---
OA_type: closed access
_id: '20079'
abstract:
- lang: eng
text: "Research question: Is LINC01638 involved in regulation of epithelial-to-mesenchymal
transition (EMT) in endometriosis?\r\nDesign: A prospective patient cohort study
was combined with functional experiments in the 12Z endometriosis epithelial cell
line to investigate the role of LINC01638 in endometriosis. Eutopic endometrial
samples were collected by curettage, and ectopic endometrial lesion samples were
collected by laparoscopic surgery from 24 control patients and 41 patients with
endometriosis. The phenotype of 12Z cells was assessed following LINC01638 knockdown
using siRNA, performing proliferation, adhesion, migration and invasion assays,
as well as assessing apoptosis and cell cycle changes with flow cytometry assays.
In order to assess the relationship between LINC01638 and histone deacetylase
class 1 enzyme (HDAC1), LINC01638 knockdown was combined with HDAC inhibition
with the specific HDAC inhibitor romidepsin.\r\nResults: LINC01638 was up-regulated
in the epithelial layer of endometriotic lesions, and LINC01638 knockdown in 12Z
cells led to reduced proliferation, adhesion, migration and invasion. The reduction
in proliferation was associated with increased p21 and p27 expression, and G1
phase arrest. Further analysis of LINC01638 control and knockdown cells revealed
that a number of transcription factors associated with EMT are down-regulated
in knockdown cells, along with the cytoskeleton regulatory gene RHOB, while HDAC1
was up-regulated. Chromatin immunoprecipitation analysis and HDAC1 inhibitory
treatment combined with LINC01638 knockdown indicated that LINC01638 regulates
RHOB expression via HDAC1-mediated promoter deacetylation. RHOB is up-regulated
in the epithelial layer of endometriotic lesions compared with eutopic endometrium,
supporting a role in the disease.\r\nConclusions: LINC01638 is an epigenetic regulator
of the pathogenesis of endometriosis, promoting proliferation and EMT of endometriotic
lesions."
acknowledgement: "The authors wish to thank all the participants and health professionals
involved in this study. In addition, the authors wish to thank technical assistants
Barbara Widmar, Matthias Witzmann-Stern and Isabella Haslinger for their work assisting
with this study; and Simon Hippenmeyer for access to bioinformatic infrastructure
and resources.\r\nOpen access funding was provided by the Medical University of
Vienna."
article_number: '104942'
article_processing_charge: No
article_type: original
author:
- first_name: Iveta
full_name: Yotova, Iveta
last_name: Yotova
- first_name: Katharina
full_name: Proestling, Katharina
last_name: Proestling
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Lisa
full_name: Rainer, Lisa
last_name: Rainer
- first_name: Leonie
full_name: Kaup, Leonie
last_name: Kaup
- first_name: Jana
full_name: Heine, Jana
last_name: Heine
- first_name: Lejla
full_name: Sandrieser, Lejla
last_name: Sandrieser
- first_name: René
full_name: Wenzl, René
last_name: Wenzl
- first_name: Quanah J.
full_name: Hudson, Quanah J.
last_name: Hudson
citation:
ama: Yotova I, Proestling K, Pauler F, et al. LINC01638 promotes epithelial-to-mesenchymal
transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression.
Reproductive Biomedicine Online. 2025;51(3). doi:10.1016/j.rbmo.2025.104942
apa: Yotova, I., Proestling, K., Pauler, F., Rainer, L., Kaup, L., Heine, J., …
Hudson, Q. J. (2025). LINC01638 promotes epithelial-to-mesenchymal transition
in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression.
Reproductive Biomedicine Online. Elsevier. https://doi.org/10.1016/j.rbmo.2025.104942
chicago: Yotova, Iveta, Katharina Proestling, Florian Pauler, Lisa Rainer, Leonie
Kaup, Jana Heine, Lejla Sandrieser, René Wenzl, and Quanah J. Hudson. “LINC01638
Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells
by up-Regulating RHOB via HDAC1 Suppression.” Reproductive Biomedicine Online.
Elsevier, 2025. https://doi.org/10.1016/j.rbmo.2025.104942.
ieee: I. Yotova et al., “LINC01638 promotes epithelial-to-mesenchymal transition
in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression,”
Reproductive Biomedicine Online, vol. 51, no. 3. Elsevier, 2025.
ista: Yotova I, Proestling K, Pauler F, Rainer L, Kaup L, Heine J, Sandrieser L,
Wenzl R, Hudson QJ. 2025. LINC01638 promotes epithelial-to-mesenchymal transition
in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression.
Reproductive Biomedicine Online. 51(3), 104942.
mla: Yotova, Iveta, et al. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition
in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.”
Reproductive Biomedicine Online, vol. 51, no. 3, 104942, Elsevier, 2025,
doi:10.1016/j.rbmo.2025.104942.
short: I. Yotova, K. Proestling, F. Pauler, L. Rainer, L. Kaup, J. Heine, L. Sandrieser,
R. Wenzl, Q.J. Hudson, Reproductive Biomedicine Online 51 (2025).
date_created: 2025-07-27T22:01:25Z
date_published: 2025-07-17T00:00:00Z
date_updated: 2025-09-30T14:10:46Z
day: '17'
department:
- _id: SiHi
doi: 10.1016/j.rbmo.2025.104942
external_id:
isi:
- '001549819000002'
pmid:
- '40680553'
fulldoi: https://doi.org/10.1016/j.rbmo.2025.104942
intvolume: ' 51'
isi: 1
issue: '3'
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: Reproductive Biomedicine Online
publication_identifier:
eissn:
- 1472-6491
issn:
- 1472-6483
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial
cells by up-regulating RHOB via HDAC1 suppression
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 51
year: '2025'
...
---
APC_amount: 3642,79 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20080'
abstract:
- lang: eng
text: "Introduction: Acid-growth theory has been postulated in the 70s to explain
the rapid elongation of plant cells in response to the hormone auxin. More recently,
it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting
acidification of the apoplast is the principal mechanism by which auxin and other
hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances,
the impact of this acidification on the mechanical properties of the cell wall
remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of
Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate
hormone-induced tissue elongation and local changes in cell wall mechanical properties.
Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase
(PME), along with calcium chelators, we investigate the effect of pectin modification
in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification
of apoplast is necessary and sufficient to induce cell elongation through promoting
cell wall softening. Moreover, we show that enhanced PME activity can induce both
cell wall softening or stiffening in extracellular calcium dependent-manner and
that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion:
Our results confirm a dual role of PME in plant cell elongation. However, further
investigation is needed to assess the status of pectin following short- or long-term
PME treatments in order to determine if pectin methyl-esterification might promote
its degradation as well as the role of PME inhibitors upon PME induction."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
acknowledgement: "The author(s) declare that financial support was received for the
research and/or publication of this article. This work was supported by grants from
the European Research Council (Starting Independent Research Grant ERC-2007-Stg-
207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe
acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge
CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127).
We gratefully acknowledge support by the Scientific Service Units at ISTA, including
the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler
for the efforts to establish immunodetection method."
article_number: '1612366'
article_processing_charge: Yes
article_type: original
author:
- first_name: Marçal
full_name: Gallemi, Marçal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi
orcid: 0000-0003-4675-6893
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Nikola
full_name: Zarevski, Nikola
id: 18e95355-e05a-11ea-a9c0-8fba1b89e83a
last_name: Zarevski
- first_name: Jan
full_name: Pribyl, Jan
last_name: Pribyl
- first_name: Petr
full_name: Skládal, Petr
last_name: Skládal
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl
esterase activity in the regulation of plant cell wall biophysical properties.
Frontiers in Plant Science. 2025;16. doi:10.3389/fpls.2025.1612366
apa: Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P.,
Hannezo, E. B., & Benková, E. (2025). Dual role of pectin methyl esterase
activity in the regulation of plant cell wall biophysical properties. Frontiers
in Plant Science. Frontiers Media. https://doi.org/10.3389/fpls.2025.1612366
chicago: Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl,
Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl
Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.”
Frontiers in Plant Science. Frontiers Media, 2025. https://doi.org/10.3389/fpls.2025.1612366.
ieee: M. Gallemi et al., “Dual role of pectin methyl esterase activity in
the regulation of plant cell wall biophysical properties,” Frontiers in Plant
Science, vol. 16. Frontiers Media, 2025.
ista: Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB,
Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation
of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366.
mla: Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the
Regulation of Plant Cell Wall Biophysical Properties.” Frontiers in Plant Science,
vol. 16, 1612366, Frontiers Media, 2025, doi:10.3389/fpls.2025.1612366.
short: M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B.
Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).
corr_author: '1'
date_created: 2025-07-27T22:01:26Z
date_published: 2025-07-04T00:00:00Z
date_updated: 2026-05-20T07:53:03Z
day: '04'
ddc:
- '580'
department:
- _id: EdHa
- _id: EvBe
- _id: CaGu
doi: 10.3389/fpls.2025.1612366
ec_funded: 1
external_id:
isi:
- '001530690900001'
pmid:
- '40688689'
file:
- access_level: open_access
checksum: 9e6b8b53ba56d4a24a9bd91cf6d2dc58
content_type: application/pdf
creator: dernst
date_created: 2025-07-31T07:28:54Z
date_updated: 2025-07-31T07:28:54Z
file_id: '20093'
file_name: 2025_FrontiersPlantSc_Gallemi.pdf
file_size: 3665187
relation: main_file
success: 1
file_date_updated: 2025-07-31T07:28:54Z
fulldoi: https://doi.org/10.3389/fpls.2025.1612366
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664-462X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dual role of pectin methyl esterase activity in the regulation of plant cell
wall biophysical properties
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'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20082'
abstract:
- lang: eng
text: Efficient immune responses rely on the capacity of leukocytes to traverse
diverse and complex tissues. To meet such changing environmental conditions, leukocytes
usually adopt an ameboid configuration, using their forward-positioned nucleus
as a probe to identify and follow the path of least resistance among pre-existing
pores. We show that, in dense environments where even the largest pores preclude
free passage, leukocytes position their nucleus behind the centrosome and organelles.
The local compression imposed on the cell body by its surroundings triggers assembly
of a central F-actin pool, located between cell front and nucleus. Central actin
pushes outward to transiently dilate a path for organelles and nucleus. Pools
of central and front actin are tightly coupled and experimental depletion of the
central pool enhances actin accumulation and protrusion formation at the cell
front. Although this shifted balance speeds up cells in permissive environments,
migration in restrictive environments is impaired, as the unleashed leading edge
dissociates from the trapped cell body. Our findings establish an actin regulatory
loop that balances path dilation with advancement of the leading edge to maintain
cellular coherence.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: This research was supported by the Scientific Service Units of ISTA
through resources provided by the Imaging and Optics, Preclinical and Lab Support
Facilities. In particular, we thank M. A. Symth and F. G. G. Leite, from the Virus
Service Team, who helped generating the lentiviral particles used in this study.
We thank all the members of the Sixt group for valuable discussions and feedback,
in particular, I. Mayer, for helping with T cell isolation and Z. (P.) Li for providing
the Actin–GFP DC line. We are also thankful to J. Mandl and C. Shen for their feedback
during the writing of this manuscript. This work was supported by a European Research
Council grant ERC-SyG 101071793 to M.S. M.J.A. was supported by an HFSP Postdoctoral
Fellowship LTF 177 2021 and A.J.G. by a Lise Meitner Fellowship of the FWF (Austrian
Science Fund). Y.F. was supported by the AMED-CREST (JP19gm1310005), the Medical
Research Center Initiative for High Depth Omics and CURE:JPMXP1323015486 for MIB,
Kyushu University. Open access funding provided by Institute of Science and Technology
(IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Patricia
full_name: Dos Reis Rodrigues, Patricia
id: 26E95904-5160-11E9-9C0B-C5B0DC97E90F
last_name: Dos Reis Rodrigues
orcid: 0000-0003-1681-508X
- first_name: Mario
full_name: Avellaneda Sarrió, Mario
id: DC4BA84C-56E6-11EA-AD5D-348C3DDC885E
last_name: Avellaneda Sarrió
orcid: 0000-0001-6406-524X
- first_name: Nikola
full_name: Canigova, Nikola
id: 3795523E-F248-11E8-B48F-1D18A9856A87
last_name: Canigova
orcid: 0000-0002-8518-5926
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Michael
full_name: Riedl, Michael
id: 3BE60946-F248-11E8-B48F-1D18A9856A87
last_name: Riedl
orcid: 0000-0003-4844-6311
- first_name: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Yoshinori
full_name: Fukui, Yoshinori
last_name: Fukui
- first_name: Alba
full_name: Juanes Garcia, Alba
id: 40F05888-F248-11E8-B48F-1D18A9856A87
last_name: Juanes Garcia
orcid: 0000-0002-1009-9652
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Dos Reis Rodrigues P, Avellaneda Sarrió M, Canigova N, et al. Migrating immune
cells globally coordinate protrusive forces. Nature Immunology. 2025;26:1258–1266.
doi:10.1038/s41590-025-02211-w
apa: Dos Reis Rodrigues, P., Avellaneda Sarrió, M., Canigova, N., Gärtner, F. R.,
Vaahtomeri, K., Riedl, M., … Sixt, M. K. (2025). Migrating immune cells globally
coordinate protrusive forces. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-025-02211-w
chicago: Dos Reis Rodrigues, Patricia, Mario Avellaneda Sarrió, Nikola Canigova,
Florian R Gärtner, Kari Vaahtomeri, Michael Riedl, Ingrid de Vries, et al. “Migrating
Immune Cells Globally Coordinate Protrusive Forces.” Nature Immunology.
Springer Nature, 2025. https://doi.org/10.1038/s41590-025-02211-w.
ieee: P. Dos Reis Rodrigues et al., “Migrating immune cells globally coordinate
protrusive forces,” Nature Immunology, vol. 26. Springer Nature, pp. 1258–1266,
2025.
ista: Dos Reis Rodrigues P, Avellaneda Sarrió M, Canigova N, Gärtner FR, Vaahtomeri
K, Riedl M, de Vries I, Merrin J, Hauschild R, Fukui Y, Juanes Garcia A, Sixt
MK. 2025. Migrating immune cells globally coordinate protrusive forces. Nature
Immunology. 26, 1258–1266.
mla: Dos Reis Rodrigues, Patricia, et al. “Migrating Immune Cells Globally Coordinate
Protrusive Forces.” Nature Immunology, vol. 26, Springer Nature, 2025,
pp. 1258–1266, doi:10.1038/s41590-025-02211-w.
short: P. Dos Reis Rodrigues, M. Avellaneda Sarrió, N. Canigova, F.R. Gärtner, K.
Vaahtomeri, M. Riedl, I. de Vries, J. Merrin, R. Hauschild, Y. Fukui, A. Juanes
Garcia, M.K. Sixt, Nature Immunology 26 (2025) 1258–1266.
corr_author: '1'
date_created: 2025-07-27T22:01:26Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2026-04-28T13:26:50Z
day: '01'
ddc:
- '570'
department:
- _id: MiSi
- _id: NanoFab
- _id: Bio
doi: 10.1038/s41590-025-02211-w
external_id:
isi:
- '001529134300001'
pmid:
- '40664976'
file:
- access_level: open_access
checksum: 0c725123dca7797c682609bff2c4c5ac
content_type: application/pdf
creator: dernst
date_created: 2025-07-31T08:00:33Z
date_updated: 2025-07-31T08:00:33Z
file_id: '20096'
file_name: 2025_NatureImmunology_ReisRodrigues.pdf
file_size: 13514646
relation: main_file
success: 1
file_date_updated: 2025-07-31T08:00:33Z
fulldoi: https://doi.org/10.1038/s41590-025-02211-w
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1258–1266
pmid: 1
project:
- _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd
grant_number: '101071793'
name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal
pushing forces'
- _id: c092d618-5a5b-11eb-8a69-f92e1e843fc8
grant_number: 944-2020
name: 'Bioelectric patrolling: the role of the local membrane potential in immune
cell migration'
publication: Nature Immunology
publication_identifier:
eissn:
- 1529-2916
issn:
- 1529-2908
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/bench-pressing-cells/
record:
- id: '20149'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Migrating immune cells globally coordinate protrusive forces
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 26
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
fulldoi: https://doi.org/10.1088/2752-5295/adec11
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: '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
fulldoi: https://doi.org/10.1016/j.csbj.2025.07.039
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
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
fulldoi: https://doi.org/10.1111/mec.70025
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
fulldoi: https://doi.org/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
fulldoi: https://doi.org/10.5281/ZENODO.13988679
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'
...
---
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
fulldoi: https://doi.org/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
_id: '20149'
abstract:
- lang: eng
text: "Immune responses depend on the coordinated and efficient migration of leukocytes.
These\r\ncells, which are embedded and tightly confined within tissues, must navigate
and traverse\r\ndiverse and complex three-dimensional environments. Leukocytes
adapt their locomotory\r\nbehavior to the mechanical, geometrical, and biochemical
characteristics of their\r\nsurroundings. In low-density environments, where the
pore size of the interstitial matrix\r\nallows free passage, these cells position
the nucleus directly behind the lamellipodium, the\r\nprotrusive actin structure
that forms the leading front of the cell. In this configuration, they\r\nuse the
nucleus as a gauge to identify the path of least resistance.\r\nHere, we show
that in high-density environments, where the pore size precludes free passage\r\nof
the cell body, leukocytes reposition the microtubule-organizing center (MTOC)
and\r\nassociated organelles in front of the nucleus. In this configuration, they
use actin structures\r\nprotruding orthogonally to the direction of migration
in order to open a path for the cell body.\r\nWe identify two distinct actin populations
that serve this purpose at different subcellular\r\nlocalizations. At the leading
edge, local indentation of the plasma membrane leads to\r\nrecruitment of the
Wiskott-Aldrich syndrome protein (WASp), which, via Arp2/3, results in\r\nthe
formation of individual actin foci. At the cell body, actin polymerization is
triggered by\r\nDOCK8, a Cdc42 exchange factor, resulting in the formation of
a central actin pool.\r\nWe demonstrate that the central and peripheral actin
pools are functionally communicating\r\nand that depletion of the central actin
pool leads to increased actin accumulation at the cell\r\nfront, resulting in
excessive extension of the leading edge."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: NanoFab
acknowledgement: "I would like to acknowledge the\r\nfinancial support of the European
Research Council through the ERC-SyG grant “Pushing from\r\nwithin: Control of cell
shape, integrity and motility by cytoskeletal pushing forces”\r\n(01071793), which
made this research possible. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Patricia
full_name: Dos Reis Rodrigues, Patricia
id: 26E95904-5160-11E9-9C0B-C5B0DC97E90F
last_name: Dos Reis Rodrigues
orcid: 0000-0003-1681-508X
citation:
ama: Dos Reis Rodrigues P. Coordination of protrusive forces in immune cell migration
. 2025. doi:10.15479/AT-ISTA-20149
apa: Dos Reis Rodrigues, P. (2025). Coordination of protrusive forces in immune
cell migration . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20149
chicago: Dos Reis Rodrigues, Patricia. “Coordination of Protrusive Forces in Immune
Cell Migration .” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20149.
ieee: P. Dos Reis Rodrigues, “Coordination of protrusive forces in immune cell migration
,” Institute of Science and Technology Austria, 2025.
ista: Dos Reis Rodrigues P. 2025. Coordination of protrusive forces in immune cell
migration . Institute of Science and Technology Austria.
mla: Dos Reis Rodrigues, Patricia. Coordination of Protrusive Forces in Immune
Cell Migration . Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20149.
short: P. Dos Reis Rodrigues, Coordination of Protrusive Forces in Immune Cell Migration
, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-08-08T09:18:02Z
date_published: 2025-08-08T00:00:00Z
date_updated: 2026-04-28T13:26:50Z
day: '08'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MiSi
doi: 10.15479/AT-ISTA-20149
file:
- access_level: open_access
checksum: fda8a1070667c3562263f4867609b41b
content_type: application/pdf
creator: prodrigu
date_created: 2025-08-27T12:59:10Z
date_updated: 2025-08-27T12:59:10Z
file_id: '20232'
file_name: 2025_ReisRodrigues_Patricia_Thesis.pdf
file_size: 63885565
relation: main_file
success: 1
- access_level: closed
checksum: e8b65affcbce846a926454df4b2867b9
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: prodrigu
date_created: 2025-08-27T13:00:30Z
date_updated: 2025-08-27T13:02:28Z
file_id: '20233'
file_name: 2025_ReisRodrigues_Patricia_Thesis.docx
file_size: 50483434
relation: source_file
file_date_updated: 2025-08-27T13:02:28Z
fulldoi: https://doi.org/10.15479/AT-ISTA-20149
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: '114'
project:
- _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd
grant_number: '101071793'
name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal
pushing forces'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10703'
relation: part_of_dissertation
status: public
- id: '20082'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: 'Coordination of protrusive forces in immune cell migration '
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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'
fulldoi: https://doi.org/10.1137/24M1700351
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
fulldoi: https://doi.org/10.1016/j.cois.2025.101411
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
fulldoi: https://doi.org/10.1038/s41467-025-62484-5
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'
fulldoi: https://doi.org/10.1038/s42003-025-08589-5
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
fulldoi: https://doi.org/10.1007/s12220-025-02148-4
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
fulldoi: https://doi.org/10.1007/s00236-025-00502-1
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
fulldoi: https://doi.org/10.1242/jcs.263779
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
fulldoi: https://doi.org/10.1007/978-3-031-98668-0_14
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'
...
---
OA_place: publisher
OA_type: diamond
PlanS_conform: '1'
_id: '20192'
abstract:
- lang: eng
text: We study the physical origin and spectroscopic impact of extreme nebular emission
in high-redshift galaxies. The nebular continuum, which can appear during an extreme
starburst, is of particular importance as it tends to redden UV slopes and has
a significant contribution to the UV luminosities of galaxies. Furthermore, its
shape can be used to infer the gas density and temperature of the interstellar
medium. First, we provide a theoretical background, showing how different stellar
populations (SPS models, initial mass functions (IMFs), and stellar temperatures)
and nebular conditions impact observed galaxy spectra. We demonstrate that, for
systems with strong nebular continuum emission, 1) UV fluxes can increase by up
to 0.7~mag (or more in the case of hot/massive stars) above the stellar continuum,
which may help reconcile the surprising abundance of bright high-redshift galaxies
and the elevated UV luminosity density at z>10, 2) at high gas densities, UV slopes
can redden from \beta<-2.5 to \beta\sim-1, 3) observational measurements of \xi_{\rm
ion} are gross underestimates, and 4) UV downturns from two-photon emission can
masquerade as damped Ly\alpha systems. Second, we present a dataset of 58 galaxies
observed with NIRSpec on JWST at 2.510 galaxies, finding
that UV slopes and UV downturns are in some cases redder or steeper than expected
from SPS models, which may hint at more exotic (e.g. hotter/more massive stars
or AGN) ionizing sources.
acknowledgement: 'HK thanks Andrey Kravtsov for insightful comments and thoughtful
discussions. We sincerely thank the PIs and Co-Is of the JWST programs where spectral
data was made publicly available on the DJA. We refer interested readers to the
following papers for survey descriptions regarding the spectral data: Bunker et
al. (2023a); D’Eugenio et al. (2024); Bezanson et al. (2022); Barrufet et al. (2024);
de Graaff et al. (2024); Finkelstein et al. (2024); Glazebrook et al. (2024); Pierel
et al. (2024); Siebert et al. (2024); Maseda et al. (2024). This work is based in
part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The
data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope
Science Institute, which is operated by the Association of Universities for Research
in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations
are associated with programs listed in Table 1. AJC and AS acknowledge funding from
the “FirstGalaxies” Advanced Grant from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (Grant agreement
No. 789056). '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Harley
full_name: Katz, Harley
last_name: Katz
- first_name: Alex J.
full_name: Cameron, Alex J.
last_name: Cameron
- first_name: Aayush
full_name: Saxena, Aayush
last_name: Saxena
- first_name: Laia
full_name: Barrufet, Laia
last_name: Barrufet
- first_name: Nicholas
full_name: Choustikov, Nicholas
last_name: Choustikov
- first_name: Nikko J.
full_name: Cleri, Nikko J.
last_name: Cleri
- first_name: Anna
full_name: De Graaff, Anna
last_name: De Graaff
- first_name: Richard S.
full_name: Ellis, Richard S.
last_name: Ellis
- first_name: Robert A.E.
full_name: Fosbury, Robert A.E.
last_name: Fosbury
- first_name: Kasper E.
full_name: Heintz, Kasper E.
last_name: Heintz
- first_name: Michael
full_name: Maseda, Michael
last_name: Maseda
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Ian
full_name: Mcconachie, Ian
last_name: Mcconachie
- first_name: Pascal A.
full_name: Oesch, Pascal A.
last_name: Oesch
citation:
ama: 'Katz H, Cameron AJ, Saxena A, et al. 21 Balmer Jump Street: The nebular continuum
at high redshift and implications for the bright galaxy problem, UV continuum
slopes, and early stellar populations. The Open Journal of Astrophysics.
2025;8. doi:10.33232/001c.142570'
apa: 'Katz, H., Cameron, A. J., Saxena, A., Barrufet, L., Choustikov, N., Cleri,
N. J., … Oesch, P. A. (2025). 21 Balmer Jump Street: The nebular continuum at
high redshift and implications for the bright galaxy problem, UV continuum slopes,
and early stellar populations. The Open Journal of Astrophysics. Maynooth
Academic Publishing. https://doi.org/10.33232/001c.142570'
chicago: 'Katz, Harley, Alex J. Cameron, Aayush Saxena, Laia Barrufet, Nicholas
Choustikov, Nikko J. Cleri, Anna De Graaff, et al. “21 Balmer Jump Street: The
Nebular Continuum at High Redshift and Implications for the Bright Galaxy Problem,
UV Continuum Slopes, and Early Stellar Populations.” The Open Journal of Astrophysics.
Maynooth Academic Publishing, 2025. https://doi.org/10.33232/001c.142570.'
ieee: 'H. Katz et al., “21 Balmer Jump Street: The nebular continuum at high
redshift and implications for the bright galaxy problem, UV continuum slopes,
and early stellar populations,” The Open Journal of Astrophysics, vol.
8. Maynooth Academic Publishing, 2025.'
ista: 'Katz H, Cameron AJ, Saxena A, Barrufet L, Choustikov N, Cleri NJ, De Graaff
A, Ellis RS, Fosbury RAE, Heintz KE, Maseda M, Matthee JJ, Mcconachie I, Oesch
PA. 2025. 21 Balmer Jump Street: The nebular continuum at high redshift and implications
for the bright galaxy problem, UV continuum slopes, and early stellar populations.
The Open Journal of Astrophysics. 8.'
mla: 'Katz, Harley, et al. “21 Balmer Jump Street: The Nebular Continuum at High
Redshift and Implications for the Bright Galaxy Problem, UV Continuum Slopes,
and Early Stellar Populations.” The Open Journal of Astrophysics, vol.
8, Maynooth Academic Publishing, 2025, doi:10.33232/001c.142570.'
short: H. Katz, A.J. Cameron, A. Saxena, L. Barrufet, N. Choustikov, N.J. Cleri,
A. De Graaff, R.S. Ellis, R.A.E. Fosbury, K.E. Heintz, M. Maseda, J.J. Matthee,
I. Mcconachie, P.A. Oesch, The Open Journal of Astrophysics 8 (2025).
date_created: 2025-08-17T22:01:37Z
date_published: 2025-07-25T00:00:00Z
date_updated: 2025-09-30T14:29:33Z
day: '25'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.33232/001c.142570
external_id:
arxiv:
- '2408.03189'
file:
- access_level: open_access
checksum: ba469d132907147f9e86d87f9124dd14
content_type: application/pdf
creator: dernst
date_created: 2025-09-30T14:28:25Z
date_updated: 2025-09-30T14:28:25Z
file_id: '20412'
file_name: 2025_OpenJourAstrophysics_Katz.pdf
file_size: 1836432
relation: main_file
success: 1
file_date_updated: 2025-09-30T14:28:25Z
fulldoi: https://doi.org/10.33232/001c.142570
has_accepted_license: '1'
intvolume: ' 8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: The Open Journal of Astrophysics
publication_identifier:
eissn:
- 2565-6120
publication_status: published
publisher: Maynooth Academic Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: '21 Balmer Jump Street: The nebular continuum at high redshift and implications
for the bright galaxy problem, UV continuum slopes, and early stellar populations'
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: 8
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20193'
abstract:
- lang: eng
text: Understanding the rapid formation of supermassive black holes in the early
Universe requires insights into stellar mass growth in host galaxies. Here we
present NIRSpec rest-frame optical spectra and NIRCam imaging from JWST of two
galaxies at z > 6, both hosting moderate-luminosity quasars. These galaxies exhibit
Balmer absorption lines, like low-redshift post-starburst galaxies. Our analyses
of the medium-resolution spectra and multiband photometry show that the bulk of
the stellar mass (log(M*/M☉) ≥ 10.6) formed in starburst episodes at redshift
9 and 7. One of the galaxies shows a clear Balmer break and lacks spatially resolved
Hα emission. It falls well below the star-formation main sequence at z = 6, indicating
quiescence. The other is transitioning to quiescence; together, these massive
galaxies are among the most distant post-starburst systems known. The blueshifted
wings of the quasar [O iii] emission lines indicate quasar-driven outflow, which
possibly influences star formation. Direct stellar velocity dispersion measurements
reveal that one galaxy follows the local black hole mass versus σ* relation whereas
the other is overmassive. The existence of massive post-starburst galaxies hosting
billion-solar-mass black holes in short-lived quasar phases indicates that supermassive
black holes and host galaxies played a principal role in each other’s rapid early
formation.
acknowledgement: We thank A. C. Carnall for supporting our use of Bagpipes. We thank
Y. Fu for his help on the use of QSOFitMORE. We thank J. Greene, S. Toft, T. Kakimoto
and M. Tanaka for fruitful discussions. This work is based on observations made
with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for
Space Telescopes at the Space Telescope Science Institute, which is operated by
the Association of Universities for Research in Astronomy, under NASA contract NAS
5-03127 for JWST. These observations are associated with programmes GO 1967 and
GO 3859. Support for these programmes was provided by NASA through a grant from
the Space Telescope Science Institute. This work was supported by World Premier
International Research Center Initiative, MEXT, Japan. This work used computing
resources at Kavli IPMU. M.O., X.D., J.D.S., Y.M., T.I., K. Ito, K.K. and H.U. are
supported by the Japan Society for the Promotion of Science (KAKENHI Grant Numbers
JP24K22894, JP22K14071, JP18H01251, JP22H01262, JP21H04494, JP20K14531, JP23K13141,
JP17H06130 and JP20H01953). M.O. and K. Inayoshi acknowledge support from the National
Natural Science Foundation of China (Grant Numbers 12150410307, 12073003, 11721303,
11991052 and 11950410493). K. Inayoshi acknowledges support from the China Manned
Space Project (Grant Numbers CMS-CSST-2021-A04 and CMS-CSST-2021-A06). S.E.I.B.
is funded by the Deutsche Forschungsgemeinschaft (German Research Foundation) under
Emmy Noether Grant Number BO 5771/1-1. Z.H., T.T. and M.S. acknowledge support from
the NSF (Grant Numbers AST-2006176, AST-1907208 and AST-2006177). A.L. acknowledges
funding from MUR (Grant Number PRIN 2022935STW). B.T. acknowledges support from
the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (Grant Agreement Number 950533) and from the Israel Science
Foundation (Grant Number 1849/19). F. Walter acknowledges support from the ERC (Grant
Cosmic_gas). J.-T.S. is supported by the Deutsche Forschungsgemeinschaft (Project
Number 518006966). M.T. acknowledges support from the NWO (Grant Number 0.16.VIDI.189.162,
ODIN). S.F. acknowledges support from NASA through the NASA Hubble Fellowship (Grant
Number HST-HF2-51505.001-A awarded by the Space Telescope Science Institute). K.
Iwasawa acknowledges support under Grant Number PID2022-136827NB-C44 funded by MCIN/AEI/10.13039/501100011033
/FEDER, EU. M. Vestergaard gratefully acknowledges financial support from the Independent
Research Fund Denmark (Grant Numbers DFF 8021-00130 and 3103-00146). F. Wang acknowledges
support from the NSF (Award Number AST-2513040). R.B. is supported by the SNSF through
the Ambizione Grant PZ00P2_223532.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Masafusa
full_name: Onoue, Masafusa
last_name: Onoue
- first_name: Xuheng
full_name: Ding, Xuheng
last_name: Ding
- first_name: John D.
full_name: Silverman, John D.
last_name: Silverman
- first_name: Yoshiki
full_name: Matsuoka, Yoshiki
last_name: Matsuoka
- first_name: Takuma
full_name: Izumi, Takuma
last_name: Izumi
- first_name: Michael A.
full_name: Strauss, Michael A.
last_name: Strauss
- first_name: Charlotte
full_name: Ward, Charlotte
last_name: Ward
- first_name: Camryn L.
full_name: Phillips, Camryn L.
last_name: Phillips
- first_name: Kei
full_name: Ito, Kei
last_name: Ito
- first_name: Irham T.
full_name: Andika, Irham T.
last_name: Andika
- first_name: Kentaro
full_name: Aoki, Kentaro
last_name: Aoki
- first_name: Junya
full_name: Arita, Junya
last_name: Arita
- first_name: Shunsuke
full_name: Baba, Shunsuke
last_name: Baba
- first_name: Rebekka
full_name: Bieri, Rebekka
last_name: Bieri
- first_name: Sarah E.I.
full_name: Bosman, Sarah E.I.
last_name: Bosman
- first_name: Anna Christina
full_name: Eilers, Anna Christina
last_name: Eilers
- first_name: Seiji
full_name: Fujimoto, Seiji
last_name: Fujimoto
- first_name: Melanie
full_name: Habouzit, Melanie
last_name: Habouzit
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
orcid: 0000-0003-3633-5403
- first_name: Masatoshi
full_name: Imanishi, Masatoshi
last_name: Imanishi
- first_name: Kohei
full_name: Inayoshi, Kohei
last_name: Inayoshi
- first_name: Kazushi
full_name: Iwasawa, Kazushi
last_name: Iwasawa
- first_name: Knud
full_name: Jahnke, Knud
last_name: Jahnke
- first_name: Nobunari
full_name: Kashikawa, Nobunari
last_name: Kashikawa
- first_name: Toshihiro
full_name: Kawaguchi, Toshihiro
last_name: Kawaguchi
- first_name: Kotaro
full_name: Kohno, Kotaro
last_name: Kohno
- first_name: Chien Hsiu
full_name: Lee, Chien Hsiu
last_name: Lee
- first_name: Junyao
full_name: Li, Junyao
last_name: Li
- first_name: Alessandro
full_name: Lupi, Alessandro
last_name: Lupi
- first_name: Jianwei
full_name: Lyu, Jianwei
last_name: Lyu
- first_name: Tohru
full_name: Nagao, Tohru
last_name: Nagao
- first_name: Roderik
full_name: Overzier, Roderik
last_name: Overzier
- first_name: Jan Torge
full_name: Schindler, Jan Torge
last_name: Schindler
- first_name: Malte
full_name: Schramm, Malte
last_name: Schramm
- first_name: Matthew T.
full_name: Scoggins, Matthew T.
last_name: Scoggins
- first_name: Kazuhiro
full_name: Shimasaku, Kazuhiro
last_name: Shimasaku
- first_name: Yoshiki
full_name: Toba, Yoshiki
last_name: Toba
- first_name: Benny
full_name: Trakhtenbrot, Benny
last_name: Trakhtenbrot
- first_name: Maxime
full_name: Trebitsch, Maxime
last_name: Trebitsch
- first_name: Tommaso
full_name: Treu, Tommaso
last_name: Treu
- first_name: Hideki
full_name: Umehata, Hideki
last_name: Umehata
- first_name: Bram
full_name: Venemans, Bram
last_name: Venemans
- first_name: Marianne
full_name: Vestergaard, Marianne
last_name: Vestergaard
- first_name: Marta
full_name: Volonteri, Marta
last_name: Volonteri
- first_name: Fabian
full_name: Walter, Fabian
last_name: Walter
- first_name: Feige
full_name: Wang, Feige
last_name: Wang
- first_name: Jinyi
full_name: Yang, Jinyi
last_name: Yang
- first_name: Haowen
full_name: Zhang, Haowen
last_name: Zhang
citation:
ama: Onoue M, Ding X, Silverman JD, et al. A post-starburst pathway for the formation
of massive galaxies and black holes at z > 6. Nature Astronomy. 2025;9:1541-1552.
doi:10.1038/s41550-025-02628-1
apa: Onoue, M., Ding, X., Silverman, J. D., Matsuoka, Y., Izumi, T., Strauss, M.
A., … Zhang, H. (2025). A post-starburst pathway for the formation of massive
galaxies and black holes at z > 6. Nature Astronomy. Springer Nature.
https://doi.org/10.1038/s41550-025-02628-1
chicago: Onoue, Masafusa, Xuheng Ding, John D. Silverman, Yoshiki Matsuoka, Takuma
Izumi, Michael A. Strauss, Charlotte Ward, et al. “A Post-Starburst Pathway for
the Formation of Massive Galaxies and Black Holes at z > 6.” Nature Astronomy.
Springer Nature, 2025. https://doi.org/10.1038/s41550-025-02628-1.
ieee: M. Onoue et al., “A post-starburst pathway for the formation of massive
galaxies and black holes at z > 6,” Nature Astronomy, vol. 9. Springer
Nature, pp. 1541–1552, 2025.
ista: Onoue M, Ding X, Silverman JD, Matsuoka Y, Izumi T, Strauss MA, Ward C, Phillips
CL, Ito K, Andika IT, Aoki K, Arita J, Baba S, Bieri R, Bosman SEI, Eilers AC,
Fujimoto S, Habouzit M, Haiman Z, Imanishi M, Inayoshi K, Iwasawa K, Jahnke K,
Kashikawa N, Kawaguchi T, Kohno K, Lee CH, Li J, Lupi A, Lyu J, Nagao T, Overzier
R, Schindler JT, Schramm M, Scoggins MT, Shimasaku K, Toba Y, Trakhtenbrot B,
Trebitsch M, Treu T, Umehata H, Venemans B, Vestergaard M, Volonteri M, Walter
F, Wang F, Yang J, Zhang H. 2025. A post-starburst pathway for the formation of
massive galaxies and black holes at z > 6. Nature Astronomy. 9, 1541–1552.
mla: Onoue, Masafusa, et al. “A Post-Starburst Pathway for the Formation of Massive
Galaxies and Black Holes at z > 6.” Nature Astronomy, vol. 9, Springer
Nature, 2025, pp. 1541–52, doi:10.1038/s41550-025-02628-1.
short: M. Onoue, X. Ding, J.D. Silverman, Y. Matsuoka, T. Izumi, M.A. Strauss, C.
Ward, C.L. Phillips, K. Ito, I.T. Andika, K. Aoki, J. Arita, S. Baba, R. Bieri,
S.E.I. Bosman, A.C. Eilers, S. Fujimoto, M. Habouzit, Z. Haiman, M. Imanishi,
K. Inayoshi, K. Iwasawa, K. Jahnke, N. Kashikawa, T. Kawaguchi, K. Kohno, C.H.
Lee, J. Li, A. Lupi, J. Lyu, T. Nagao, R. Overzier, J.T. Schindler, M. Schramm,
M.T. Scoggins, K. Shimasaku, Y. Toba, B. Trakhtenbrot, M. Trebitsch, T. Treu,
H. Umehata, B. Venemans, M. Vestergaard, M. Volonteri, F. Walter, F. Wang, J.
Yang, H. Zhang, Nature Astronomy 9 (2025) 1541–1552.
date_created: 2025-08-17T22:01:38Z
date_published: 2025-10-01T00:00:00Z
date_updated: 2025-12-30T13:08:12Z
day: '01'
department:
- _id: ZoHa
doi: 10.1038/s41550-025-02628-1
external_id:
arxiv:
- '2409.07113'
isi:
- '001548138600001'
fulldoi: https://doi.org/10.1038/s41550-025-02628-1
intvolume: ' 9'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2409.07113
month: '10'
oa: 1
oa_version: Preprint
page: 1541-1552
publication: Nature Astronomy
publication_identifier:
eissn:
- 2397-3366
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A post-starburst pathway for the formation of massive galaxies and black holes
at z > 6
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2025'
...