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

pmid:37641878

The cold-inducible RNA-binding protein-Thioredoxin 1 pathway ameliorates mitochondrial dysfunction and mitochondrial dynamin-related protein 1 level in the hippocampus of aged mice with perioperative neurocognitive dysfunction.

Jingyao Huang · Yongliang Zhu · Yongxin Liu · Rui Zhang · Zhenjiang Zhang · Jie Liu · Zhihao Zhang · Yingxia Liang · Baoyu Ma

CNS neuroscience & therapeutics · 2024 doi:10.1111/cns.14433

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:37641878
kind
science-record
content_hash
sha256:ff7492f12a9a8f8116d702687c7a58015ecbfd9949f792715b0ce6795a0b5264
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T19:02:25Z
updated_at
2026-11-01T22:52:36Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
The cold-inducible RNA-binding protein-Thioredoxin 1 pathway ameliorates mitochondrial dysfunction and mitochondrial dynamin-related protein 1 level in the hippocampus of aged mice with perioperative neurocognitive dysfunction.
doi
10.1111/cns.14433
pmid
37641878
authors array · 9 items
[0]
Jingyao Huang
[1]
Yongliang Zhu
[2]
Yongxin Liu
[3]
Rui Zhang
[4]
Zhenjiang Zhang
[5]
Jie Liu
[6]
Zhihao Zhang
[7]
Yingxia Liang
[8]
Baoyu Ma
journal
CNS neuroscience & therapeutics
year
2024
abstract
BACKGROUND: As a multi-disease model, neuroinflammation, mitochondrial dysfunction, and oxidative stress might be involved in the pathogenic process of perioperative neurocognitive dysfunction (PND). Dynamin-related protein 1 (Drp1) could mediate mitochondrial fission and play important roles in mitochondrial dynamic homeostasis and mitochondria function. The Drp1 may be involved in PND development. The cold-inducible RNA-binding protein (Cirbp) could bind to the 3'-UTR of the thioredoxin 1 (Trx1) mRNA, control oxidative stress, and improve mitochondrial function. In this study, we hypothesized that the Cirbp-Trx1 pathway could ameliorate mitochondrial dysfunction and Drp1 levels in PND mice. METHODS: Differentially expressed genes were screened using the Gene Expression Omnibus (GEO) database GSE95426 and validated using PCR. Eighteen-month-old C57BL/6 mice were subjected to tibial fracture surgery to generate a PND model. Cirbp was upregulated by hippocampal stereotaxic injections of over-Cirbp plasmid according to the manufacturer's instructions for the in vivo DNA transfection reagent. Cirbp expression was measured using western blot (WB) and immunofluorescence (IF). The Morris water maze (MWM) was used to assess cognitive function. After behavioral testing, the hippocampal tissue was extracted to examine changes in mitochondrial Drp1, mitochondrial function, neuroinflammation, and oxidative stress. RESULTS: Differential gene screening showed that Cirbp expression was significantly downregulated (fold change >1.5, p = 0.003272) in the PND model. In this study, we also found that Cirbp protein levels were downregulated, accompanied by an impairment of cognition, a decrease in superoxide dismutase (SOD) activity, and an increase in malondialdehyde (MDA) content, mitochondrial Drp1 levels, neuroinflammation, and apoptosis. Cirbp overexpression increased Trx1 protein levels and reversed the damage. However, this protective effect was abolished by PX-12 treatment with a Trx1 inhibitor. CONCLUSIONS: The Cirbp-Trx1 pathway may regulate mitochondrial dysfunction and mitochondrial Drp1 expression in the hippocampus of PND mice to ameliorate cognitive dysfunction.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
The qRT‐PCR results were analyzed using unpaired Student's t‐tests, and data between multiple groups were analyzed using one‐way ANOVA followed by Tukey's post‐hoc test.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:37641878
locator
sections[18] "Statistical analysis" paragraph 2
quote
The qRT‐PCR results were analyzed using unpaired Student's t‐tests, and data between multiple groups were analyzed using one‐way ANOVA followed by Tukey's post‐hoc test.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
All data about this study are included in the article, and further inquiries can be directed to the corresponding authors.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:37641878
locator
sections[32] "DATA AVAILABILITY STATEMENT" paragraph 2
quote
All data about this study are included in the article, and further inquiries can be directed to the corresponding authors.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
The Cirbp‐Trx1 pathway may regulate mitochondrial dysfunction and mitochondrial Drp1 expression in the hippocampus of PND mice to ameliorate cognitive dysfunction.
kind
quantitative
target object · 4 fields
value
0.003272
unit
p-value
tolerance
null
source
Differential gene screening showed that Cirbp expression was significantly downregulated (fold change >1.5, p = 0.003272) in the PND model.
evidence array · 2 items
[0] object · 3 fields
asset
source:pmid:37641878
locator
sections[0] "Abstract" paragraph 4
quote
The Cirbp‐Trx1 pathway may regulate mitochondrial dysfunction and mitochondrial Drp1 expression in the hippocampus of PND mice to ameliorate cognitive dysfunction.
[1] object · 3 fields
asset
source:pmid:37641878
locator
sections[0] "Abstract" paragraph 3
quote
Differential gene screening showed that Cirbp expression was significantly downregulated (fold change >1.5, p = 0.003272) in the PND model.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
objective
The Cirbp‐Trx1 pathway may regulate mitochondrial dysfunction and mitochondrial Drp1 expression in the hippocampus of PND mice to ameliorate cognitive dysfunction.
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:37641878
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:GSE95426
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:student_t
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:GSE95426
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:student_t
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:37641878
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1111/cns.14433
sha256
sha256:7da60a4511b9d154952672d00e5b61d26e95ce9d10a1b26b4ae402f0df25658d
bytes
40417
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1111/cns.14433
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
PMC10915978
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE95426
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=GSE95426
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE95426
version
null
note
All data about this study are included in the article, and further inquiries can be directed to the corresponding authors.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
All data about this study are included in the article, and further inquiries can be directed to the corresponding authors.
access_statement_kind
data_availability_statement
sample_accessions array · 12 items
[0]
GSM2510565
[1]
GSM2510566
[2]
GSM2510567
[3]
GSM2510568
[4]
GSM2510569
[5]
GSM2510570
[6]
GSM2510571
[7]
GSM2510572
[8]
GSM2510573
[9]
GSM2510574
[10]
GSM2510575
[11]
GSM2510576
sample_count
12
group_sizes
null
group_sizes_basis
null
platform
22782
taxon
Mus musculus
title
Comprehensive analysis of differentially expressed lncRNAs and mRNAs in aged mice
resolution_checked_at
2026-11-01T19:09:46Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE95426 not downloaded
[1]
asset:data:geo:GSE95426 licence not read
analysis object · 4 fields
state
partial
methods array · 2 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
student_t_test
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
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
The qRT‐PCR results were analyzed using unpaired Student's t‐tests, and data between multiple groups were analyzed using one‐way ANOVA followed by Tukey's post‐hoc test.
[1] object · 10 fields
id
method-2
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
0.8
band
high
quote
ANOVA
targets array · 1 item
[0] object · 8 fields
id
target-published-estimate
claim_id
claim-target-result
operation
bootstrap_mean_difference
expected_value
0.003272
unit
p-value
tolerance
null
state
complete
note
The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold.
gaps array · 1 item
[0]
method.student_t
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]
student_t
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test.
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]
GSE95426
resolved_accessions array · 1 item
[0]
GSE95426
statements array · 1 item
[0]
All data about this study are included in the article, and further inquiries can be directed to the corresponding authors.
basis
The paper names GSE95426 in Gene Expression Omnibus (GEO) database 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:37641878
[1]
data:geo:GSE95426
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
operation
student_t
priority
null
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE95426
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
2026-11-01T18:51:47Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
11257
completion_tokens
1794
cached_tokens
264
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:37641878
type
paper
label
pmid:37641878
[1] object · 3 fields
id
source:pmid:37641878
type
manuscript
label
PMID 37641878 full text
[2] object · 3 fields
id
data:geo:GSE95426
type
dataset
label
GEO GSE95426
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:37641878
type
paper
label
pmid:37641878
[1] object · 3 fields
id
source:pmid:37641878
type
manuscript
label
PMID 37641878 full text
[2] object · 3 fields
id
data:geo:GSE95426
type
dataset
label
GEO GSE95426
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-37641878
type
extraction
used array · 1 item
[0]
source:pmid:37641878
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE95426
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE95426
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:37641878
parent_hash
sha256:abf6aecfc470f97253c4b1d5009f13553c50561ebc31b54e5b3e3b46e26a64f4
fork_of
null
gaps array · 8 items
[0]
asset:data:geo:GSE95426 licence not read
[1]
asset:data:geo:GSE95426 not downloaded
[2]
execution.not_run
[3]
method.student_t
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
[7]
step:run_analysis blocked on method:student_t
assays array · 6 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]
idated using PCR. Eighteen-month-old C57BL/6 mice were subjected to tibial fracture surgery to gene
[1]
g to the manufacturer's instructions for the in vivo DNA transfection reagent. Cirbp expression w
[2]
fracture surgery. One day after surgery, all mice were sacrificed, and total hippocampal RNA was extracted to
[3]
al Centre of Weifang Medical University. The mice were housed in an environment of temperature and
order_basis
paper_text_order:1049
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
transfection
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]
ufacturer's instructions for the in vivo DNA transfection reagent. Cirbp expression was measured using
order_basis
paper_text_order:1268
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 · 2 items
[0]
reagent. Cirbp expression was measured using western blot (WB) and immunofluorescence (IF). The Morris
[1]
l Cirbp and Trx1 expression were detected by western blot (WB) and immunofluorescence (IF). For the be
order_basis
paper_text_order:1326
id
assay:3
[3] 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 · 3 items
[0]
ion was measured using western blot (WB) and immunofluorescence (IF). The Morris water maze (MWM) was used t
[1]
ssion were detected by western blot (WB) and immunofluorescence (IF). For the behavioral test, the mice firs
[2]
teral stereotaxic delivery of over‐Cirbp and immunostaining for Cirbp (green). (C) Volcanic plot of mRNA
order_basis
paper_text_order:1348
id
assay:4
[4] 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
0.69
evidence array · 1 item
[0]
hondrial Drp1 levels, neuroinflammation, and apoptosis. Cirbp overexpression increased Trx1 protein
order_basis
paper_text_order:2028
id
assay:5
[5] 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]
The qRT‐PCR results were analyzed using unpaired Student's t‐tests, and data between multiple groups were analyzed using one‐way ANOVA followed by Tukey's post‐hoc test.
order_basis
consumes_earlier_output
id
assay:6
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37641878", "kind": "science-record", "revision": 5, "content_hash": "sha256:ff7492f12a9a8f8116d702687c7a58015ecbfd9949f792715b0ce6795a0b5264", "created_at": "2026-11-01T19:02:25Z", "updated_at": "2026-11-01T22:52:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The cold-inducible RNA-binding protein-Thioredoxin 1 pathway ameliorates mitochondrial dysfunction and mitochondrial dynamin-related protein 1 level in the hippocampus of aged mice with perioperative neurocognitive dysfunction.", "doi": "10.1111/cns.14433", "pmid": "37641878", "authors": ["Jingyao Huang", "Yongliang Zhu", "Yongxin Liu", "Rui Zhang", "Zhenjiang Zhang", "Jie Liu", "Zhihao Zhang", "Yingxia Liang", "Baoyu Ma"], "journal": "CNS neuroscience & therapeutics", "year": 2024, "abstract": "BACKGROUND: As a multi-disease model, neuroinflammation, mitochondrial dysfunction, and oxidative stress might be involved in the pathogenic process of perioperative neurocognitive dysfunction (PND). Dynamin-related protein 1 (Drp1) could mediate mitochondrial fission and play important roles in mitochondrial dynamic homeostasis and mitochondria function. The Drp1 may be involved in PND development. The cold-inducible RNA-binding protein (Cirbp) could bind to the 3'-UTR of the thioredoxin 1 (Trx1) mRNA, control oxidative stress, and improve mitochondrial function. In this study, we hypothesized that the Cirbp-Trx1 pathway could ameliorate mitochondrial dysfunction and Drp1 levels in PND mice.\nMETHODS: Differentially expressed genes were screened using the Gene Expression Omnibus (GEO) database GSE95426 and validated using PCR. Eighteen-month-old C57BL/6 mice were subjected to tibial fracture surgery to generate a PND model. Cirbp was upregulated by hippocampal stereotaxic injections of over-Cirbp plasmid according to the manufacturer's instructions for the in vivo DNA transfection reagent. Cirbp expression was measured using western blot (WB) and immunofluorescence (IF). The Morris water maze (MWM) was used to assess cognitive function. After behavioral testing, the hippocampal tissue was extracted to examine changes in mitochondrial Drp1, mitochondrial function, neuroinflammation, and oxidative stress.\nRESULTS: Differential gene screening showed that Cirbp expression was significantly downregulated (fold change >1.5, p = 0.003272) in the PND model. In this study, we also found that Cirbp protein levels were downregulated, accompanied by an impairment of cognition, a decrease in superoxide dismutase (SOD) activity, and an increase in malondialdehyde (MDA) content, mitochondrial Drp1 levels, neuroinflammation, and apoptosis. Cirbp overexpression increased Trx1 protein levels and reversed the damage. However, this protective effect was abolished by PX-12 treatment with a Trx1 inhibitor.\nCONCLUSIONS: The Cirbp-Trx1 pathway may regulate mitochondrial dysfunction and mitochondrial Drp1 expression in the hippocampus of PND mice to ameliorate cognitive dysfunction.", "claims": [{"id": "claim-method", "statement": "The qRT‐PCR results were analyzed using unpaired Student's t‐tests, and data between multiple groups were analyzed using one‐way ANOVA followed by Tukey's post‐hoc test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37641878", "locator": "sections[18] \"Statistical analysis\" paragraph 2", "quote": "The qRT‐PCR results were analyzed using unpaired Student's t‐tests, and data between multiple groups were analyzed using one‐way ANOVA followed by Tukey's post‐hoc test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data about this study are included in the article, and further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37641878", "locator": "sections[32] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "All data about this study are included in the article, and further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The Cirbp‐Trx1 pathway may regulate mitochondrial dysfunction and mitochondrial Drp1 expression in the hippocampus of PND mice to ameliorate cognitive dysfunction.", "kind": "quantitative", "target": {"value": 0.003272, "unit": "p-value", "tolerance": null, "source": "Differential gene screening showed that Cirbp expression was significantly downregulated (fold change >1.5, p = 0.003272) in the PND model."}, "evidence": [{"asset": "source:pmid:37641878", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The Cirbp‐Trx1 pathway may regulate mitochondrial dysfunction and mitochondrial Drp1 expression in the hippocampus of PND mice to ameliorate cognitive dysfunction."}, {"asset": "source:pmid:37641878", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Differential gene screening showed that Cirbp expression was significantly downregulated (fold change >1.5, p = 0.003272) in the PND model."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The Cirbp‐Trx1 pathway may regulate mitochondrial dysfunction and mitochondrial Drp1 expression in the hippocampus of PND mice to ameliorate cognitive dysfunction.", "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:37641878"], "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:GSE95426"], "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:student_t", "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:GSE95426"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37641878", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/cns.14433", "sha256": "sha256:7da60a4511b9d154952672d00e5b61d26e95ce9d10a1b26b4ae402f0df25658d", "bytes": 40417, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/cns.14433", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10915978", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE95426", "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=GSE95426", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE95426", "version": null, "note": "All data about this study are included in the article, and further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data about this study are included in the article, and further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2510565", "GSM2510566", "GSM2510567", "GSM2510568", "GSM2510569", "GSM2510570", "GSM2510571", "GSM2510572", "GSM2510573", "GSM2510574", "GSM2510575", "GSM2510576"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "22782", "taxon": "Mus musculus", "title": "Comprehensive analysis of differentially expressed  lncRNAs and mRNAs  in aged mice", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE95426 not downloaded", "asset:data:geo:GSE95426 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The qRT‐PCR results were analyzed using unpaired Student's t‐tests, and data between multiple groups were analyzed using one‐way ANOVA followed by Tukey's post‐hoc test."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "ANOVA"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 0.003272, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.student_t"]}, "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": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE95426"], "resolved_accessions": ["GSE95426"], "statements": ["All data about this study are included in the article, and further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE95426 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:37641878", "data:geo:GSE95426"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE95426"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:51:47Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11257, "completion_tokens": 1794, "cached_tokens": 264}}, "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:37641878", "type": "paper", "label": "pmid:37641878"}, {"id": "source:pmid:37641878", "type": "manuscript", "label": "PMID 37641878 full text"}, {"id": "data:geo:GSE95426", "type": "dataset", "label": "GEO GSE95426"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37641878", "type": "paper", "label": "pmid:37641878"}, {"id": "source:pmid:37641878", "type": "manuscript", "label": "PMID 37641878 full text"}, {"id": "data:geo:GSE95426", "type": "dataset", "label": "GEO GSE95426"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37641878", "type": "extraction", "used": ["source:pmid:37641878"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE95426", "type": "accession_resolution", "used": ["data:geo:GSE95426"], "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:37641878", "parent_hash": "sha256:abf6aecfc470f97253c4b1d5009f13553c50561ebc31b54e5b3e3b46e26a64f4", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE95426 licence not read", "asset:data:geo:GSE95426 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": ["idated using PCR. Eighteen-month-old C57BL/6 mice were subjected to tibial fracture surgery to gene", "g to the manufacturer's instructions for the in vivo DNA transfection reagent. Cirbp expression w", "fracture surgery. One day after surgery, all mice were sacrificed, and total hippocampal RNA was extracted to", "al Centre of Weifang Medical University. The mice were housed in an environment of temperature and"], "order_basis": "paper_text_order:1049", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["ufacturer's instructions for the in vivo DNA transfection reagent. Cirbp expression was measured using"], "order_basis": "paper_text_order:1268", "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": ["reagent. Cirbp expression was measured using western blot (WB) and immunofluorescence (IF). The Morris", "l Cirbp and Trx1 expression were detected by western blot (WB) and immunofluorescence (IF). For the be"], "order_basis": "paper_text_order:1326", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ion was measured using western blot (WB) and immunofluorescence (IF). The Morris water maze (MWM) was used t", "ssion were detected by western blot (WB) and immunofluorescence (IF). For the behavioral test, the mice firs", "teral stereotaxic delivery of over‐Cirbp and immunostaining for Cirbp (green). (C) Volcanic plot of mRNA"], "order_basis": "paper_text_order:1348", "id": "assay:4"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["hondrial Drp1 levels, neuroinflammation, and apoptosis. Cirbp overexpression increased Trx1 protein"], "order_basis": "paper_text_order:2028", "id": "assay:5"}, {"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": ["The qRT‐PCR results were analyzed using unpaired Student's t‐tests, and data between multiple groups were analyzed using one‐way ANOVA followed by Tukey's post‐hoc test."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}