run the analysis programme
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analysis
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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:39979267
parameters object · 0 fields
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[0]
the registered result
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[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:39979267' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
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source:pmid:39979267
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manuscript
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xml
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application/xml
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https://doi.org/10.1038/s41419-025-07452-z
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null
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reader_required
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10.1038/s41419-025-07452-z
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null
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Source read by the package builder: full_text.
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access_state
full_text
[1] object · 16 fields
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asset:table:pmid:39979267:1
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jats-table
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section[15]/table-wrap[1]#Tab1
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null
note
primer sequences used in real-time PCR.
structure object · 5 fields
pmcid
PMC11842871
section_index
15
section_title
Real-time PCR
row_count
3
column_count
3
table object · 8 fields
label
Table 1
caption
primer sequences used in real-time PCR.
rows array · 3 items
[0] array · 3 items
[0]
primer
[1]
Forward
[2]
Reverse
[1] array · 3 items
[0]
mus Arg-1mus CD163mus CD206mus HNF4Amus NCOA2
[1]
TATCTGCCAAAGACATCGCAGCTTCGCTTGGTAGGGCAAGTGATTTGGAGGCTTGGTCGAGTGGGCCAAGTACTCATCCGTTCTCAGACTACTA
[2]
ATCACCTTGCCAATCCCCACATTGGCATCAGTCATAATAGGAAACGGGAGAACCGTGCCGAGGGACGATGTAGATGCCCATTTGTTCCTTT
[2] array · 3 items
[0]
mus Stab1mus iNOSmus MHCIImus GAPDH
[1]
TGCTTCACTCCCTCAACTCACCACCCTCCTCGTTCCAGCCAAGATCAAAGTGCGTGTTCCTACCCCCAATGTGTCCGTC
[2]
CCCAAGGCTAACTACACCCAATCCACAACTCGCTCCGCCAAGCCCGAGGAAGACTGGTCCTCAGTGTAGCCCAAGATG
locator
section[15]/table-wrap[1]#Tab1
gaps array · 1 item
[0]
asset:source:pmid:39979267 not verified
analysis object · 4 fields
state
absent
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gaps array · 2 items
[0]
method
[1]
targets
capability object · 3 fields
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absent
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[0]
capability
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partial
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null
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null
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[0]
source:pmid:39979267
[1]
asset:table:pmid:39979267:1
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[0]
read_published_estimate
must_build object · 5 fields
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[0]
xml
capabilities array · 0 items
data_gaps array · 1 item
[0]
source:pmid:39979267
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
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partial
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blocked
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minimax
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MiniMax-M3.1-Flash
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full-text-reading-v1
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1cb8ab65f2ddf8684878368a3823eb67eb965bbdcb32cf71c1fd8d406dd46ff7
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sha256:0b2608b5d5232de35e63b090d6c23c7044d7320d72d982dfc1bd46243c78fcd0
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3505
[1] object · 7 fields
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minimax_alt
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MiniMax-M3
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full-text-reading-v1
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a5c03eff9dbfc62aa27bc60194ff12264cfc39ad59699c9fbcbc099d8d4ba592
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minimax
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MiniMax-M3.1-Flash
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{"parent_value":0,"unit":"","evidence":"","target_result":"The paper states that HNF4A overexpression resulted in a higher survival rate in septic mice and amelioration of pulmonary damage, but it does not state the numerical survival rate or another headline numerical result for the main finding.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
The paper states that HNF4A overexpression resulted in a higher survival rate in septic mice and amelioration of pulmonary damage, but it does not state the numerical survival rate or another headline numerical result for the main finding.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:30:58.428773+00:00
[1] object · 8 fields
provider
minimax_alt
model
MiniMax-M3
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replication-target-v2
prompt_hash
251f9c4f4528b478c62cc4796af20bc8cbb182dd9f4e63d1704b49c6a04c0e3a
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a5c03eff9dbfc62aa27bc60194ff12264cfc39ad59699c9fbcbc099d8d4ba592
raw_response
<think>We need answer JSON only. Need determine source text contains headline numerical result for registered target? Source is abstract/methods snippets, no quantitative headline result except perhaps no survival rate numerical percentage, no main effect value. Need say number_stated false, parent_value 0, unit/evidence empty, target_result what text states instead. Need exact? Evidence empty due instruction if no number. target_result can summarize text states qualitative findings. Need not invent. JSON valid. Question nuanced: "find the single numerical result that a replication of registered target has to reproduce. Report headline number only: value paper itself states for registered target". The supplied text lacks headline numeric result. Could there be thresholds, 10 DEGs, but not headline main finding. So false. Need make target_result perhaps "The text states that HNF4A overexpression resulted in a higher survival rate in septic mice and amelioration of pulmonary damage..." Maybe mention mechanistic axis. Since asks "say in target_result what the text does state instead." Could use wording concise. Ensure no numerical claims? It says no number. We can state no numerical main-finding result; text reports qualitative outcomes. Evidence empty. Unit empty. Need perhaps exact contiguous quote? Evidence only required exact quotation containing number; absent means empty. target_result likely prose. JSON with schema.</think> {"parent_value":0,"unit":"","evidence":"","target_result":"No numerical value is stated for the main finding. The text reports that HNF4A overexpression resulted in a higher survival rate in septic mice, ameliorated pulmonary damage, reduced inflammatory-cell infiltration, impeded M1 polarization, and facilitated M2 polarization.","number_stated":false}
reading object · 6 fields
parent_value
0
unit
evidence
target_result
No numerical value is stated for the main finding. The text reports that HNF4A overexpression resulted in a higher survival rate in septic mice, ameliorated pulmonary damage, reduced inflammatory-cell infiltration, impeded M1 polarization, and facilitated M2 polarization.
number_stated
false
source_locator
null
recorded_at
2026-10-31T15:30:59.793594+00:00
agreement
false
disagreements object · 4 fields
target_result object · 3 fields
minimax
HNF4A overexpression resulted in a higher survival rate in septic mice, although no numerical survival value was reported.
minimax_alt
unclear — the closest headline result stated is that "HNF4A overexpression resulted in a higher survival rate in septic mice," but no numerical survival value or effect size is provided in the supplied text.
decisive
false
physical_methods object · 3 fields
minimax array · 5 items
[0]
Cecal ligation and puncture mouse sepsis model
[1]
Adenoviral HNF4A overexpression in mice
[2]
Western blot analysis
[3]
Flow cytometer analysis of macrophage polarization
[4]
Interleukin-4 treatment of bone marrow-derived macrophages
minimax_alt array · 6 items
[0]
Cecal ligation and puncture (CLP) mouse sepsis model
[1]
Adenovirus-vector-mediated HNF4A overexpression injected into mice
[2]
In vitro interleukin-4 treatment of bone marrow-derived macrophages
[3]
Transcriptome sequencing (mRNA-seq)
[4]
Western blot analysis
[5]
Flow cytometry analysis
decisive
false
analysis_methods object · 3 fields
minimax array · 5 items
[0]
Transcriptomic analysis of lung tissues
[1]
Differential expressed gene analysis using ∣log2FoldChange∣> 1 and −log10 (p-value) > 2.5
[2]
Gene Ontology enrichment analysis
[3]
Venn diagram analysis
[4]
Transcriptome sequencing analysis
minimax_alt array · 8 items
[0]
Transcriptomic differential-expression analysis of CLP and sham lung tissues (|log2FoldChange| > 1 and −log10(p-value) > 2.5)
[1]
Gene Ontology enrichment analysis of biological process and molecular function terms
[2]
Venn diagram overlap analysis
[3]
Western-blot band optical-density quantification using Gel-Pro-Analyzer
[4]
Flow-cytometric assessment of M1/M2 macrophage polarization
[5]
Two-group comparisons using two-tailed unpaired Student t-tests
[6]
Three-or-more-group comparisons using one-way ANOVA with post hoc Tukey's tests
[7]
Survival-curve comparison using the log-rank test and Kaplan–Meier plotting
decisive
false
statistical_method object · 3 fields
minimax
log-rank test
minimax_alt
Log-rank test for the survival comparison; Kaplan–Meier method for plotting the survival curve.
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
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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
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not_run
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null
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[0]
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type
sep_package
label
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activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:39979267
type
conversion
used array · 1 item
[0]
package:0ac1f16e4cc6c0c62af99adcf55f5d4577e06674aa56e42284d55bb8e8656f98
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[1] object · 3 fields
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agent:minimax_alt
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model
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minimax_alt
[2] object · 3 fields
id
agent:corpus-assay-engine
type
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source_run_id
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dsl_catalogue_fingerprint
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lineage object · 4 fields
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gaps array · 13 items
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abstract
[1]
asset:source:pmid:39979267 not verified
[2]
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[3]
capability
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step:obtain_source_data blocked on data:not_downloaded
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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:39979267' does not resolve to a declared asset
[12]
targets
Complete file
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"prompt_version": "full-text-reading-v1", "prompt_hash": "6be38c3f825e1f7263531219fc05bc2ac44230e621605ea77a39cc29ddd22db3", "source_hash": "a5c03eff9dbfc62aa27bc60194ff12264cfc39ad59699c9fbcbc099d8d4ba592", "raw_response_sha256": "sha256:2960135d7c0921b3b17b917a7d8d62c02a2d0a1e2e3f760cc11c6d8312768429", "raw_response_chars": 50911}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "d1191e5a3dc2da54a9a615840070deca10f4af593eff7bba10e3cac853c1353a", "source_hash": "a5c03eff9dbfc62aa27bc60194ff12264cfc39ad59699c9fbcbc099d8d4ba592", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that HNF4A overexpression resulted in a higher survival rate in septic mice and amelioration of pulmonary damage, but it does not state the numerical survival rate or another headline numerical result for the main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that HNF4A overexpression resulted in a higher survival rate in septic mice and amelioration of pulmonary damage, but it does not state the numerical survival rate or another headline numerical result for the main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:30:58.428773+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "251f9c4f4528b478c62cc4796af20bc8cbb182dd9f4e63d1704b49c6a04c0e3a", "source_hash": "a5c03eff9dbfc62aa27bc60194ff12264cfc39ad59699c9fbcbc099d8d4ba592", "raw_response": "<think>We need answer JSON only. Need determine source text contains headline numerical result for registered target? Source is abstract/methods snippets, no quantitative headline result except perhaps no survival rate numerical percentage, no main effect value. Need say number_stated false, parent_value 0, unit/evidence empty, target_result what text states instead. Need exact? Evidence empty due instruction if no number. target_result can summarize text states qualitative findings. Need not invent. JSON valid.\n\nQuestion nuanced: \"find the single numerical result that a replication of registered target has to reproduce. Report headline number only: value paper itself states for registered target\". The supplied text lacks headline numeric result. Could there be thresholds, 10 DEGs, but not headline main finding. So false.\n\nNeed make target_result perhaps \"The text states that HNF4A overexpression resulted in a higher survival rate in septic mice and amelioration of pulmonary damage...\" Maybe mention mechanistic axis. Since asks \"say in target_result what the text does state instead.\" Could use wording concise. Ensure no numerical claims? It says no number. We can state no numerical main-finding result; text reports qualitative outcomes. Evidence empty. Unit empty.\n\nNeed perhaps exact contiguous quote? Evidence only required exact quotation containing number; absent means empty. target_result likely prose. JSON with schema.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"No numerical value is stated for the main finding. The text reports that HNF4A overexpression resulted in a higher survival rate in septic mice, ameliorated pulmonary damage, reduced inflammatory-cell infiltration, impeded M1 polarization, and facilitated M2 polarization.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "No numerical value is stated for the main finding. The text reports that HNF4A overexpression resulted in a higher survival rate in septic mice, ameliorated pulmonary damage, reduced inflammatory-cell infiltration, impeded M1 polarization, and facilitated M2 polarization.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:30:59.793594+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "HNF4A overexpression resulted in a higher survival rate in septic mice, although no numerical survival value was reported.", "minimax_alt": "unclear — the closest headline result stated is that \"HNF4A overexpression resulted in a higher survival rate in septic mice,\" but no numerical survival value or effect size is provided in the supplied text.", "decisive": false}, "physical_methods": {"minimax": ["Cecal ligation and puncture mouse sepsis model", "Adenoviral HNF4A overexpression in mice", "Western blot analysis", "Flow cytometer analysis of macrophage polarization", "Interleukin-4 treatment of bone marrow-derived macrophages"], "minimax_alt": ["Cecal ligation and puncture (CLP) mouse sepsis model", "Adenovirus-vector-mediated HNF4A overexpression injected into mice", "In vitro interleukin-4 treatment of bone marrow-derived macrophages", "Transcriptome sequencing (mRNA-seq)", "Western blot analysis", "Flow cytometry analysis"], "decisive": false}, "analysis_methods": {"minimax": ["Transcriptomic analysis of lung tissues", "Differential expressed gene analysis using ∣log2FoldChange∣> 1 and −log10 (p-value) > 2.5", "Gene Ontology enrichment analysis", "Venn diagram analysis", "Transcriptome sequencing analysis"], "minimax_alt": ["Transcriptomic differential-expression analysis of CLP and sham lung tissues (|log2FoldChange| > 1 and −log10(p-value) > 2.5)", "Gene Ontology enrichment analysis of biological process and molecular function terms", "Venn diagram overlap analysis", "Western-blot band optical-density quantification using Gel-Pro-Analyzer", "Flow-cytometric assessment of M1/M2 macrophage polarization", "Two-group comparisons using two-tailed unpaired Student t-tests", "Three-or-more-group comparisons using one-way ANOVA with post hoc Tukey's tests", "Survival-curve comparison using the log-rank test and Kaplan–Meier plotting"], "decisive": false}, "statistical_method": {"minimax": "log-rank test", "minimax_alt": "Log-rank test for the survival comparison; Kaplan–Meier method for plotting the survival curve.", "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:0ac1f16e4cc6c0c62af99adcf55f5d4577e06674aa56e42284d55bb8e8656f98", "type": "sep_package", "label": "SEP v1 package for pmid:39979267"}], "activities": [{"id": "activity:conversion:pmid:39979267", "type": "conversion", "used": ["package:0ac1f16e4cc6c0c62af99adcf55f5d4577e06674aa56e42284d55bb8e8656f98"], "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:39979267", "parent_hash": "sha256:ac54179ed04682156e9f192bac66e8f748bc5a99689fa62131cb21794bf85504", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39979267 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:39979267' does not resolve to a declared asset", "targets"]}