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

pmid:38672131

Increased Circulating CD14+ Monocytes in Patients with Psoriatic Arthritis Presenting Impaired Apoptosis Activity.

Shang-Hung Lin · Chung-Yuan Hsu · Sung-Chou Li

Biomedicines · 2024 doi:10.3390/biomedicines12040775

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:38672131
kind
science-record
content_hash
sha256:fa1081ec0ebc6823ab3de57b181ddd45300652e1e8d20fc911bc051200085943
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T19:20:38Z
updated_at
2026-11-01T22:54:13Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Increased Circulating CD14+ Monocytes in Patients with Psoriatic Arthritis Presenting Impaired Apoptosis Activity.
doi
10.3390/biomedicines12040775
pmid
38672131
authors array · 3 items
[0]
Shang-Hung Lin
[1]
Chung-Yuan Hsu
[2]
Sung-Chou Li
journal
Biomedicines
year
2024
abstract
Psoriatic arthritis (PsA) is a chronic inflammatory arthritis primarily affecting peripheral and axial joints. The osteolytic effect in the damaged joint is mediated by osteoclast activation. We aimed to investigate differential gene expression in peripheral CD14+ monocytes between patients with psoriatic arthritis (n = 15) and healthy controls (HCs; n = 15). Circulating CD14+ monocytes were isolated from peripheral blood mononuclear cells using CD14+ magnetic beads. Cell apoptosis was measured via Annexin V using flow cytometry. The gene expression profiling was analyzed via microarray (available in the NCBI GEO database; accession number GSE261765), and the candidate genes were validated using PCR. The results showed a higher number of peripheral CD14+ monocytes in patients with PsA than in the HCs. By analyzing the microarray data, identifying the differentially expressed genes, and conducting pathway enrichment analysis, we found that the apoptosis signaling pathway in CD14+ cells was significantly impaired in patients with PsA compared to the HCs. Among the candidate genes in the apoptotic signaling pathway, the relative expression level of cathepsin L was confirmed to be significantly lower in the PsAs than in the HCs. We concluded that the numbers of peripheral CD14+ monocytes increased, and their apoptosis activity was impaired in patients with PsA, which could lead to enhanced macrophage maturation and osteoclast activation. The resistance of apoptotic death in peripheral CD14+ monocytes may contribute to active joint inflammation in PsA.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
The generated raw CEL files were analyzed using Transcription Analysis Console 4.0 (Thermo Fisher Scientific, Inc., Carlsbad, CA, USA) to conduct ANOVA, identify the differentially expressed genes, and generate the volcano plot. In addition, we also used Partek Genomics Suite 7.0 (Partek, St. Louis, MO, USA) to conduct pathway enrichment analysis.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:38672131
locator
sections[6] "2.4. Microarray Assay and Analysis" paragraph 2
quote
The generated raw CEL files were analyzed using Transcription Analysis Console 4.0 (Thermo Fisher Scientific, Inc., Carlsbad, CA, USA) to conduct ANOVA, identify the differentially expressed genes, and generate the volcano plot. In addition, we also used Partek Genomics Suite 7.0 (Partek, St. Louis, MO, USA) to conduct pathway enrichment analysis.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:38672131
locator
sections[23] "Data Availability Statement" paragraph 2
quote
Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
The study found that the apoptosis signaling pathway was impaired in PsA CD14+ monocytes, with cathepsin L expression significantly lower than in healthy controls, and the microarray raw data were deposited in NCBI GEO under accession GSE261765.
kind
qualitative
target
null
evidence array · 3 items
[0] object · 3 fields
asset
source:pmid:38672131
locator
sections[0] "Abstract" paragraph 1
quote
By analyzing the microarray data, identifying the differentially expressed genes, and conducting pathway enrichment analysis, we found that the apoptosis signaling pathway in CD14+ cells was significantly impaired in patients with PsA compared to the HCs.
[1] object · 3 fields
asset
source:pmid:38672131
locator
sections[0] "Abstract" paragraph 1
quote
Among the candidate genes in the apoptotic signaling pathway, the relative expression level of cathepsin L was confirmed to be significantly lower in the PsAs than in the HCs.
[2] object · 3 fields
asset
source:pmid:38672131
locator
sections[0] "Abstract" paragraph 1
quote
The gene expression profiling was analyzed via microarray (available in the NCBI GEO database; accession number GSE261765), and the candidate genes were validated using PCR.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
The study found that the apoptosis signaling pathway was impaired in PsA CD14+ monocytes, with cathepsin L expression significantly lower than in healthy controls, and the microarray raw data were deposited in NCBI GEO under accession GSE261765.
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:38672131
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:GSE261765
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:GSE261765
outputs array · 1 item
[0]
the replicated result and its comparison
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:38672131
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3390/biomedicines12040775
sha256
sha256:0661ac3cb4faee1c767fc2e8f2153bd5da54ca37c9faf4dc7a47b498016e5253
bytes
38080
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3390/biomedicines12040775
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
PMC11048590
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE261765
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=GSE261765
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE261765
version
null
note
Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765.
access_statement_kind
data_availability_statement
sample_accessions array · 4 items
[0]
GSM8150918
[1]
GSM8150919
[2]
GSM8150920
[3]
GSM8150921
sample_count
4
group_sizes
null
group_sizes_basis
null
platform
23126
taxon
Homo sapiens
title
Gene expression profile in monocyte of PsA patients
resolution_checked_at
2026-11-01T20:16:08Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE261765 not downloaded
[1]
asset:data:geo:GSE261765 licence not read
analysis object · 4 fields
state
complete
methods array · 2 items
[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
The generated raw CEL files were analyzed using Transcription Analysis Console 4.0 (Thermo Fisher Scientific, Inc., Carlsbad, CA, USA) to conduct ANOVA, identify the differentially expressed genes, and generate the volcano plot. In addition, we also used Partek Genomics Suite 7.0 (Partek, St. Louis, MO, USA) to conduct pathway enrichment analysis.
[1] object · 10 fields
id
method-2
family
network_analysis
specific
pathway_enrichment
label
Network / pathway analysis
dsl_operations array · 1 item
[0]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.7
band
medium
quote
pathway enrichment
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 · 1 item
[0]
GSE261765
resolved_accessions array · 1 item
[0]
GSE261765
statements array · 1 item
[0]
Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765.
basis
The paper names GSE261765 in NCBI 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:38672131
[1]
data:geo:GSE261765
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:GSE261765
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-01T19:16:59Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
12072
completion_tokens
1376
cached_tokens
128
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:38672131
type
paper
label
pmid:38672131
[1] object · 3 fields
id
source:pmid:38672131
type
manuscript
label
PMID 38672131 full text
[2] object · 3 fields
id
data:geo:GSE261765
type
dataset
label
GEO GSE261765
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:38672131
type
paper
label
pmid:38672131
[1] object · 3 fields
id
source:pmid:38672131
type
manuscript
label
PMID 38672131 full text
[2] object · 3 fields
id
data:geo:GSE261765
type
dataset
label
GEO GSE261765
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-38672131
type
extraction
used array · 1 item
[0]
source:pmid:38672131
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE261765
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE261765
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:38672131
parent_hash
sha256:35b6f0e31ff1fef7105e1684ea9ed394de4f957662076da736af092b3f4de9ac
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:GSE261765 licence not read
[1]
asset:data:geo:GSE261765 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 5 items
[0] 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
0.99
evidence array · 4 items
[0]
with Psoriatic Arthritis Presenting Impaired Apoptosis Activity.
[1]
clear cells using CD14+ magnetic beads. Cell apoptosis was measured via Annexin V using flow cytome
[2]
thway enrichment analysis, we found that the apoptosis signaling pathway in CD14+ cells was signifi
[3]
ipheral CD14+ monocytes increased, and their apoptosis activity was impaired in patients with PsA,
order_basis
paper_text_order:50
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
flow_cytometry
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]
l apoptosis was measured via Annexin V using flow cytometry. The gene expression profiling was analyzed
order_basis
paper_text_order:590
id
assay:2
[2] 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
0.99
evidence array · 4 items
[0]
e gene expression profiling was analyzed via microarray (available in the NCBI GEO database; accessi
[1]
s with PsA than in the HCs. By analyzing the microarray data, identifying the differentially express
[2]
er of monocytes than the HCs, we conducted a microarray assay (Clariom D Human) on the monocyte samp
[3]
gene expression profiles were examined using microarray and qPCR assays. (A) We used a volcano plot
order_basis
paper_text_order:653
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 · 4 items
[0]
apoptosis-related genes, CTSL and IKBKB, for qPCR validation since they had the largest expres
[1]
) and HCs (n = 15). As shown in Figure 3B,C, qPCR validation confirmed that CTSL was downregul
[2]
profiles were examined using microarray and qPCR assays. (A) We used a volcano plot (generate
[3]
y (p value < 0.05 based on ANOVA). (B,C) The qPCR results compared nine HC and nine PsA monocy
order_basis
paper_text_order:5830
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]
The generated raw CEL files were analyzed using Transcription Analysis Console 4.0 (Thermo Fisher Scientific, Inc., Carlsbad, CA, USA) to conduct ANOVA, identify the differentially expressed genes, and generate the volcano plot. In addition, we also used Partek Genomics Suite 7.0 (Partek, St. Louis, MO, USA) to conduct pathway enrichment analysis.
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:38672131", "kind": "science-record", "revision": 5, "content_hash": "sha256:fa1081ec0ebc6823ab3de57b181ddd45300652e1e8d20fc911bc051200085943", "created_at": "2026-11-01T19:20:38Z", "updated_at": "2026-11-01T22:54:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Increased Circulating CD14+ Monocytes in Patients with Psoriatic Arthritis Presenting Impaired Apoptosis Activity.", "doi": "10.3390/biomedicines12040775", "pmid": "38672131", "authors": ["Shang-Hung Lin", "Chung-Yuan Hsu", "Sung-Chou Li"], "journal": "Biomedicines", "year": 2024, "abstract": "Psoriatic arthritis (PsA) is a chronic inflammatory arthritis primarily affecting peripheral and axial joints. The osteolytic effect in the damaged joint is mediated by osteoclast activation. We aimed to investigate differential gene expression in peripheral CD14+ monocytes between patients with psoriatic arthritis (n = 15) and healthy controls (HCs; n = 15). Circulating CD14+ monocytes were isolated from peripheral blood mononuclear cells using CD14+ magnetic beads. Cell apoptosis was measured via Annexin V using flow cytometry. The gene expression profiling was analyzed via microarray (available in the NCBI GEO database; accession number GSE261765), and the candidate genes were validated using PCR. The results showed a higher number of peripheral CD14+ monocytes in patients with PsA than in the HCs. By analyzing the microarray data, identifying the differentially expressed genes, and conducting pathway enrichment analysis, we found that the apoptosis signaling pathway in CD14+ cells was significantly impaired in patients with PsA compared to the HCs. Among the candidate genes in the apoptotic signaling pathway, the relative expression level of cathepsin L was confirmed to be significantly lower in the PsAs than in the HCs. We concluded that the numbers of peripheral CD14+ monocytes increased, and their apoptosis activity was impaired in patients with PsA, which could lead to enhanced macrophage maturation and osteoclast activation. The resistance of apoptotic death in peripheral CD14+ monocytes may contribute to active joint inflammation in PsA.", "claims": [{"id": "claim-method", "statement": "The generated raw CEL files were analyzed using Transcription Analysis Console 4.0 (Thermo Fisher Scientific, Inc., Carlsbad, CA, USA) to conduct ANOVA, identify the differentially expressed genes, and generate the volcano plot. In addition, we also used Partek Genomics Suite 7.0 (Partek, St. Louis, MO, USA) to conduct pathway enrichment analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38672131", "locator": "sections[6] \"2.4. Microarray Assay and Analysis\" paragraph 2", "quote": "The generated raw CEL files were analyzed using Transcription Analysis Console 4.0 (Thermo Fisher Scientific, Inc., Carlsbad, CA, USA) to conduct ANOVA, identify the differentially expressed genes, and generate the volcano plot. In addition, we also used Partek Genomics Suite 7.0 (Partek, St. Louis, MO, USA) to conduct pathway enrichment analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38672131", "locator": "sections[23] \"Data Availability Statement\" paragraph 2", "quote": "Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study found that the apoptosis signaling pathway was impaired in PsA CD14+ monocytes, with cathepsin L expression significantly lower than in healthy controls, and the microarray raw data were deposited in NCBI GEO under accession GSE261765.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38672131", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "By analyzing the microarray data, identifying the differentially expressed genes, and conducting pathway enrichment analysis, we found that the apoptosis signaling pathway in CD14+ cells was significantly impaired in patients with PsA compared to the HCs."}, {"asset": "source:pmid:38672131", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Among the candidate genes in the apoptotic signaling pathway, the relative expression level of cathepsin L was confirmed to be significantly lower in the PsAs than in the HCs."}, {"asset": "source:pmid:38672131", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The gene expression profiling was analyzed via microarray (available in the NCBI GEO database; accession number GSE261765), and the candidate genes were validated using PCR."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study found that the apoptosis signaling pathway was impaired in PsA CD14+ monocytes, with cathepsin L expression significantly lower than in healthy controls, and the microarray raw data were deposited in NCBI GEO under accession GSE261765.", "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:38672131"], "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:GSE261765"], "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:GSE261765"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38672131", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/biomedicines12040775", "sha256": "sha256:0661ac3cb4faee1c767fc2e8f2153bd5da54ca37c9faf4dc7a47b498016e5253", "bytes": 38080, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/biomedicines12040775", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11048590", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE261765", "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=GSE261765", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE261765", "version": null, "note": "Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM8150918", "GSM8150919", "GSM8150920", "GSM8150921"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "23126", "taxon": "Homo sapiens", "title": "Gene expression profile in monocyte of PsA patients", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE261765 not downloaded", "asset:data:geo:GSE261765 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": "The generated raw CEL files were analyzed using Transcription Analysis Console 4.0 (Thermo Fisher Scientific, Inc., Carlsbad, CA, USA) to conduct ANOVA, identify the differentially expressed genes, and generate the volcano plot. In addition, we also used Partek Genomics Suite 7.0 (Partek, St. Louis, MO, USA) to conduct pathway enrichment analysis."}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "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": ["GSE261765"], "resolved_accessions": ["GSE261765"], "statements": ["Please contact Sung-Chou Li (raymond.pinus@gmail.com) for data requests. The microarray raw data are available in the NCBI GEO database, accession number GSE261765."], "basis": "The paper names GSE261765 in NCBI 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:38672131", "data:geo:GSE261765"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE261765"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:16:59Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12072, "completion_tokens": 1376, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38672131", "type": "paper", "label": "pmid:38672131"}, {"id": "source:pmid:38672131", "type": "manuscript", "label": "PMID 38672131 full text"}, {"id": "data:geo:GSE261765", "type": "dataset", "label": "GEO GSE261765"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38672131", "type": "paper", "label": "pmid:38672131"}, {"id": "source:pmid:38672131", "type": "manuscript", "label": "PMID 38672131 full text"}, {"id": "data:geo:GSE261765", "type": "dataset", "label": "GEO GSE261765"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38672131", "type": "extraction", "used": ["source:pmid:38672131"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE261765", "type": "accession_resolution", "used": ["data:geo:GSE261765"], "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:38672131", "parent_hash": "sha256:35b6f0e31ff1fef7105e1684ea9ed394de4f957662076da736af092b3f4de9ac", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE261765 licence not read", "asset:data:geo:GSE261765 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["with Psoriatic Arthritis Presenting Impaired Apoptosis Activity.", "clear cells using CD14+ magnetic beads. Cell apoptosis was measured via Annexin V using flow cytome", "thway enrichment analysis, we found that the apoptosis signaling pathway in CD14+ cells was signifi", "ipheral CD14+ monocytes increased, and their apoptosis activity was impaired in patients with PsA,"], "order_basis": "paper_text_order:50", "id": "assay:1"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["l apoptosis was measured via Annexin V using flow cytometry. The gene expression profiling was analyzed"], "order_basis": "paper_text_order:590", "id": "assay:2"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e gene expression profiling was analyzed via microarray (available in the NCBI GEO database; accessi", "s with PsA than in the HCs. By analyzing the microarray data, identifying the differentially express", "er of monocytes than the HCs, we conducted a microarray assay (Clariom D Human) on the monocyte samp", "gene expression profiles were examined using microarray and qPCR assays. (A) We used a volcano plot"], "order_basis": "paper_text_order:653", "id": "assay:3"}, {"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": ["apoptosis-related genes, CTSL and IKBKB, for qPCR validation since they had the largest expres", ") and HCs (n = 15). As shown in Figure 3B,C, qPCR validation confirmed that CTSL was downregul", "profiles were examined using microarray and qPCR assays. (A) We used a volcano plot (generate", "y (p value < 0.05 based on ANOVA). (B,C) The qPCR results compared nine HC and nine PsA monocy"], "order_basis": "paper_text_order:5830", "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": ["The generated raw CEL files were analyzed using Transcription Analysis Console 4.0 (Thermo Fisher Scientific, Inc., Carlsbad, CA, USA) to conduct ANOVA, identify the differentially expressed genes, and generate the volcano plot. In addition, we also used Partek Genomics Suite 7.0 (Partek, St. Louis, MO, USA) to conduct pathway enrichment analysis."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}