---
OA_place: repository
OA_type: green
_id: '20081'
abstract:
- lang: eng
text: 'Information measures can be constructed from Rényi divergences much like
mutual information from Kullback-Leibler divergence. One such information measure
is known as Sibson α-mutual information and has received renewed attention recently
in several contexts: concentration of measure under dependence, statistical learning,
hypothesis testing, and estimation theory. In this paper, we survey and extend
the state of the art. In particular, we introduce variational representations
for Sibson α-mutual information and employ them in each described context to derive
novel results. Namely, we produce generalized Transportation-Cost inequalities
and Fano-type inequalities. We also present an overview of known applications,
spanning from learning theory and Bayesian risk to universal prediction.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Amedeo Roberto
full_name: Esposito, Amedeo Roberto
id: 9583e921-e1ad-11ec-9862-cef099626dc9
last_name: Esposito
- first_name: Michael
full_name: Gastpar, Michael
last_name: Gastpar
- first_name: Ibrahim
full_name: Issa, Ibrahim
last_name: Issa
citation:
ama: Esposito AR, Gastpar M, Issa I. Sibson α-mutual information and its variational
representations. IEEE Transactions on Information Theory. 2025. doi:10.1109/TIT.2025.3587340
apa: Esposito, A. R., Gastpar, M., & Issa, I. (2025). Sibson α-mutual information
and its variational representations. IEEE Transactions on Information Theory.
IEEE. https://doi.org/10.1109/TIT.2025.3587340
chicago: Esposito, Amedeo Roberto, Michael Gastpar, and Ibrahim Issa. “Sibson α-Mutual
Information and Its Variational Representations.” IEEE Transactions on Information
Theory. IEEE, 2025. https://doi.org/10.1109/TIT.2025.3587340.
ieee: A. R. Esposito, M. Gastpar, and I. Issa, “Sibson α-mutual information and
its variational representations,” IEEE Transactions on Information Theory.
IEEE, 2025.
ista: Esposito AR, Gastpar M, Issa I. 2025. Sibson α-mutual information and its
variational representations. IEEE Transactions on Information Theory.
mla: Esposito, Amedeo Roberto, et al. “Sibson α-Mutual Information and Its Variational
Representations.” IEEE Transactions on Information Theory, IEEE, 2025,
doi:10.1109/TIT.2025.3587340.
short: A.R. Esposito, M. Gastpar, I. Issa, IEEE Transactions on Information Theory
(2025).
date_created: 2025-07-27T22:01:26Z
date_published: 2025-07-11T00:00:00Z
date_updated: 2026-02-16T11:49:40Z
day: '11'
department:
- _id: MaMo
doi: 10.1109/TIT.2025.3587340
external_id:
arxiv:
- '2405.08352'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.08352
month: '07'
oa: 1
oa_version: Preprint
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: epub_ahead
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sibson α-mutual information and its variational representations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20098'
abstract:
- lang: eng
text: Climate change is causing wildfires to become more frequent and intense. While
predicting burned areas using bioclimatic and anthropogenic factors is an active
research area, few studies have examined what drives the economic damages of wildfires.
Our study aims to fill this gap by analyzing key factors influencing global economic
wildfire damages and projecting future damages under three shared socioeconomic
pathways (SSPs). We apply regression analyses to identify significant predictors
of economic wildfire damages at country levels and use the fitted model to project
future damages under SSP126, SSP245, and SSP370. Results show that the human vulnerability
index (HVI), reflecting socioeconomic conditions, is the strongest predictor of
historical wildfire damages, followed by water vapor pressure deficit during the
fire season and population density around forested areas. We found high population
density to be associated with lower damages. These findings contrast with studies
of burned areas, where climate factors are more dominant. Our model projects that
by 2070, average global economic wildfire damages will be three times higher under
SSP370 than SSP126. Our model also shows that following SSP126 not only reduces
wildfire damages but also lessens the inequalities in damage distribution across
countries. This pathway’s dual focus on equitable socioeconomic progress and climate
action potentially enhances a country’s resilience that helps mitigate wildfire
damages. Our analyses also indicate that strong socioeconomic development can
offset wildfire damages associated with climate hazards, although this is less
certain under SSP370. SSP126’s integrated approach improves both socioeconomic
conditions and limits global warming, providing substantial benefits to less developed
countries while still reducing damages in developed nations, despite their already
low HVI scores. Our work complements existing research on burned areas and underscores
the importance of sustainable development and international collaboration in reducing
the economic damages of wildfires.
acknowledgement: We thank Marina Andrijevic, Giacomo Falchetta, Samuel Lüthi, Caroline
Muller, Carl Schleussner, and Adriano Vinca for providing useful ideas and feedback
for this work. YLH is supported by funding from the European Union’s Horizon 2020
research and innovation programme under the Marie Skłodowska‐Curie Grant No. 101034413.
EB, MW, and YQ are supported by the European Union’s Horizon Europe research and
innovation programme under Grant Agreement No. 101081369 (SPARCCLE). We also thank
the two anonymous reviewers for providing helpful feedback that greatly improved
this manuscript.
article_number: '035005'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yi-Ling
full_name: Hwong, Yi-Ling
id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22
last_name: Hwong
orcid: 0000-0001-9281-3479
- first_name: Edward
full_name: Byers, Edward
last_name: Byers
- first_name: Michaela
full_name: Werning, Michaela
last_name: Werning
- first_name: Yann
full_name: Quilcaille, Yann
last_name: Quilcaille
citation:
ama: 'Hwong Y-L, Byers E, Werning M, Quilcaille Y. Sustainable development key to
limiting climate change-driven wildfire damages. Environmental Research: Climate.
2025;4(3). doi:10.1088/2752-5295/adec11'
apa: 'Hwong, Y.-L., Byers, E., Werning, M., & Quilcaille, Y. (2025). Sustainable
development key to limiting climate change-driven wildfire damages. Environmental
Research: Climate. IOP Publishing. https://doi.org/10.1088/2752-5295/adec11'
chicago: 'Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Sustainable
Development Key to Limiting Climate Change-Driven Wildfire Damages.” Environmental
Research: Climate. IOP Publishing, 2025. https://doi.org/10.1088/2752-5295/adec11.'
ieee: 'Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Sustainable development
key to limiting climate change-driven wildfire damages,” Environmental Research:
Climate, vol. 4, no. 3. IOP Publishing, 2025.'
ista: 'Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Sustainable development
key to limiting climate change-driven wildfire damages. Environmental Research:
Climate. 4(3), 035005.'
mla: 'Hwong, Yi-Ling, et al. “Sustainable Development Key to Limiting Climate Change-Driven
Wildfire Damages.” Environmental Research: Climate, vol. 4, no. 3, 035005,
IOP Publishing, 2025, doi:10.1088/2752-5295/adec11.'
short: 'Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, Environmental Research:
Climate 4 (2025).'
corr_author: '1'
date_created: 2025-07-31T14:03:16Z
date_published: 2025-07-15T00:00:00Z
date_updated: 2025-08-04T07:46:33Z
day: '15'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1088/2752-5295/adec11
ec_funded: 1
file:
- access_level: open_access
checksum: ca679496767021e792b0378c48fdee8c
content_type: application/pdf
creator: dernst
date_created: 2025-08-04T07:38:14Z
date_updated: 2025-08-04T07:38:14Z
file_id: '20108'
file_name: 2025_EnvironResearchClimate_Hwong.pdf
file_size: 2807041
relation: main_file
success: 1
file_date_updated: 2025-08-04T07:38:14Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 'Environmental Research: Climate'
publication_identifier:
eissn:
- 2752-5295
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
- id: '20107'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Sustainable development key to limiting climate change-driven wildfire damages
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20099'
abstract:
- lang: eng
text: The hippocampus, critical for learning and memory, is dogmatically described
as a trisynaptic circuit where dentate gyrus granule cells (GCs), CA3 pyramidal
neurons (PNs), and CA1 PNs are serially connected. However, CA3 also forms an
autoassociative network, and its PNs have diverse morphologies, intrinsic properties,
and GC input levels. How PN subtypes compose this recurrent network is unknown.
To determine the synaptic arrangement of identified CA3 PNs, we combine multicellular
patch-clamp recording and post hoc morphological analysis in mouse hippocampal
slices. PNs can be divided into distinct “superficial” and “deep” subclasses,
the latter including previously reported “athorny” cells. Subclasses have distinct
input-output transformations and asymmetric connectivity, which is more abundant
from superficial to deep PNs, splitting CA3 locally into two parallel recurrent
networks. Coincident spontaneous inhibition occurs frequently within but not between
subclasses, implying subclass-specific inhibitory innervation. Our results suggest
two separately controlled sublayers for parallel information processing in hippocampal
CA3.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
acknowledgement: We thank Andrea Navas-Olive and Rebecca J. Morse-Mora for critically
reading an earlier version of the manuscript. We also thank Florian Marr and Christina
Altmutter for excellent technical assistance, Alois Schlögl for programming and
data-handling assistance, Todor Asenov for technical support, and Eleftheria Kralli-Beller
for manuscript editing. This research was supported by the Scientific Services Units
(SSUs) of ISTA. We are particularly grateful for assistance from the Imaging and
Optics Facility, Preclinical Facility, Lab Support Facility, and Miba Machine Shop.
The project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation program (grant agreement no.
692692 to P.J., Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635
to J.F.W., and an ISTplus Fellowship through Marie Skłodowska-Curie grant agreement
no. 754411 to V.V.-B.), the Austrian Science Fund (P 36232-B, PAT 4178023, and Cluster
of Excellence 10.55776/COE16 to P.J.), and a CONACyT fellowship (289638 to V.V.-B.)
and was supported by a non-stipendiary EMBO fellowship (ALTF 756–2020 to J.F.W.).
article_number: '116080'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Watson J, Vargas Barroso VM, Jonas PM. Cell-specific wiring routes information
flow through hippocampal CA3. Cell Reports. 2025;44(8). doi:10.1016/j.celrep.2025.116080
apa: Watson, J., Vargas Barroso, V. M., & Jonas, P. M. (2025). Cell-specific
wiring routes information flow through hippocampal CA3. Cell Reports. Elsevier.
https://doi.org/10.1016/j.celrep.2025.116080
chicago: Watson, Jake, Victor M Vargas Barroso, and Peter M Jonas. “Cell-Specific
Wiring Routes Information Flow through Hippocampal CA3.” Cell Reports.
Elsevier, 2025. https://doi.org/10.1016/j.celrep.2025.116080.
ieee: J. Watson, V. M. Vargas Barroso, and P. M. Jonas, “Cell-specific wiring routes
information flow through hippocampal CA3,” Cell Reports, vol. 44, no. 8.
Elsevier, 2025.
ista: Watson J, Vargas Barroso VM, Jonas PM. 2025. Cell-specific wiring routes information
flow through hippocampal CA3. Cell Reports. 44(8), 116080.
mla: Watson, Jake, et al. “Cell-Specific Wiring Routes Information Flow through
Hippocampal CA3.” Cell Reports, vol. 44, no. 8, 116080, Elsevier, 2025,
doi:10.1016/j.celrep.2025.116080.
short: J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (2025).
corr_author: '1'
date_created: 2025-08-03T22:01:30Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2025-09-30T14:12:02Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2025.116080
ec_funded: 1
external_id:
isi:
- '001544472300002'
file:
- access_level: open_access
checksum: 556ff9760661ecd23949d75031043b1f
content_type: application/pdf
creator: dernst
date_created: 2025-08-04T06:53:07Z
date_updated: 2025-08-04T06:53:07Z
file_id: '20106'
file_name: 2025_CellReports_Watson.pdf
file_size: 27695214
relation: main_file
success: 1
file_date_updated: 2025-08-04T06:53:07Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell-specific wiring routes information flow through hippocampal CA3
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 44
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20100'
abstract:
- lang: eng
text: A key step in protein structure prediction involves the detection of co-evolving
pairs of residues, a signal for spatial proximity. This information is gleaned
from multiple sequence alignment and underscores Alphafold’s structure prediction
for almost every known protein. A simple means to create proteins beyond those
found in nature, is by unnaturally fusing together two known proteins or protein
parts. Here we demonstrate that structured peptides are predicted with significantly
reduced accuracy when added to the terminal ends of scaffold proteins. Appending
the multiple sequence alignment for the individual peptide tags to that of the
scaffold protein often restores prediction accuracy. This work suggests that this
windowed multiple sequence alignment approach can be a useful tool for predicting
the structure of fused, chimeric proteins.
acknowledgement: AM acknowledges the financial support of the Helmsley Fellowships
Program for Sustainability and Health. AMB is supported by the Schmidt Chair in
Artificial Intelligence.
article_processing_charge: Yes
article_type: original
author:
- first_name: Sanketh
full_name: Vedula, Sanketh
id: 94f2fe44-70fa-11f0-b76b-92922c09452b
last_name: Vedula
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Ailie
full_name: Marx, Ailie
last_name: Marx
citation:
ama: Vedula S, Bronstein AM, Marx A. Improving prediction accuracy in chimeric proteins
with windowed multiple sequence alignment. Computational and Structural Biotechnology
Journal. 2025;27:3292-3298. doi:10.1016/j.csbj.2025.07.039
apa: Vedula, S., Bronstein, A. M., & Marx, A. (2025). Improving prediction accuracy
in chimeric proteins with windowed multiple sequence alignment. Computational
and Structural Biotechnology Journal. Elsevier. https://doi.org/10.1016/j.csbj.2025.07.039
chicago: Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Improving Prediction
Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” Computational
and Structural Biotechnology Journal. Elsevier, 2025. https://doi.org/10.1016/j.csbj.2025.07.039.
ieee: S. Vedula, A. M. Bronstein, and A. Marx, “Improving prediction accuracy in
chimeric proteins with windowed multiple sequence alignment,” Computational
and Structural Biotechnology Journal, vol. 27. Elsevier, pp. 3292–3298, 2025.
ista: Vedula S, Bronstein AM, Marx A. 2025. Improving prediction accuracy in chimeric
proteins with windowed multiple sequence alignment. Computational and Structural
Biotechnology Journal. 27, 3292–3298.
mla: Vedula, Sanketh, et al. “Improving Prediction Accuracy in Chimeric Proteins
with Windowed Multiple Sequence Alignment.” Computational and Structural Biotechnology
Journal, vol. 27, Elsevier, 2025, pp. 3292–98, doi:10.1016/j.csbj.2025.07.039.
short: S. Vedula, A.M. Bronstein, A. Marx, Computational and Structural Biotechnology
Journal 27 (2025) 3292–3298.
date_created: 2025-08-03T22:01:31Z
date_published: 2025-06-27T00:00:00Z
date_updated: 2025-11-27T14:09:59Z
day: '27'
ddc:
- '000'
- '570'
department:
- _id: AlBr
doi: 10.1016/j.csbj.2025.07.039
external_id:
isi:
- '001583543100001'
file:
- access_level: open_access
checksum: 78d01f30fc1dc11dd2bd1d7bb7ac8a62
content_type: application/pdf
creator: dernst
date_created: 2025-08-04T06:25:23Z
date_updated: 2025-08-04T06:25:23Z
file_id: '20104'
file_name: 2025_CompStrucBiotechJour_Vedula.pdf
file_size: 6609770
relation: main_file
success: 1
file_date_updated: 2025-08-04T06:25:23Z
has_accepted_license: '1'
intvolume: ' 27'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 3292-3298
publication: Computational and Structural Biotechnology Journal
publication_identifier:
eissn:
- 2001-0370
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/sankethvedula/AFChimera
record:
- id: '20103'
relation: software
status: public
scopus_import: '1'
status: public
title: Improving prediction accuracy in chimeric proteins with windowed multiple sequence
alignment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20101'
abstract:
- lang: eng
text: 'Evading imminent threat from predators is critical for animal survival. Effective
defensive strategies can vary, even between closely related species. However,
the neural basis of such species-specific behaviours remains poorly understood1,2,3,4.
Here we find that two sister species of deer mice (genus Peromyscus)5 show different
responses to the same looming stimulus: Peromyscus maniculatus, which occupies
densely vegetated habitats, predominantly escapes, whereas the open field specialist,
Peromyscus polionotus, briefly freezes. This difference arises from species-specific
escape thresholds, is largely context-independent, and can be triggered by both
visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological
recordings, we find that although visual threat activates the superior colliculus
in both species, the role of the dorsal periaqueductal grey (dPAG) in driving
behaviour differs. Whereas dPAG activity scales with running speed in P. maniculatus,
neural activity in the dPAG of P. polionotus correlates poorly with movement,
including during visually triggered escape. Moreover, optogenetic activation of
dPAG neurons elicits acceleration in P. maniculatus but not in P. polionotus,
and their chemogenetic inhibition during a looming stimulus delays escape onset
in P. maniculatus to match that of P. polionotus. Together, we trace species-specific
escape thresholds to a central circuit node, downstream of peripheral sensory
neurons, localizing an ecologically relevant behavioural difference to a specific
region of the mammalian brain.'
acknowledgement: The authors thank M. Yilmaz, M. Meister, M. Joesch and T. Branco
for advice on the behavioural experiments; C. Dulac, V. Bitsikas, E. Diel and J.
Chen for advice on the immunohistochemistry and RNAscope experiments; J. Greenwood
and E. Soucy for technical and engineering help; A. Chrzanowska for help and advice
on optogenetic experiments; A. Calzoni for help aligning histological sections to
a brain atlas; S. Worthington for statistical advice; P. Gonçalves for advice with
the electrophysiology analysis; I. Vlaemick for help with whole cell experiments;
R. Hellmiss for figure design; B. Sabatini, V. Stempel, K. Tyssowski and N. Sanguinetti
for feedback on the manuscript; and Y. M. Lee and A. Tomcho for photos of P. maniculatus
and P. leucopus habitats (Fig. 1). F.B. was supported by an HHMI International Student
Research Fellowship, a Grant-in-Aid of the American Society of Mammalogy, a Herchel
Smith Graduate Fellowship, a Robert A. Chapman Memorial Scholarship, and a Joan
Brockman Williamson Fellowship. This project received funding from the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
grant agreement 665501 and by the FWO (12S7917N and 12S7920N) to K.R. and from European
Research Council (ERC) (grant agreement 101075848) to K.R. V.T. was supported by
a Harvard PRISE fellowship and a Harvard Museum of Comparative Zoology grant for
undergraduate research. K.F. is supported by the FWO (G094616N and G091719N) and
the NIH (1R01EY032101). This work was supported by the Howard Hughes Medical Institute,
of which H.E.H. was an Investigator.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Felix
full_name: Baier, Felix
last_name: Baier
- first_name: Katja
full_name: Reinhard, Katja
last_name: Reinhard
- first_name: Bram
full_name: Nuttin, Bram
last_name: Nuttin
- first_name: Arnau
full_name: Sans-Dublanc, Arnau
last_name: Sans-Dublanc
- first_name: Chen
full_name: Liu, Chen
last_name: Liu
- first_name: Victoria
full_name: Tong, Victoria
last_name: Tong
- first_name: Julie Stefanie
full_name: Murmann, Julie Stefanie
id: 1d390868-f128-11eb-9611-a0ca5f7833b5
last_name: Murmann
- first_name: Keimpe
full_name: Wierda, Keimpe
last_name: Wierda
- first_name: Karl
full_name: Farrow, Karl
last_name: Farrow
- first_name: Hopi E.
full_name: Hoekstra, Hopi E.
last_name: Hoekstra
citation:
ama: Baier F, Reinhard K, Nuttin B, et al. The neural basis of species-specific
defensive behaviour in Peromyscus mice. Nature. 2025;645:439-447. doi:10.1038/s41586-025-09241-2
apa: Baier, F., Reinhard, K., Nuttin, B., Sans-Dublanc, A., Liu, C., Tong, V., …
Hoekstra, H. E. (2025). The neural basis of species-specific defensive behaviour
in Peromyscus mice. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-09241-2
chicago: Baier, Felix, Katja Reinhard, Bram Nuttin, Arnau Sans-Dublanc, Chen Liu,
Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi E.
Hoekstra. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus
Mice.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-09241-2.
ieee: F. Baier et al., “The neural basis of species-specific defensive behaviour
in Peromyscus mice,” Nature, vol. 645. Springer Nature, pp. 439–447, 2025.
ista: Baier F, Reinhard K, Nuttin B, Sans-Dublanc A, Liu C, Tong V, Murmann JS,
Wierda K, Farrow K, Hoekstra HE. 2025. The neural basis of species-specific defensive
behaviour in Peromyscus mice. Nature. 645, 439–447.
mla: Baier, Felix, et al. “The Neural Basis of Species-Specific Defensive Behaviour
in Peromyscus Mice.” Nature, vol. 645, Springer Nature, 2025, pp. 439–47,
doi:10.1038/s41586-025-09241-2.
short: F. Baier, K. Reinhard, B. Nuttin, A. Sans-Dublanc, C. Liu, V. Tong, J.S.
Murmann, K. Wierda, K. Farrow, H.E. Hoekstra, Nature 645 (2025) 439–447.
date_created: 2025-08-03T22:01:31Z
date_published: 2025-07-23T00:00:00Z
date_updated: 2026-01-05T11:38:40Z
day: '23'
ddc:
- '570'
department:
- _id: GradSch
doi: 10.1038/s41586-025-09241-2
external_id:
pmid:
- '40702175'
file:
- access_level: open_access
checksum: 7ea846a7a49b3b2a248f6a27ab13d591
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T07:39:45Z
date_updated: 2025-12-30T07:39:45Z
file_id: '20884'
file_name: 2025_Nature_Baier.pdf
file_size: 53301589
relation: main_file
success: 1
file_date_updated: 2025-12-30T07:39:45Z
has_accepted_license: '1'
intvolume: ' 645'
language:
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license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 439-447
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: The neural basis of species-specific defensive behaviour in Peromyscus mice
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 645
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20102'
abstract:
- lang: eng
text: 'Speciation is rarely observable directly. A way forward is to compare pairs
of ecotypes that evolved in parallel in similar contexts but have reached different
degrees of reproductive isolation. Such comparisons are possible in the marine
snail Littorina saxatilis by contrasting barriers to gene flow between parallel
ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved
to withstand either crab predation or wave action. Here, we explore transects
spanning contact zones between the Crab and the Wave ecotypes using low-coverage
whole-genome sequencing, morphological and behavioural traits. Despite parallel
phenotypic divergence, distinct patterns of differentiation between the ecotypes
emerged: a continuous cline in Sweden indicating a weak barrier to gene flow,
but two highly genetically and phenotypically divergent, and partly spatially
overlapping clusters in Spain suggesting a much stronger barrier to gene flow.
The absence of Spanish early-generation hybrids supported strong isolation, but
a low level of gene flow is evident from molecular data. In both countries, highly
differentiated loci were located in both shared and country-specific chromosomal
inversions but were also present in collinear regions. Despite being considered
the same species and showing similar levels of phenotypic divergence, the Spanish
ecotypes are much closer to full reproductive isolation than the Swedish ones.
Barriers to gene flow of very different strengths between ecotypes within the
same species might be explained by dissimilarities in the spatial arrangement
of habitats, the selection gradients or the ages of the systems.'
acknowledgement: 'This study was supported by European Research Council grant 693030-BARRIERS
to RKB; the Swedish Research Council (grant number 2021-04191) to KJ; the Portuguese
Foundation for Science and Technology (FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021)
to RF; grant PID2022-137935NB-I00 by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU
(ED431C 2020-05) to JG, grant PID2021-124930NB-I00 funded by MICIU/AEI/ 10.13039/501100011033/and
ERDF/EU to ERA, Xunta de Galicia (ED431C 2024/22), Centro singular de Investigación
de Galicia accreditation 2024-2027 (ED431G 2023/07), ‘ERDF A way of making Europe’
and Norwegian Research Council RCN, project 315287 to AMW.'
article_number: e70025
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Francesca
full_name: Raffini, Francesca
last_name: Raffini
- first_name: Aurélien
full_name: De Jode, Aurélien
last_name: De Jode
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Zuzanna B.
full_name: Zagrodzka, Zuzanna B.
last_name: Zagrodzka
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Juan
full_name: Galindo, Juan
last_name: Galindo
- first_name: Emilio
full_name: Rolán-Alvarez, Emilio
last_name: Rolán-Alvarez
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Raffini F, De Jode A, Johannesson K, et al. Phenotypic divergence and genomic
architecture between parallel ecotypes at two different points on the speciation
continuum in a marine snail. Molecular Ecology. 2025;34(21). doi:10.1111/mec.70025
apa: Raffini, F., De Jode, A., Johannesson, K., Faria, R., Zagrodzka, Z. B., Westram,
A. M., … Butlin, R. K. (2025). Phenotypic divergence and genomic architecture
between parallel ecotypes at two different points on the speciation continuum
in a marine snail. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.70025
chicago: Raffini, Francesca, Aurélien De Jode, Kerstin Johannesson, Rui Faria, Zuzanna
B. Zagrodzka, Anja M Westram, Juan Galindo, Emilio Rolán-Alvarez, and Roger K.
Butlin. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes
at Two Different Points on the Speciation Continuum in a Marine Snail.” Molecular
Ecology. Wiley, 2025. https://doi.org/10.1111/mec.70025.
ieee: F. Raffini et al., “Phenotypic divergence and genomic architecture
between parallel ecotypes at two different points on the speciation continuum
in a marine snail,” Molecular Ecology, vol. 34, no. 21. Wiley, 2025.
ista: Raffini F, De Jode A, Johannesson K, Faria R, Zagrodzka ZB, Westram AM, Galindo
J, Rolán-Alvarez E, Butlin RK. 2025. Phenotypic divergence and genomic architecture
between parallel ecotypes at two different points on the speciation continuum
in a marine snail. Molecular Ecology. 34(21), e70025.
mla: Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture
between Parallel Ecotypes at Two Different Points on the Speciation Continuum
in a Marine Snail.” Molecular Ecology, vol. 34, no. 21, e70025, Wiley,
2025, doi:10.1111/mec.70025.
short: F. Raffini, A. De Jode, K. Johannesson, R. Faria, Z.B. Zagrodzka, A.M. Westram,
J. Galindo, E. Rolán-Alvarez, R.K. Butlin, Molecular Ecology 34 (2025).
date_created: 2025-08-03T22:01:31Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2025-12-30T09:25:45Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.70025
external_id:
isi:
- '001538172800001'
file:
- access_level: open_access
checksum: ec01edda64cfbc6cbc8adf300f719644
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T09:25:17Z
date_updated: 2025-12-30T09:25:17Z
file_id: '20906'
file_name: 2025_MolecEcology_Raffini.pdf
file_size: 2767745
relation: main_file
success: 1
file_date_updated: 2025-12-30T09:25:17Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '21'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phenotypic divergence and genomic architecture between parallel ecotypes at
two different points on the speciation continuum in a marine snail
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2025'
...
---
OA_place: repository
_id: '20103'
abstract:
- lang: eng
text: Official implementation, windowed MSAs, and the predictions as reported in
the manuscript titled "Improving Prediction Accuracy in Chimeric Proteins with
Windowed Multiple Sequence Alignment". (2025-06-27)
article_processing_charge: No
author:
- first_name: Sanketh
full_name: Vedula, Sanketh
id: 94f2fe44-70fa-11f0-b76b-92922c09452b
last_name: Vedula
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Ailie
full_name: Marx, Ailie
last_name: Marx
citation:
ama: 'Vedula S, Bronstein AM, Marx A. Replication Data for: “Improving Prediction
Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” 2025.
doi:10.7910/DVN/DYEBVM'
apa: 'Vedula, S., Bronstein, A. M., & Marx, A. (2025). Replication Data for:
“Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence
Alignment.” Harvard Dataverse. https://doi.org/10.7910/DVN/DYEBVM'
chicago: 'Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Replication Data
for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple
Sequence Alignment.’” Harvard Dataverse, 2025. https://doi.org/10.7910/DVN/DYEBVM.'
ieee: 'S. Vedula, A. M. Bronstein, and A. Marx, “Replication Data for: ‘Improving
Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.’”
Harvard Dataverse, 2025.'
ista: 'Vedula S, Bronstein AM, Marx A. 2025. Replication Data for: ‘Improving Prediction
Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment’, Harvard
Dataverse, 10.7910/DVN/DYEBVM.'
mla: 'Vedula, Sanketh, et al. Replication Data for: “Improving Prediction Accuracy
in Chimeric Proteins with Windowed Multiple Sequence Alignment.” Harvard Dataverse,
2025, doi:10.7910/DVN/DYEBVM.'
short: S. Vedula, A.M. Bronstein, A. Marx, (2025).
date_created: 2025-08-04T06:18:55Z
date_published: 2025-06-27T00:00:00Z
date_updated: 2025-11-27T14:09:58Z
day: '27'
ddc:
- '000'
department:
- _id: AlBr
doi: 10.7910/DVN/DYEBVM
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.7910/DVN/DYEBVM
month: '06'
oa: 1
oa_version: Published Version
publisher: Harvard Dataverse
related_material:
record:
- id: '20100'
relation: used_for_analysis_in
status: public
status: public
title: 'Replication Data for: "Improving Prediction Accuracy in Chimeric Proteins
with Windowed Multiple Sequence Alignment"'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20107'
abstract:
- lang: eng
text: 'This repository contains the data and scripts required to reproduce the results
of the manuscript "Sustainable Development Key to Limiting Climate Change-Driven
Wildfire Damages" submitted to the Environmental Research Climate Journal (ERCL). '
article_processing_charge: No
author:
- first_name: Yi-Ling
full_name: Hwong, Yi-Ling
id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22
last_name: Hwong
orcid: 0000-0001-9281-3479
- first_name: Edward
full_name: Byers, Edward
last_name: Byers
- first_name: Michaela
full_name: Werning, Michaela
last_name: Werning
- first_name: Yann
full_name: Quilcaille, Yann
last_name: Quilcaille
citation:
ama: Hwong Y-L, Byers E, Werning M, Quilcaille Y. Data - Sustainable Development
Key to Limiting Climate Change-Driven Wildfire Damages. 2025. doi:10.5281/ZENODO.13988679
apa: Hwong, Y.-L., Byers, E., Werning, M., & Quilcaille, Y. (2025). Data - Sustainable
Development Key to Limiting Climate Change-Driven Wildfire Damages. Zenodo. https://doi.org/10.5281/ZENODO.13988679
chicago: Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Data
- Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.”
Zenodo, 2025. https://doi.org/10.5281/ZENODO.13988679.
ieee: Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Data - Sustainable
Development Key to Limiting Climate Change-Driven Wildfire Damages.” Zenodo, 2025.
ista: Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Data - Sustainable Development
Key to Limiting Climate Change-Driven Wildfire Damages, Zenodo, 10.5281/ZENODO.13988679.
mla: Hwong, Yi-Ling, et al. Data - Sustainable Development Key to Limiting Climate
Change-Driven Wildfire Damages. Zenodo, 2025, doi:10.5281/ZENODO.13988679.
short: Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, (2025).
corr_author: '1'
date_created: 2025-08-04T07:34:39Z
date_published: 2025-05-21T00:00:00Z
date_updated: 2025-08-04T07:46:33Z
day: '21'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.5281/ZENODO.13988679
ec_funded: 1
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.15409324
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publisher: Zenodo
related_material:
record:
- id: '20098'
relation: used_in_publication
status: public
status: public
title: Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire
Damages
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20116'
abstract:
- lang: eng
text: Auxin regulates various aspects of plant growth and development by modulating
the transcription of target genes through the degradation of auxin/indole-3-acetic
acid (Aux/IAA) repressors via the 26S proteasome. Proteasome regulator 1 (PTRE1),
a positive regulator of proteasome activity, has been implicated in auxin-mediated
proteasome suppression; however, the mechanism by which auxin modulates PTRE1
function remains unclear. Here, we demonstrate that auxin promotes the interaction
between germin-like protein 1 (GLP1) and PTRE1, facilitating PTRE1 retention at
the plasma membrane. The relocation of PTRE1 results in reduced nuclear 26S proteasome
activity, and thus the attenuated Aux/IAA degradation and altered Aux/IAA homeostasis,
ultimately resulting in suppressed auxin-mediated transcriptional regulation.
Our findings uncover a previously uncharacterized regulatory axis in auxin signaling
that controls Aux/IAA protein stability, functioning alongside the TIR1- and TRANSMEMBRANE
KINASE 1 (TMK1)-mediated pathways, and highlight the coordination of auxin signaling
from the cell surface to the nucleus via auxin-induced PTRE1 relocation, which
fine-tunes Aux/IAA protein homeostasis and auxin responses.
acknowledgement: The study was supported by the National Natural Science Foundation
of China (NSFC; 32230011, 91954206, and 31721001). We thank Dr. Deli Lin (Shanghai
Jiao Tong University) for kind help with the laser confocal microscope observation
and the Arabidopsis Biological Resource Center (ABRC) for providing T-DNA insertional
mutants.
article_number: '116056'
article_processing_charge: Yes
article_type: original
author:
- first_name: Faqing
full_name: Xu, Faqing
last_name: Xu
- first_name: Yongqiang
full_name: Yu, Yongqiang
last_name: Yu
- first_name: Bin
full_name: Guan, Bin
id: 56aad729-cca2-11ed-a45a-9b4138991a48
last_name: Guan
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Zhihong
full_name: Xu, Zhihong
last_name: Xu
- first_name: Hongwei
full_name: Xue, Hongwei
last_name: Xue
citation:
ama: Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. Germin-like protein 1 interacts with
proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis.
Cell Reports. 2025;44(8). doi:10.1016/j.celrep.2025.116056
apa: Xu, F., Yu, Y., Guan, B., Xu, T., Xu, Z., & Xue, H. (2025). Germin-like
protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by
controlling Aux/IAA homeostasis. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2025.116056
chicago: Xu, Faqing, Yongqiang Yu, Bin Guan, Tongda Xu, Zhihong Xu, and Hongwei
Xue. “Germin-like Protein 1 Interacts with Proteasome Regulator 1 to Regulate
Auxin Signaling by Controlling Aux/IAA Homeostasis.” Cell Reports. Elsevier,
2025. https://doi.org/10.1016/j.celrep.2025.116056.
ieee: F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, and H. Xue, “Germin-like protein 1 interacts
with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA
homeostasis,” Cell Reports, vol. 44, no. 8. Elsevier, 2025.
ista: Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. 2025. Germin-like protein 1 interacts
with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA
homeostasis. Cell Reports. 44(8), 116056.
mla: Xu, Faqing, et al. “Germin-like Protein 1 Interacts with Proteasome Regulator
1 to Regulate Auxin Signaling by Controlling Aux/IAA Homeostasis.” Cell Reports,
vol. 44, no. 8, 116056, Elsevier, 2025, doi:10.1016/j.celrep.2025.116056.
short: F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, H. Xue, Cell Reports 44 (2025).
date_created: 2025-08-04T13:39:11Z
date_published: 2025-07-24T00:00:00Z
date_updated: 2025-09-30T14:13:45Z
day: '24'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.celrep.2025.116056
external_id:
isi:
- '001542038500001'
pmid:
- '40714631'
file:
- access_level: open_access
checksum: 3c43e040a4a7a65ec67ae1d2bb81261a
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T06:15:09Z
date_updated: 2025-08-05T06:15:09Z
file_id: '20120'
file_name: 2025_CellReports_Xu.pdf
file_size: 24178018
relation: main_file
success: 1
file_date_updated: 2025-08-05T06:15:09Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin
signaling by controlling Aux/IAA homeostasis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 44
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20143'
abstract:
- lang: eng
text: Bacteria and archaea deploy diverse antiviral defense systems, many of which
remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread
two-component system composed of the transmembrane sensor KwaA and the DNA-binding
effector KwaB. Cryogenic electron microscopy (cryo-EM) analysis reveals that KwaA
and KwaB assemble into a large, membrane-associated supercomplex. Upon phage binding,
KwaA senses infection at the membrane, leading to KwaB binding of ejected phage
DNA and inhibition of replication and late transcription, without inducing host
cell death. Although KwaB can bind DNA independently, its antiviral activity requires
association with KwaA, suggesting spatial or conformational regulation. We show
that the phage-encoded DNA-mimic protein Gam directly binds and inhibits KwaB
but that co-expression with the Gam-targeted RecBCD system restores protection
by Kiwa. Our findings support a model in which Kiwa coordinates membrane-associated
detection of phage infection with downstream DNA binding by its effector, forming
a spatially coordinated antiviral mechanism.
acknowledgement: We thank Rotem Sorek (Weizmann Institute of Science) for the Lambda
Gam mutant and Ian Molineux (University of Texas) for T4Δgp2. We thank You Yu (Zhejiang
University-University of Edinburgh Institute) and J. De La Cruz (MSK) for assistance
with cryo-EM data collection and Lyuqin Zheng (MSK) for discussions on structural
analysis. We thank the Imaging and Microscopy Centre (IMC) at the University of
Southampton. This work was supported by Royal Society grant RGS\R2\222312 to F.L.N.;
Welch Foundation grant F-1938 and National Institutes of Health R35GM138348 to D.W.T.;
Wessex Medical Research Innovation grant AE06 to T.A.; and NIH grant GM145888 and
Maloris Foundation and Memorial Sloan-Kettering Core grant (P30-CA008748) to D.J.P.
In addition to MSKCC cryo-EM resources, some of this work was performed at the National
Center for CryoEM Access and Training (NCCAT) and the Simons Electron Microscopy
Center located at the New York Structural Biology Center, supported by the NIH Common
Fund Transformative High Resolution Cryo-Electron Microscopy program (U24 GM129539)
and Simons Foundation (SF349247) and NY State Assembly grants. This research used
NSLS-II MX X-ray User Resources (FMX) of the National Synchrotron Light Source II,
operated for the DOE Office of Science by Brookhaven National Laboratory under contract
no. DE-SC0012704. The Center for BioMolecular Structure (CBMS) is primarily supported
by the NIH, the National Institute of General Medical Sciences (NIGMS) through a
Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental
Research (KP1605010). R.K. and E.V.K. are supported by the Intramural Research Program
of the NIH (National Library of Medicine).
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Zhiying
full_name: Zhang, Zhiying
last_name: Zhang
- first_name: Thomas C.
full_name: Todeschini, Thomas C.
last_name: Todeschini
- first_name: Yi
full_name: Wu, Yi
last_name: Wu
- first_name: Roman
full_name: Kogay, Roman
last_name: Kogay
- first_name: Ameena
full_name: Naji, Ameena
last_name: Naji
- first_name: Joaquin
full_name: Cardenas Rodriguez, Joaquin
last_name: Cardenas Rodriguez
- first_name: Rupavidhya
full_name: Mondi, Rupavidhya
last_name: Mondi
- first_name: Daniel
full_name: Kaganovich, Daniel
last_name: Kaganovich
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Marianna
full_name: Teplova, Marianna
last_name: Teplova
- first_name: Triana
full_name: Amen, Triana
last_name: Amen
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
- first_name: Dinshaw J.
full_name: Patel, Dinshaw J.
last_name: Patel
- first_name: Franklin L.
full_name: Nobrega, Franklin L.
last_name: Nobrega
citation:
ama: Zhang Z, Todeschini TC, Wu Y, et al. Kiwa is a membrane-embedded defense supercomplex
activated at phage attachment sites. Cell. 2025;188(21):5862-5877.e23.
doi:10.1016/j.cell.2025.07.002
apa: Zhang, Z., Todeschini, T. C., Wu, Y., Kogay, R., Naji, A., Cardenas Rodriguez,
J., … Nobrega, F. L. (2025). Kiwa is a membrane-embedded defense supercomplex
activated at phage attachment sites. Cell. Elsevier. https://doi.org/10.1016/j.cell.2025.07.002
chicago: Zhang, Zhiying, Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji,
Joaquin Cardenas Rodriguez, Rupavidhya Mondi, et al. “Kiwa Is a Membrane-Embedded
Defense Supercomplex Activated at Phage Attachment Sites.” Cell. Elsevier,
2025. https://doi.org/10.1016/j.cell.2025.07.002.
ieee: Z. Zhang et al., “Kiwa is a membrane-embedded defense supercomplex
activated at phage attachment sites,” Cell, vol. 188, no. 21. Elsevier,
p. 5862–5877.e23, 2025.
ista: Zhang Z, Todeschini TC, Wu Y, Kogay R, Naji A, Cardenas Rodriguez J, Mondi
R, Kaganovich D, Taylor DW, Bravo JPK, Teplova M, Amen T, Koonin E, Patel DJ,
Nobrega FL. 2025. Kiwa is a membrane-embedded defense supercomplex activated at
phage attachment sites. Cell. 188(21), 5862–5877.e23.
mla: Zhang, Zhiying, et al. “Kiwa Is a Membrane-Embedded Defense Supercomplex Activated
at Phage Attachment Sites.” Cell, vol. 188, no. 21, Elsevier, 2025, p.
5862–5877.e23, doi:10.1016/j.cell.2025.07.002.
short: Z. Zhang, T.C. Todeschini, Y. Wu, R. Kogay, A. Naji, J. Cardenas Rodriguez,
R. Mondi, D. Kaganovich, D.W. Taylor, J.P.K. Bravo, M. Teplova, T. Amen, E. Koonin,
D.J. Patel, F.L. Nobrega, Cell 188 (2025) 5862–5877.e23.
date_created: 2025-08-07T05:00:04Z
date_published: 2025-10-16T00:00:00Z
date_updated: 2025-12-29T14:15:58Z
day: '16'
ddc:
- '570'
department:
- _id: JaBr
doi: 10.1016/j.cell.2025.07.002
external_id:
isi:
- '001603560700005'
pmid:
- '40730155'
file:
- access_level: open_access
checksum: b944de5fbd7455f58e1ff338ad352239
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T14:15:25Z
date_updated: 2025-12-29T14:15:25Z
file_id: '20875'
file_name: 2025_Cell_Zhang.pdf
file_size: 32104588
relation: main_file
success: 1
file_date_updated: 2025-12-29T14:15:25Z
has_accepted_license: '1'
intvolume: ' 188'
isi: 1
issue: '21'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 5862-5877.e23
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Kiwa is a membrane-embedded defense supercomplex activated at phage attachment
sites
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 188
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '20146'
abstract:
- lang: eng
text: "This criteria catalogue and the accompanying assessment questions were developed
by a working group of KEMÖ (Kooperation E-Medien Österreich, the Austrian Academic
Library Consortium). They are intended to support research institutions and organisations
in the evaluation of Open Science Infrastructures. The 20 criteria outlined in
the catalogue provide a structured basis for making informed decisions regarding
the financial support of these infrastructures.\r\n\r\nThe assessment questions
are intended to be completed by Open Science Infrastructures and can be shared
with them accordingly."
article_processing_charge: No
author:
- first_name: Paul
full_name: Gredler, Paul
last_name: Gredler
- first_name: Christian
full_name: Kaier, Christian
last_name: Kaier
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Michael
full_name: Zoyer, Michael
last_name: Zoyer
- first_name: Katharina
full_name: Rieck, Katharina
last_name: Rieck
- first_name: Andreas
full_name: Ferus, Andreas
last_name: Ferus
- first_name: Elisabeth
full_name: Rosenberger, Elisabeth
last_name: Rosenberger
- first_name: Alexander
full_name: Löffler, Alexander
last_name: Löffler
- first_name: Lisa
full_name: Hofer, Lisa
last_name: Hofer
- first_name: Laura
full_name: Still, Laura
last_name: Still
citation:
ama: Gredler P, Kaier C, Danowski P, et al. Catalogue of Criteria for Assessing
the Funding Eligibility of Open Science Infrastructures. Zenodo; 2025. doi:10.5281/zenodo.15269364
apa: Gredler, P., Kaier, C., Danowski, P., Zoyer, M., Rieck, K., Ferus, A., … Still,
L. (2025). Catalogue of criteria for assessing the funding eligibility of Open
Science infrastructures. Zenodo. https://doi.org/10.5281/zenodo.15269364
chicago: Gredler, Paul, Christian Kaier, Patrick Danowski, Michael Zoyer, Katharina
Rieck, Andreas Ferus, Elisabeth Rosenberger, Alexander Löffler, Lisa Hofer, and
Laura Still. Catalogue of Criteria for Assessing the Funding Eligibility of
Open Science Infrastructures. Zenodo, 2025. https://doi.org/10.5281/zenodo.15269364.
ieee: P. Gredler et al., Catalogue of criteria for assessing the funding
eligibility of Open Science infrastructures. Zenodo, 2025.
ista: Gredler P, Kaier C, Danowski P, Zoyer M, Rieck K, Ferus A, Rosenberger E,
Löffler A, Hofer L, Still L. 2025. Catalogue of criteria for assessing the funding
eligibility of Open Science infrastructures, Zenodo,p.
mla: Gredler, Paul, et al. Catalogue of Criteria for Assessing the Funding Eligibility
of Open Science Infrastructures. Zenodo, 2025, doi:10.5281/zenodo.15269364.
short: P. Gredler, C. Kaier, P. Danowski, M. Zoyer, K. Rieck, A. Ferus, E. Rosenberger,
A. Löffler, L. Hofer, L. Still, Catalogue of Criteria for Assessing the Funding
Eligibility of Open Science Infrastructures, Zenodo, 2025.
date_created: 2025-08-07T11:10:14Z
date_published: 2025-08-07T00:00:00Z
date_updated: 2025-08-11T07:20:03Z
day: '07'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.5281/zenodo.15269364
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.15269364
month: '08'
oa: 1
oa_version: Published Version
publication_status: published
publisher: Zenodo
status: public
title: Catalogue of criteria for assessing the funding eligibility of Open Science
infrastructures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: working_paper
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20154'
abstract:
- lang: eng
text: In long-lived mammals, including humans, brain cell homeostasis is critical
for maintaining brain function throughout life. Most neurons are generated during
development and must maintain their cellular identity and plasticity to preserve
brain function. Although extensive studies indicate the importance of recycling
and regenerating cellular molecules to maintain cellular homeostasis, recent evidence
has shown that some proteins and RNAs do not turn over for months and even years.
We propose that these long-lived cellular molecules may be the basis for maintaining
brain function in the long term, but also a potential convergent target of brain
aging. We highlight key discoveries and challenges, and propose potential directions
to unravel the mystery of brain cell longevity.
acknowledgement: The work was supported by the Deutsche Forschungsgemeinschaft (DFG,
German Research Foundation) (470322152 – T1347/3-1; 497658532 – T1347/4-1; 507965872
– T1347/5-1; and 460333672 – CRC1540 Exploring Brain Mechanics) to T.T., the Schram
Foundation (T.T.), the European Research Council (ERC-2018-STG, 804468 EAGER; ERC-2023-COG,
101125034 NEUTIME) to T.T., the Hans-Georg Geis und Xue Hong Dong-Geis Foundation
and Forschungsstiftung Medizin am Universitätsklinikum Erlangen to T.T., and the
Interdisciplinary Centre for Clinical Research Erlangen (Interdisziplinäres Zentrum
für Klinische Forschung, Universitätsklinikum Erlangen; P162 to T.T.). We thank
Dr Laura J. Harrison for editing assistance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
- first_name: Tomohisa
full_name: Toda, Tomohisa
last_name: Toda
citation:
ama: Hetzer M, Toda T. Long-lived cellular molecules in the brain. Trends in
Neurosciences. 2025;48(9):645-654. doi:10.1016/j.tins.2025.07.004
apa: Hetzer, M., & Toda, T. (2025). Long-lived cellular molecules in the brain.
Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2025.07.004
chicago: Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the
Brain.” Trends in Neurosciences. Elsevier, 2025. https://doi.org/10.1016/j.tins.2025.07.004.
ieee: M. Hetzer and T. Toda, “Long-lived cellular molecules in the brain,” Trends
in Neurosciences, vol. 48, no. 9. Elsevier, pp. 645–654, 2025.
ista: Hetzer M, Toda T. 2025. Long-lived cellular molecules in the brain. Trends
in Neurosciences. 48(9), 645–654.
mla: Hetzer, Martin, and Tomohisa Toda. “Long-Lived Cellular Molecules in the Brain.”
Trends in Neurosciences, vol. 48, no. 9, Elsevier, 2025, pp. 645–54, doi:10.1016/j.tins.2025.07.004.
short: M. Hetzer, T. Toda, Trends in Neurosciences 48 (2025) 645–654.
corr_author: '1'
date_created: 2025-08-10T22:01:29Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2025-12-29T13:47:58Z
day: '01'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1016/j.tins.2025.07.004
external_id:
isi:
- '001568965400001'
pmid:
- '40744775'
file:
- access_level: open_access
checksum: 90942491b499f70b0bf48b8aec2e7387
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T13:47:27Z
date_updated: 2025-12-29T13:47:27Z
file_id: '20873'
file_name: 2025_TrendsNeurosciences_Hetzer.pdf
file_size: 327847
relation: main_file
success: 1
file_date_updated: 2025-12-29T13:47:27Z
has_accepted_license: '1'
intvolume: ' 48'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 645-654
pmid: 1
publication: Trends in Neurosciences
publication_identifier:
eissn:
- 1878-108X
issn:
- 0166-2236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Long-lived cellular molecules in the brain
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20155'
abstract:
- lang: eng
text: We study time averages for the norm of solutions to kinetic Fokker–Planck
equations associated with general Hamiltonians. We provide fully explicit and
constructive decay estimates for systems subject to a confining potential, allowing
fat-tail, subexponential and (super-)exponential local equilibria, which also
include the classic Maxwellian case. The key step in our estimates is a modified
Poincaré inequality, obtained via a Lions–Poincaré inequality and an averaging
lemma.
acknowledgement: The first author was funded by the European Union's Horizon 2020
research andinnovation program under the Marie Sklodowska-Curie grant agreements
754362 and 101034413,and partially by Project EFI (ANR-17-CE40-0030) of the French
National Research Agency (ANR).The work of the second author was partially funded
by the European Research Council (ERC) underthe European Union's Horizon 2020 research
and innovation programme (grant agreement 810367),and by the Agence Nationale de
la Recherche under grants ANR-19-CE40-0010 (QuAMProcs) andANR-21-CE40-0006 (SINEQ).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giovanni
full_name: Brigati, Giovanni
id: 63ff57e8-1fbb-11ee-88f2-f558ffc59cf1
last_name: Brigati
- first_name: Gabriel
full_name: Stoltz, Gabriel
last_name: Stoltz
citation:
ama: Brigati G, Stoltz G. How to construct explicit decay rates for kinetic Fokker–Planck
equations? SIAM Journal on Mathematical Analysis. 2025;57(4):3587-3622.
doi:10.1137/24M1700351
apa: Brigati, G., & Stoltz, G. (2025). How to construct explicit decay rates
for kinetic Fokker–Planck equations? SIAM Journal on Mathematical Analysis.
Society for Industrial and Applied Mathematics. https://doi.org/10.1137/24M1700351
chicago: Brigati, Giovanni, and Gabriel Stoltz. “How to Construct Explicit Decay
Rates for Kinetic Fokker–Planck Equations?” SIAM Journal on Mathematical Analysis.
Society for Industrial and Applied Mathematics, 2025. https://doi.org/10.1137/24M1700351.
ieee: G. Brigati and G. Stoltz, “How to construct explicit decay rates for kinetic
Fokker–Planck equations?,” SIAM Journal on Mathematical Analysis, vol.
57, no. 4. Society for Industrial and Applied Mathematics, pp. 3587–3622, 2025.
ista: Brigati G, Stoltz G. 2025. How to construct explicit decay rates for kinetic
Fokker–Planck equations? SIAM Journal on Mathematical Analysis. 57(4), 3587–3622.
mla: Brigati, Giovanni, and Gabriel Stoltz. “How to Construct Explicit Decay Rates
for Kinetic Fokker–Planck Equations?” SIAM Journal on Mathematical Analysis,
vol. 57, no. 4, Society for Industrial and Applied Mathematics, 2025, pp. 3587–622,
doi:10.1137/24M1700351.
short: G. Brigati, G. Stoltz, SIAM Journal on Mathematical Analysis 57 (2025) 3587–3622.
corr_author: '1'
date_created: 2025-08-10T22:01:29Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2025-11-05T13:51:40Z
day: '01'
department:
- _id: JaMa
doi: 10.1137/24M1700351
ec_funded: 1
external_id:
arxiv:
- '2302.14506'
isi:
- '001550830900006'
intvolume: ' 57'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2302.14506
month: '08'
oa: 1
oa_version: Preprint
page: 3587-3622
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: SIAM Journal on Mathematical Analysis
publication_identifier:
eissn:
- 1095-7154
issn:
- 0036-1410
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: How to construct explicit decay rates for kinetic Fokker–Planck equations?
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20182'
abstract:
- lang: eng
text: Sex chromosomes have evolved many times throughout the tree of life, and understanding
what has shaped their unusual morphological, sequence, and regulatory features
has been a long-standing goal. Most early insights into insect sex chromosome
biology came from a few model species, such as the fruit fly Drosophila melanogaster,
which limited broad-scale evolutionary inferences. More recently, extensive comparative
genomics studies have uncovered several unexpected patterns, which we highlight
in this review. First, we describe the conservation of the ancestral X chromosome
over 450 million years but also its recurrent turnover (i.e. its reversal to an
autosome when a new X chromosome arose) in at least one order. We then summarize
classical and more recent findings on how insects modulate the expression of X-linked
genes following the degradation of the Y chromosome and how the diverse mechanisms
of dosage compensation identified may elucidate important principles of sex chromosome
regulatory evolution.
acknowledgement: This work was supported by an Austrian Research Fund (FWF) grant
to B.V. (PAT 8748323) and by the Louisiana Board of Regents Research Competitiveness
Subprogram (LEQSF(2025-28)-RD-A-20) to MAT.
article_number: '101411'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Toups MA, Vicoso B. Insect sex chromosome evolution: Conservation, turnover,
and mechanisms of dosage compensation. Current Opinion in Insect Science.
2025;72. doi:10.1016/j.cois.2025.101411'
apa: 'Toups, M. A., & Vicoso, B. (2025). Insect sex chromosome evolution: Conservation,
turnover, and mechanisms of dosage compensation. Current Opinion in Insect
Science. Elsevier. https://doi.org/10.1016/j.cois.2025.101411'
chicago: 'Toups, Melissa A, and Beatriz Vicoso. “Insect Sex Chromosome Evolution:
Conservation, Turnover, and Mechanisms of Dosage Compensation.” Current Opinion
in Insect Science. Elsevier, 2025. https://doi.org/10.1016/j.cois.2025.101411.'
ieee: 'M. A. Toups and B. Vicoso, “Insect sex chromosome evolution: Conservation,
turnover, and mechanisms of dosage compensation,” Current Opinion in Insect
Science, vol. 72. Elsevier, 2025.'
ista: 'Toups MA, Vicoso B. 2025. Insect sex chromosome evolution: Conservation,
turnover, and mechanisms of dosage compensation. Current Opinion in Insect Science.
72, 101411.'
mla: 'Toups, Melissa A., and Beatriz Vicoso. “Insect Sex Chromosome Evolution: Conservation,
Turnover, and Mechanisms of Dosage Compensation.” Current Opinion in Insect
Science, vol. 72, 101411, Elsevier, 2025, doi:10.1016/j.cois.2025.101411.'
short: M.A. Toups, B. Vicoso, Current Opinion in Insect Science 72 (2025).
corr_author: '1'
date_created: 2025-08-17T22:01:35Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2025-12-30T13:14:38Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1016/j.cois.2025.101411
external_id:
isi:
- '001582424100001'
file:
- access_level: open_access
checksum: 262640abc34277686b56eb60102976f6
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T13:14:20Z
date_updated: 2025-12-30T13:14:20Z
file_id: '20917'
file_name: 2025_CurrOpinionInsectScience_Toups.pdf
file_size: 897079
relation: main_file
success: 1
file_date_updated: 2025-12-30T13:14:20Z
has_accepted_license: '1'
intvolume: ' 72'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 8ed82125-16d5-11f0-9cad-fbcae312235b
grant_number: PAT 8748323
name: Sex chromosomes in evolution and development
publication: Current Opinion in Insect Science
publication_identifier:
eissn:
- 2214-5753
issn:
- 2214-5745
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Insect sex chromosome evolution: Conservation, turnover, and mechanisms of
dosage compensation'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 72
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20183'
abstract:
- lang: eng
text: The unequal segregation of organelles has been proposed to be an intrinsic
mechanism that contributes to cell fate divergence during asymmetric cell division;
however, in vivo evidence is sparse. Using super-resolution microscopy, we analysed
the segregation of organelles during the division of the neuroblast QL.p in C.
elegans larvae. QL.p divides to generate a daughter that survives, QL.pa, and
a daughter that dies, QL.pp. We found that mitochondria segregate unequally by
density and morphology and that this is dependent on mitochondrial dynamics. Furthermore,
we found that mitochondrial density in QL.pp correlates with the time it takes
QL.pp to die. We propose that low mitochondrial density in QL.pp promotes the
cell death fate and ensures that QL.pp dies in a highly reproducible and timely
manner. Our results provide in vivo evidence that the unequal segregation of mitochondria
can contribute to cell fate divergence during asymmetric cell division in a developing
animal.
acknowledgement: We thank members of the Conradt lab, the Center for Cell and Molecular
Dynamics (https://www.uclccmd.co.uk/) and T. Schedl for discussions and comments
on the manuscript. We thank L. McGuinness for excellent technical support. Some
strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded
by NIH Office of Research Infrastructure Programs (P40 OD010440). We thank Alex
Hajnal (University of Zurich, Switzerland) and Andrew deMello (ETH Zurich, Switzerland)
for their support of S.B. This work was supported by a predoctoral fellowship from
the Studienstiftung des deutschen Volkes to NM, funds from UCL (Division of Biosciences,
UCL LSM Capital Equipment Fund) to B.C., and a Wolfson Fellowship from the Royal
Society (https://royalsociety.org/) to B.C. (RSWF\R1\180008), and the Biotechnology
and Biological Sciences Research Council (https://bbsrc.ukri.org/) (BB/V007572/1
and BB/V015648/1to B.C.).
article_number: '7174'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ioannis
full_name: Segos, Ioannis
last_name: Segos
- first_name: Jens
full_name: Van Eeckhoven, Jens
last_name: Van Eeckhoven
- first_name: Simon
full_name: Berger, Simon
last_name: Berger
- first_name: Nikhil
full_name: Mishra, Nikhil
id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E
last_name: Mishra
orcid: 0000-0002-6425-5788
- first_name: Eric J.
full_name: Lambie, Eric J.
last_name: Lambie
- first_name: Barbara
full_name: Conradt, Barbara
last_name: Conradt
citation:
ama: Segos I, Van Eeckhoven J, Berger S, Mishra N, Lambie EJ, Conradt B. Unequal
segregation of mitochondria during asymmetric cell division contributes to cell
fate divergence in sister cells in vivo. Nature Communications. 2025;16.
doi:10.1038/s41467-025-62484-5
apa: Segos, I., Van Eeckhoven, J., Berger, S., Mishra, N., Lambie, E. J., &
Conradt, B. (2025). Unequal segregation of mitochondria during asymmetric cell
division contributes to cell fate divergence in sister cells in vivo. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-025-62484-5
chicago: Segos, Ioannis, Jens Van Eeckhoven, Simon Berger, Nikhil Mishra, Eric J.
Lambie, and Barbara Conradt. “Unequal Segregation of Mitochondria during Asymmetric
Cell Division Contributes to Cell Fate Divergence in Sister Cells in Vivo.” Nature
Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-62484-5.
ieee: I. Segos, J. Van Eeckhoven, S. Berger, N. Mishra, E. J. Lambie, and B. Conradt,
“Unequal segregation of mitochondria during asymmetric cell division contributes
to cell fate divergence in sister cells in vivo,” Nature Communications,
vol. 16. Springer Nature, 2025.
ista: Segos I, Van Eeckhoven J, Berger S, Mishra N, Lambie EJ, Conradt B. 2025.
Unequal segregation of mitochondria during asymmetric cell division contributes
to cell fate divergence in sister cells in vivo. Nature Communications. 16, 7174.
mla: Segos, Ioannis, et al. “Unequal Segregation of Mitochondria during Asymmetric
Cell Division Contributes to Cell Fate Divergence in Sister Cells in Vivo.” Nature
Communications, vol. 16, 7174, Springer Nature, 2025, doi:10.1038/s41467-025-62484-5.
short: I. Segos, J. Van Eeckhoven, S. Berger, N. Mishra, E.J. Lambie, B. Conradt,
Nature Communications 16 (2025).
date_created: 2025-08-17T22:01:35Z
date_published: 2025-08-04T00:00:00Z
date_updated: 2025-09-01T09:47:29Z
day: '04'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1038/s41467-025-62484-5
external_id:
pmid:
- '40759648'
file:
- access_level: open_access
checksum: f28e73963ea1f55876d0d1afca0f706a
content_type: application/pdf
creator: dernst
date_created: 2025-09-01T09:46:44Z
date_updated: 2025-09-01T09:46:44Z
file_id: '20261'
file_name: 2025_NatureComm_Segos.pdf
file_size: 3775190
relation: main_file
success: 1
file_date_updated: 2025-09-01T09:46:44Z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unequal segregation of mitochondria during asymmetric cell division contributes
to cell fate divergence in sister cells in vivo
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20184'
abstract:
- lang: eng
text: Specialized DNA polymerases facilitate various cellular processes. Despite
extensive research, the mutagenic effects of these error-prone enzymes on genomes
are not fully understood. Here we show that Pol IV promotes genomic instability
in Pseudomonas aeruginosa by misincorporating oxidized guanine nucleotides. This
activity led to a distinctive mutational signature, characterized by A-to-C transversions
occurring preferentially at AT sites flanked by a 5’G and/or 3’C. Furthermore,
Pol IV preferentially targeted pathogenicity genes located at specific chromosomal
locations near the replication termination region and rRNA-encoding operons. Half
of the mutation events catalyzed by Pol IV impaired gene function. This can be
attributed to the bias of Pol IV for mutating codons with its preferred sequence
contexts, leading to substitutions to unreactive alanine and glycine residues.
Remarkably, mutation signatures identified for Pol IV were found in clinical isolate
genomes of P. aeruginosa, providing compelling evidence for its role in genetic
diversification during pathogen adaptation.
acknowledgement: "This work was supported by the Secretaría de Ciencia y Técnica (33620230100926CB),
Universidad Nacional de Córdoba; and the Agencia Nacional de Promoción Científica
y Técnica (PICT 2018-4527).\r\n\r\n"
article_number: '1148'
article_processing_charge: Yes
article_type: original
author:
- first_name: Sofía D.
full_name: Castell, Sofía D.
last_name: Castell
- first_name: Consuelo M.
full_name: Fernandez, Consuelo M.
last_name: Fernandez
- first_name: Ignacio N.
full_name: Tumas, Ignacio N.
last_name: Tumas
- first_name: Lucía M.
full_name: Margara, Lucía M.
last_name: Margara
- first_name: Maria C
full_name: Miserendino, Maria C
id: 273e0cbd-72f0-11ef-b75a-f9f932e292fa
last_name: Miserendino
- first_name: Danilo G.
full_name: Ceschin, Danilo G.
last_name: Ceschin
- first_name: Roberto J.
full_name: Pezza, Roberto J.
last_name: Pezza
- first_name: Mariela R.
full_name: Monti, Mariela R.
last_name: Monti
citation:
ama: Castell SD, Fernandez CM, Tumas IN, et al. The low-fidelity DNA Pol IV accelerates
evolution of pathogenicity genes in Pseudomonas aeruginosa. Communications
Biology. 2025;8. doi:10.1038/s42003-025-08589-5
apa: Castell, S. D., Fernandez, C. M., Tumas, I. N., Margara, L. M., Miserendino,
M. C., Ceschin, D. G., … Monti, M. R. (2025). The low-fidelity DNA Pol IV accelerates
evolution of pathogenicity genes in Pseudomonas aeruginosa. Communications
Biology. Springer Nature. https://doi.org/10.1038/s42003-025-08589-5
chicago: Castell, Sofía D., Consuelo M. Fernandez, Ignacio N. Tumas, Lucía M. Margara,
Maria C Miserendino, Danilo G. Ceschin, Roberto J. Pezza, and Mariela R. Monti.
“The Low-Fidelity DNA Pol IV Accelerates Evolution of Pathogenicity Genes in Pseudomonas
Aeruginosa.” Communications Biology. Springer Nature, 2025. https://doi.org/10.1038/s42003-025-08589-5.
ieee: S. D. Castell et al., “The low-fidelity DNA Pol IV accelerates evolution
of pathogenicity genes in Pseudomonas aeruginosa,” Communications Biology,
vol. 8. Springer Nature, 2025.
ista: Castell SD, Fernandez CM, Tumas IN, Margara LM, Miserendino MC, Ceschin DG,
Pezza RJ, Monti MR. 2025. The low-fidelity DNA Pol IV accelerates evolution of
pathogenicity genes in Pseudomonas aeruginosa. Communications Biology. 8, 1148.
mla: Castell, Sofía D., et al. “The Low-Fidelity DNA Pol IV Accelerates Evolution
of Pathogenicity Genes in Pseudomonas Aeruginosa.” Communications Biology,
vol. 8, 1148, Springer Nature, 2025, doi:10.1038/s42003-025-08589-5.
short: S.D. Castell, C.M. Fernandez, I.N. Tumas, L.M. Margara, M.C. Miserendino,
D.G. Ceschin, R.J. Pezza, M.R. Monti, Communications Biology 8 (2025).
date_created: 2025-08-17T22:01:35Z
date_published: 2025-08-02T00:00:00Z
date_updated: 2025-09-30T14:18:46Z
day: '02'
ddc:
- '570'
department:
- _id: PaSc
- _id: GradSch
doi: 10.1038/s42003-025-08589-5
external_id:
isi:
- '001541878500001'
pmid:
- '40753298'
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s42003-025-08589-5
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The low-fidelity DNA Pol IV accelerates evolution of pathogenicity genes in
Pseudomonas aeruginosa
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20185'
abstract:
- lang: eng
text: We show a local rigidity result for the integrability of symplectic billiards.
We prove that any domain which is close to an ellipse, and for which the symplectic
billiard map is rationally integrable must be an ellipse as well. This is in spirit
of the result of [2] for Birkhoff billiards.
acknowledgement: The author would like to thank Corentin Fierobe, Vadim Kaloshin,
Illya Koval and Yunzhe Li for useful discussions. The author would also like to
thank the referee for useful remarks. Open access funding provided by Institute
of Science and Technology (IST Austria). European Research Council (885707) Mr Daniel
Tsodikovich
article_number: '306'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Daniel
full_name: Tsodikovich, Daniel
id: 04531810-fb3e-11ef-87f0-800a4ce333db
last_name: Tsodikovich
citation:
ama: Tsodikovich D. Local rigidity for symplectic billiards. Journal of Geometric
Analysis. 2025;35(10). doi:10.1007/s12220-025-02148-4
apa: Tsodikovich, D. (2025). Local rigidity for symplectic billiards. Journal
of Geometric Analysis. Springer Nature. https://doi.org/10.1007/s12220-025-02148-4
chicago: Tsodikovich, Daniel. “Local Rigidity for Symplectic Billiards.” Journal
of Geometric Analysis. Springer Nature, 2025. https://doi.org/10.1007/s12220-025-02148-4.
ieee: D. Tsodikovich, “Local rigidity for symplectic billiards,” Journal of Geometric
Analysis, vol. 35, no. 10. Springer Nature, 2025.
ista: Tsodikovich D. 2025. Local rigidity for symplectic billiards. Journal of Geometric
Analysis. 35(10), 306.
mla: Tsodikovich, Daniel. “Local Rigidity for Symplectic Billiards.” Journal
of Geometric Analysis, vol. 35, no. 10, 306, Springer Nature, 2025, doi:10.1007/s12220-025-02148-4.
short: D. Tsodikovich, Journal of Geometric Analysis 35 (2025).
corr_author: '1'
date_created: 2025-08-17T22:01:35Z
date_published: 2025-08-07T00:00:00Z
date_updated: 2025-12-30T09:29:27Z
day: '07'
ddc:
- '510'
department:
- _id: VaKa
doi: 10.1007/s12220-025-02148-4
ec_funded: 1
external_id:
arxiv:
- '2501.08849'
isi:
- '001546433200002'
file:
- access_level: open_access
checksum: ed86500742b3fd93db3287558a630383
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T09:28:58Z
date_updated: 2025-12-30T09:28:58Z
file_id: '20907'
file_name: 2025_JourGeomAnalysis_Tsodikovich.pdf
file_size: 484344
relation: main_file
success: 1
file_date_updated: 2025-12-30T09:28:58Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '10'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A
call_identifier: H2020
grant_number: '885707'
name: Spectral rigidity and integrability for billiards and geodesic flows
publication: Journal of Geometric Analysis
publication_identifier:
issn:
- 1050-6926
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local rigidity for symplectic billiards
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20186'
abstract:
- lang: eng
text: Enforcement of information-flow policies has been extensively studied by language-based
approaches over the past few decades. In this paper, we propose an alternative,
novel, general, and effective approach using enforcement of hyperproperties– a
powerful formalism for expressing and reasoning about a wide range of information-flow
security policies. We study black- vs. gray- vs. white-box enforcement of hyperproperties
expressed by nondeterministic finite-word hyperautomata (NFH), where the enforcer
has null, some, or complete information about the implementation of the system
under scrutiny. Given an NFH, in order to generate a runtime enforcer, we reduce
the problem to controller synthesis for hyperproperties and subsequently to the
satisfiability problem for quantified Boolean formulas (QBFs). The resulting enforcers
are transferable with low-overhead. We conduct a rich set of case studies, including
information-flow control for JavaScript code, as well as synthesizing obfuscators
for control plants.
acknowledgement: This project was funded in part by the Austrian Science Fund (FWF)
SFB project SpyCoDe F8502, Vienna Science and Technology Fund (WWTF) [10.47379/ICT19018]
(ProbInG) and WWTF project ICT22-023 (TAIGER), National Science Foundation (NSF)
CPS Award 1837680, NSF award ECCS-2144416 and NSF SaTC Award 2245114. Open access
funding provided by Institute of Science and Technology (IST Austria).
article_number: '30'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Tzu Han
full_name: Hsu, Tzu Han
last_name: Hsu
- first_name: Ana A
full_name: Oliveira Da Costa, Ana A
id: 8b282559-50b0-11ef-861e-d6ace0d92e9b
last_name: Oliveira Da Costa
- first_name: Andrew
full_name: Wintenberg, Andrew
last_name: Wintenberg
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Borzoo
full_name: Bonakdarpour, Borzoo
last_name: Bonakdarpour
citation:
ama: Hsu TH, Oliveira da Costa AA, Wintenberg A, Bartocci E, Bonakdarpour B. Gray-box
runtime enforcement of hyperproperties. Acta Informatica. 2025;62(3). doi:10.1007/s00236-025-00502-1
apa: Hsu, T. H., Oliveira da Costa, A. A., Wintenberg, A., Bartocci, E., & Bonakdarpour,
B. (2025). Gray-box runtime enforcement of hyperproperties. Acta Informatica.
Springer Nature. https://doi.org/10.1007/s00236-025-00502-1
chicago: Hsu, Tzu Han, Ana A Oliveira da Costa, Andrew Wintenberg, Ezio Bartocci,
and Borzoo Bonakdarpour. “Gray-Box Runtime Enforcement of Hyperproperties.” Acta
Informatica. Springer Nature, 2025. https://doi.org/10.1007/s00236-025-00502-1.
ieee: T. H. Hsu, A. A. Oliveira da Costa, A. Wintenberg, E. Bartocci, and B. Bonakdarpour,
“Gray-box runtime enforcement of hyperproperties,” Acta Informatica, vol.
62, no. 3. Springer Nature, 2025.
ista: Hsu TH, Oliveira da Costa AA, Wintenberg A, Bartocci E, Bonakdarpour B. 2025.
Gray-box runtime enforcement of hyperproperties. Acta Informatica. 62(3), 30.
mla: Hsu, Tzu Han, et al. “Gray-Box Runtime Enforcement of Hyperproperties.” Acta
Informatica, vol. 62, no. 3, 30, Springer Nature, 2025, doi:10.1007/s00236-025-00502-1.
short: T.H. Hsu, A.A. Oliveira da Costa, A. Wintenberg, E. Bartocci, B. Bonakdarpour,
Acta Informatica 62 (2025).
corr_author: '1'
date_created: 2025-08-17T22:01:36Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2025-09-30T14:20:11Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/s00236-025-00502-1
external_id:
isi:
- '001546115300001'
file:
- access_level: open_access
checksum: 90a43350fd4a8c5cb5b1b0e1aea7970d
content_type: application/pdf
creator: dernst
date_created: 2025-09-02T05:53:47Z
date_updated: 2025-09-02T05:53:47Z
file_id: '20267'
file_name: 2025_ActaInformatica_Hsu.pdf
file_size: 6505049
relation: main_file
success: 1
file_date_updated: 2025-09-02T05:53:47Z
has_accepted_license: '1'
intvolume: ' 62'
isi: 1
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 34a1b658-11ca-11ed-8bc3-c75229f0241e
grant_number: F8502
name: Interface Theory for Security and Privacy
publication: Acta Informatica
publication_identifier:
eissn:
- 1432-0525
issn:
- 0001-5903
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gray-box runtime enforcement of hyperproperties
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 62
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20188'
abstract:
- lang: eng
text: Collective cell migration is coordinated by the front-to-rear intercellular
propagation of EGFR-Ras-ERK pathway activation. However, the molecular mechanisms
integrating front-to-rear information into this intercellular signaling cascade,
particularly the determinants of cellular front-side specification, remain elusive.
We visualized the activity of EGFR, Ras, Rac1 and Rab5A (hereafter Rab5) by using
FRET biosensors and chemogenetic tools. Whereas EGFR activation was uniformly
observed within cells, Ras activation was biased to the front side within cells.
The polarized Ras activation depended on Merlin and Rac1, which also showed front-biased
activation. Furthermore, Rab5, a crucial regulator of cell migration, demonstrated
similar front-biased activation and was found to function downstream of Ras while
being necessary for Rac1 activation. Thus, the positive feedback loop consisting
of Ras, Rab5 and Rac1 is activated primarily at the front of collectively migrating
cells. These findings offer new spatio-temporal insight into processing front–rear
information during collective cell migration.
acknowledgement: We are grateful to the members of the Matsuda Laboratory for their
helpful input, to K. Hirano, T. Uesugi and K. Takakura, who provided technical assistance,
and to the Medical Research Support Center of Kyoto University for DNA sequence
analysis. This work was supported by the Kyoto University Live Imaging Center. Financial
support was provided by Japan Society for the Promotion of Science (JSPS) KAKENHI
grants (21H05226 to K.T., 19H00993 and 20H05898 to M.M.), a Japan Science and Technology
Agency (JST) CREST grant (JPMJCR1654 to M.M.), and a JST Moonshot Research and Development
Program grant (JPMJPS2022 to M.M.). Open Access funding provided by Tokushima University.
Deposited in PMC for immediate release.
article_number: '263779'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yuya
full_name: Jikko, Yuya
last_name: Jikko
- first_name: Eriko
full_name: Deguchi, Eriko
last_name: Deguchi
- first_name: Kimiya
full_name: Matsuda, Kimiya
last_name: Matsuda
- first_name: Naoya
full_name: Hino, Naoya
id: 5299a9ce-7679-11eb-a7bc-d1e62b936307
last_name: Hino
- first_name: Shinya
full_name: Tsukiji, Shinya
last_name: Tsukiji
- first_name: Michiyuki
full_name: Matsuda, Michiyuki
last_name: Matsuda
- first_name: Kenta
full_name: Terai, Kenta
last_name: Terai
citation:
ama: Jikko Y, Deguchi E, Matsuda K, et al. Front-biased activation of the Ras-Rab5-Rac1
loop coordinates collective cell migration. Journal of Cell Science. 2025;138(15).
doi:10.1242/jcs.263779
apa: Jikko, Y., Deguchi, E., Matsuda, K., Hino, N., Tsukiji, S., Matsuda, M., &
Terai, K. (2025). Front-biased activation of the Ras-Rab5-Rac1 loop coordinates
collective cell migration. Journal of Cell Science. The Company of Biologists.
https://doi.org/10.1242/jcs.263779
chicago: Jikko, Yuya, Eriko Deguchi, Kimiya Matsuda, Naoya Hino, Shinya Tsukiji,
Michiyuki Matsuda, and Kenta Terai. “Front-Biased Activation of the Ras-Rab5-Rac1
Loop Coordinates Collective Cell Migration.” Journal of Cell Science. The
Company of Biologists, 2025. https://doi.org/10.1242/jcs.263779.
ieee: Y. Jikko et al., “Front-biased activation of the Ras-Rab5-Rac1 loop
coordinates collective cell migration,” Journal of Cell Science, vol. 138,
no. 15. The Company of Biologists, 2025.
ista: Jikko Y, Deguchi E, Matsuda K, Hino N, Tsukiji S, Matsuda M, Terai K. 2025.
Front-biased activation of the Ras-Rab5-Rac1 loop coordinates collective cell
migration. Journal of Cell Science. 138(15), 263779.
mla: Jikko, Yuya, et al. “Front-Biased Activation of the Ras-Rab5-Rac1 Loop Coordinates
Collective Cell Migration.” Journal of Cell Science, vol. 138, no. 15,
263779, The Company of Biologists, 2025, doi:10.1242/jcs.263779.
short: Y. Jikko, E. Deguchi, K. Matsuda, N. Hino, S. Tsukiji, M. Matsuda, K. Terai,
Journal of Cell Science 138 (2025).
date_created: 2025-08-17T22:01:36Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2025-11-27T14:12:24Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1242/jcs.263779
external_id:
isi:
- '001567723900009'
pmid:
- '40667649'
file:
- access_level: open_access
checksum: 29f42619dab5ce251a20c769ed4581c0
content_type: application/pdf
creator: dernst
date_created: 2025-09-01T10:02:24Z
date_updated: 2025-09-01T10:02:24Z
file_id: '20262'
file_name: 2025_JourCellScience_Jikko.pdf
file_size: 12393297
relation: main_file
success: 1
file_date_updated: 2025-09-01T10:02:24Z
has_accepted_license: '1'
intvolume: ' 138'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- ' 0021-9533'
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Front-biased activation of the Ras-Rab5-Rac1 loop coordinates collective cell
migration
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 138
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20189'
abstract:
- lang: eng
text: Certification was made mandatory for the first time in the latest hardware
model checking competition. In this case study, we investigate the trade-offs
of requiring certificates for both passing and failing properties in the competition.
Our evaluation shows that participating model checkers were able to produce compact,
correct certificates that could be verified with minimal overhead. Furthermore,
the certifying winner of the competition outperforms the previous non-certifying
state-of-the-art model checker, demonstrating that certification can be adopted
without compromising model checking efficiency.
acknowledgement: "This work is supported in part by the ERC-2020-AdG 101020093, the
LIT AI Lab funded by the State of Upper Austria, the Research Council of Finland
under the project 336092, and a gift from Intel Corporation.\r\nFurthermore we of
course also owe a big thank-you to the submitters of model checkers and benchmarks
to the competition over all these years. Without their enthusiasm and support neither
the competition nor this study would exist."
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nils
full_name: Froleyks, Nils
last_name: Froleyks
- first_name: Zhengqi
full_name: Yu, Zhengqi
id: 20aa2ae8-f2f1-11ed-bbfa-8205053f1342
last_name: Yu
orcid: 0000-0002-4993-773X
- first_name: Mathias
full_name: Preiner, Mathias
last_name: Preiner
- first_name: Armin
full_name: Biere, Armin
last_name: Biere
- first_name: Keijo
full_name: Heljanko, Keijo
last_name: Heljanko
citation:
ama: 'Froleyks N, Yu E, Preiner M, Biere A, Heljanko K. Introducing certificates
to the hardware model checking competition. In: 37th International Conference
on Computer Aided Verification. Vol 15931. Springer Nature; 2025:281-295.
doi:10.1007/978-3-031-98668-0_14'
apa: 'Froleyks, N., Yu, E., Preiner, M., Biere, A., & Heljanko, K. (2025). Introducing
certificates to the hardware model checking competition. In 37th International
Conference on Computer Aided Verification (Vol. 15931, pp. 281–295). Zagreb,
Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-98668-0_14'
chicago: Froleyks, Nils, Emily Yu, Mathias Preiner, Armin Biere, and Keijo Heljanko.
“Introducing Certificates to the Hardware Model Checking Competition.” In 37th
International Conference on Computer Aided Verification, 15931:281–95. Springer
Nature, 2025. https://doi.org/10.1007/978-3-031-98668-0_14.
ieee: N. Froleyks, E. Yu, M. Preiner, A. Biere, and K. Heljanko, “Introducing certificates
to the hardware model checking competition,” in 37th International Conference
on Computer Aided Verification, Zagreb, Croatia, 2025, vol. 15931, pp. 281–295.
ista: 'Froleyks N, Yu E, Preiner M, Biere A, Heljanko K. 2025. Introducing certificates
to the hardware model checking competition. 37th International Conference on Computer
Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 15931, 281–295.'
mla: Froleyks, Nils, et al. “Introducing Certificates to the Hardware Model Checking
Competition.” 37th International Conference on Computer Aided Verification,
vol. 15931, Springer Nature, 2025, pp. 281–95, doi:10.1007/978-3-031-98668-0_14.
short: N. Froleyks, E. Yu, M. Preiner, A. Biere, K. Heljanko, in:, 37th International
Conference on Computer Aided Verification, Springer Nature, 2025, pp. 281–295.
conference:
end_date: 2025-07-25
location: Zagreb, Croatia
name: 'CAV: Computer Aided Verification'
start_date: 2025-07-23
date_created: 2025-08-17T22:01:36Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-12-01T12:34:05Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-98668-0_14
ec_funded: 1
external_id:
isi:
- '001562507100014'
file:
- access_level: open_access
checksum: 15ec1bc9b9409d3b2736f4c9d5f42fd1
content_type: application/pdf
creator: dernst
date_created: 2025-09-02T05:46:10Z
date_updated: 2025-09-02T05:46:10Z
file_id: '20266'
file_name: 2025_CAV_Froleyks.pdf
file_size: 1078274
relation: main_file
success: 1
file_date_updated: 2025-09-02T05:46:10Z
has_accepted_license: '1'
intvolume: ' 15931'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 281-295
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 37th International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031986673'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introducing certificates to the hardware model checking competition
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15931
year: '2025'
...