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

pmid:29552626

Neutrophil-Hepatic Stellate Cell Interactions Promote Fibrosis in Experimental Steatohepatitis.

Zhou Zhou · Ming-Jiang Xu · Yan Cai · Wei Wang · Joy X Jiang · Zoltan V Varga · Dechun Feng · Pal Pacher · George Kunos · Natalie J Torok · Bin Gao

Cellular and molecular gastroenterology and hepatology · 2018 doi:10.1016/j.jcmgh.2018.01.003

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

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:29552626
kind
science-record
content_hash
sha256:8aae2da988ee763a7ae659f35fd18662748696f9a028363428b19d437471fde4
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:32Z
updated_at
2026-11-01T22:43:19Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Neutrophil-Hepatic Stellate Cell Interactions Promote Fibrosis in Experimental Steatohepatitis.
doi
10.1016/j.jcmgh.2018.01.003
pmid
29552626
authors array · 11 items
[0]
Zhou Zhou
[1]
Ming-Jiang Xu
[2]
Yan Cai
[3]
Wei Wang
[4]
Joy X Jiang
[5]
Zoltan V Varga
[6]
Dechun Feng
[7]
Pal Pacher
[8]
George Kunos
[9]
Natalie J Torok
[10]
Bin Gao
journal
Cellular and molecular gastroenterology and hepatology
year
2018
abstract
BACKGROUND & AIMS: Hepatic infiltration of neutrophils is a hallmark of steatohepatitis; however, the role of neutrophils in the progression of steatohepatitis remains unknown. METHODS: A clinically relevant mouse model of steatohepatitis induced by high-fat diet (HFD) plus binge ethanol feeding was used. Liver fibrosis was examined. In vitro cell culture was used to analyze the interaction of hepatic stellate cells (HSCs) and neutrophils. RESULTS: HFD plus one binge ethanol (HFD+1B) feeding induced significant hepatic neutrophil infiltration, liver injury, and fibrosis. HFD plus multiple binges of ethanol (HFD+mB) caused more pronounced liver fibrosis. Microarray analyses showed that the most highly activated signaling pathway in this HFD+1B model was related to liver fibrosis and HSC activation. Blockade of chemokine (C-X-C motif) ligand 1 or intercellular adhesion molecule-1 expression reduced hepatic neutrophil infiltration and ameliorated liver injury and fibrosis. Disruption of the p47phox gene (also called neutrophil cytosolic factor 1), a critical component of reactive oxygen species producing nicotinamide adenine dinucleotide phosphate-oxidase in neutrophils, diminished HFD+1B-induced liver injury and fibrosis. Co-culture of HSCs with neutrophils, but not with neutrophil apoptotic bodies, induced HSC activation and prolonged neutrophil survival. Mechanistic studies showed that activated HSCs produce granulocyte-macrophage colony-stimulating factor and interleukin-15 to prolong the survival of neutrophils, which may serve as a positive forward loop to promote liver damage and fibrosis. CONCLUSIONS: The current data from a mouse model of HFD plus binge ethanol feeding suggest that obesity and binge drinking synergize to promote liver fibrosis, which is partially mediated via the interaction of neutrophils and HSCs. Microarray data in this article have been uploaded to NCBI's Gene Expression Omnibus (GEO accession number: GSE98153).
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:29552626
locator
sections[17] "Statistical Analysis" paragraph 2
quote
Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:29552626
locator
sections[8] "Microarray Analyses of Mouse Liver Samples" paragraph 2
quote
Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153).
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Headline result: Obesity and binge drinking synergistically promote liver fibrosis, partially through interactions between neutrophils and hepatic stellate cells. Statistical method: two-group comparisons used an unpaired t test; multiple-group comparisons used one-way analysis of variance followed by the Tukey post hoc test, with P < .05 considered significant. Route to source data: the microarray data were uploaded to NCBI’s Gene Expression Omnibus under accession GSE98153, and all authors had access to the study data.
kind
qualitative
target
null
evidence array · 4 items
[0] object · 3 fields
asset
source:pmid:29552626
locator
sections[0] "Abstract" paragraph 4
quote
The current data from a mouse model of HFD plus binge ethanol feeding suggest that obesity and binge drinking synergize to promote liver fibrosis, which is partially mediated via the interaction of neutrophils and HSCs.
[1] object · 3 fields
asset
source:pmid:29552626
locator
sections[17] "Statistical Analysis" paragraph 2
quote
Data are shown as means ± SEM. Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test. P < .05 was considered a significant difference.
[2] object · 3 fields
asset
source:pmid:29552626
locator
sections[0] "Abstract" paragraph 4
quote
Microarray data in this article have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153).
[3] object · 3 fields
asset
source:pmid:29552626
locator
sections[18] "Data" paragraph 2
quote
All authors had access to the study data and reviewed and approved the final manuscript.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
Headline result: Obesity and binge drinking synergistically promote liver fibrosis, partially through interactions between neutrophils and hepatic stellate cells. Statistical method: two-group comparisons used an unpaired t test; multiple-group comparisons used one-way analysis of variance followed by the Tukey post hoc test, with P < .05 considered significant. Route to source data: the microarray data were uploaded to NCBI’s Gene Expression Omnibus under accession GSE98153, and all authors had access to the study data.
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:29552626
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
complete
blocked_on
null
description
The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE98153
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the published analysis
kind
analysis
state
complete
blocked_on
null
description
Apply the paper's statistical method to the resolved series and compare the result with the published target.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE98153
outputs array · 1 item
[0]
the replicated result and its comparison
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 · 0 items
data object · 3 fields
state
partial
assets array · 3 items
[0] object · 15 fields
id
source:pmid:29552626
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.jcmgh.2018.01.003
sha256
sha256:acb0a1a863a5c4eae2a1cd6682bb9647dbb11ea2547a3df3492e6f3c5b14096c
bytes
55043
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.jcmgh.2018.01.003
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC5852390
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE98153
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98153
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE98153
version
null
note
Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153).
access_statement_kind
repository_route_statement
sample_accessions array · 17 items
[0]
GSM2588732
[1]
GSM2588733
[2]
GSM2588734
[3]
GSM2588735
[4]
GSM2588736
[5]
GSM2588737
[6]
GSM2588738
[7]
GSM2588739
[8]
GSM2588740
[9]
GSM2588741
[10]
GSM2588742
[11]
GSM2588743
[12]
GSM2588744
[13]
GSM2588745
[14]
GSM2588746
[15]
GSM2588747
[16]
GSM2588748
sample_count
17
group_sizes
null
group_sizes_basis
null
platform
7202
taxon
Mus musculus
title
Interaction of neutrophils and hepatic stellate cells promotes fibrosis in a mouse model of steatohepatitis
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:29552626:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:d8caa93335b250a9d80f99d0218bdc3d8720b3c8b963801972178cd0dc02dc3a
bytes
1365
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[16]/table-wrap[1]#tbl1
version
null
note
Real-Time Quantitative PCR Primer Sequence Used in the Present Study
structure object · 5 fields
pmcid
PMC5852390
section_index
16
section_title
Real-Time Quantitative PCR
row_count
19
column_count
3
table object · 8 fields
label
Table 1
caption
Real-Time Quantitative PCR Primer Sequence Used in the Present Study
rows array · 19 items
[0] array · 3 items
[0]
Gene name
[1]
Forward
[2]
Reverse
[1] array · 3 items
[0]
Acta2 (encodes α-SMA)
[1]
TCCTGACGCTGAAGTATCCGATA
[2]
GGTGCCAGATCTTTTCCATGTC
[2] array · 3 items
[0]
collagen 1a1
[1]
TAGGCCATTGTGTATGCAGC
[2]
ACATGTTCAGCTTTGTGGACC
[3] array · 3 items
[0]
collagen 1a2
[1]
GGTGAGCCTGGTCAAACGG
[2]
ACTGTGTCCTTTCACGCCTTT
[4] array · 3 items
[0]
collagen 3a1
[1]
TAGGACTGACCAAGGTGGCT
[2]
GGAACCTGGTTTCTTCTCACC
[5] array · 3 items
[0]
collagen 4a1
[1]
CACATTTTCCACAGCCAGAG
[2]
GTCTGGCTTCTGCTGCTCTT
[6] array · 3 items
[0]
collagen 5a2
[1]
CATGGAGAAGGTTTCCAAATG
[2]
AAAGCCCAGGAACAAGAGAA
[7] array · 3 items
[0]
collagen 12a1
[1]
TGAGGTCTGGGTAAAGGCAA
[2]
GTATGAGGTCACCGTCCAGG
[8] array · 3 items
[0]
Ly6g
[1]
TGCGTTGCTCTGGAGATAGA
[2]
CAGAGTAGTGGGGCAGATG
[9] array · 3 items
[0]
Csf2 (encodes GM-CSF)
[1]
CTGCTCTTCTCCACGCTACTG
[2]
GAGACTCGCCGGTGTATCC
[10] array · 3 items
[0]
Csf3 (encodes G-CSF)
[1]
CTGATCTTCTTGCTACTCCCCA
[2]
GGTGTAGTTCAAGTGAGGCAG
[11] array · 3 items
[0]
IL3
[1]
GGGATACCCACCGTTTAACCA
[2]
AGGTTTACTCTCCGAAAGCTCTT
[12] array · 3 items
[0]
IL15
[1]
ACATCCATCTCGTGCTACTTGT
[2]
GCCTCTGTTTTAGGGAGACCT
[13] array · 3 items
[0]
Egf
[1]
AGCATCTCTCGGATTGACCCA
[2]
CCTGTCCCGTTAAGGAAAACTCT
[14] array · 3 items
[0]
Hgf
[1]
ATGTGGGGGACCAAACTTCTG
[2]
GGATGGCGACATGAAGCAG
[15] array · 3 items
[0]
IL17a
[1]
TTTAACTCCCTTGGCGCAAAA
[2]
CTTTCCCTCCGCATTGACAC
[16] array · 3 items
[0]
IL17f
[1]
TGCTACTGTTGATGTTGGGAC
[2]
AATGCCCTGGTTTTGGTTGAA
[17] array · 3 items
[0]
Ly6g
[1]
TGCGTTGCTCTGGAGATAGA
[2]
CAGAGTAGTGGGGCAGATGG
[18] array · 3 items
[0]
18s
[1]
GTAACCCGTTGAACCCCATT
[2]
CCATCCAATCGGTAGTAGCG
locator
section[16]/table-wrap[1]#tbl1
gaps array · 2 items
[0]
asset:data:geo:GSE98153 not downloaded
[1]
asset:data:geo:GSE98153 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test.
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
GSE98153
resolved_accessions array · 1 item
[0]
GSE98153
statements array · 1 item
[0]
Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153).
basis
The paper names GSE98153 in NCBI’s Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 3 items
[0]
source:pmid:29552626
[1]
data:geo:GSE98153
[2]
asset:table:pmid:29552626:1
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE98153
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:34:15Z
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
null
calls
8
usage object · 3 fields
prompt_tokens
114393
completion_tokens
2962
cached_tokens
1560
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
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 · 3 items
[0] object · 3 fields
id
pmid:29552626
type
paper
label
pmid:29552626
[1] object · 3 fields
id
source:pmid:29552626
type
manuscript
label
PMID 29552626 full text
[2] object · 3 fields
id
data:geo:GSE98153
type
dataset
label
GEO GSE98153
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:29552626
type
paper
label
pmid:29552626
[1] object · 3 fields
id
source:pmid:29552626
type
manuscript
label
PMID 29552626 full text
[2] object · 3 fields
id
data:geo:GSE98153
type
dataset
label
GEO GSE98153
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-29552626
type
extraction
used array · 1 item
[0]
source:pmid:29552626
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE98153
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE98153
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:29552626
parent_hash
sha256:58baff2016486dee9f652aa48adfdd214065ce2f2d04a5f36c60ae3b36c2e082
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:GSE98153 licence not read
[1]
asset:data:geo:GSE98153 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 4 items
[0] object · 11 fields
role
data_generation
definition_id
animal_model
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
ains unknown. METHODS: A clinically relevant mouse model of steatohepatitis induced by high-fat diet
[1]
brosis. CONCLUSIONS: The current data from a mouse model of HFD plus binge ethanol feeding suggest th
[2]
ains unknown. METHODS: A clinically relevant mouse model of steatohepatitis induced by high-fat
[3]
brosis. CONCLUSIONS: The current data from a mouse model of HFD plus binge ethanol feeding sugg
order_basis
paper_text_order:259
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
microarray
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
D+mB) caused more pronounced liver fibrosis. Microarray analyses showed that the most highly activat
[1]
via the interaction of neutrophils and HSCs. Microarray data in this article have been uploaded to N
[2]
Materials and Methods Microarray Analyses of Mouse Liver Samples Total RNAs w
[3]
bridized to an Agilent 44K mouse 60-meroligo microarray (Agilent Technologies, Santa Clara, CA). The
order_basis
paper_text_order:713
id
assay:2
[2] object · 11 fields
role
data_generation
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
on Omnibus (GEO accession number: GSE98153). Enzyme-Linked Immunosorbent Assay Analysis of GM-CSF The concentration of GM-C
[1]
pernatant of HSCs was measured with a GM-CSF enzyme-linked immunosorbent assay kit (R&D) according to the manufacturer's in
order_basis
paper_text_order:3105
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test.
order_basis
consumes_earlier_output
id
assay:4
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29552626", "kind": "science-record", "revision": 9, "content_hash": "sha256:8aae2da988ee763a7ae659f35fd18662748696f9a028363428b19d437471fde4", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T22:43:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Neutrophil-Hepatic Stellate Cell Interactions Promote Fibrosis in Experimental Steatohepatitis.", "doi": "10.1016/j.jcmgh.2018.01.003", "pmid": "29552626", "authors": ["Zhou Zhou", "Ming-Jiang Xu", "Yan Cai", "Wei Wang", "Joy X Jiang", "Zoltan V Varga", "Dechun Feng", "Pal Pacher", "George Kunos", "Natalie J Torok", "Bin Gao"], "journal": "Cellular and molecular gastroenterology and hepatology", "year": 2018, "abstract": "BACKGROUND & AIMS: Hepatic infiltration of neutrophils is a hallmark of steatohepatitis; however, the role of neutrophils in the progression of steatohepatitis remains unknown.\nMETHODS: A clinically relevant mouse model of steatohepatitis induced by high-fat diet (HFD) plus binge ethanol feeding was used. Liver fibrosis was examined. In vitro cell culture was used to analyze the interaction of hepatic stellate cells (HSCs) and neutrophils.\nRESULTS: HFD plus one binge ethanol (HFD+1B) feeding induced significant hepatic neutrophil infiltration, liver injury, and fibrosis. HFD plus multiple binges of ethanol (HFD+mB) caused more pronounced liver fibrosis. Microarray analyses showed that the most highly activated signaling pathway in this HFD+1B model was related to liver fibrosis and HSC activation. Blockade of chemokine (C-X-C motif) ligand 1 or intercellular adhesion molecule-1 expression reduced hepatic neutrophil infiltration and ameliorated liver injury and fibrosis. Disruption of the p47phox gene (also called neutrophil cytosolic factor 1), a critical component of reactive oxygen species producing nicotinamide adenine dinucleotide phosphate-oxidase in neutrophils, diminished HFD+1B-induced liver injury and fibrosis. Co-culture of HSCs with neutrophils, but not with neutrophil apoptotic bodies, induced HSC activation and prolonged neutrophil survival. Mechanistic studies showed that activated HSCs produce granulocyte-macrophage colony-stimulating factor and interleukin-15 to prolong the survival of neutrophils, which may serve as a positive forward loop to promote liver damage and fibrosis.\nCONCLUSIONS: The current data from a mouse model of HFD plus binge ethanol feeding suggest that obesity and binge drinking synergize to promote liver fibrosis, which is partially mediated via the interaction of neutrophils and HSCs. Microarray data in this article have been uploaded to NCBI's Gene Expression Omnibus (GEO accession number: GSE98153).", "claims": [{"id": "claim-method", "statement": "Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29552626", "locator": "sections[17] \"Statistical Analysis\" paragraph 2", "quote": "Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29552626", "locator": "sections[8] \"Microarray Analyses of Mouse Liver Samples\" paragraph 2", "quote": "Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Headline result: Obesity and binge drinking synergistically promote liver fibrosis, partially through interactions between neutrophils and hepatic stellate cells. Statistical method: two-group comparisons used an unpaired t test; multiple-group comparisons used one-way analysis of variance followed by the Tukey post hoc test, with P < .05 considered significant. Route to source data: the microarray data were uploaded to NCBI’s Gene Expression Omnibus under accession GSE98153, and all authors had access to the study data.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29552626", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The current data from a mouse model of HFD plus binge ethanol feeding suggest that obesity and binge drinking synergize to promote liver fibrosis, which is partially mediated via the interaction of neutrophils and HSCs."}, {"asset": "source:pmid:29552626", "locator": "sections[17] \"Statistical Analysis\" paragraph 2", "quote": "Data are shown as means ± SEM. Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test. P < .05 was considered a significant difference."}, {"asset": "source:pmid:29552626", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Microarray data in this article have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153)."}, {"asset": "source:pmid:29552626", "locator": "sections[18] \"Data\" paragraph 2", "quote": "All authors had access to the study data and reviewed and approved the final manuscript."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Headline result: Obesity and binge drinking synergistically promote liver fibrosis, partially through interactions between neutrophils and hepatic stellate cells. Statistical method: two-group comparisons used an unpaired t test; multiple-group comparisons used one-way analysis of variance followed by the Tukey post hoc test, with P < .05 considered significant. Route to source data: the microarray data were uploaded to NCBI’s Gene Expression Omnibus under accession GSE98153, and all authors had access to the study data.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29552626"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE98153"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE98153"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29552626", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.jcmgh.2018.01.003", "sha256": "sha256:acb0a1a863a5c4eae2a1cd6682bb9647dbb11ea2547a3df3492e6f3c5b14096c", "bytes": 55043, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.jcmgh.2018.01.003", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5852390", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE98153", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98153", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE98153", "version": null, "note": "Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2588732", "GSM2588733", "GSM2588734", "GSM2588735", "GSM2588736", "GSM2588737", "GSM2588738", "GSM2588739", "GSM2588740", "GSM2588741", "GSM2588742", "GSM2588743", "GSM2588744", "GSM2588745", "GSM2588746", "GSM2588747", "GSM2588748"], "sample_count": 17, "group_sizes": null, "group_sizes_basis": null, "platform": "7202", "taxon": "Mus musculus", "title": "Interaction of neutrophils and hepatic stellate cells promotes fibrosis in a mouse model of steatohepatitis", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29552626:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d8caa93335b250a9d80f99d0218bdc3d8720b3c8b963801972178cd0dc02dc3a", "bytes": 1365, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#tbl1", "version": null, "note": "Real-Time Quantitative PCR Primer Sequence Used in the Present Study", "structure": {"pmcid": "PMC5852390", "section_index": 16, "section_title": "Real-Time Quantitative PCR", "row_count": 19, "column_count": 3}, "table": {"label": "Table 1", "caption": "Real-Time Quantitative PCR Primer Sequence Used in the Present Study", "rows": [["Gene name", "Forward", "Reverse"], ["Acta2 (encodes α-SMA)", "TCCTGACGCTGAAGTATCCGATA", "GGTGCCAGATCTTTTCCATGTC"], ["collagen 1a1", "TAGGCCATTGTGTATGCAGC", "ACATGTTCAGCTTTGTGGACC"], ["collagen 1a2", "GGTGAGCCTGGTCAAACGG", "ACTGTGTCCTTTCACGCCTTT"], ["collagen 3a1", "TAGGACTGACCAAGGTGGCT", "GGAACCTGGTTTCTTCTCACC"], ["collagen 4a1", "CACATTTTCCACAGCCAGAG", "GTCTGGCTTCTGCTGCTCTT"], ["collagen 5a2", "CATGGAGAAGGTTTCCAAATG", "AAAGCCCAGGAACAAGAGAA"], ["collagen 12a1", "TGAGGTCTGGGTAAAGGCAA", "GTATGAGGTCACCGTCCAGG"], ["Ly6g", "TGCGTTGCTCTGGAGATAGA", "CAGAGTAGTGGGGCAGATG"], ["Csf2 (encodes GM-CSF)", "CTGCTCTTCTCCACGCTACTG", "GAGACTCGCCGGTGTATCC"], ["Csf3 (encodes G-CSF)", "CTGATCTTCTTGCTACTCCCCA", "GGTGTAGTTCAAGTGAGGCAG"], ["IL3", "GGGATACCCACCGTTTAACCA", "AGGTTTACTCTCCGAAAGCTCTT"], ["IL15", "ACATCCATCTCGTGCTACTTGT", "GCCTCTGTTTTAGGGAGACCT"], ["Egf", "AGCATCTCTCGGATTGACCCA", "CCTGTCCCGTTAAGGAAAACTCT"], ["Hgf", "ATGTGGGGGACCAAACTTCTG", "GGATGGCGACATGAAGCAG"], ["IL17a", "TTTAACTCCCTTGGCGCAAAA", "CTTTCCCTCCGCATTGACAC"], ["IL17f", "TGCTACTGTTGATGTTGGGAC", "AATGCCCTGGTTTTGGTTGAA"], ["Ly6g", "TGCGTTGCTCTGGAGATAGA", "CAGAGTAGTGGGGCAGATGG"], ["18s", "GTAACCCGTTGAACCCCATT", "CCATCCAATCGGTAGTAGCG"]], "row_count": 19, "column_count": 3, "numeric_cells": 10, "header_rows": 1, "locator": "section[16]/table-wrap[1]#tbl1"}}], "gaps": ["asset:data:geo:GSE98153 not downloaded", "asset:data:geo:GSE98153 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE98153"], "resolved_accessions": ["GSE98153"], "statements": ["Full microarray data have been uploaded to NCBI’s Gene Expression Omnibus (GEO accession number: GSE98153)."], "basis": "The paper names GSE98153 in NCBI’s Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:29552626", "data:geo:GSE98153", "asset:table:pmid:29552626:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE98153"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:15Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 114393, "completion_tokens": 2962, "cached_tokens": 1560}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:29552626", "type": "paper", "label": "pmid:29552626"}, {"id": "source:pmid:29552626", "type": "manuscript", "label": "PMID 29552626 full text"}, {"id": "data:geo:GSE98153", "type": "dataset", "label": "GEO GSE98153"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29552626", "type": "paper", "label": "pmid:29552626"}, {"id": "source:pmid:29552626", "type": "manuscript", "label": "PMID 29552626 full text"}, {"id": "data:geo:GSE98153", "type": "dataset", "label": "GEO GSE98153"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29552626", "type": "extraction", "used": ["source:pmid:29552626"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE98153", "type": "accession_resolution", "used": ["data:geo:GSE98153"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:29552626", "parent_hash": "sha256:58baff2016486dee9f652aa48adfdd214065ce2f2d04a5f36c60ae3b36c2e082", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE98153 licence not read", "asset:data:geo:GSE98153 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ains unknown. METHODS: A clinically relevant mouse model of steatohepatitis induced by high-fat diet", "brosis. CONCLUSIONS: The current data from a mouse model of HFD plus binge ethanol feeding suggest th", "ains unknown. METHODS: A clinically relevant mouse model of steatohepatitis induced by high-fat", "brosis. CONCLUSIONS: The current data from a mouse model of HFD plus binge ethanol feeding sugg"], "order_basis": "paper_text_order:259", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["D+mB) caused more pronounced liver fibrosis. Microarray analyses showed that the most highly activat", "via the interaction of neutrophils and HSCs. Microarray data in this article have been uploaded to N", "Materials and Methods Microarray Analyses of Mouse Liver Samples Total RNAs w", "bridized to an Agilent 44K mouse 60-meroligo microarray (Agilent Technologies, Santa Clara, CA). The"], "order_basis": "paper_text_order:713", "id": "assay:2"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on Omnibus (GEO accession number: GSE98153). Enzyme-Linked Immunosorbent Assay Analysis of GM-CSF The concentration of GM-C", "pernatant of HSCs was measured with a GM-CSF enzyme-linked immunosorbent assay kit (R&D) according to the manufacturer's in"], "order_basis": "paper_text_order:3105", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Data from 2 groups were compared with an unpaired t test. Data from multiple groups were compared with 1-way analysis of variance followed by the Tukey post hoc test."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}