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

pmid:35708762

A miR-125/Sirtuin-7 pathway drives the pro-calcific potential of myeloid cells in diabetic vascular disease.

Saula Vigili de Kreutzenberg · Alessandra Giannella · Giulio Ceolotto · Elisabetta Faggin · Roberta Cappellari · Marta Mazzucato · Chiara Fraccaro · Giuseppe Tarantini · Angelo Avogaro · Gian Paolo Fadini

Diabetologia · 2022 doi:10.1007/s00125-022-05733-2

Paper

complete

Experiment

complete

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:35708762
kind
science-record
content_hash
sha256:9d9d84196d683841529a29d990f03404b66d1898fb0b7710d704268e89db234e
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T18:14:41Z
updated_at
2026-11-01T22:06:46Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
A miR-125/Sirtuin-7 pathway drives the pro-calcific potential of myeloid cells in diabetic vascular disease.
doi
10.1007/s00125-022-05733-2
pmid
35708762
authors array · 10 items
[0]
Saula Vigili de Kreutzenberg
[1]
Alessandra Giannella
[2]
Giulio Ceolotto
[3]
Elisabetta Faggin
[4]
Roberta Cappellari
[5]
Marta Mazzucato
[6]
Chiara Fraccaro
[7]
Giuseppe Tarantini
[8]
Angelo Avogaro
[9]
Gian Paolo Fadini
journal
Diabetologia
year
2022
abstract
AIMS/HYPOTHESIS: Ectopic calcification is a typical feature of diabetic vascular disease and resembles an accelerated ageing phenotype. We previously found an excess of myeloid calcifying cells in diabetic individuals. We herein examined molecular and cellular pathways linking atherosclerotic calcification with calcification by myeloid cells in the diabetic milieu. METHODS: We first examined the associations among coronary calcification, myeloid calcifying cell levels and mononuclear cell gene expression in a cross-sectional study of 87 participants with type 2 diabetes undergoing elective coronary angiography. Then, we undertook in vitro studies on mesenchymal stem cells and the THP-1 myeloid cell line to verify the causal relationships of the observed associations. RESULTS: Coronary calcification was associated with 2.8-times-higher myeloid calcifying cell levels (p=0.037) and 50% elevated expression of the osteogenic gene RUNX2 in mononuclear cells, whereas expression of Sirtuin-7 (SIRT7) was inversely correlated with calcification. In standard differentiation assays of mesenchymal stem cells, SIRT7 knockdown activated the osteogenic program and worsened calcification, especially in the presence of high (20 mmol/l) glucose. In the myeloid cell line THP-1, SIRT7 downregulation drove a pro-calcific phenotype, whereas SIRT7 overexpression prevented high-glucose-induced calcification. Through the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway, high glucose induced miR-125b-5p, which in turn targeted SIRT7 in myeloid cells and was directly associated with coronary calcification. CONCLUSIONS/INTERPRETATION: We describe a new pathway elicited by high glucose through the JAK/STAT cascade, involving regulation of SIRT7 by miR-125b-5p and driving calcification by myeloid cells. This pathway is associated with coronary calcification in diabetic individuals and may be a target against diabetic vascular disease. DATA AVAILABILITY: RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510 ).
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Comparison between two group means was performed using unpaired two-tailed Student’s t test. ANOVA with least square difference post hoc test was used to compare three or more groups. Differences between categorical data were assessed by χ2 test. Linear correlation between two continuous variables was explored with Pearson's r and age-adjusted using the partial correlation function.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35708762
locator
sections[16] "Statistical analysis" paragraph 2
quote
Comparison between two group means was performed using unpaired two-tailed Student’s t test. ANOVA with least square difference post hoc test was used to compare three or more groups. Differences between categorical data were assessed by χ2 test. Linear correlation between two continuous variables was explored with Pearson's r and age-adjusted using the partial correlation function.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35708762
locator
sections[32] "Data availability" paragraph 2
quote
RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
We describe a new pathway elicited by high glucose through the JAK/STAT cascade, involving regulation of SIRT7 by miR-125b-5p and driving calcification by myeloid cells.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:35708762
locator
sections[0] "Abstract" paragraph 4
quote
We describe a new pathway elicited by high glucose through the JAK/STAT cascade, involving regulation of SIRT7 by miR-125b-5p and driving calcification by myeloid cells.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
We describe a new pathway elicited by high glucose through the JAK/STAT cascade, involving regulation of SIRT7 by miR-125b-5p and driving calcification by myeloid cells.
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:35708762
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:GSE193510
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:GSE193510
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:35708762
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1007/s00125-022-05733-2
sha256
sha256:84ce4258a4fe48ddb60c61761f4a2542682b969ca9c653a21dd5639c7a205f88
bytes
52185
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1007/s00125-022-05733-2
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
PMC9345831
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE193510
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=GSE193510
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE193510
version
null
note
RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request.
access_statement_kind
data_availability_statement
sample_accessions array · 8 items
[0]
GSM5811726
[1]
GSM5811727
[2]
GSM5811728
[3]
GSM5811729
[4]
GSM5811730
[5]
GSM5811731
[6]
GSM5811732
[7]
GSM5811733
sample_count
8
group_sizes
null
group_sizes_basis
null
platform
21697
taxon
Homo sapiens
title
A miR-125 / Sirtuin-7 pathway drives pro-calcific potential of myeloid cells in diabetic vascular disease
resolution_checked_at
2026-11-01T18:06:43Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE193510 not downloaded
[1]
asset:data:geo:GSE193510 licence not read
analysis object · 4 fields
state
partial
methods array · 3 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
0.8
band
high
quote
ANOVA
[1] object · 10 fields
id
method-2
family
contingency_analysis
specific
chi_square
label
Categorical (contingency table) analysis
dsl_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
categorical_cross_tabulation
evidence object · 3 fields
score
0.8
band
high
quote
χ2
[2] object · 10 fields
id
method-3
family
null
specific
null
label
Comparison between two group means was performed using unpaired two-tailed Student’s t test; correlations between continuous variables were explored with Pearson's r and age-adjusted using the partial correlation function.
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
Comparison between two group means was performed using unpaired two-tailed Student’s t test. ANOVA with least square difference post hoc test was used to compare three or more groups. Differences between categorical data were assessed by χ2 test. Linear correlation between two continuous variables was explored with Pearson's r and age-adjusted using the partial correlation function.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
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]
GSE193510
resolved_accessions array · 1 item
[0]
GSE193510
statements array · 1 item
[0]
RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request.
basis
The paper names GSE193510 in 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:35708762
[1]
data:geo:GSE193510
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:GSE193510
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
2026-11-01T17:50:30Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
15416
completion_tokens
941
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:35708762
type
paper
label
pmid:35708762
[1] object · 3 fields
id
source:pmid:35708762
type
manuscript
label
PMID 35708762 full text
[2] object · 3 fields
id
data:geo:GSE193510
type
dataset
label
GEO GSE193510
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:35708762
type
paper
label
pmid:35708762
[1] object · 3 fields
id
source:pmid:35708762
type
manuscript
label
PMID 35708762 full text
[2] object · 3 fields
id
data:geo:GSE193510
type
dataset
label
GEO GSE193510
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-35708762
type
extraction
used array · 1 item
[0]
source:pmid:35708762
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE193510
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE193510
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:35708762
parent_hash
sha256:a186eea1fa17a099eeb51581480329082a51833dc20f8bb099ecf488af14bb64
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE193510 licence not read
[1]
asset:data:geo:GSE193510 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 3 items
[0] 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]
tion assays of mesenchymal stem cells, SIRT7 knockdown activated the osteogenic program and worsene
order_basis
paper_text_order:1184
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
rna_seq
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]
iabetic vascular disease. DATA AVAILABILITY: RNA sequencing data are deposited in GEO (accession number
order_basis
paper_text_order:2055
id
assay:2
[2] 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]
ANOVA
order_basis
consumes_earlier_output
id
assay:3
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35708762", "kind": "science-record", "revision": 4, "content_hash": "sha256:9d9d84196d683841529a29d990f03404b66d1898fb0b7710d704268e89db234e", "created_at": "2026-11-01T18:14:41Z", "updated_at": "2026-11-01T22:06:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A miR-125/Sirtuin-7 pathway drives the pro-calcific potential of myeloid cells in diabetic vascular disease.", "doi": "10.1007/s00125-022-05733-2", "pmid": "35708762", "authors": ["Saula Vigili de Kreutzenberg", "Alessandra Giannella", "Giulio Ceolotto", "Elisabetta Faggin", "Roberta Cappellari", "Marta Mazzucato", "Chiara Fraccaro", "Giuseppe Tarantini", "Angelo Avogaro", "Gian Paolo Fadini"], "journal": "Diabetologia", "year": 2022, "abstract": "AIMS/HYPOTHESIS: Ectopic calcification is a typical feature of diabetic vascular disease and resembles an accelerated ageing phenotype. We previously found an excess of myeloid calcifying cells in diabetic individuals. We herein examined molecular and cellular pathways linking atherosclerotic calcification with calcification by myeloid cells in the diabetic milieu.\nMETHODS: We first examined the associations among coronary calcification, myeloid calcifying cell levels and mononuclear cell gene expression in a cross-sectional study of 87 participants with type 2 diabetes undergoing elective coronary angiography. Then, we undertook in vitro studies on mesenchymal stem cells and the THP-1 myeloid cell line to verify the causal relationships of the observed associations.\nRESULTS: Coronary calcification was associated with 2.8-times-higher myeloid calcifying cell levels (p=0.037) and 50% elevated expression of the osteogenic gene RUNX2 in mononuclear cells, whereas expression of Sirtuin-7 (SIRT7) was inversely correlated with calcification. In standard differentiation assays of mesenchymal stem cells, SIRT7 knockdown activated the osteogenic program and worsened calcification, especially in the presence of high (20 mmol/l) glucose. In the myeloid cell line THP-1, SIRT7 downregulation drove a pro-calcific phenotype, whereas SIRT7 overexpression prevented high-glucose-induced calcification. Through the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway, high glucose induced miR-125b-5p, which in turn targeted SIRT7 in myeloid cells and was directly associated with coronary calcification.\nCONCLUSIONS/INTERPRETATION: We describe a new pathway elicited by high glucose through the JAK/STAT cascade, involving regulation of SIRT7 by miR-125b-5p and driving calcification by myeloid cells. This pathway is associated with coronary calcification in diabetic individuals and may be a target against diabetic vascular disease.\nDATA AVAILABILITY: RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510 ).", "claims": [{"id": "claim-method", "statement": "Comparison between two group means was performed using unpaired two-tailed Student’s t test. ANOVA with least square difference post hoc test was used to compare three or more groups. Differences between categorical data were assessed by χ2 test. Linear correlation between two continuous variables was explored with Pearson's r and age-adjusted using the partial correlation function.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35708762", "locator": "sections[16] \"Statistical analysis\" paragraph 2", "quote": "Comparison between two group means was performed using unpaired two-tailed Student’s t test. ANOVA with least square difference post hoc test was used to compare three or more groups. Differences between categorical data were assessed by χ2 test. Linear correlation between two continuous variables was explored with Pearson's r and age-adjusted using the partial correlation function."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35708762", "locator": "sections[32] \"Data availability\" paragraph 2", "quote": "RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We describe a new pathway elicited by high glucose through the JAK/STAT cascade, involving regulation of SIRT7 by miR-125b-5p and driving calcification by myeloid cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35708762", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We describe a new pathway elicited by high glucose through the JAK/STAT cascade, involving regulation of SIRT7 by miR-125b-5p and driving calcification by myeloid cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We describe a new pathway elicited by high glucose through the JAK/STAT cascade, involving regulation of SIRT7 by miR-125b-5p and driving calcification by myeloid cells.", "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:35708762"], "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:GSE193510"], "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:GSE193510"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35708762", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s00125-022-05733-2", "sha256": "sha256:84ce4258a4fe48ddb60c61761f4a2542682b969ca9c653a21dd5639c7a205f88", "bytes": 52185, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s00125-022-05733-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9345831", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE193510", "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=GSE193510", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE193510", "version": null, "note": "RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5811726", "GSM5811727", "GSM5811728", "GSM5811729", "GSM5811730", "GSM5811731", "GSM5811732", "GSM5811733"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "21697", "taxon": "Homo sapiens", "title": "A miR-125 / Sirtuin-7 pathway drives pro-calcific potential of myeloid cells in diabetic vascular disease", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE193510 not downloaded", "asset:data:geo:GSE193510 licence not read"]}, "analysis": {"state": "partial", "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": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-2", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "χ2"}}, {"id": "method-3", "family": null, "specific": null, "label": "Comparison between two group means was performed using unpaired two-tailed Student’s t test; correlations between continuous variables were explored with Pearson's r and age-adjusted using the partial correlation function.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Comparison between two group means was performed using unpaired two-tailed Student’s t test. ANOVA with least square difference post hoc test was used to compare three or more groups. Differences between categorical data were assessed by χ2 test. Linear correlation between two continuous variables was explored with Pearson's r and age-adjusted using the partial correlation function."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["GSE193510"], "resolved_accessions": ["GSE193510"], "statements": ["RNA sequencing data are deposited in GEO (accession number GSE193510; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193510). Original data are available from the corresponding author on reasonable request."], "basis": "The paper names GSE193510 in 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:35708762", "data:geo:GSE193510"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE193510"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:50:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15416, "completion_tokens": 941, "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:35708762", "type": "paper", "label": "pmid:35708762"}, {"id": "source:pmid:35708762", "type": "manuscript", "label": "PMID 35708762 full text"}, {"id": "data:geo:GSE193510", "type": "dataset", "label": "GEO GSE193510"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35708762", "type": "paper", "label": "pmid:35708762"}, {"id": "source:pmid:35708762", "type": "manuscript", "label": "PMID 35708762 full text"}, {"id": "data:geo:GSE193510", "type": "dataset", "label": "GEO GSE193510"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35708762", "type": "extraction", "used": ["source:pmid:35708762"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE193510", "type": "accession_resolution", "used": ["data:geo:GSE193510"], "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:35708762", "parent_hash": "sha256:a186eea1fa17a099eeb51581480329082a51833dc20f8bb099ecf488af14bb64", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE193510 licence not read", "asset:data:geo:GSE193510 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["tion assays of mesenchymal stem cells, SIRT7 knockdown activated the osteogenic program and worsene"], "order_basis": "paper_text_order:1184", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["iabetic vascular disease. DATA AVAILABILITY: RNA sequencing data are deposited in GEO (accession number"], "order_basis": "paper_text_order:2055", "id": "assay:2"}, {"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": 0.8, "evidence": ["ANOVA"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}