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

pmid:39554548

Proteomics dataset of lysolecithin-induced demyelinated lesions in corpus callosum of Lewis rats, treated with Vagus nerve stimulation or sham treatment.

Helen Bachmann · Boris Vandemoortele · Vanessa Vermeirssen · Evelien Carrette · Kristl Vonck · Paul Boon · Robrecht Raedt · Guy Laureys

Data in brief · 2024 doi:10.1016/j.dib.2024.111048

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:39554548
kind
science-record
content_hash
sha256:95721693fbfa1fb2da1dee6317a9945d109dd019c12125cdddb929f27224dda0
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:29:49Z
updated_at
2026-11-01T22:55:37Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Proteomics dataset of lysolecithin-induced demyelinated lesions in corpus callosum of Lewis rats, treated with Vagus nerve stimulation or sham treatment.
doi
10.1016/j.dib.2024.111048
pmid
39554548
authors array · 8 items
[0]
Helen Bachmann
[1]
Boris Vandemoortele
[2]
Vanessa Vermeirssen
[3]
Evelien Carrette
[4]
Kristl Vonck
[5]
Paul Boon
[6]
Robrecht Raedt
[7]
Guy Laureys
journal
Data in brief
year
2024
abstract
This article presents a comprehensive proteomics dataset from a lysolecithin (LPC)-induced demyelination model in the corpus callosum of female Lewis rats. The LPC model, widely used in preclinical studies of toxic demyelination, serves as a valuable tool for investigating processes of demyelination and remyelination, as well as for testing potential remyelination therapies for diseases like Multiple Sclerosis. In this study, rats received either Vagus Nerve Stimulation (VNS) or a sham treatment. Proteomic analysis via LC-MS/MS was performed to assess the impact of these treatments on inflammation and remyelination and to further explore the mechanism of VNS action. This dataset complements the findings reported in the article "Vagus Nerve Stimulation enhances remyelination and decreases innate neuroinflammation in lysolecithin-induced demyelination" [1], providing a detailed account of the proteomics methods and results, including the quantification of 8172 proteins. This dataset allows for further exploration of key mechanisms in the LPC model by comparing different time points within the sham group. Additionally, comparisons between the sham and VNS groups can be extended or combined with other published datasets to gain deeper insights into the effects of VNS. Raw data are available via ProteomeXchange with identifier PXD050858.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Statistical analyses were performed on log2-transformed, imputed PG.MaxLFQ values using the package limma (empirical Bayes procedure with Benjamini & Hochberg multiple testing correction) [8].
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:39554548
locator
sections[5] "Data Description" paragraph 11
quote
Statistical analyses were performed on log2-transformed, imputed PG.MaxLFQ values using the package limma (empirical Bayes procedure with Benjamini & Hochberg multiple testing correction) [8].
state
complete
[1] object · 6 fields
id
claim-data-access
statement
ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:39554548
locator
sections[16] "Data Availability" paragraph 2
quote
ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
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:39554548
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:PXD050858
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:PXD050858
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 · 2 items
[0] object · 15 fields
id
source:pmid:39554548
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1016/j.dib.2024.111048
sha256
sha256:7f3697ac2833c3611758a49306bd528520e89613fd93dffa92f87eacac226671
bytes
25808
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1016/j.dib.2024.111048
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
PMC11567096
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD050858
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=PXD050858
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD050858
version
null
note
ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data).
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
Vagus Nerve Stimulation enhances remyelination and decreases innate neuroinflammation in a Multiple Sclerosis rodent model.
resolution_checked_at
2026-11-01T20:16:17Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:PXD050858 not downloaded
[1]
asset:data:geo:PXD050858 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
differential_expression
specific
limma_voom
label
Differential expression analysis
dsl_operations array · 3 items
[0]
normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
count_matrix_with_condition
evidence object · 3 fields
score
1
band
verbatim
quote
Statistical analyses were performed on log2-transformed, imputed PG.MaxLFQ values using the package limma (empirical Bayes procedure with Benjamini & Hochberg multiple testing correction) [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
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 3 items
[0]
normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
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: limma_voom.
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]
PXD050858
resolved_accessions array · 1 item
[0]
PXD050858
statements array · 1 item
[0]
ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data).
basis
The paper names PXD050858 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 3 items
[0]
normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
assets array · 2 items
[0]
source:pmid:39554548
[1]
data:geo:PXD050858
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:PXD050858
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
2026-11-01T19:39:02Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
8192
completion_tokens
1884
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:39554548
type
paper
label
pmid:39554548
[1] object · 3 fields
id
source:pmid:39554548
type
manuscript
label
PMID 39554548 full text
[2] object · 3 fields
id
data:geo:PXD050858
type
dataset
label
GEO PXD050858
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:39554548
type
paper
label
pmid:39554548
[1] object · 3 fields
id
source:pmid:39554548
type
manuscript
label
PMID 39554548 full text
[2] object · 3 fields
id
data:geo:PXD050858
type
dataset
label
GEO PXD050858
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-39554548
type
extraction
used array · 1 item
[0]
source:pmid:39554548
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD050858
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD050858
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:39554548
parent_hash
sha256:d1f7a7c73d796b5cf6117bbb9701336ebf23e9e2025780a90196d58f46df8331
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:PXD050858 licence not read
[1]
asset:data:geo:PXD050858 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 3 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]
elinated lesions in corpus callosum of Lewis rats, treated with Vagus nerve stimulation or sha
[1]
model in the corpus callosum of female Lewis rats. The LPC model, widely used in preclinical s
[2]
ases like Multiple Sclerosis. In this study, rats received either Vagus Nerve Stimulation (VNS
[3]
the effective stimulation of the electrode. Rats were euthanized at 3 or 11 dpi for the demyelinat
order_basis
paper_text_order:47
id
assay:1
[1] 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
0.85
evidence array · 1 item
[0]
ble 2). For each rat, one slice, next to the immunostained slices, was washed with phosphate-buffered s
order_basis
paper_text_order:3221
id
assay:2
[2] object · 11 fields
role
analysis
definition_id
differential_expression
definition_version
f2132e96ae6c7a4e
required_operations array · 3 items
[0]
normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Statistical analyses were performed on log2-transformed, imputed PG.MaxLFQ values using the package limma (empirical Bayes procedure with Benjamini & Hochberg multiple testing correction) [8].
order_basis
consumes_earlier_output
id
assay:3
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39554548", "kind": "science-record", "revision": 4, "content_hash": "sha256:95721693fbfa1fb2da1dee6317a9945d109dd019c12125cdddb929f27224dda0", "created_at": "2026-11-01T20:29:49Z", "updated_at": "2026-11-01T22:55:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomics dataset of lysolecithin-induced demyelinated lesions in corpus callosum of Lewis rats, treated with Vagus nerve stimulation or sham treatment.", "doi": "10.1016/j.dib.2024.111048", "pmid": "39554548", "authors": ["Helen Bachmann", "Boris Vandemoortele", "Vanessa Vermeirssen", "Evelien Carrette", "Kristl Vonck", "Paul Boon", "Robrecht Raedt", "Guy Laureys"], "journal": "Data in brief", "year": 2024, "abstract": "This article presents a comprehensive proteomics dataset from a lysolecithin (LPC)-induced demyelination model in the corpus callosum of female Lewis rats. The LPC model, widely used in preclinical studies of toxic demyelination, serves as a valuable tool for investigating processes of demyelination and remyelination, as well as for testing potential remyelination therapies for diseases like Multiple Sclerosis. In this study, rats received either Vagus Nerve Stimulation (VNS) or a sham treatment. Proteomic analysis via LC-MS/MS was performed to assess the impact of these treatments on inflammation and remyelination and to further explore the mechanism of VNS action. This dataset complements the findings reported in the article \"Vagus Nerve Stimulation enhances remyelination and decreases innate neuroinflammation in lysolecithin-induced demyelination\" [1], providing a detailed account of the proteomics methods and results, including the quantification of 8172 proteins. This dataset allows for further exploration of key mechanisms in the LPC model by comparing different time points within the sham group. Additionally, comparisons between the sham and VNS groups can be extended or combined with other published datasets to gain deeper insights into the effects of VNS. Raw data are available via ProteomeXchange with identifier PXD050858.", "claims": [{"id": "claim-method", "statement": "Statistical analyses were performed on log2-transformed, imputed PG.MaxLFQ values using the package limma (empirical Bayes procedure with Benjamini & Hochberg multiple testing correction) [8].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39554548", "locator": "sections[5] \"Data Description\" paragraph 11", "quote": "Statistical analyses were performed on log2-transformed, imputed PG.MaxLFQ values using the package limma (empirical Bayes procedure with Benjamini & Hochberg multiple testing correction) [8]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39554548", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:39554548"], "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:PXD050858"], "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:PXD050858"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39554548", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2024.111048", "sha256": "sha256:7f3697ac2833c3611758a49306bd528520e89613fd93dffa92f87eacac226671", "bytes": 25808, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2024.111048", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11567096", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD050858", "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=PXD050858", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD050858", "version": null, "note": "ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Vagus Nerve Stimulation enhances remyelination and decreases innate neuroinflammation in a Multiple Sclerosis rodent model.", "resolution_checked_at": "2026-11-01T20:16:17Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD050858 not downloaded", "asset:data:geo:PXD050858 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical analyses were performed on log2-transformed, imputed PG.MaxLFQ values using the package limma (empirical Bayes procedure with Benjamini & Hochberg multiple testing correction) [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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["PXD050858"], "resolved_accessions": ["PXD050858"], "statements": ["ProteomeXchange Consortium via the PRIDE partner repositoryPXD050858 (Original data)."], "basis": "The paper names PXD050858 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:39554548", "data:geo:PXD050858"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD050858"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:39:02Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8192, "completion_tokens": 1884, "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:39554548", "type": "paper", "label": "pmid:39554548"}, {"id": "source:pmid:39554548", "type": "manuscript", "label": "PMID 39554548 full text"}, {"id": "data:geo:PXD050858", "type": "dataset", "label": "GEO PXD050858"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39554548", "type": "paper", "label": "pmid:39554548"}, {"id": "source:pmid:39554548", "type": "manuscript", "label": "PMID 39554548 full text"}, {"id": "data:geo:PXD050858", "type": "dataset", "label": "GEO PXD050858"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39554548", "type": "extraction", "used": ["source:pmid:39554548"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD050858", "type": "accession_resolution", "used": ["data:geo:PXD050858"], "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:39554548", "parent_hash": "sha256:d1f7a7c73d796b5cf6117bbb9701336ebf23e9e2025780a90196d58f46df8331", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD050858 licence not read", "asset:data:geo:PXD050858 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": ["elinated lesions in corpus callosum of Lewis rats, treated with Vagus nerve stimulation or sha", "model in the corpus callosum of female Lewis rats. The LPC model, widely used in preclinical s", "ases like Multiple Sclerosis. In this study, rats received either Vagus Nerve Stimulation (VNS", "the effective stimulation of the electrode. Rats were euthanized at 3 or 11 dpi for the demyelinat"], "order_basis": "paper_text_order:47", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["ble 2). For each rat, one slice, next to the immunostained slices, was washed with phosphate-buffered s"], "order_basis": "paper_text_order:3221", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Statistical analyses were performed on log2-transformed, imputed PG.MaxLFQ values using the package limma (empirical Bayes procedure with Benjamini & Hochberg multiple testing correction) [8]."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}