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

pmid:40725160

Quantitative Proteomics Reveals Fh15 as an Antagonist of TLR4 Downregulating the Activation of NF-κB, Inducible Nitric Oxide, Phagosome Signaling Pathways, and Oxidative Stress of LPS-Stimulated Macrophages.

Albersy Armina-Rodriguez · Bianca N Valdés Fernandez · Carlimar Ocasio-Malavé · Yadira M Cantres Rosario · Kelvin Carrasquillo Carrión · Loyda M Meléndez · Abiel Roche Lima · Eduardo L Tosado Rodriguez · Ana M Espino

International journal of molecular sciences · 2025 doi:10.3390/ijms26146914

Paper

complete

Experiment

partial

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:40725160
kind
science-record
content_hash
sha256:4ae33cd74b4967a46f74a974dcbc8ad9169a96a8ea96a19821c069b4e61bba39
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:30:49Z
updated_at
2026-11-01T22:56:54Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Quantitative Proteomics Reveals Fh15 as an Antagonist of TLR4 Downregulating the Activation of NF-κB, Inducible Nitric Oxide, Phagosome Signaling Pathways, and Oxidative Stress of LPS-Stimulated Macrophages.
doi
10.3390/ijms26146914
pmid
40725160
authors array · 9 items
[0]
Albersy Armina-Rodriguez
[1]
Bianca N Valdés Fernandez
[2]
Carlimar Ocasio-Malavé
[3]
Yadira M Cantres Rosario
[4]
Kelvin Carrasquillo Carrión
[5]
Loyda M Meléndez
[6]
Abiel Roche Lima
[7]
Eduardo L Tosado Rodriguez
[8]
Ana M Espino
journal
International journal of molecular sciences
year
2025
abstract
There is a present need to develop alternative biotherapeutic drugs to mitigate the exacerbated inflammatory immune responses characteristic of sepsis. The potent endotoxin lipopolysaccharide (LPS), a major component of Gram-negative bacterial outer membrane, activates the immune system via Toll-like receptor 4 (TLR4), triggering macrophages and a persistent cascade of inflammatory mediators. Our previous studies have demonstrated that Fh15, a recombinant member of the Fasciola hepatica fatty acid binding protein family, can significantly increase the survival rate by suppressing many inflammatory mediators induced by LPS in a septic shock mouse model. Although Fh15 has been proposed as a TLR4 antagonist, the specific mechanisms underlying its immunomodulatory effect remained unclear. In the present study, we employed a quantitative proteomics approach using tandem mass tag (TMT) followed by LC-MS/MS analysis to identify and quantify differentially expressed proteins that participate in signaling pathways downstream TLR4 of macrophages, which can be dysregulated by Fh15. Data are available via ProteomeXchange with identifier PXD065520. Based on significant fold change (FC) cut-off of 1.5 and p-value ≤ 0.05 criteria, we focused our attention to 114 proteins that were upregulated by LPS and downregulated by Fh15. From these proteins, TNFα, IL-1α, Lck, NOS2, SOD2 and CD36 were selected for validation by Western blot on murine bone marrow-derived macrophages due to their relevant roles in the NF-κB, iNOS, oxidative stress, and phagosome signaling pathways, which are closely associated with sepsis pathogenesis. These results suggest that Fh15 exerts a broad spectrum of action by simultaneously targeting multiple downstream pathways activated by TLR4, thereby modulating various aspects of the inflammatory responses during sepsis.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Data were analyzed using one-way ANOVA with multiple comparisons and the Tukey test, employing GraphPad Prism software (version 8).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40725160
locator
sections[20] "4.11. Statistical Analysis" paragraph 2
quote
Data were analyzed using one-way ANOVA with multiple comparisons and the Tukey test, employing GraphPad Prism software (version 8).
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [92] partner repository with the dataset identifier PXD065520 and 10.6019/PXD065520. This information was incorporated in the Methods section or just before Acknowledgements and in the Abstract, e.g., Data are available via ProteomeXchange with identifier PSD065520.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40725160
locator
sections[28] "Data Availability Statement" paragraph 2
quote
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [92] partner repository with the dataset identifier PXD065520 and 10.6019/PXD065520. This information was incorporated in the Methods section or just before Acknowledgements and in the Abstract, e.g., Data are available via ProteomeXchange with identifier PSD065520.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Using a fold-change cutoff of 1.5 and p-value ≤ 0.05, the study identified 114 proteins that were upregulated by LPS and downregulated by Fh15.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40725160
locator
sections[0] "Abstract" paragraph 1
quote
Based on significant fold change (FC) cut-off of 1.5 and p-value ≤ 0.05 criteria, we focused our attention to 114 proteins that were upregulated by LPS and downregulated by Fh15.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
Using a fold-change cutoff of 1.5 and p-value ≤ 0.05, the study identified 114 proteins that were upregulated by LPS and downregulated by Fh15.
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:40725160
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
blocked
blocked_on
data:accession_absent
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 · 0 items
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 · 0 items
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 · 1 item
[0]
step:obtain_source_data blocked on data:accession_absent
data object · 3 fields
state
partial
assets array · 1 item
[0] object · 15 fields
id
source:pmid:40725160
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3390/ijms26146914
sha256
sha256:f2268eefc95011e9f21734cc17f8cbf0ea88b239b133bdcb674d63573c1d0587
bytes
77300
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3390/ijms26146914
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
PMC12294962
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
gaps array · 0 items
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 were analyzed using one-way ANOVA with multiple comparisons and the Tukey test, employing GraphPad Prism software (version 8).
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
blocked
tier
R4
blocked_on
data:accession_absent
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
R4
reachable
false
accessions array · 1 item
[0]
PXD065520 and 10.6019/PXD065520
resolved_accessions array · 0 items
statements array · 1 item
[0]
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [92] partner repository with the dataset identifier PXD065520 and 10.6019/PXD065520. This information was incorporated in the Methods section or just before Acknowledgements and in the Abstract, e.g., Data are available via ProteomeXchange with identifier PSD065520.
basis
The paper names PXD065520 and 10.6019/PXD065520, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. 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 · 1 item
[0]
source:pmid:40725160
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:None
gaps array · 1 item
[0]
data:accession_absent
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
2026-11-01T19:57:58Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
22539
completion_tokens
1026
cached_tokens
128
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:40725160
type
paper
label
pmid:40725160
[1] object · 3 fields
id
source:pmid:40725160
type
manuscript
label
PMID 40725160 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
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:40725160
type
paper
label
pmid:40725160
[1] object · 3 fields
id
source:pmid:40725160
type
manuscript
label
PMID 40725160 full text
[2] object · 3 fields
id
data:geo:None
type
dataset
label
GEO None
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-40725160
type
extraction
used array · 1 item
[0]
source:pmid:40725160
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-None
type
accession_resolution
used array · 1 item
[0]
data:geo:None
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:40725160
parent_hash
sha256:275c1970a209eba44817688dae10c71f9062771f55b70e4ba06fae11f54a7ded
fork_of
null
gaps array · 5 items
[0]
execution.not_run
[1]
review.human_critique
[2]
review.independent_reader
[3]
review.machine_critique
[4]
step:obtain_source_data blocked on data:accession_absent
assays array · 4 items
[0] object · 11 fields
role
data_generation
definition_id
mass_spectrometry
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]
Quantitative Proteomics Reveals Fh15 as an Antagonist of TLR4 Downre
[1]
he present study, we employed a quantitative proteomics approach using tandem mass tag (TMT) followe
[2]
2.1. Quantitative Proteomics Analysis of Macrophages-like Cells Exposed t
[3]
e TMT-labeling protocol for the quantitative proteomics approach. RAW 264.7 cells were treated with
order_basis
paper_text_order:0
id
assay:1
[1] 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 · 3 items
[0]
y mediators induced by LPS in a septic shock mouse model. Although Fh15 has been proposed as a TLR4 a
[1]
e selected for validation by Western blot on murine bone marrow-derived macrophages due to their
[2]
y mediators induced by LPS in a septic shock mouse model. Although Fh15 has been proposed as a
order_basis
paper_text_order:811
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
western_blot
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
OD2 and CD36 were selected for validation by Western blot on murine bone marrow-derived macrophages du
order_basis
paper_text_order:1587
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 were analyzed using one-way ANOVA with multiple comparisons and the Tukey test, employing GraphPad Prism software (version 8).
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:40725160", "kind": "science-record", "revision": 4, "content_hash": "sha256:4ae33cd74b4967a46f74a974dcbc8ad9169a96a8ea96a19821c069b4e61bba39", "created_at": "2026-11-01T20:30:49Z", "updated_at": "2026-11-01T22:56:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative Proteomics Reveals Fh15 as an Antagonist of TLR4 Downregulating the Activation of NF-κB, Inducible Nitric Oxide, Phagosome Signaling Pathways, and Oxidative Stress of LPS-Stimulated Macrophages.", "doi": "10.3390/ijms26146914", "pmid": "40725160", "authors": ["Albersy Armina-Rodriguez", "Bianca N Valdés Fernandez", "Carlimar Ocasio-Malavé", "Yadira M Cantres Rosario", "Kelvin Carrasquillo Carrión", "Loyda M Meléndez", "Abiel Roche Lima", "Eduardo L Tosado Rodriguez", "Ana M Espino"], "journal": "International journal of molecular sciences", "year": 2025, "abstract": "There is a present need to develop alternative biotherapeutic drugs to mitigate the exacerbated inflammatory immune responses characteristic of sepsis. The potent endotoxin lipopolysaccharide (LPS), a major component of Gram-negative bacterial outer membrane, activates the immune system via Toll-like receptor 4 (TLR4), triggering macrophages and a persistent cascade of inflammatory mediators. Our previous studies have demonstrated that Fh15, a recombinant member of the Fasciola hepatica fatty acid binding protein family, can significantly increase the survival rate by suppressing many inflammatory mediators induced by LPS in a septic shock mouse model. Although Fh15 has been proposed as a TLR4 antagonist, the specific mechanisms underlying its immunomodulatory effect remained unclear. In the present study, we employed a quantitative proteomics approach using tandem mass tag (TMT) followed by LC-MS/MS analysis to identify and quantify differentially expressed proteins that participate in signaling pathways downstream TLR4 of macrophages, which can be dysregulated by Fh15. Data are available via ProteomeXchange with identifier PXD065520. Based on significant fold change (FC) cut-off of 1.5 and p-value ≤ 0.05 criteria, we focused our attention to 114 proteins that were upregulated by LPS and downregulated by Fh15. From these proteins, TNFα, IL-1α, Lck, NOS2, SOD2 and CD36 were selected for validation by Western blot on murine bone marrow-derived macrophages due to their relevant roles in the NF-κB, iNOS, oxidative stress, and phagosome signaling pathways, which are closely associated with sepsis pathogenesis. These results suggest that Fh15 exerts a broad spectrum of action by simultaneously targeting multiple downstream pathways activated by TLR4, thereby modulating various aspects of the inflammatory responses during sepsis.", "claims": [{"id": "claim-method", "statement": "Data were analyzed using one-way ANOVA with multiple comparisons and the Tukey test, employing GraphPad Prism software (version 8).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40725160", "locator": "sections[20] \"4.11. Statistical Analysis\" paragraph 2", "quote": "Data were analyzed using one-way ANOVA with multiple comparisons and the Tukey test, employing GraphPad Prism software (version 8)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [92] partner repository with the dataset identifier PXD065520 and 10.6019/PXD065520. This information was incorporated in the Methods section or just before Acknowledgements and in the Abstract, e.g., Data are available via ProteomeXchange with identifier PSD065520.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40725160", "locator": "sections[28] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [92] partner repository with the dataset identifier PXD065520 and 10.6019/PXD065520. This information was incorporated in the Methods section or just before Acknowledgements and in the Abstract, e.g., Data are available via ProteomeXchange with identifier PSD065520."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using a fold-change cutoff of 1.5 and p-value ≤ 0.05, the study identified 114 proteins that were upregulated by LPS and downregulated by Fh15.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40725160", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Based on significant fold change (FC) cut-off of 1.5 and p-value ≤ 0.05 criteria, we focused our attention to 114 proteins that were upregulated by LPS and downregulated by Fh15."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using a fold-change cutoff of 1.5 and p-value ≤ 0.05, the study identified 114 proteins that were upregulated by LPS and downregulated by Fh15.", "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:40725160"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40725160", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms26146914", "sha256": "sha256:f2268eefc95011e9f21734cc17f8cbf0ea88b239b133bdcb674d63573c1d0587", "bytes": 77300, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms26146914", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12294962", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "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 were analyzed using one-way ANOVA with multiple comparisons and the Tukey test, employing GraphPad Prism software (version 8)."}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "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": "R4", "reachable": false, "accessions": ["PXD065520 and 10.6019/PXD065520"], "resolved_accessions": [], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [92] partner repository with the dataset identifier PXD065520 and 10.6019/PXD065520. This information was incorporated in the Methods section or just before Acknowledgements and in the Abstract, e.g., Data are available via ProteomeXchange with identifier PSD065520."], "basis": "The paper names PXD065520 and 10.6019/PXD065520, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. 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:40725160"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:57:58Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 22539, "completion_tokens": 1026, "cached_tokens": 128}}, "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:40725160", "type": "paper", "label": "pmid:40725160"}, {"id": "source:pmid:40725160", "type": "manuscript", "label": "PMID 40725160 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40725160", "type": "paper", "label": "pmid:40725160"}, {"id": "source:pmid:40725160", "type": "manuscript", "label": "PMID 40725160 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40725160", "type": "extraction", "used": ["source:pmid:40725160"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:40725160", "parent_hash": "sha256:275c1970a209eba44817688dae10c71f9062771f55b70e4ba06fae11f54a7ded", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Quantitative Proteomics Reveals Fh15 as an Antagonist of TLR4 Downre", "he present study, we employed a quantitative proteomics approach using tandem mass tag (TMT) followe", "2.1. Quantitative Proteomics Analysis of Macrophages-like Cells Exposed t", "e TMT-labeling protocol for the quantitative proteomics approach. RAW 264.7 cells were treated with"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"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": ["y mediators induced by LPS in a septic shock mouse model. Although Fh15 has been proposed as a TLR4 a", "e selected for validation by Western blot on murine bone marrow-derived macrophages due to their", "y mediators induced by LPS in a septic shock mouse model. Although Fh15 has been proposed as a"], "order_basis": "paper_text_order:811", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["OD2 and CD36 were selected for validation by Western blot on murine bone marrow-derived macrophages du"], "order_basis": "paper_text_order:1587", "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 were analyzed using one-way ANOVA with multiple comparisons and the Tukey test, employing GraphPad Prism software (version 8)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}