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

pmid:41537777

Transient ER stress cell-autonomously promotes beta cell cycling in mice.

Stephanie Bourgeois · Annelore Van Mulders · Yves Heremans · Gunter Leuckx · Lien Willems · Sophie Coenen · Laure Degroote · Julie Pierreux · Daliya Kancheva · Isabelle Scheyltjens · Kiavash Movahedi · Françoise Carlotti · Eelco de Koning · Xiaoyan Yi · Chiara Vinci · Yue Tong · Miriam Cnop · Harry Heimberg · Nico De Leu · Willem Staels

Diabetologia · 2026 doi:10.1007/s00125-025-06649-3

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:41537777
kind
science-record
content_hash
sha256:1262577e50c935df7464f48e057813ac7879d24e9a57296e6d21466bc973ab7e
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:31:30Z
updated_at
2026-11-01T22:57:44Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Transient ER stress cell-autonomously promotes beta cell cycling in mice.
doi
10.1007/s00125-025-06649-3
pmid
41537777
authors array · 20 items
[0]
Stephanie Bourgeois
[1]
Annelore Van Mulders
[2]
Yves Heremans
[3]
Gunter Leuckx
[4]
Lien Willems
[5]
Sophie Coenen
[6]
Laure Degroote
[7]
Julie Pierreux
[8]
Daliya Kancheva
[9]
Isabelle Scheyltjens
[10]
Kiavash Movahedi
[11]
Françoise Carlotti
[12]
Eelco de Koning
[13]
Xiaoyan Yi
[14]
Chiara Vinci
[15]
Yue Tong
[16]
Miriam Cnop
[17]
Harry Heimberg
[18]
Nico De Leu
[19]
Willem Staels
journal
Diabetologia
year
2026
abstract
AIMS/HYPOTHESIS: Regenerating endogenous pancreatic beta cells is a potentially curative yet currently elusive strategy for diabetes therapy. Mimicking the microenvironment of the developing pancreas and leveraging vascular signals that support pancreatic endocrinogenesis may promote beta cell regeneration. We aimed to investigate whether recovery from experimental hypovascularisation of the endocrine pancreas could trigger mouse beta cell proliferation. METHODS: A doxycycline (DOX)-inducible transgenic mouse model was used to induce conditional intra-islet hypovascularisation. In this model, vascular endothelial growth factor (VEGF)-A signalling within pancreatic islets is antagonised through beta cell-specific overexpression of a VEGF-A decoy receptor, soluble fms-like tyrosine kinase 1 (sFLT1). Cessation of sFLT1 overexpression was induced by DOX withdrawal. sFLT1 expression, vessel kinetics and beta cell proliferation upon DOX administration and withdrawal were analysed using quantitative RT-PCR and immunostaining. Single-cell RNA-seq was used to investigate the effects on the islet cells' transcriptome and perform pathway enrichment analysis. RIP-rtTA;TetO-GFP mice were studied in parallel to assess the dependency of cell cycle induction on vessel manipulation. Additionally, in vitro experiments were conducted to further elucidate and validate our in vivo findings. RESULTS: Serendipitously, we discovered that sFLT1 overexpression in beta cells induces endoplasmic reticulum (ER) stress and activates proliferation-associated pathways. Upon cessation of sFLT1 overexpression, ER stress decreased and beta cell proliferation was promoted independently of vessel recovery, as shown by cumulative BrdU labelling over 7 days (mean ± SEM vs control: 14.3 ± 1.3% vs 5.2 ± 0.6%) during the DOX withdrawal period. Transient GFP overexpression also induced ER stress and a subsequent reduction thereof resulted in increased beta cell proliferation (mean ± SEM vs control: 7.2 ± 0.4% vs 5.1 ± 0.5%). Chemical, transient induction of ER stress in vitro by ER-stress-inducing compounds reproduced this beta cell cycling response, as assessed by cumulative EdU labelling during a 3 day washout period (mean ± SEM vs control: 2.6 ± 0.4% vs 0.8 ± 0.2% for thapsigargin and 3.8 ± 0.9% vs 1.0 ± 0.2% for tunicamycin), which further increased under high-glucose conditions when islets were exposed to thapsigargin (mean ± SEM vs control: 9.0 ± 1.2% vs 2.0 ± 0.4%). CONCLUSIONS/INTERPRETATION: Our findings uncover a link between transgene (over)expression, ER stress, glucose and cell cycle activation in mouse beta cells. DATA AND CODE AVAILABILITY: The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
Data were analysed in GraphPad Prism v9.1.0 using unpaired t tests, one- or two-way ANOVA, or mixed-model analysis with Tukey’s post hoc test as appropriate.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41537777
locator
sections[12] "Statistics" paragraph 2
quote
Data were analysed in GraphPad Prism v9.1.0 using unpaired t tests, one- or two-way ANOVA, or mixed-model analysis with Tukey’s post hoc test as appropriate.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41537777
locator
sections[26] "notes" paragraph 1
quote
The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Upon cessation of sFLT1 overexpression, ER stress decreased and beta cell proliferation was promoted independently of vessel recovery, as shown by cumulative BrdU labelling over 7 days (mean ± SEM vs control: 14.3 ± 1.3% vs 5.2 ± 0.6%) during the DOX withdrawal period.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:41537777
locator
sections[0] "Abstract" paragraph 3
quote
Upon cessation of sFLT1 overexpression, ER stress decreased and beta cell proliferation was promoted independently of vessel recovery, as shown by cumulative BrdU labelling over 7 days (mean ± SEM vs control: 14.3 ± 1.3% vs 5.2 ± 0.6%) during the DOX withdrawal period.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
Upon cessation of sFLT1 overexpression, ER stress decreased and beta cell proliferation was promoted independently of vessel recovery, as shown by cumulative BrdU labelling over 7 days (mean ± SEM vs control: 14.3 ± 1.3% vs 5.2 ± 0.6%) during the DOX withdrawal period.
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:41537777
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:GSE274443
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:GSE274443
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:41537777
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1007/s00125-025-06649-3
sha256
sha256:1a389a4d32ed7f229a0e5614091e38a8b6b02bb57e4ed927a33660816b37fcbf
bytes
53948
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1007/s00125-025-06649-3
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
PMC13005877
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE274443
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=GSE274443
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE274443
version
null
note
The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability.
access_statement_kind
data_availability_statement
sample_accessions array · 6 items
[0]
GSM8449324
[1]
GSM8449325
[2]
GSM8449326
[3]
GSM8449327
[4]
GSM8449328
[5]
GSM8449329
sample_count
6
group_sizes
null
group_sizes_basis
null
platform
24247
taxon
Mus musculus
title
Transient ER stress cell-autonomously promotes beta cell cycling
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:GSE274443 not downloaded
[1]
asset:data:geo:GSE274443 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
Data were analysed in GraphPad Prism v9.1.0 using unpaired t tests, one- or two-way ANOVA, or mixed-model analysis with Tukey’s post hoc test as appropriate.
[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]
GSE274443
resolved_accessions array · 1 item
[0]
GSE274443
statements array · 1 item
[0]
The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability.
basis
The paper names GSE274443 in GEO (NCBI) 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:41537777
[1]
data:geo:GSE274443
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:GSE274443
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
2026-11-01T20:10:02Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
15307
completion_tokens
1364
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:41537777
type
paper
label
pmid:41537777
[1] object · 3 fields
id
source:pmid:41537777
type
manuscript
label
PMID 41537777 full text
[2] object · 3 fields
id
data:geo:GSE274443
type
dataset
label
GEO GSE274443
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:41537777
type
paper
label
pmid:41537777
[1] object · 3 fields
id
source:pmid:41537777
type
manuscript
label
PMID 41537777 full text
[2] object · 3 fields
id
data:geo:GSE274443
type
dataset
label
GEO GSE274443
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-41537777
type
extraction
used array · 1 item
[0]
source:pmid:41537777
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE274443
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE274443
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:41537777
parent_hash
sha256:8644619255b2cd5005308131938a6e03398b35b1558efc8e72027e9b9bf37e9a
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:GSE274443 licence not read
[1]
asset:data:geo:GSE274443 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
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]
cell-autonomously promotes beta cell cycling in mice.
[1]
DS: A doxycycline (DOX)-inducible transgenic mouse model was used to induce conditional intra-islet h
[2]
thway enrichment analysis. RIP-rtTA;TetO-GFP mice were studied in parallel to assess the dependency
[3]
ducted to further elucidate and validate our in vivo findings. RESULTS: Serendipitously, we disco
order_basis
paper_text_order:20
id
assay:1
[1] object · 11 fields
role
data_generation
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.85
evidence array · 1 item
[0]
were analysed using quantitative RT-PCR and immunostaining. Single-cell RNA-seq was used to investigate
order_basis
paper_text_order:1049
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
scrna_seq
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
unsupported
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
sing quantitative RT-PCR and immunostaining. Single-cell RNA-seq was used to investigate the effects on the i
[1]
beta cells. DATA AND CODE AVAILABILITY: The single-cell RNA-seq data generated in this study are deposited a
order_basis
paper_text_order:1064
id
assay:3
[3] 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
0.99
evidence array · 3 items
[0]
ative RT-PCR and immunostaining. Single-cell RNA-seq was used to investigate the effects on the i
[1]
DATA AND CODE AVAILABILITY: The single-cell RNA-seq data generated in this study are deposited a
[2]
investigate the effects on the islet cells' transcriptome and perform pathway enrichment analysis. RIP
order_basis
paper_text_order:1076
id
assay:4
[4] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Data were analysed in GraphPad Prism v9.1.0 using unpaired t tests, one- or two-way ANOVA, or mixed-model analysis with Tukey’s post hoc test as appropriate.
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:41537777", "kind": "science-record", "revision": 4, "content_hash": "sha256:1262577e50c935df7464f48e057813ac7879d24e9a57296e6d21466bc973ab7e", "created_at": "2026-11-01T20:31:30Z", "updated_at": "2026-11-01T22:57:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transient ER stress cell-autonomously promotes beta cell cycling in mice.", "doi": "10.1007/s00125-025-06649-3", "pmid": "41537777", "authors": ["Stephanie Bourgeois", "Annelore Van Mulders", "Yves Heremans", "Gunter Leuckx", "Lien Willems", "Sophie Coenen", "Laure Degroote", "Julie Pierreux", "Daliya Kancheva", "Isabelle Scheyltjens", "Kiavash Movahedi", "Françoise Carlotti", "Eelco de Koning", "Xiaoyan Yi", "Chiara Vinci", "Yue Tong", "Miriam Cnop", "Harry Heimberg", "Nico De Leu", "Willem Staels"], "journal": "Diabetologia", "year": 2026, "abstract": "AIMS/HYPOTHESIS: Regenerating endogenous pancreatic beta cells is a potentially curative yet currently elusive strategy for diabetes therapy. Mimicking the microenvironment of the developing pancreas and leveraging vascular signals that support pancreatic endocrinogenesis may promote beta cell regeneration. We aimed to investigate whether recovery from experimental hypovascularisation of the endocrine pancreas could trigger mouse beta cell proliferation.\nMETHODS: A doxycycline (DOX)-inducible transgenic mouse model was used to induce conditional intra-islet hypovascularisation. In this model, vascular endothelial growth factor (VEGF)-A signalling within pancreatic islets is antagonised through beta cell-specific overexpression of a VEGF-A decoy receptor, soluble fms-like tyrosine kinase 1 (sFLT1). Cessation of sFLT1 overexpression was induced by DOX withdrawal. sFLT1 expression, vessel kinetics and beta cell proliferation upon DOX administration and withdrawal were analysed using quantitative RT-PCR and immunostaining. Single-cell RNA-seq was used to investigate the effects on the islet cells' transcriptome and perform pathway enrichment analysis. RIP-rtTA;TetO-GFP mice were studied in parallel to assess the dependency of cell cycle induction on vessel manipulation. Additionally, in vitro experiments were conducted to further elucidate and validate our in vivo findings.\nRESULTS: Serendipitously, we discovered that sFLT1 overexpression in beta cells induces endoplasmic reticulum (ER) stress and activates proliferation-associated pathways. Upon cessation of sFLT1 overexpression, ER stress decreased and beta cell proliferation was promoted independently of vessel recovery, as shown by cumulative BrdU labelling over 7 days (mean ± SEM vs control: 14.3 ± 1.3% vs 5.2 ± 0.6%) during the DOX withdrawal period. Transient GFP overexpression also induced ER stress and a subsequent reduction thereof resulted in increased beta cell proliferation (mean ± SEM vs control: 7.2 ± 0.4% vs 5.1 ± 0.5%). Chemical, transient induction of ER stress in vitro by ER-stress-inducing compounds reproduced this beta cell cycling response, as assessed by cumulative EdU labelling during a 3 day washout period (mean ± SEM vs control: 2.6 ± 0.4% vs 0.8 ± 0.2% for thapsigargin and 3.8 ± 0.9% vs 1.0 ± 0.2% for tunicamycin), which further increased under high-glucose conditions when islets were exposed to thapsigargin (mean ± SEM vs control: 9.0 ± 1.2% vs 2.0 ± 0.4%).\nCONCLUSIONS/INTERPRETATION: Our findings uncover a link between transgene (over)expression, ER stress, glucose and cell cycle activation in mouse beta cells.\nDATA AND CODE AVAILABILITY: The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443.", "claims": [{"id": "claim-method", "statement": "Data were analysed in GraphPad Prism v9.1.0 using unpaired t tests, one- or two-way ANOVA, or mixed-model analysis with Tukey’s post hoc test as appropriate.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41537777", "locator": "sections[12] \"Statistics\" paragraph 2", "quote": "Data were analysed in GraphPad Prism v9.1.0 using unpaired t tests, one- or two-way ANOVA, or mixed-model analysis with Tukey’s post hoc test as appropriate."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41537777", "locator": "sections[26] \"notes\" paragraph 1", "quote": "The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Upon cessation of sFLT1 overexpression, ER stress decreased and beta cell proliferation was promoted independently of vessel recovery, as shown by cumulative BrdU labelling over 7 days (mean ± SEM vs control: 14.3 ± 1.3% vs 5.2 ± 0.6%) during the DOX withdrawal period.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41537777", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Upon cessation of sFLT1 overexpression, ER stress decreased and beta cell proliferation was promoted independently of vessel recovery, as shown by cumulative BrdU labelling over 7 days (mean ± SEM vs control: 14.3 ± 1.3% vs 5.2 ± 0.6%) during the DOX withdrawal period."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Upon cessation of sFLT1 overexpression, ER stress decreased and beta cell proliferation was promoted independently of vessel recovery, as shown by cumulative BrdU labelling over 7 days (mean ± SEM vs control: 14.3 ± 1.3% vs 5.2 ± 0.6%) during the DOX withdrawal period.", "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:41537777"], "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:GSE274443"], "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:GSE274443"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41537777", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s00125-025-06649-3", "sha256": "sha256:1a389a4d32ed7f229a0e5614091e38a8b6b02bb57e4ed927a33660816b37fcbf", "bytes": 53948, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s00125-025-06649-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC13005877", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE274443", "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=GSE274443", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE274443", "version": null, "note": "The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM8449324", "GSM8449325", "GSM8449326", "GSM8449327", "GSM8449328", "GSM8449329"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "24247", "taxon": "Mus musculus", "title": "Transient ER stress cell-autonomously promotes beta cell cycling", "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:GSE274443 not downloaded", "asset:data:geo:GSE274443 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Data were analysed in GraphPad Prism v9.1.0 using unpaired t tests, one- or two-way ANOVA, or mixed-model analysis with Tukey’s post hoc test as appropriate."}}, {"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": ["GSE274443"], "resolved_accessions": ["GSE274443"], "statements": ["The single-cell RNA-seq data generated in this study are deposited at GEO (NCBI) with accession code GSE274443. Other data that support the findings of this study are available from the corresponding author upon request. There are no restrictions on data availability."], "basis": "The paper names GSE274443 in GEO (NCBI) 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:41537777", "data:geo:GSE274443"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE274443"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:10:02Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15307, "completion_tokens": 1364, "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:41537777", "type": "paper", "label": "pmid:41537777"}, {"id": "source:pmid:41537777", "type": "manuscript", "label": "PMID 41537777 full text"}, {"id": "data:geo:GSE274443", "type": "dataset", "label": "GEO GSE274443"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41537777", "type": "paper", "label": "pmid:41537777"}, {"id": "source:pmid:41537777", "type": "manuscript", "label": "PMID 41537777 full text"}, {"id": "data:geo:GSE274443", "type": "dataset", "label": "GEO GSE274443"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41537777", "type": "extraction", "used": ["source:pmid:41537777"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE274443", "type": "accession_resolution", "used": ["data:geo:GSE274443"], "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:41537777", "parent_hash": "sha256:8644619255b2cd5005308131938a6e03398b35b1558efc8e72027e9b9bf37e9a", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE274443 licence not read", "asset:data:geo:GSE274443 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["cell-autonomously promotes beta cell cycling in mice.", "DS: A doxycycline (DOX)-inducible transgenic mouse model was used to induce conditional intra-islet h", "thway enrichment analysis. RIP-rtTA;TetO-GFP mice were studied in parallel to assess the dependency", "ducted to further elucidate and validate our in vivo findings. RESULTS: Serendipitously, we disco"], "order_basis": "paper_text_order:20", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["were analysed using quantitative RT-PCR and immunostaining. Single-cell RNA-seq was used to investigate"], "order_basis": "paper_text_order:1049", "id": "assay:2"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["sing quantitative RT-PCR and immunostaining. Single-cell RNA-seq was used to investigate the effects on the i", "beta cells. DATA AND CODE AVAILABILITY: The single-cell RNA-seq data generated in this study are deposited a"], "order_basis": "paper_text_order:1064", "id": "assay:3"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ative RT-PCR and immunostaining. Single-cell RNA-seq was used to investigate the effects on the i", "DATA AND CODE AVAILABILITY: The single-cell RNA-seq data generated in this study are deposited a", "investigate the effects on the islet cells' transcriptome and perform pathway enrichment analysis. RIP"], "order_basis": "paper_text_order:1076", "id": "assay:4"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Data were analysed in GraphPad Prism v9.1.0 using unpaired t tests, one- or two-way ANOVA, or mixed-model analysis with Tukey’s post hoc test as appropriate."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}