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

pmid:37926093

Bone Marrow Mesenchymal Stem Cells Release miR-378a-5p-Carried Extracellular Vesicles to Alleviate Rheumatoid Arthritis.

Yaqin Zhang · Ziying Jiao · Shanshan Wang

Journal of innate immunity · 2023 doi:10.1159/000534830

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:37926093
kind
science-record
content_hash
sha256:298d354d9aab30c30473035bd93ecf9a1c6ad33b8f167243590487f1c12fa124
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T19:02:48Z
updated_at
2026-11-01T22:53:01Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Bone Marrow Mesenchymal Stem Cells Release miR-378a-5p-Carried Extracellular Vesicles to Alleviate Rheumatoid Arthritis.
doi
10.1159/000534830
pmid
37926093
authors array · 3 items
[0]
Yaqin Zhang
[1]
Ziying Jiao
[2]
Shanshan Wang
journal
Journal of innate immunity
year
2023
abstract
This study investigates whether bone marrow mesenchymal stem cell (BMSC)-derived extracellular vesicles (EVs) can affect rheumatoid arthritis (RA) by delivering microRNA (miR)-378a-5p to regulate the interferon regulatory factor 1/signal transducer and transcription 1 (IRF1/STAT1) axis. We identified RA-associated miRNAs using the GEO microarray dataset GSE121894. We found the most important miRNAs in RA synovial tissues using RT-qPCR. BMSC-derived EVs were ultracentrifuged and cocultured with human synovial microvascular endothelial cells (HSMECs) in vitro. Dual-luciferase and RNA immunoprecipitation studies examined miR-378a-5p's specific binding to IRF1. We also measured angiogenesis, migration, and proliferation using CCK-8, Transwell, and tube formation assays. Collagen-induced arthritis (CIA) mice models were created by inducing arthritis and scoring it. RA synovial tissues had low miR-378a-5p expression, whereas BMSC-derived EVs had high levels. The transfer of miR-378a-5p by BMSC-derived EVs to HSMECs boosted proliferation, migration, and angiogenesis. miR-378a-5p inhibited IRF1. MiR-378a-5p-containing BMSC-derived EVs decreased STAT1 phosphorylation and HSMEC IRF1 expression. EVs with miR-378a-5p mimic promoted HSMEC proliferation, migration, and angiogenesis, whereas dexmedetomidine inhibited STAT1 phosphorylation. In CIA mice, BMSC-derived EVs containing miR-378a-5p enhanced synovial vascular remodeling and histopathology. Thus, miR-378a-5p from BMSC-derived EVs promotes HSMEC proliferation, migration, and angiogenesis, inactivating the IRF1/STAT1 axis and preventing RA.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Data between groups were analyzed using an unpaired t test. One-way ANOVA was used to compare data among multiple groups, followed by Tukey’s post hoc tests. Data between groups at different time points were compared using repeated measures ANOVA combined with Bonferroni post hoc tests.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:37926093
locator
sections[22] "Statistical Analysis" paragraph 2
quote
Data between groups were analyzed using an unpaired t test. One-way ANOVA was used to compare data among multiple groups, followed by Tukey’s post hoc tests. Data between groups at different time points were compared using repeated measures ANOVA combined with Bonferroni post hoc tests.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:37926093
locator
sections[36] "Data Availability Statement" paragraph 2
quote
Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.
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:37926093
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:GSE121894
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:GSE121894
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 · 4 items
[0] object · 15 fields
id
source:pmid:37926093
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1159/000534830
sha256
sha256:e2b118f51d0bfe7e9b59c46d0f7bb1ce9bccf58081becfa128f1c8797e722ef2
bytes
70936
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1159/000534830
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
PMC10715757
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE121894
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=GSE121894
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE121894
version
null
note
Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.
access_statement_kind
data_availability_statement
sample_accessions array · 58 items
[0]
GSM3449621
[1]
GSM3449622
[2]
GSM3449623
[3]
GSM3449624
[4]
GSM3449625
[5]
GSM3449626
[6]
GSM3449627
[7]
GSM3449628
[8]
GSM3449629
[9]
GSM3449630
[10]
GSM3449631
[11]
GSM3449632
[12]
GSM3449633
[13]
GSM3449634
[14]
GSM3449635
[15]
GSM3449636
[16]
GSM3449637
[17]
GSM3449638
[18]
GSM3449639
[19]
GSM3449640
[20]
GSM3449641
[21]
GSM3449642
[22]
GSM3449643
[23]
GSM3449644
[24]
GSM3449645
[25]
GSM3449646
[26]
GSM3449647
[27]
GSM3449648
[28]
GSM3449649
[29]
GSM3449650
[30]
GSM3449651
[31]
GSM3449652
[32]
GSM3449653
[33]
GSM3449654
[34]
GSM3449655
[35]
GSM3449656
[36]
GSM3449657
[37]
GSM3449658
[38]
GSM3449659
[39]
GSM3449660
[40]
GSM3449661
[41]
GSM3449662
[42]
GSM3449663
[43]
GSM3449664
[44]
GSM3449665
[45]
GSM3449666
[46]
GSM3449667
[47]
GSM3449668
[48]
GSM3449669
[49]
GSM3449670
[50]
GSM3449671
[51]
GSM3449672
[52]
GSM3449673
[53]
GSM3449674
[54]
GSM3449675
[55]
GSM3449676
[56]
GSM3449677
[57]
GSM3449678
sample_count
58
group_sizes
null
group_sizes_basis
null
platform
25734
taxon
Homo sapiens
title
Gene expression profile of endothelial cells derived from circulating progenitors issued from patients with rheumatoid arthritis
resolution_checked_at
2026-11-01T18:46:34Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 15 fields
id
data:geo:GSE185059
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=GSE185059
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE185059
version
null
note
Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.
access_statement_kind
data_availability_statement
sample_accessions array · 6 items
[0]
GSM5604914
[1]
GSM5604915
[2]
GSM5604916
[3]
GSM5604917
[4]
GSM5604918
[5]
GSM5604919
sample_count
6
group_sizes
null
group_sizes_basis
null
platform
29371
taxon
Homo sapiens
title
Identification of exosomal mRNA, lncRNA and circRNA signatures in an osteoarthritis synovial fluid-exosomal study
resolution_checked_at
2026-11-01T19:09:46Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[3] object · 15 fields
id
data:geo:GSE44711
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=GSE44711
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE44711
version
null
note
Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.
access_statement_kind
data_availability_statement
sample_accessions array · 16 items
[0]
GSM1089229
[1]
GSM1089230
[2]
GSM1089231
[3]
GSM1089232
[4]
GSM1089233
[5]
GSM1089234
[6]
GSM1089235
[7]
GSM1089236
[8]
GSM1089237
[9]
GSM1089238
[10]
GSM1089239
[11]
GSM1089240
[12]
GSM1089241
[13]
GSM1089242
[14]
GSM1089243
[15]
GSM1089244
sample_count
16
group_sizes
null
group_sizes_basis
null
platform
10558
taxon
Homo sapiens
title
Gene expression in Early-Onset Preeclampsia Placentas and Controls
resolution_checked_at
2026-11-01T18:46:34Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 6 items
[0]
asset:data:geo:GSE121894 not downloaded
[1]
asset:data:geo:GSE121894 licence not read
[2]
asset:data:geo:GSE185059 not downloaded
[3]
asset:data:geo:GSE185059 licence not read
[4]
asset:data:geo:GSE44711 not downloaded
[5]
asset:data:geo:GSE44711 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
Data between groups were analyzed using an unpaired t test. One-way ANOVA was used to compare data among multiple groups, followed by Tukey’s post hoc tests. Data between groups at different time points were compared using repeated measures ANOVA combined with Bonferroni post hoc tests.
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 3 items
[0]
GSE121894
[1]
GSE185059
[2]
GSE44711
resolved_accessions array · 3 items
[0]
GSE121894
[1]
GSE185059
[2]
GSE44711
statements array · 1 item
[0]
Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.
basis
The paper names GSE121894, GSE185059, GSE44711 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 2 items
[0]
source:pmid:37926093
[1]
data:geo:GSE121894
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:GSE121894
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
2026-11-01T18:58:13Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
20887
completion_tokens
1171
cached_tokens
188
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:37926093
type
paper
label
pmid:37926093
[1] object · 3 fields
id
source:pmid:37926093
type
manuscript
label
PMID 37926093 full text
[2] object · 3 fields
id
data:geo:GSE121894
type
dataset
label
GEO GSE121894
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:37926093
type
paper
label
pmid:37926093
[1] object · 3 fields
id
source:pmid:37926093
type
manuscript
label
PMID 37926093 full text
[2] object · 3 fields
id
data:geo:GSE121894
type
dataset
label
GEO GSE121894
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-37926093
type
extraction
used array · 1 item
[0]
source:pmid:37926093
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE121894
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE121894
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:37926093
parent_hash
sha256:7682ad169eb3c5b2a85146432f57372428f584a6da2319e834ca4cc2546c9a84
fork_of
null
gaps array · 10 items
[0]
asset:data:geo:GSE121894 licence not read
[1]
asset:data:geo:GSE121894 not downloaded
[2]
asset:data:geo:GSE185059 licence not read
[3]
asset:data:geo:GSE185059 not downloaded
[4]
asset:data:geo:GSE44711 licence not read
[5]
asset:data:geo:GSE44711 not downloaded
[6]
execution.not_run
[7]
review.human_critique
[8]
review.independent_reader
[9]
review.machine_critique
assays array · 5 items
[0] object · 11 fields
role
data_generation
definition_id
microarray
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
dentified RA-associated miRNAs using the GEO microarray dataset GSE121894. We found the most importa
order_basis
paper_text_order:413
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
0.99
evidence array · 2 items
[0]
mportant miRNAs in RA synovial tissues using RT-qPCR. BMSC-derived EVs were ultracentrifuged and
[1]
rtant miRNAs in RA synovial tissues using RT-qPCR. BMSC-derived EVs were ultracentrifuged and
order_basis
paper_text_order:507
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
apoptosis_assay
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]
ogenesis, migration, and proliferation using CCK-8, Transwell, and tube formation assays. Colla
order_basis
paper_text_order:808
id
assay:3
[3] object · 11 fields
role
data_generation
definition_id
cell_culture
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]
BMSCs (ATCC, Manassas, VA; PCS-500-012) were cultured in complete Dulbecco’s modified Eagle medium (D
[1]
from Genechem (Shanghai, China). HSMECs were cultured in cell culture dishes in a 6-well plate at a s
[2]
from Genechem (Shanghai, China). HSMECs were cultured in cell culture dishes in a 6-well plate at
[3]
ence, the cells were subcultured in DMEM and passaged into new flasks. Cell collection was perform
order_basis
paper_text_order:2381
id
assay:4
[4] 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 between groups were analyzed using an unpaired t test. One-way ANOVA was used to compare data among multiple groups, followed by Tukey’s post hoc tests. Data between groups at different time points were compared using repeated measures ANOVA combined with Bonferroni post hoc tests.
order_basis
consumes_earlier_output
id
assay:5
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37926093", "kind": "science-record", "revision": 5, "content_hash": "sha256:298d354d9aab30c30473035bd93ecf9a1c6ad33b8f167243590487f1c12fa124", "created_at": "2026-11-01T19:02:48Z", "updated_at": "2026-11-01T22:53:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bone Marrow Mesenchymal Stem Cells Release miR-378a-5p-Carried Extracellular Vesicles to Alleviate Rheumatoid Arthritis.", "doi": "10.1159/000534830", "pmid": "37926093", "authors": ["Yaqin Zhang", "Ziying Jiao", "Shanshan Wang"], "journal": "Journal of innate immunity", "year": 2023, "abstract": "This study investigates whether bone marrow mesenchymal stem cell (BMSC)-derived extracellular vesicles (EVs) can affect rheumatoid arthritis (RA) by delivering microRNA (miR)-378a-5p to regulate the interferon regulatory factor 1/signal transducer and transcription 1 (IRF1/STAT1) axis. We identified RA-associated miRNAs using the GEO microarray dataset GSE121894. We found the most important miRNAs in RA synovial tissues using RT-qPCR. BMSC-derived EVs were ultracentrifuged and cocultured with human synovial microvascular endothelial cells (HSMECs) in vitro. Dual-luciferase and RNA immunoprecipitation studies examined miR-378a-5p's specific binding to IRF1. We also measured angiogenesis, migration, and proliferation using CCK-8, Transwell, and tube formation assays. Collagen-induced arthritis (CIA) mice models were created by inducing arthritis and scoring it. RA synovial tissues had low miR-378a-5p expression, whereas BMSC-derived EVs had high levels. The transfer of miR-378a-5p by BMSC-derived EVs to HSMECs boosted proliferation, migration, and angiogenesis. miR-378a-5p inhibited IRF1. MiR-378a-5p-containing BMSC-derived EVs decreased STAT1 phosphorylation and HSMEC IRF1 expression. EVs with miR-378a-5p mimic promoted HSMEC proliferation, migration, and angiogenesis, whereas dexmedetomidine inhibited STAT1 phosphorylation. In CIA mice, BMSC-derived EVs containing miR-378a-5p enhanced synovial vascular remodeling and histopathology. Thus, miR-378a-5p from BMSC-derived EVs promotes HSMEC proliferation, migration, and angiogenesis, inactivating the IRF1/STAT1 axis and preventing RA.", "claims": [{"id": "claim-method", "statement": "Data between groups were analyzed using an unpaired t test. One-way ANOVA was used to compare data among multiple groups, followed by Tukey’s post hoc tests. Data between groups at different time points were compared using repeated measures ANOVA combined with Bonferroni post hoc tests.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37926093", "locator": "sections[22] \"Statistical Analysis\" paragraph 2", "quote": "Data between groups were analyzed using an unpaired t test. One-way ANOVA was used to compare data among multiple groups, followed by Tukey’s post hoc tests. Data between groups at different time points were compared using repeated measures ANOVA combined with Bonferroni post hoc tests."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37926093", "locator": "sections[36] \"Data Availability Statement\" paragraph 2", "quote": "Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author."}], "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:37926093"], "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:GSE121894"], "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:GSE121894"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37926093", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1159/000534830", "sha256": "sha256:e2b118f51d0bfe7e9b59c46d0f7bb1ce9bccf58081becfa128f1c8797e722ef2", "bytes": 70936, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1159/000534830", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10715757", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE121894", "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=GSE121894", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE121894", "version": null, "note": "Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3449621", "GSM3449622", "GSM3449623", "GSM3449624", "GSM3449625", "GSM3449626", "GSM3449627", "GSM3449628", "GSM3449629", "GSM3449630", "GSM3449631", "GSM3449632", "GSM3449633", "GSM3449634", "GSM3449635", "GSM3449636", "GSM3449637", "GSM3449638", "GSM3449639", "GSM3449640", "GSM3449641", "GSM3449642", "GSM3449643", "GSM3449644", "GSM3449645", "GSM3449646", "GSM3449647", "GSM3449648", "GSM3449649", "GSM3449650", "GSM3449651", "GSM3449652", "GSM3449653", "GSM3449654", "GSM3449655", "GSM3449656", "GSM3449657", "GSM3449658", "GSM3449659", "GSM3449660", "GSM3449661", "GSM3449662", "GSM3449663", "GSM3449664", "GSM3449665", "GSM3449666", "GSM3449667", "GSM3449668", "GSM3449669", "GSM3449670", "GSM3449671", "GSM3449672", "GSM3449673", "GSM3449674", "GSM3449675", "GSM3449676", "GSM3449677", "GSM3449678"], "sample_count": 58, "group_sizes": null, "group_sizes_basis": null, "platform": "25734", "taxon": "Homo sapiens", "title": "Gene expression profile of endothelial cells derived from circulating progenitors issued from patients with rheumatoid arthritis", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE185059", "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=GSE185059", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE185059", "version": null, "note": "Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5604914", "GSM5604915", "GSM5604916", "GSM5604917", "GSM5604918", "GSM5604919"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "29371", "taxon": "Homo sapiens", "title": "Identification of exosomal mRNA, lncRNA and circRNA signatures in an osteoarthritis synovial fluid-exosomal study", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE44711", "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=GSE44711", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE44711", "version": null, "note": "Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1089229", "GSM1089230", "GSM1089231", "GSM1089232", "GSM1089233", "GSM1089234", "GSM1089235", "GSM1089236", "GSM1089237", "GSM1089238", "GSM1089239", "GSM1089240", "GSM1089241", "GSM1089242", "GSM1089243", "GSM1089244"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Gene expression in Early-Onset Preeclampsia Placentas and Controls", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE121894 not downloaded", "asset:data:geo:GSE121894 licence not read", "asset:data:geo:GSE185059 not downloaded", "asset:data:geo:GSE185059 licence not read", "asset:data:geo:GSE44711 not downloaded", "asset:data:geo:GSE44711 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Data between groups were analyzed using an unpaired t test. One-way ANOVA was used to compare data among multiple groups, followed by Tukey’s post hoc tests. Data between groups at different time points were compared using repeated measures ANOVA combined with Bonferroni post hoc tests."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE121894", "GSE185059", "GSE44711"], "resolved_accessions": ["GSE121894", "GSE185059", "GSE44711"], "statements": ["Data are not publicly available due to ethical reasons. Further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE121894, GSE185059, GSE44711 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:37926093", "data:geo:GSE121894"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE121894"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:58:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 20887, "completion_tokens": 1171, "cached_tokens": 188}}, "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:37926093", "type": "paper", "label": "pmid:37926093"}, {"id": "source:pmid:37926093", "type": "manuscript", "label": "PMID 37926093 full text"}, {"id": "data:geo:GSE121894", "type": "dataset", "label": "GEO GSE121894"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37926093", "type": "paper", "label": "pmid:37926093"}, {"id": "source:pmid:37926093", "type": "manuscript", "label": "PMID 37926093 full text"}, {"id": "data:geo:GSE121894", "type": "dataset", "label": "GEO GSE121894"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37926093", "type": "extraction", "used": ["source:pmid:37926093"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE121894", "type": "accession_resolution", "used": ["data:geo:GSE121894"], "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:37926093", "parent_hash": "sha256:7682ad169eb3c5b2a85146432f57372428f584a6da2319e834ca4cc2546c9a84", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE121894 licence not read", "asset:data:geo:GSE121894 not downloaded", "asset:data:geo:GSE185059 licence not read", "asset:data:geo:GSE185059 not downloaded", "asset:data:geo:GSE44711 licence not read", "asset:data:geo:GSE44711 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["dentified RA-associated miRNAs using the GEO microarray dataset GSE121894. We found the most importa"], "order_basis": "paper_text_order:413", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["mportant miRNAs in RA synovial tissues using RT-qPCR. BMSC-derived EVs were ultracentrifuged and", "rtant miRNAs in RA synovial tissues using RT-qPCR. BMSC-derived EVs were ultracentrifuged and"], "order_basis": "paper_text_order:507", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ogenesis, migration, and proliferation using CCK-8, Transwell, and tube formation assays. Colla"], "order_basis": "paper_text_order:808", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["BMSCs (ATCC, Manassas, VA; PCS-500-012) were cultured in complete Dulbecco’s modified Eagle medium (D", "from Genechem (Shanghai, China). HSMECs were cultured in cell culture dishes in a 6-well plate at a s", "from Genechem (Shanghai, China). HSMECs were cultured in cell culture dishes in a 6-well plate at", "ence, the cells were subcultured in DMEM and passaged into new flasks. Cell collection was perform"], "order_basis": "paper_text_order:2381", "id": "assay:4"}, {"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 between groups were analyzed using an unpaired t test. One-way ANOVA was used to compare data among multiple groups, followed by Tukey’s post hoc tests. Data between groups at different time points were compared using repeated measures ANOVA combined with Bonferroni post hoc tests."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}