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

pmid:30535257

Small Extracellular Vesicles in Rat Serum Contain Astrocyte-Derived Protein Biomarkers of Repetitive Stress.

Cristóbal Gómez-Molina · Mauricio Sandoval · Roberto Henzi · Juan Pablo Ramírez · Manuel Varas-Godoy · Alejandro Luarte · Carlos Andres Lafourcade · Alejandra Lopez-Verrilli · Karl-Heinz Smalla · Thilo Kaehne · Ursula Wyneken

The international journal of neuropsychopharmacology · 2019 doi:10.1093/ijnp/pyy098

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

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:30535257
kind
science-record
content_hash
sha256:1ae987b4de89c091f07684455ca7ca92c7ac916f008b956c2d505801fc0c7206
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:39Z
updated_at
2026-11-01T22:43:39Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Small Extracellular Vesicles in Rat Serum Contain Astrocyte-Derived Protein Biomarkers of Repetitive Stress.
doi
10.1093/ijnp/pyy098
pmid
30535257
authors array · 11 items
[0]
Cristóbal Gómez-Molina
[1]
Mauricio Sandoval
[2]
Roberto Henzi
[3]
Juan Pablo Ramírez
[4]
Manuel Varas-Godoy
[5]
Alejandro Luarte
[6]
Carlos Andres Lafourcade
[7]
Alejandra Lopez-Verrilli
[8]
Karl-Heinz Smalla
[9]
Thilo Kaehne
[10]
Ursula Wyneken
journal
The international journal of neuropsychopharmacology
year
2019
abstract
BACKGROUND: Stress precipitates mood disorders, characterized by a range of symptoms present in different combinations, suggesting the existence of disease subtypes. Using an animal model, we previously described that repetitive stress via restraint or immobilization induced depressive-like behaviors in rats that were differentially reverted by a serotonin- or noradrenaline-based antidepressant drug, indicating that different neurobiological mechanisms may be involved. The forebrain astrocyte protein aldolase C, contained in small extracellular vesicles, was identified as a potential biomarker in the cerebrospinal fluid; however, its specific origin remains unknown. Here, we propose to investigate whether serum small extracellular vesicles contain a stress-specific protein cargo and whether serum aldolase C has a brain origin. METHODS: We isolated and characterized serum small extracellular vesicles from rats exposed to restraint, immobilization, or no stress, and their proteomes were identified by mass spectrometry. Data available via ProteomeXchange with identifier PXD009085 were validated, in part, by western blot. In utero electroporation was performed to study the direct transfer of recombinant aldolase C-GFP from brain cells to blood small extracellular vesicles. RESULTS: A differential proteome was identified among the experimental groups, including aldolase C, astrocytic glial fibrillary acidic protein, synaptophysin, and reelin. Additionally, we observed that, when expressed in the brain, aldolase C tagged with green fluorescent protein could be recovered in serum small extracellular vesicles. CONCLUSION: The protein cargo of serum small extracellular vesicles constitutes a valuable source of biomarkers of stress-induced diseases, including those characterized by depressive-like behaviors. Brain-to-periphery signaling mediated by a differential molecular cargo of small extracellular vesicles is a novel and challenging mechanism by which the brain might communicate health and disease states to the rest of the body.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Semiquantitative analysis of western blots was evaluated by comparing the relative optic densities of bands (fold change of stress over no stress) after restraint and immobilization using the Mann-Whitney test. In turn, the significant differences in each dataset, with a hypothetical value of 1 (no change), were assessed with a Wilcoxon-signed rank test.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:30535257
locator
sections[16] "Statistical Analysis" paragraph 2
quote
Semiquantitative analysis of western blots was evaluated by comparing the relative optic densities of bands (fold change of stress over no stress) after restraint and immobilization using the Mann-Whitney test. In turn, the significant differences in each dataset, with a hypothetical value of 1 (no change), were assessed with a Wilcoxon-signed rank test.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:30535257
locator
sections[14] "High-Resolution Proteomic Analysis" paragraph 6
quote
The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
null
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:30535257
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:PXD009085
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
blocked
blocked_on
method:group_comparison_mann_whitney
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:PXD009085
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:run_analysis blocked on method:group_comparison_mann_whitney
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:30535257
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1093/ijnp/pyy098
sha256
sha256:f5b6afb5004c5d414dc182786c1d2d091dcdf6c23691ba7f7a709f5d9635a572
bytes
56731
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1093/ijnp/pyy098
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
PMC6403096
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD009085
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=PXD009085
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD009085
version
null
note
The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085.
access_statement_kind
repository_route_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
rat serum exosomes after restriction stress
resolution_checked_at
2026-10-31T18:35:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:PXD009085 not downloaded
[1]
asset:data:geo:PXD009085 licence not read
analysis object · 4 fields
state
partial
methods array · 4 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
mann_whitney
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_mann_whitney
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
Semiquantitative analysis of western blots was evaluated by comparing the relative optic densities of bands (fold change of stress over no stress) after restraint and immobilization using the Mann-Whitney test. In turn, the significant differences in each dataset, with a hypothetical value of 1 (no change), were assessed with a Wilcoxon-signed rank test.
[1] object · 10 fields
id
method-2
family
group_comparison
specific
wilcoxon
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_wilcoxon
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.8
band
high
quote
Wilcoxon
[2] object · 10 fields
id
method-3
family
image_quantification
specific
densitometry
label
Image analysis / quantification
dsl_operations array · 2 items
[0]
segment_objects
[1]
quantify_intensity
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
image_stack
evidence object · 3 fields
score
0.8
band
high
quote
densitometr
[3] object · 10 fields
id
method-4
family
multi_omics_integration
specific
pathway_progeny
label
Multi-omics integration
dsl_operations array · 2 items
[0]
multiomics_factor_analysis
[1]
joint_pathway_score
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
aligned_multi_layer_matrices
evidence object · 3 fields
score
0.8
band
high
quote
progeny
targets array · 0 items
gaps array · 1 item
[0]
method.group_comparison_mann_whitney
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
false
required_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_mann_whitney
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney.
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]
PXD009085
resolved_accessions array · 1 item
[0]
PXD009085
statements array · 1 item
[0]
The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085.
basis
The paper names PXD009085 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 · 0 items
assets array · 2 items
[0]
source:pmid:30535257
[1]
data:geo:PXD009085
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
operation
group_comparison_mann_whitney
priority
null
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:PXD009085
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
2026-10-31T18:13:05Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
null
calls
3
usage object · 3 fields
prompt_tokens
41602
completion_tokens
1319
cached_tokens
14192
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:30535257
type
paper
label
pmid:30535257
[1] object · 3 fields
id
source:pmid:30535257
type
manuscript
label
PMID 30535257 full text
[2] object · 3 fields
id
data:geo:PXD009085
type
dataset
label
GEO PXD009085
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:30535257
type
paper
label
pmid:30535257
[1] object · 3 fields
id
source:pmid:30535257
type
manuscript
label
PMID 30535257 full text
[2] object · 3 fields
id
data:geo:PXD009085
type
dataset
label
GEO PXD009085
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-30535257
type
extraction
used array · 1 item
[0]
source:pmid:30535257
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD009085
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD009085
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:30535257
parent_hash
sha256:cb0b0b54114cb841a1d317fcffdef81206600e250f6faa0a8048c2248e7eb65e
fork_of
null
gaps array · 8 items
[0]
asset:data:geo:PXD009085 licence not read
[1]
asset:data:geo:PXD009085 not downloaded
[2]
execution.not_run
[3]
method.group_comparison_mann_whitney
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
[7]
step:run_analysis blocked on method:group_comparison_mann_whitney
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]
Small Extracellular Vesicles in Rat Serum Contain Astrocyte-Derived Protein Biom
[1]
bilization induced depressive-like behaviors in rats that were differentially reverted by a serot
[2]
ization induced depressive-like behaviors in rats that were differentially reverted by a serot
[3]
ized serum small extracellular vesicles from rats exposed to restraint, immobilization, or no
order_basis
paper_text_order:0
id
assay:1
[1] 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
0.93
evidence array · 1 item
[0]
ress, and their proteomes were identified by mass spectrometry. Data available via ProteomeXchange with ide
order_basis
paper_text_order:1078
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
0.99
evidence array · 4 items
[0]
tifier PXD009085 were validated, in part, by western blot. In utero electroporation was performed to s
[1]
6 independent samples per animal group. (d) Western blots and (e) the corresponding densitometric quan
[2]
clonal antibody against aldolase C, which in western blots recognizes a polypeptide antigen of 36 kD te
[3]
the mean ± SEM. Semiquantitative analysis of western blots was evaluated by comparing the relative opti
order_basis
paper_text_order:1186
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Semiquantitative analysis of western blots was evaluated by comparing the relative optic densities of bands (fold change of stress over no stress) after restraint and immobilization using the Mann-Whitney test. In turn, the significant differences in each dataset, with a hypothetical value of 1 (no change), were assessed with a Wilcoxon-signed rank 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:30535257", "kind": "science-record", "revision": 9, "content_hash": "sha256:1ae987b4de89c091f07684455ca7ca92c7ac916f008b956c2d505801fc0c7206", "created_at": "2026-11-01T15:40:39Z", "updated_at": "2026-11-01T22:43:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Small Extracellular Vesicles in Rat Serum Contain Astrocyte-Derived Protein Biomarkers of Repetitive Stress.", "doi": "10.1093/ijnp/pyy098", "pmid": "30535257", "authors": ["Cristóbal Gómez-Molina", "Mauricio Sandoval", "Roberto Henzi", "Juan Pablo Ramírez", "Manuel Varas-Godoy", "Alejandro Luarte", "Carlos Andres Lafourcade", "Alejandra Lopez-Verrilli", "Karl-Heinz Smalla", "Thilo Kaehne", "Ursula Wyneken"], "journal": "The international journal of neuropsychopharmacology", "year": 2019, "abstract": "BACKGROUND: Stress precipitates mood disorders, characterized by a range of symptoms present in different combinations, suggesting the existence of disease subtypes. Using an animal model, we previously described that repetitive stress via restraint or immobilization induced depressive-like behaviors in rats that were differentially reverted by a serotonin- or noradrenaline-based antidepressant drug, indicating that different neurobiological mechanisms may be involved. The forebrain astrocyte protein aldolase C, contained in small extracellular vesicles, was identified as a potential biomarker in the cerebrospinal fluid; however, its specific origin remains unknown. Here, we propose to investigate whether serum small extracellular vesicles contain a stress-specific protein cargo and whether serum aldolase C has a brain origin.\nMETHODS: We isolated and characterized serum small extracellular vesicles from rats exposed to restraint, immobilization, or no stress, and their proteomes were identified by mass spectrometry. Data available via ProteomeXchange with identifier PXD009085 were validated, in part, by western blot. In utero electroporation was performed to study the direct transfer of recombinant aldolase C-GFP from brain cells to blood small extracellular vesicles.\nRESULTS: A differential proteome was identified among the experimental groups, including aldolase C, astrocytic glial fibrillary acidic protein, synaptophysin, and reelin. Additionally, we observed that, when expressed in the brain, aldolase C tagged with green fluorescent protein could be recovered in serum small extracellular vesicles.\nCONCLUSION: The protein cargo of serum small extracellular vesicles constitutes a valuable source of biomarkers of stress-induced diseases, including those characterized by depressive-like behaviors. Brain-to-periphery signaling mediated by a differential molecular cargo of small extracellular vesicles is a novel and challenging mechanism by which the brain might communicate health and disease states to the rest of the body.", "claims": [{"id": "claim-method", "statement": "Semiquantitative analysis of western blots was evaluated by comparing the relative optic densities of bands (fold change of stress over no stress) after restraint and immobilization using the Mann-Whitney test. In turn, the significant differences in each dataset, with a hypothetical value of 1 (no change), were assessed with a Wilcoxon-signed rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30535257", "locator": "sections[16] \"Statistical Analysis\" paragraph 2", "quote": "Semiquantitative analysis of western blots was evaluated by comparing the relative optic densities of bands (fold change of stress over no stress) after restraint and immobilization using the Mann-Whitney test. In turn, the significant differences in each dataset, with a hypothetical value of 1 (no change), were assessed with a Wilcoxon-signed rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30535257", "locator": "sections[14] \"High-Resolution Proteomic Analysis\" paragraph 6", "quote": "The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:30535257"], "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:PXD009085"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_mann_whitney", "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:PXD009085"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_mann_whitney"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30535257", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/ijnp/pyy098", "sha256": "sha256:f5b6afb5004c5d414dc182786c1d2d091dcdf6c23691ba7f7a709f5d9635a572", "bytes": 56731, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/ijnp/pyy098", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6403096", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD009085", "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=PXD009085", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD009085", "version": null, "note": "The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085.", "access_statement_kind": "repository_route_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "rat serum exosomes after restriction stress", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD009085 not downloaded", "asset:data:geo:PXD009085 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Semiquantitative analysis of western blots was evaluated by comparing the relative optic densities of bands (fold change of stress over no stress) after restraint and immobilization using the Mann-Whitney test. In turn, the significant differences in each dataset, with a hypothetical value of 1 (no change), were assessed with a Wilcoxon-signed rank test."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "image_quantification", "specific": "densitometry", "label": "Image analysis / quantification", "dsl_operations": ["segment_objects", "quantify_intensity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["image_stack"], "evidence": {"score": 0.8, "band": "high", "quote": "densitometr"}}, {"id": "method-4", "family": "multi_omics_integration", "specific": "pathway_progeny", "label": "Multi-omics integration", "dsl_operations": ["multiomics_factor_analysis", "joint_pathway_score"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["aligned_multi_layer_matrices"], "evidence": {"score": 0.8, "band": "high", "quote": "progeny"}}], "targets": [], "gaps": ["method.group_comparison_mann_whitney"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney."}, "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": ["PXD009085"], "resolved_accessions": ["PXD009085"], "statements": ["The MS proteomics data obtained in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009085 (Vizcaino et al., 2016). The ProteomeXchange dataset has been made public via the PRIDE database, with the following details: ProteomeXchange title: rat serum exosomes after restriction stress, ProteomeXchange accession: PXD009085, PubMed ID: Not applicable, Publication DOI: Not applicable, Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD009085, FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD009085."], "basis": "The paper names PXD009085 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": [], "assets": ["source:pmid:30535257", "data:geo:PXD009085"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_mann_whitney", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD009085"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:05Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 41602, "completion_tokens": 1319, "cached_tokens": 14192}}, "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:30535257", "type": "paper", "label": "pmid:30535257"}, {"id": "source:pmid:30535257", "type": "manuscript", "label": "PMID 30535257 full text"}, {"id": "data:geo:PXD009085", "type": "dataset", "label": "GEO PXD009085"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30535257", "type": "paper", "label": "pmid:30535257"}, {"id": "source:pmid:30535257", "type": "manuscript", "label": "PMID 30535257 full text"}, {"id": "data:geo:PXD009085", "type": "dataset", "label": "GEO PXD009085"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30535257", "type": "extraction", "used": ["source:pmid:30535257"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD009085", "type": "accession_resolution", "used": ["data:geo:PXD009085"], "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:30535257", "parent_hash": "sha256:cb0b0b54114cb841a1d317fcffdef81206600e250f6faa0a8048c2248e7eb65e", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:PXD009085 licence not read", "asset:data:geo:PXD009085 not downloaded", "execution.not_run", "method.group_comparison_mann_whitney", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_mann_whitney"], "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": ["Small Extracellular Vesicles in Rat Serum Contain Astrocyte-Derived Protein Biom", "bilization induced depressive-like behaviors in rats that were differentially reverted by a serot", "ization induced depressive-like behaviors in rats that were differentially reverted by a serot", "ized serum small extracellular vesicles from rats exposed to restraint, immobilization, or no"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ress, and their proteomes were identified by mass spectrometry. Data available via ProteomeXchange with ide"], "order_basis": "paper_text_order:1078", "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": 0.99, "evidence": ["tifier PXD009085 were validated, in part, by western blot. In utero electroporation was performed to s", "6 independent samples per animal group. (d) Western blots and (e) the corresponding densitometric quan", "clonal antibody against aldolase C, which in western blots recognizes a polypeptide antigen of 36 kD te", "the mean ± SEM. Semiquantitative analysis of western blots was evaluated by comparing the relative opti"], "order_basis": "paper_text_order:1186", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Semiquantitative analysis of western blots was evaluated by comparing the relative optic densities of bands (fold change of stress over no stress) after restraint and immobilization using the Mann-Whitney test. In turn, the significant differences in each dataset, with a hypothetical value of 1 (no change), were assessed with a Wilcoxon-signed rank test."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}