---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19404'
abstract:
- lang: eng
text: Cell migration is a fundamental process during embryonic development. Most
studies in vivo have focused on the migration of cells using the extracellular
matrix (ECM) as their substrate for migration. In contrast, much less is known
about how cells migrate on other cells, as found in early embryos when the ECM
has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the
early zebrafish gastrula use the ectoderm as their substrate for migration. We
show that the lateral ectoderm is permissive for the animal-pole-directed migration
of LME cells, while the ectoderm at the animal pole halts it. These differences
in permissiveness depend on the lateral ectoderm being more cohesive than the
animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling
within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion
as one critical factor in regulating LME migration during zebrafish gastrulation.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
acknowledgement: 'We are grateful to the colleagues who contributed to this work with
discussions, technical advice, and feedback on the manuscript: Irene Steccari, David
Labrousse Arias and the other members of the Heisenberg lab, Nicole Amberg, Florian
Pauler, Nicoletta Petridou, Elena Scarpa, and Edouard Hannezo. We also thank the
Imaging and Optics Facility, the Life Science Facility, and the Scientific Computing
Unit at ISTA for support. The Next Generation Sequencing Facility at Vienna BioCenter
Core Facilities performed the RNA-seq for animal and lateral ectoderm. D.B.B. was
supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral
Fellowship (ALTF 343-2022). S. Tavano was supported by an EMBO Postdoctoral Fellowship
(ALTF 1159-2018).'
article_number: '115387'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ste
full_name: Tavano, Ste
id: 2F162F0C-F248-11E8-B48F-1D18A9856A87
last_name: Tavano
orcid: 0000-0001-9970-7804
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Xin
full_name: Tong, Xin
id: 50F65CDC-AA30-11E9-A72B-8A12E6697425
last_name: Tong
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Tavano S, Brückner D, Tasciyan S, et al. BMP-dependent patterning of ectoderm
tissue material properties modulates lateral mesendoderm cell migration during
early zebrafish gastrulation. Cell Reports. 2025;44(3). doi:10.1016/j.celrep.2025.115387
apa: Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A.,
… Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material
properties modulates lateral mesendoderm cell migration during early zebrafish
gastrulation. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2025.115387
chicago: Tavano, Ste, David Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra
Schauer, Robert Hauschild, and Carl-Philipp J Heisenberg. “BMP-Dependent Patterning
of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration
during Early Zebrafish Gastrulation.” Cell Reports. Elsevier, 2025. https://doi.org/10.1016/j.celrep.2025.115387.
ieee: S. Tavano et al., “BMP-dependent patterning of ectoderm tissue material
properties modulates lateral mesendoderm cell migration during early zebrafish
gastrulation,” Cell Reports, vol. 44, no. 3. Elsevier, 2025.
ista: Tavano S, Brückner D, Tasciyan S, Tong X, Kardos R, Schauer A, Hauschild R,
Heisenberg C-PJ. 2025. BMP-dependent patterning of ectoderm tissue material properties
modulates lateral mesendoderm cell migration during early zebrafish gastrulation.
Cell Reports. 44(3), 115387.
mla: Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties
Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.”
Cell Reports, vol. 44, no. 3, 115387, Elsevier, 2025, doi:10.1016/j.celrep.2025.115387.
short: S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild,
C.-P.J. Heisenberg, Cell Reports 44 (2025).
corr_author: '1'
date_created: 2025-03-16T23:01:24Z
date_published: 2025-03-25T00:00:00Z
date_updated: 2025-10-22T07:00:04Z
day: '25'
ddc:
- '570'
department:
- _id: CaHe
- _id: EdHa
- _id: MiSi
- _id: Bio
doi: 10.1016/j.celrep.2025.115387
external_id:
isi:
- '001443652700001'
pmid:
- '40057955'
file:
- access_level: open_access
checksum: 57e05dd1598c807af0afdb32cec039d3
content_type: application/pdf
creator: dernst
date_created: 2025-03-17T10:26:54Z
date_updated: 2025-03-17T10:26:54Z
file_id: '19413'
file_name: 2025_CellReports_Tavano.pdf
file_size: 9067797
relation: main_file
success: 1
file_date_updated: 2025-03-17T10:26:54Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
- _id: 269CD5C4-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1159-2018
name: 'Mechanosensation in cell migration: the role of friction forces in cell polarization
and directed migration'
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: BMP-dependent patterning of ectoderm tissue material properties modulates lateral
mesendoderm cell migration during early zebrafish gastrulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19405'
abstract:
- lang: eng
text: "In the third APOKASC catalog, we present data for the complete sample of
15,808 evolved stars with APOGEE spectroscopic parameters and Kepler asteroseismology.
We used 10 independent asteroseismic analysis techniques and anchor our system
on fundamental radii derived from Gaia L and spectroscopic Teff. We provide evolutionary
state, asteroseismic surface gravity, mass, radius, age, and the data used to
derive them for 12,418 stars. This includes 10,036 exceptionally precise measurements,
with median fractional uncertainties in \r\nvmax, Δν, mass, radius, and age of
0.6%, 0.6%, 3.8%, 1.8%, and 11.1%, respectively. We provide more limited data
for 1624 additional stars that either have lower-quality data or are outside of
our primary calibration domain. Using lower red giant branch (RGB) stars, we find
a median age for the chemical thick disk of 9.14 ± 0.05(ran) ± 0.9(sys) Gyr with
an age dispersion of 1.1 Gyr, consistent with our error model. We calibrate our
red clump (RC) mass loss to derive an age consistent with the lower RGB and provide
asymptotic GB and RGB ages for luminous stars. We also find a sharp upper-age
boundary in the chemical thin disk. We find that scaling relations are precise
and accurate on the lower RGB and RC, but they become more model dependent for
more luminous giants and break down at the tip of the RGB. We recommend the use
of multiple methods, calibration to a fundamental scale, and the use of stellar
models to interpret frequency spacings."
acknowledgement: "We thank the anonymous referee for providing constructive comments
that improved the paper. This paper includes data collected by the Kepler mission
and obtained from the MAST data archive at the Space Telescope Science Institute
(STScI). Funding for the Kepler mission is provided by the NASA Science Mission
Directorate. STScI is operated by the Association of Universities for Research in
Astronomy, Inc., under NASA contract NAS 5-26555. M.H.P. acknowledges support from
NASA grants 80NSSC24K0637 and 80NSSC18K1582. M.H.P., J.T., and P.M.F. acknowledge
that part of this work was performed at the Aspen Center for Physics, which is supported
by National Science Foundation grant PHY-1607611. M.H.P. acknowledges support from
the Fundación Occident and the Instituto de Astrofísica de Canarias under the Visiting
Researcher Programme 2022-2025 agreed between both institutions. A.S. acknowledges
support by the Spanish Ministry of Science, Innovation and Universities through
the grant PID2023-149918NB-I00 and the program Unidad de Excelencia Marìa de Maeztu
CEX2020-001058-M, and by Generalitat de Catalunya through grant 2021-SGR-1526. S.B.
acknowledges NSF grant AST-2205026. P.G.B. acknowledges support by the Spanish Ministry
of Science and Innovation with the Ramón y Cajal fellowship Nos. RYC-2021-033137-I
and MRR4032204. D.S. is supported by the Australian Research Council (DP190100666).
P.G.B., D.G.R., and R.A.G. acknowledge support from the Spanish Ministry of Science
and Innovation from grant No. PID2023-146453NB-100 (PLAtoSOnG). M.V. acknowledges
support from NASA grant 80NSSC18K1582 and funding from the European Research Council
(ERC) under the European Union's Horizon 2020 research and innovation program (grant
agreement No. 101019653). T.C.B. acknowledges partial support for this work from
grant PHY 14-30152; Physics Frontier Center/JINA Center for the Evolution of the
Elements (JINA-CEE), and OISE-1927130: The International Research Network for Nuclear
Astrophysics (IReNA), awarded by the US National Science Foundation. The research
leading to the presented results has received funding from the ERC Consolidator
Grant DipolarSound (grant agreement No. 101000296). P.F. and T.S. acknowledges support
from the National Science Foundation Astronomy and Astrophysics grants AST-1715662
and AST-2206541. S.M. acknowledges support by the Spanish Ministry of Science and
Innovation with the Ramon y Cajal fellowship Nos. RYC-2015-17697, PID2019-107061GB-C66,
and PID2023-149439NB-C41, and through AEI under the Severo Ochoa Centres of Excellence
Programme 2020–2023 (CEX2019-000920-S). S.M. and D.G.R. acknowledge support from
the Spanish Ministry of Science and Innovation (MICINN) from grant No. PID2019-107187GB-I00.
D.G.R. acknowledges support from the Spanish Ministry of Science and Innovation
(MICINN) with the Juan de la Cierva program under contract JDC2022-049054-I. L.B.
gratefully acknowledges support from the European Research Council (ERC) under the
Horizon Europe program (Calcifer; Starting grant agreement No. 101165631). A.R.G.S.
acknowledges the support from the FCT through national funds and FEDER through COMPETE2020
(UIDB/04434/2020, UIDP/04434/2020, and 2022.03993.PTDC) and the support from the
FCT through work contract No. 2020.02480.CEECIND/CP1631/CT0001.\r\n\r\nFunding for
the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation,
the U.S. Department of Energy Office of Science, and the Participating Institutions.
SDSS acknowledges support and resources from the Center for High-Performance Computing
at the University of Utah. The SDSS website is www.sdss4.org.\r\n\r\nSDSS is managed
by the Astrophysical Research Consortium for the Participating Institutions of the
SDSS Collaboration including the Brazilian Participation Group, the Carnegie Institution
for Science, Carnegie Mellon University, Center for Astrophysics—Harvard & Smithsonian
(CfA), the Chilean Participation Group, the French Participation Group, Instituto
de Astrofísica de Canarias, The Johns Hopkins University, Kavli Institute for the
Physics and Mathematics of the Universe (IPMU)/University of Tokyo, the Korean Participation
Group, Lawrence Berkeley National Laboratory, Leibniz Institut für Astrophysik Potsdam
(AIP), Max-Planck-Institut für Astronomie (MPIA Heidelberg), Max-Planck-Institut
für Astrophysik (MPA Garching), Max-Planck-Institut für Extraterrestrische Physik
(MPE), National Astronomical Observatories of China, New Mexico State University,
New York University, University of Notre Dame, Observatório Nacional/MCTI, The Ohio
State University, Pennsylvania State University, Shanghai Astronomical Observatory,
United Kingdom Participation Group, Universidad Nacional Autónoma de México, University
of Arizona, University of Colorado Boulder, University of Oxford, University of
Portsmouth, University of Utah, University of Virginia, University of Washington,
University of Wisconsin, Vanderbilt University, and Yale University."
article_number: '69'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Marc H.
full_name: Pinsonneault, Marc H.
last_name: Pinsonneault
- first_name: Joel C.
full_name: Zinn, Joel C.
last_name: Zinn
- first_name: Jamie
full_name: Tayar, Jamie
last_name: Tayar
- first_name: Aldo
full_name: Serenelli, Aldo
last_name: Serenelli
- first_name: Rafael A.
full_name: García, Rafael A.
last_name: García
- first_name: Savita
full_name: Mathur, Savita
last_name: Mathur
- first_name: Mathieu
full_name: Vrard, Mathieu
last_name: Vrard
- first_name: Yvonne P.
full_name: Elsworth, Yvonne P.
last_name: Elsworth
- first_name: Benoit
full_name: Mosser, Benoit
last_name: Mosser
- first_name: Dennis
full_name: Stello, Dennis
last_name: Stello
- first_name: Keaton J.
full_name: Bell, Keaton J.
last_name: Bell
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
- first_name: Enrico
full_name: Corsaro, Enrico
last_name: Corsaro
- first_name: Patrick
full_name: Gaulme, Patrick
last_name: Gaulme
- first_name: Saskia
full_name: Hekker, Saskia
last_name: Hekker
- first_name: Marc
full_name: Hon, Marc
last_name: Hon
- first_name: Daniel
full_name: Huber, Daniel
last_name: Huber
- first_name: Thomas
full_name: Kallinger, Thomas
last_name: Kallinger
- first_name: Kaili
full_name: Cao, Kaili
last_name: Cao
- first_name: Jennifer A.
full_name: Johnson, Jennifer A.
last_name: Johnson
- first_name: Bastien
full_name: Liagre, Bastien
last_name: Liagre
- first_name: Rachel A.
full_name: Patton, Rachel A.
last_name: Patton
- first_name: Ângela R.G.
full_name: Santos, Ângela R.G.
last_name: Santos
- first_name: Sarbani
full_name: Basu, Sarbani
last_name: Basu
- first_name: Paul G.
full_name: Beck, Paul G.
last_name: Beck
- first_name: Timothy C.
full_name: Beers, Timothy C.
last_name: Beers
- first_name: William J.
full_name: Chaplin, William J.
last_name: Chaplin
- first_name: Katia
full_name: Cunha, Katia
last_name: Cunha
- first_name: Peter M.
full_name: Frinchaboy, Peter M.
last_name: Frinchaboy
- first_name: Léo
full_name: Girardi, Léo
last_name: Girardi
- first_name: Diego
full_name: Godoy-Rivera, Diego
last_name: Godoy-Rivera
- first_name: Jon A.
full_name: Holtzman, Jon A.
last_name: Holtzman
- first_name: Henrik
full_name: Jönsson, Henrik
last_name: Jönsson
- first_name: Szabolcs
full_name: Mészáros, Szabolcs
last_name: Mészáros
- first_name: Claudia
full_name: Reyes, Claudia
last_name: Reyes
- first_name: Hans Walter
full_name: Rix, Hans Walter
last_name: Rix
- first_name: Matthew
full_name: Shetrone, Matthew
last_name: Shetrone
- first_name: Verne V.
full_name: Smith, Verne V.
last_name: Smith
- first_name: Taylor
full_name: Spoo, Taylor
last_name: Spoo
- first_name: Keivan G.
full_name: Stassun, Keivan G.
last_name: Stassun
- first_name: Ji
full_name: Wang, Ji
last_name: Wang
citation:
ama: 'Pinsonneault MH, Zinn JC, Tayar J, et al. APOKASC-3: The third joint spectroscopic
and asteroseismic catalog for evolved stars in the Kepler fields. Astrophysical
Journal, Supplement Series. 2025;276(2). doi:10.3847/1538-4365/ad9fef'
apa: 'Pinsonneault, M. H., Zinn, J. C., Tayar, J., Serenelli, A., García, R. A.,
Mathur, S., … Wang, J. (2025). APOKASC-3: The third joint spectroscopic and asteroseismic
catalog for evolved stars in the Kepler fields. Astrophysical Journal, Supplement
Series. IOP Publishing. https://doi.org/10.3847/1538-4365/ad9fef'
chicago: 'Pinsonneault, Marc H., Joel C. Zinn, Jamie Tayar, Aldo Serenelli, Rafael
A. García, Savita Mathur, Mathieu Vrard, et al. “APOKASC-3: The Third Joint Spectroscopic
and Asteroseismic Catalog for Evolved Stars in the Kepler Fields.” Astrophysical
Journal, Supplement Series. IOP Publishing, 2025. https://doi.org/10.3847/1538-4365/ad9fef.'
ieee: 'M. H. Pinsonneault et al., “APOKASC-3: The third joint spectroscopic
and asteroseismic catalog for evolved stars in the Kepler fields,” Astrophysical
Journal, Supplement Series, vol. 276, no. 2. IOP Publishing, 2025.'
ista: 'Pinsonneault MH, Zinn JC, Tayar J, Serenelli A, García RA, Mathur S, Vrard
M, Elsworth YP, Mosser B, Stello D, Bell KJ, Bugnet LA, Corsaro E, Gaulme P, Hekker
S, Hon M, Huber D, Kallinger T, Cao K, Johnson JA, Liagre B, Patton RA, Santos
ÂRG, Basu S, Beck PG, Beers TC, Chaplin WJ, Cunha K, Frinchaboy PM, Girardi L,
Godoy-Rivera D, Holtzman JA, Jönsson H, Mészáros S, Reyes C, Rix HW, Shetrone
M, Smith VV, Spoo T, Stassun KG, Wang J. 2025. APOKASC-3: The third joint spectroscopic
and asteroseismic catalog for evolved stars in the Kepler fields. Astrophysical
Journal, Supplement Series. 276(2), 69.'
mla: 'Pinsonneault, Marc H., et al. “APOKASC-3: The Third Joint Spectroscopic and
Asteroseismic Catalog for Evolved Stars in the Kepler Fields.” Astrophysical
Journal, Supplement Series, vol. 276, no. 2, 69, IOP Publishing, 2025, doi:10.3847/1538-4365/ad9fef.'
short: M.H. Pinsonneault, J.C. Zinn, J. Tayar, A. Serenelli, R.A. García, S. Mathur,
M. Vrard, Y.P. Elsworth, B. Mosser, D. Stello, K.J. Bell, L.A. Bugnet, E. Corsaro,
P. Gaulme, S. Hekker, M. Hon, D. Huber, T. Kallinger, K. Cao, J.A. Johnson, B.
Liagre, R.A. Patton, Â.R.G. Santos, S. Basu, P.G. Beck, T.C. Beers, W.J. Chaplin,
K. Cunha, P.M. Frinchaboy, L. Girardi, D. Godoy-Rivera, J.A. Holtzman, H. Jönsson,
S. Mészáros, C. Reyes, H.W. Rix, M. Shetrone, V.V. Smith, T. Spoo, K.G. Stassun,
J. Wang, Astrophysical Journal, Supplement Series 276 (2025).
date_created: 2025-03-16T23:01:24Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-09-30T11:03:01Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.3847/1538-4365/ad9fef
external_id:
arxiv:
- '2410.00102'
isi:
- '001414132600001'
file:
- access_level: open_access
checksum: a01a6645c6cb0b5cc75490f3339a2244
content_type: application/pdf
creator: dernst
date_created: 2025-03-17T10:40:41Z
date_updated: 2025-03-17T10:40:41Z
file_id: '19414'
file_name: 2025_AstrophysicalJourSuppl_Pinsonneault.pdf
file_size: 4993506
relation: main_file
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file_date_updated: 2025-03-17T10:40:41Z
has_accepted_license: '1'
intvolume: ' 276'
isi: 1
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
publication: Astrophysical Journal, Supplement Series
publication_identifier:
issn:
- 0067-0049
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'APOKASC-3: The third joint spectroscopic and asteroseismic catalog for evolved
stars in the Kepler fields'
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: 276
year: '2025'
...
---
OA_type: closed access
_id: '19406'
abstract:
- lang: eng
text: "Polyploidization is a common occurrence in the evolutionary history of flowering
plants, significantly contributing to their adaptability and diversity. However,
the molecular mechanisms behind these adaptive advantages are not well understood.\r\nThrough
comprehensive phenotyping of diploid and tetraploid clones from Citrus and Poncirus
genera, we discovered that genome doubling significantly enhances salt stress
resilience. Epigenetic and transcriptomic analyses revealed that increased ethylene
production in the roots of tetraploid plants was associated with hypomethylation
and enhanced chromatin accessibility of the ACO1 gene. This increased ethylene
production activates the transcription of reactive oxygen species scavenging genes
and stress-related hormone biosynthesis genes. Consequently, tetraploid plants
exhibited superior root functionality under salt stress, maintaining improved
cytosolic K+/Na+ homeostasis.\r\nTo genetically validate the link between salt
stress resilience and ACO1 expression, we generated overexpression and knockout
lines, confirming the central role of ACO1 expression regulation following genome
doubling in salt stress resilience.\r\nOur work elucidates the molecular mechanisms
underlying the role of genome doubling in stress resilience. We also highlight
the importance of chromatin dynamics in fine-tuning ethylene gene expression and
activating salt stress resilience pathways, offering valuable insights into plant
adaptation and crop genome evolution."
acknowledgement: We thank Prof. Qi Xie from the Institute of Genetics and Development,
Chinese Academy of Sciences, for providing the YAO promoter-driven CRISPR/Cas9 vector,
our colleague Dr Robert M. Larkin from Huazhong Agricultural University, and Dr
Olivier Martin from IPS2 (INRAE, France) for critical reading of the manuscript.
This research was financially supported by grants from the National Key Research
& Development Program of China (2024YFD1200501), the National Natural Science Foundation
of China (32172525 and 32202432), the Foundation of Hubei Hongshan laboratory (2021hszd009),
the China Agricultural Research System (CARS-26) and the Department of Science and
Technology of Hubei Province (2022BBA0019). A. Bendahmane is funded by the ANR BioAdapt
(ANR-21-LCV3-0003), LabEx Saclay Plant Sciences (SPS) (ANR-10-LABX-40-SPS), and
the NectarGland ERC Project (101095736).
article_processing_charge: No
article_type: original
author:
- first_name: Xin
full_name: Song, Xin
last_name: Song
- first_name: Miao
full_name: Zhang, Miao
last_name: Zhang
- first_name: Ting Ting
full_name: Wang, Ting Ting
last_name: Wang
- first_name: Yao Yuan
full_name: Duan, Yao Yuan
last_name: Duan
- first_name: Jie
full_name: Ren, Jie
last_name: Ren
- first_name: Hu
full_name: Gao, Hu
last_name: Gao
- first_name: Yan Jie
full_name: Fan, Yan Jie
last_name: Fan
- first_name: Qiang Ming
full_name: Xia, Qiang Ming
last_name: Xia
- first_name: Hui Xiang
full_name: Cao, Hui Xiang
last_name: Cao
- first_name: Kai Dong
full_name: Xie, Kai Dong
last_name: Xie
- first_name: Xiao Meng
full_name: Wu, Xiao Meng
last_name: Wu
- first_name: Fei
full_name: Zhang, Fei
last_name: Zhang
- first_name: Si Qi
full_name: Zhang, Si Qi
last_name: Zhang
- first_name: Ying
full_name: Huang, Ying
id: 11b5bbff-8b61-11ed-b69e-d8ddd6bce951
last_name: Huang
- first_name: Adnane
full_name: Boualem, Adnane
last_name: Boualem
- first_name: Abdelhafid
full_name: Bendahmane, Abdelhafid
last_name: Bendahmane
- first_name: Feng Quan
full_name: Tan, Feng Quan
last_name: Tan
- first_name: Wen Wu
full_name: Guo, Wen Wu
last_name: Guo
citation:
ama: Song X, Zhang M, Wang TT, et al. Polyploidization leads to salt stress resilience
via ethylene signaling in citrus plants. New Phytologist. 2025;246(1):176-191.
doi:10.1111/nph.20428
apa: Song, X., Zhang, M., Wang, T. T., Duan, Y. Y., Ren, J., Gao, H., … Guo, W.
W. (2025). Polyploidization leads to salt stress resilience via ethylene signaling
in citrus plants. New Phytologist. Wiley. https://doi.org/10.1111/nph.20428
chicago: Song, Xin, Miao Zhang, Ting Ting Wang, Yao Yuan Duan, Jie Ren, Hu Gao,
Yan Jie Fan, et al. “Polyploidization Leads to Salt Stress Resilience via Ethylene
Signaling in Citrus Plants.” New Phytologist. Wiley, 2025. https://doi.org/10.1111/nph.20428.
ieee: X. Song et al., “Polyploidization leads to salt stress resilience via
ethylene signaling in citrus plants,” New Phytologist, vol. 246, no. 1.
Wiley, pp. 176–191, 2025.
ista: Song X, Zhang M, Wang TT, Duan YY, Ren J, Gao H, Fan YJ, Xia QM, Cao HX, Xie
KD, Wu XM, Zhang F, Zhang SQ, Huang Y, Boualem A, Bendahmane A, Tan FQ, Guo WW.
2025. Polyploidization leads to salt stress resilience via ethylene signaling
in citrus plants. New Phytologist. 246(1), 176–191.
mla: Song, Xin, et al. “Polyploidization Leads to Salt Stress Resilience via Ethylene
Signaling in Citrus Plants.” New Phytologist, vol. 246, no. 1, Wiley, 2025,
pp. 176–91, doi:10.1111/nph.20428.
short: X. Song, M. Zhang, T.T. Wang, Y.Y. Duan, J. Ren, H. Gao, Y.J. Fan, Q.M. Xia,
H.X. Cao, K.D. Xie, X.M. Wu, F. Zhang, S.Q. Zhang, Y. Huang, A. Boualem, A. Bendahmane,
F.Q. Tan, W.W. Guo, New Phytologist 246 (2025) 176–191.
date_created: 2025-03-16T23:01:25Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-09-30T11:00:06Z
day: '01'
department:
- _id: XiFe
doi: 10.1111/nph.20428
external_id:
isi:
- '001424915600001'
pmid:
- '39969116'
intvolume: ' 246'
isi: 1
issue: '1'
language:
- iso: eng
month: '04'
oa_version: None
page: 176-191
pmid: 1
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Polyploidization leads to salt stress resilience via ethylene signaling in
citrus plants
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 246
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19407'
abstract:
- lang: eng
text: We discuss, in a non-Archimedean setting, the distribution of the coefficients
of L-polynomials of curves of genus g over Fq . Among other results, this allows
us to prove that the Q-vector space spanned by such characteristic polynomials
has dimension g + 1. We also state a conjecture about the Archimedean distribution
of the number of rational points of curves over finite fields.
acknowledgement: We thank Umberto Zannier for bringing the problem to our attention,
for many useful suggestions, and especially for pointing out the relevance of the
equidistribution results of Katz–Sarnak, noting that they imply the case q≫g0 of
theorem 1.4. In addition, the first author would like to thank Umberto Zannier for
his guidance during his undergraduate studies, on a topic that ultimately inspired
much of the work in this article. We are grateful to J. Kaczorowski and A. Perelli
for sharing their work [Reference Kaczorowski and Perelli28] before publication.
We thank Christophe Ritzenthaler and Elisa Lorenzo García for their interesting
comments on the first version of this article, Zhao Yu Ma for a comment about remark
3.12, and the anonymous referees for their helpful suggestions.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Francesco
full_name: Ballini, Francesco
last_name: Ballini
- first_name: Davide
full_name: Lombardo, Davide
last_name: Lombardo
- first_name: Matteo
full_name: Verzobio, Matteo
id: 7aa8f170-131e-11ed-88e1-a9efd01027cb
last_name: Verzobio
orcid: 0000-0002-0854-0306
citation:
ama: 'Ballini F, Lombardo D, Verzobio M. On the L-polynomials of curves over finite
fields. Proceedings of the Royal Society of Edinburgh Section A: Mathematics.
2025. doi:10.1017/prm.2025.7'
apa: 'Ballini, F., Lombardo, D., & Verzobio, M. (2025). On the L-polynomials
of curves over finite fields. Proceedings of the Royal Society of Edinburgh
Section A: Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2025.7'
chicago: 'Ballini, Francesco, Davide Lombardo, and Matteo Verzobio. “On the L-Polynomials
of Curves over Finite Fields.” Proceedings of the Royal Society of Edinburgh
Section A: Mathematics. Cambridge University Press, 2025. https://doi.org/10.1017/prm.2025.7.'
ieee: 'F. Ballini, D. Lombardo, and M. Verzobio, “On the L-polynomials of curves
over finite fields,” Proceedings of the Royal Society of Edinburgh Section
A: Mathematics. Cambridge University Press, 2025.'
ista: 'Ballini F, Lombardo D, Verzobio M. 2025. On the L-polynomials of curves over
finite fields. Proceedings of the Royal Society of Edinburgh Section A: Mathematics.'
mla: 'Ballini, Francesco, et al. “On the L-Polynomials of Curves over Finite Fields.”
Proceedings of the Royal Society of Edinburgh Section A: Mathematics, Cambridge
University Press, 2025, doi:10.1017/prm.2025.7.'
short: 'F. Ballini, D. Lombardo, M. Verzobio, Proceedings of the Royal Society of
Edinburgh Section A: Mathematics (2025).'
corr_author: '1'
date_created: 2025-03-16T23:01:25Z
date_published: 2025-02-06T00:00:00Z
date_updated: 2025-09-30T11:00:35Z
day: '06'
department:
- _id: TiBr
doi: 10.1017/prm.2025.7
external_id:
isi:
- '001414690400001'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1017/prm.2025.7
month: '02'
oa: 1
oa_version: Published Version
publication: 'Proceedings of the Royal Society of Edinburgh Section A: Mathematics'
publication_identifier:
eissn:
- 1473-7124
issn:
- 0308-2105
publication_status: epub_ahead
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the L-polynomials of curves over finite fields
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '19416'
abstract:
- lang: eng
text: 'Recently, Biagioli and Tompkins (2023, https://doi.org/10.1029/2022ms003231)
used a simple stochastic model to derive a dimensionless parameter to predict
convective self aggregation (SA) development, which was based on the derivation
of the maximum free convective distance ($d_{clr}$) expected in the pre-aggregated,
random state. Our goal is to test and further investigate this hypothesis, namely
that $d_{clr}$ can predict SA occurrence, using an ensemble of twenty-four distinct
combinations of horizontal mixing, planetary boundary layer (PBL), and microphysical
parameterizations. We conclude that the key impact of parameterization schemes
on SA is through their control of the number of convective cores and their relative
spacing, $d_{clr}$, which itself is impacted by cold-pool (CP) properties and
mean updraft core size. SA is more likely when the convective core count is small,
while CPs modify convective spacing via suppression in their interiors and triggering
by gust-front convergence and collisions. Each parameterization scheme emphasizes
a different mechanism. Subgrid-scale horizontal turbulent mixing mainly affects
SA through the determination of convective core size and thus spacing. The sensitivity
to the microphysics is mainly through rain evaporation and the subsequent impact
on CPs, while perturbations to the ice cloud microphysics have a limited effect.
Non-local PBL mixing schemes promote SA primarily by increasing convective inhibition
through inversion entrainment and altering low cloud amounts, leading to fewer
convective cores and larger $d_{clr}$. '
acknowledgement: This article is based on chapter 3 of AC Ph.D. thesis. The authors
thank Graziano Giuliani for his coding assistance. We also thank Daniel Hernández-Deckers,
Paolina Cerlini, and especially to Giovanni Biagioli for discussions and feedback.
We also thank two reviewers for their insightful comments. AC was supported by a
fellowship awarded by ICTP and by the European Union Horizon 2020 Marie Skłodowska-Curie
grant agreement No. 101034413. CM acknowledges funding from the European Research
Council (ERC) under the European Union's Horizon 2020 research and innovation program
(Project CLUSTER, Grant Agreement No. 805041).
article_number: e2024MS004791
article_processing_charge: Yes
article_type: original
author:
- first_name: Alejandro
full_name: Casallas Garcia, Alejandro
id: 92081129-2d75-11ef-a48d-b04dd7a2385a
last_name: Casallas Garcia
orcid: 0000-0002-1988-5035
- first_name: A.M.
full_name: Tompkins, A.M.
last_name: Tompkins
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: G.
full_name: Thompson, G.
last_name: Thompson
citation:
ama: Casallas Garcia A, Tompkins AM, Muller CJ, Thompson G. Sensitivity of self-aggregation
and the key role of the free convection distance. Journal of Advances in Modeling
Earth Systems. 2025;17(3). doi:10.1029/2024MS004791
apa: Casallas Garcia, A., Tompkins, A. M., Muller, C. J., & Thompson, G. (2025).
Sensitivity of self-aggregation and the key role of the free convection distance.
Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2024MS004791
chicago: Casallas Garcia, Alejandro, A.M. Tompkins, Caroline J Muller, and G. Thompson.
“Sensitivity of Self-Aggregation and the Key Role of the Free Convection Distance.”
Journal of Advances in Modeling Earth Systems. Wiley, 2025. https://doi.org/10.1029/2024MS004791.
ieee: A. Casallas Garcia, A. M. Tompkins, C. J. Muller, and G. Thompson, “Sensitivity
of self-aggregation and the key role of the free convection distance,” Journal
of Advances in Modeling Earth Systems, vol. 17, no. 3. Wiley, 2025.
ista: Casallas Garcia A, Tompkins AM, Muller CJ, Thompson G. 2025. Sensitivity of
self-aggregation and the key role of the free convection distance. Journal of
Advances in Modeling Earth Systems. 17(3), e2024MS004791.
mla: Casallas Garcia, Alejandro, et al. “Sensitivity of Self-Aggregation and the
Key Role of the Free Convection Distance.” Journal of Advances in Modeling
Earth Systems, vol. 17, no. 3, e2024MS004791, Wiley, 2025, doi:10.1029/2024MS004791.
short: A. Casallas Garcia, A.M. Tompkins, C.J. Muller, G. Thompson, Journal of Advances
in Modeling Earth Systems 17 (2025).
corr_author: '1'
date_created: 2025-03-19T07:58:38Z
date_published: 2025-03-18T00:00:00Z
date_updated: 2025-09-30T11:04:38Z
day: '18'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1029/2024MS004791
ec_funded: 1
external_id:
isi:
- '001447023900001'
file:
- access_level: open_access
checksum: bc32677e63f8abb07b330f4a08da796d
content_type: application/pdf
creator: acasalla
date_created: 2025-03-19T07:58:21Z
date_updated: 2025-03-19T07:58:21Z
file_id: '19417'
file_name: Casallas_et_al_2025_dclr.pdf
file_size: 18285343
relation: main_file
file_date_updated: 2025-03-19T07:58:21Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
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'
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: Organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
eissn:
- 1942-2466
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sensitivity of self-aggregation and the key role of the free convection distance
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: 17
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19418'
abstract:
- lang: eng
text: The size-Ramsey number r^(H) of a graph H is the smallest number of edges
a (host) graph G can have, such that for any red/blue colouring of G, there is
a monochromatic copy of H in G. Recently, Conlon, Nenadov and Trujić showed that
if H is a graph on n vertices and maximum degree three, then r^(H)=O(n8/5), improving
upon the upper bound of n5/3+o(1) by Kohayakawa, Rödl, Schacht and Szemerédi.
In this paper we show that r^(H)≤n3/2+o(1). While the previously used host graphs
were vanilla binomial random graphs, we prove our result using a novel host graph
construction. Our bound hits a natural barrier of the existing methods.
acknowledgement: 'We would like to thank Rajko Nenadov and Miloš Trujić for helpful
comments and discussions, as well as the anonymous referees for their very useful
feedback, which improved the paper considerably. This research was supported by
SNSF Project 217926. Part of this research was conducted while Nemanja Draganić
was at ETH Zürich, Switzerland, and partially supported by SNSF Grant 200021_196965.
This project has received funding from the European Union''s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement Number:
101034413. Part of this research was conducted while Kalina Petrova was at the Department
of Computer Science, ETH Zürich, Switzerland, supported by SNSF Grant CRSII5 173721.'
article_number: e70116
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nemanja
full_name: Draganić, Nemanja
last_name: Draganić
- first_name: Kalina H
full_name: Petrova, Kalina H
id: 554ff4e4-f325-11ee-b0c4-a10dbd523381
last_name: Petrova
citation:
ama: Draganić N, Petrova KH. Size‐Ramsey numbers of graphs with maximum degree three.
Journal of the London Mathematical Society. 2025;111(3). doi:10.1112/jlms.70116
apa: Draganić, N., & Petrova, K. H. (2025). Size‐Ramsey numbers of graphs with
maximum degree three. Journal of the London Mathematical Society. Wiley.
https://doi.org/10.1112/jlms.70116
chicago: Draganić, Nemanja, and Kalina H Petrova. “Size‐Ramsey Numbers of Graphs
with Maximum Degree Three.” Journal of the London Mathematical Society.
Wiley, 2025. https://doi.org/10.1112/jlms.70116.
ieee: N. Draganić and K. H. Petrova, “Size‐Ramsey numbers of graphs with maximum
degree three,” Journal of the London Mathematical Society, vol. 111, no.
3. Wiley, 2025.
ista: Draganić N, Petrova KH. 2025. Size‐Ramsey numbers of graphs with maximum degree
three. Journal of the London Mathematical Society. 111(3), e70116.
mla: Draganić, Nemanja, and Kalina H. Petrova. “Size‐Ramsey Numbers of Graphs with
Maximum Degree Three.” Journal of the London Mathematical Society, vol.
111, no. 3, e70116, Wiley, 2025, doi:10.1112/jlms.70116.
short: N. Draganić, K.H. Petrova, Journal of the London Mathematical Society 111
(2025).
date_created: 2025-03-19T09:03:37Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-09-30T11:05:07Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1112/jlms.70116
ec_funded: 1
external_id:
arxiv:
- '2207.05048'
isi:
- '001450645400019'
file:
- access_level: open_access
checksum: d8e0a03286a44c4f672709e3c829206e
content_type: application/pdf
creator: dernst
date_created: 2025-03-20T09:46:20Z
date_updated: 2025-03-20T09:46:20Z
file_id: '19427'
file_name: 2025_JournLondonMath_Draganic.pdf
file_size: 625974
relation: main_file
success: 1
file_date_updated: 2025-03-20T09:46:20Z
has_accepted_license: '1'
intvolume: ' 111'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
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: Journal of the London Mathematical Society
publication_identifier:
eissn:
- 1469-7750
issn:
- 0024-6107
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Size‐Ramsey numbers of graphs with maximum degree three
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: 111
year: '2025'
...
---
OA_type: closed access
_id: '19420'
abstract:
- lang: eng
text: Auxin and its PIN-FORMED (PIN) exporters are essential for tissue repair and
regeneration in flowering plants. To gain insight into the evolution of this mechanism,
we investigated their roles in leaves excised from Physcomitrium patens, a bryophyte
known for its remarkable cell reprogramming capacity. We used various approaches
to manipulate auxin levels, including exogenous application, pharmacological manipulations,
and auxin biosynthesis mutants. We observed no significant effect on the rate
of cell reprogramming. Rather, our analysis of auxin dynamics revealed a decrease
in auxin levels upon excision, which was followed by a local increase before the
reprogramming process began. Mutant analysis revealed that PpPINs are required
for effective cell reprogramming, and endogenously expressed PpPINA-GFP accumulates
polarly at sites that will develop into future filamentous stem cells. In addition,
hyperpolarized PpPINA variants carrying mutated phosphorylation sites showed a
marked delay in reprogramming, whereas endogenous or nonpolar versions do not
have this effect. These results underscore that both the levels and the polarity
of PpPINA are important for efficient cell reprogramming. Overall, these findings
highlight the pivotal role of PIN polarity in plant regeneration. Furthermore,
they suggest that understanding polarity mechanisms could have broader implications
for improving regenerative processes across various plant species.
acknowledgement: "The authors sincerely thank Dr Barbara Kloeckener Gruissem’s time
and efforts in critical reading and constructive advice on the manuscript. The authors
gratefully acknowledge Dr. Eva Sundberg for generously providing transgenic plants
to support this study.\r\nThis work was supported by the European Research Council
Advanced Grant (ETAP-742985 to H.T. and J.F.) and the Taiwan National Science and
Technology Council (NSTC 112-2311-B-005-008 to H.T. and L.-H.C.)."
article_number: pcaf008
article_processing_charge: No
article_type: original
author:
- first_name: Han
full_name: Tang, Han
id: 19BDF720-25A0-11EA-AC6E-928F3DDC885E
last_name: Tang
orcid: 0000-0001-6152-6637
- first_name: L
full_name: Chen, L
last_name: Chen
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tang H, Chen L, Friml J. Auxin fluctuation and PIN polarization in moss leaf
cell reprogramming. Plant and Cell Physiology. 2025. doi:10.1093/pcp/pcaf008
apa: Tang, H., Chen, L., & Friml, J. (2025). Auxin fluctuation and PIN polarization
in moss leaf cell reprogramming. Plant and Cell Physiology. Oxford University
Press. https://doi.org/10.1093/pcp/pcaf008
chicago: Tang, Han, L Chen, and Jiří Friml. “Auxin Fluctuation and PIN Polarization
in Moss Leaf Cell Reprogramming.” Plant and Cell Physiology. Oxford University
Press, 2025. https://doi.org/10.1093/pcp/pcaf008.
ieee: H. Tang, L. Chen, and J. Friml, “Auxin fluctuation and PIN polarization in
moss leaf cell reprogramming.,” Plant and Cell Physiology. Oxford University
Press, 2025.
ista: Tang H, Chen L, Friml J. 2025. Auxin fluctuation and PIN polarization in moss
leaf cell reprogramming. Plant and Cell Physiology., pcaf008.
mla: Tang, Han, et al. “Auxin Fluctuation and PIN Polarization in Moss Leaf Cell
Reprogramming.” Plant and Cell Physiology, pcaf008, Oxford University Press,
2025, doi:10.1093/pcp/pcaf008.
short: H. Tang, L. Chen, J. Friml, Plant and Cell Physiology (2025).
corr_author: '1'
date_created: 2025-03-19T09:44:19Z
date_published: 2025-03-05T00:00:00Z
date_updated: 2025-09-30T11:05:55Z
day: '05'
department:
- _id: JiFr
doi: 10.1093/pcp/pcaf008
ec_funded: 1
external_id:
isi:
- '001436802900001'
pmid:
- '39829340'
isi: 1
language:
- iso: eng
month: '03'
oa_version: None
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant and Cell Physiology
publication_identifier:
eissn:
- 1471-9053
issn:
- 0032-0781
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin fluctuation and PIN polarization in moss leaf cell reprogramming.
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19422'
abstract:
- lang: eng
text: Nitrogen (N) is an essential macronutrient for plant development and, ultimately,
yield. Identifying the genetic components and mechanisms underlying N use efficiency
in maize (Zea mays L.) is thus of great importance. Nitrate (NO3−) is the preferred
inorganic N source in maize. Here we performed a genome-wide association study
of shoot NO3− accumulation in maize seedlings grown under low-NO3− conditions,
identifying the ferredoxin family gene ZmFd4 as a major contributor to this trait.
ZmFd4 interacts and co-localizes with nitrite reductases (ZmNiRs) in chloroplasts
to promote their enzymatic activity. Furthermore, ZmFd4 forms a high-affinity
heterodimer with its closest paralogue, ZmFd9, in a NO3−-sensitive manner. Although
ZmFd4 exerts similar biochemical functions as ZmFd9, ZmFd4 and ZmFd9 interaction
limits their ability to associate with ZmNiRs and stimulate their activity. Knockout
lines for ZmFd4 with decreased NO3− contents exhibit more efficient NO3− assimilation,
and field experiments show consistently improved N utilization and grain yield
under N-deficient conditions. Our work thus provides molecular and mechanistic
insights into the natural variation in N utilization, instrumental for genetic
improvement of yield in maize and, potentially, in other crops.
acknowledgement: We thank X. Yang for providing published inbred lines and helping
with data analysis; and S. Huang, C. Jiang, G. Bi, C. Liu and S. Zhang for helpful
discussions. The transgenic maize lines were generated by the Center for Crop Functional
Genomics and Molecular Breeding of China Agricultural University. This work was
supported by grants from the National Key Research and Development Program of China
(2021YFF1000500 to J.Z.), the National Natural Science Foundation of China (32170265
and 32441022 to J.Z.), the Chinese Universities Scientific Fund (2024TC084 to J.Z.),
the Pinduoduo-China Agricultural University Research Fund (PC2024B01005 to J.Z.),
the Hainan Provincial Natural Science Foundation of China (323CXTD379 to J.Z.),
and the Central Guidance on Local Science and Technology Development Fund of Shanxi
Province (YDZJSX2024D040 to C.T. and J.Z.).
article_number: '5207'
article_processing_charge: No
article_type: original
author:
- first_name: G
full_name: Jia, G
last_name: Jia
- first_name: G
full_name: Chen, G
last_name: Chen
- first_name: Z
full_name: Zhang, Z
last_name: Zhang
- first_name: C
full_name: Tian, C
last_name: Tian
- first_name: Y
full_name: Wang, Y
last_name: Wang
- first_name: J
full_name: Luo, J
last_name: Luo
- first_name: K
full_name: Zhang, K
last_name: Zhang
- first_name: X
full_name: Zhao, X
last_name: Zhao
- first_name: X
full_name: Zhao, X
last_name: Zhao
- first_name: Z
full_name: Li, Z
last_name: Li
- first_name: L
full_name: Sun, L
last_name: Sun
- first_name: W
full_name: Yang, W
last_name: Yang
- first_name: Y
full_name: Guo, Y
last_name: Guo
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Z
full_name: Gong, Z
last_name: Gong
- first_name: J
full_name: Zhang, J
last_name: Zhang
citation:
ama: Jia G, Chen G, Zhang Z, et al. Ferredoxin-mediated mechanism for efficient
nitrogen utilization in maize. Nature Plants. 2025;11. doi:10.1038/s41477-025-01934-w
apa: Jia, G., Chen, G., Zhang, Z., Tian, C., Wang, Y., Luo, J., … Zhang, J. (2025).
Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize. Nature
Plants. Springer Nature. https://doi.org/10.1038/s41477-025-01934-w
chicago: Jia, G, G Chen, Z Zhang, C Tian, Y Wang, J Luo, K Zhang, et al. “Ferredoxin-Mediated
Mechanism for Efficient Nitrogen Utilization in Maize.” Nature Plants.
Springer Nature, 2025. https://doi.org/10.1038/s41477-025-01934-w.
ieee: G. Jia et al., “Ferredoxin-mediated mechanism for efficient nitrogen
utilization in maize,” Nature Plants, vol. 11. Springer Nature, 2025.
ista: Jia G, Chen G, Zhang Z, Tian C, Wang Y, Luo J, Zhang K, Zhao X, Zhao X, Li
Z, Sun L, Yang W, Guo Y, Friml J, Gong Z, Zhang J. 2025. Ferredoxin-mediated mechanism
for efficient nitrogen utilization in maize. Nature Plants. 11, 5207.
mla: Jia, G., et al. “Ferredoxin-Mediated Mechanism for Efficient Nitrogen Utilization
in Maize.” Nature Plants, vol. 11, 5207, Springer Nature, 2025, doi:10.1038/s41477-025-01934-w.
short: G. Jia, G. Chen, Z. Zhang, C. Tian, Y. Wang, J. Luo, K. Zhang, X. Zhao, X.
Zhao, Z. Li, L. Sun, W. Yang, Y. Guo, J. Friml, Z. Gong, J. Zhang, Nature Plants
11 (2025).
date_created: 2025-03-19T09:44:55Z
date_published: 2025-03-05T00:00:00Z
date_updated: 2025-11-12T07:52:06Z
day: '05'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41477-025-01934-w
external_id:
isi:
- '001437953800001'
pmid:
- '40044942'
file:
- access_level: open_access
checksum: caeaf1a8bc3e1435e8c995d1d9df5390
content_type: application/pdf
creator: dernst
date_created: 2025-11-12T07:50:45Z
date_updated: 2025-11-12T07:50:45Z
file_id: '20634'
file_name: 2025_NaturePlants_Jia_submitted.pdf
file_size: 2714177
relation: main_file
success: 1
file_date_updated: 2025-11-12T07:50:45Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Nature Plants
publication_identifier:
issn:
- 2055-0278
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19423'
abstract:
- lang: eng
text: "Auxin, indole-3-acetic acid (IAA), is a key phytohormone with diverse morphogenic
roles in land plants, but its function and transport mechanisms in algae remain
poorly understood. We therefore aimed to explore the role of IAA in a complex,
streptophyte algae Chara braunii.\r\nHere, we described novel responses of C.
braunii to IAA and characterized two homologs of PIN auxin efflux carriers: CbPINa
and CbPINc. We determined their localization in C. braunii using epitope-specific
antibodies and tested their function in heterologous land plant models. Further,
using phosphoproteomic analysis, we identified IAA-induced phosphorylation events.\r\nThe
thallus regeneration assay showed that IAA promotes thallus elongation and side
branch development. Immunolocalization of CbPINa and CbPINc confirmed their presence
on the plasma membrane of vegetative and generative cells of C. braunii. However,
functional assays in tobacco BY-2 cells demonstrated that CbPINa affects auxin
transport, whereas CbPINc does not. The IAA is effective in the acceleration of
cytoplasmic streaming and the phosphorylation of evolutionary conserved targets
such as homolog of RAF-like kinase.\r\nThese findings suggest that, although canonical
PIN-mediated auxin transport mechanisms might not be fully conserved in Chara,
IAA is involved in morphogenesis and fast signaling processes."
acknowledgement: 'This work was supported by funding from the Czech Science Foundation
project no. 20-13587S to JP and SV, Charles University Grant Agency projects no.
289523 to KK and no. 393422 to VS, a DOC fellowship of the Austrian Academy of Sciences
to AS, and the Austrian Science Fund (FWF): I 6123-B to JF. The authors acknowledge
the Imaging Facility of the Institute of Experimental Botany AS CR supported by
the MEYS CR (LM2023050 Czech-BioImaging), the Czech Academy of Sciences and IEB
AS CR, and Viničná Microscopy Core Facility cofinanced by the Czech-BioImaging large
RI project LM2023050. Computational resources were provided by the e-INFRA CZ project
(ID:90254), supported by the MEYS CR. The authors would like to thank Ilse Foissner
and Margit Höftberger for discussing details of immunostaining protocol, Katarzyna
Retzer and Jan Martinek for help with western blots, Anna Kampová for help with
phosphoproteome sampling, Anja Holzhausen and MadLAnd for providing Chara braunii
strain S276, and Roman Skokan for valuable discussion. Open access publishing facilitated
by Univerzita Karlova, as part of the Wiley - CzechELib agreement.'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: K
full_name: Kurtović, K
last_name: Kurtović
- first_name: S
full_name: Vosolsobě, S
last_name: Vosolsobě
- first_name: D
full_name: Nedvěd, D
last_name: Nedvěd
- first_name: K
full_name: Müller, K
last_name: Müller
- first_name: PI
full_name: Dobrev, PI
last_name: Dobrev
- first_name: V
full_name: Schmidt, V
last_name: Schmidt
- first_name: P
full_name: Piszczek, P
last_name: Piszczek
- first_name: A
full_name: Kuhn, A
last_name: Kuhn
- first_name: Adrijana
full_name: Smoljan, Adrijana
id: cced8a85-223e-11ed-af04-b0596c55053b
last_name: Smoljan
- first_name: TJ
full_name: Fisher, TJ
last_name: Fisher
- first_name: D
full_name: Weijers, D
last_name: Weijers
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: JL
full_name: Bowman, JL
last_name: Bowman
- first_name: J
full_name: Petrášek, J
last_name: Petrášek
citation:
ama: Kurtović K, Vosolsobě S, Nedvěd D, et al. The role of indole-3-acetic acid
and characterization of PIN transporters in complex streptophyte alga Chara braunii.
New Phytologist. 2025;246(3):1066-1083. doi:10.1111/nph.70019
apa: Kurtović, K., Vosolsobě, S., Nedvěd, D., Müller, K., Dobrev, P., Schmidt, V.,
… Petrášek, J. (2025). The role of indole-3-acetic acid and characterization of
PIN transporters in complex streptophyte alga Chara braunii. New Phytologist.
Wiley. https://doi.org/10.1111/nph.70019
chicago: Kurtović, K, S Vosolsobě, D Nedvěd, K Müller, PI Dobrev, V Schmidt, P Piszczek,
et al. “The Role of Indole-3-Acetic Acid and Characterization of PIN Transporters
in Complex Streptophyte Alga Chara Braunii.” New Phytologist. Wiley, 2025.
https://doi.org/10.1111/nph.70019.
ieee: K. Kurtović et al., “The role of indole-3-acetic acid and characterization
of PIN transporters in complex streptophyte alga Chara braunii,” New Phytologist,
vol. 246, no. 3. Wiley, pp. 1066–1083, 2025.
ista: Kurtović K, Vosolsobě S, Nedvěd D, Müller K, Dobrev P, Schmidt V, Piszczek
P, Kuhn A, Smoljan A, Fisher T, Weijers D, Friml J, Bowman J, Petrášek J. 2025.
The role of indole-3-acetic acid and characterization of PIN transporters in complex
streptophyte alga Chara braunii. New Phytologist. 246(3), 1066–1083.
mla: Kurtović, K., et al. “The Role of Indole-3-Acetic Acid and Characterization
of PIN Transporters in Complex Streptophyte Alga Chara Braunii.” New Phytologist,
vol. 246, no. 3, Wiley, 2025, pp. 1066–83, doi:10.1111/nph.70019.
short: K. Kurtović, S. Vosolsobě, D. Nedvěd, K. Müller, P. Dobrev, V. Schmidt, P.
Piszczek, A. Kuhn, A. Smoljan, T. Fisher, D. Weijers, J. Friml, J. Bowman, J.
Petrášek, New Phytologist 246 (2025) 1066–1083.
date_created: 2025-03-19T09:45:11Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2025-09-30T11:11:18Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.70019
external_id:
isi:
- '001438711600001'
pmid:
- '40047465'
file:
- access_level: open_access
checksum: 861c9bf47e7a7766ed03e6d85bd4f6dc
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T08:03:36Z
date_updated: 2025-04-16T08:03:36Z
file_id: '19571'
file_name: 2025_NewPhytologist_Kurtovic.pdf
file_size: 12841729
relation: main_file
success: 1
file_date_updated: 2025-04-16T08:03:36Z
has_accepted_license: '1'
intvolume: ' 246'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1066-1083
pmid: 1
project:
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptors for auxin canalization in Arabidopsis
publication: New Phytologist
publication_identifier:
issn:
- 1469-8137
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The role of indole-3-acetic acid and characterization of PIN transporters in
complex streptophyte alga Chara braunii
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: 246
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '19433'
abstract:
- lang: eng
text: An ordered r-matching is an r-uniform hypergraph matching equipped with an
ordering on its vertices. These objects can be viewed as natural generalisations
of r-dimensional orders. The theory of ordered 2-matchings is well developed and
has connections and applications to extremal and enumerative combinatorics, probability
and geometry. On the other hand, in the case r≥3 much less is known, largely
due to a lack of powerful bijective tools. Recently, Dudek, Grytczuk and Ruciński
made some first steps towards a general theory of ordered r-matchings, and in
this paper we substantially improve several of their results and introduce some
new directions of study. Many intriguing open questions remain.
acknowledgement: We would like to thank Timo Seppäläinen for some illuminating discussion
about random high-dimensional orders and for bringing our attention to [59]. We
would also like to thank the referees for helpful feedback. Michael Anastos is supported
by the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie grant agreement No. 101034413. Matthew Kwan is supported
by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777, also funded by the European Union.
Zhihan Jin and Benny Sudakov are supported by SNSF grant 200021-228014.
article_number: e55
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: Zhihan
full_name: Jin, Zhihan
last_name: Jin
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Anastos M, Jin Z, Kwan MA, Sudakov B. Extremal, enumerative and probabilistic
results on ordered hypergraph matchings. Forum of Mathematics, Sigma. 2025;13.
doi:10.1017/fms.2024.144
apa: Anastos, M., Jin, Z., Kwan, M. A., & Sudakov, B. (2025). Extremal, enumerative
and probabilistic results on ordered hypergraph matchings. Forum of Mathematics,
Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2024.144
chicago: Anastos, Michael, Zhihan Jin, Matthew Alan Kwan, and Benny Sudakov. “Extremal,
Enumerative and Probabilistic Results on Ordered Hypergraph Matchings.” Forum
of Mathematics, Sigma. Cambridge University Press, 2025. https://doi.org/10.1017/fms.2024.144.
ieee: M. Anastos, Z. Jin, M. A. Kwan, and B. Sudakov, “Extremal, enumerative and
probabilistic results on ordered hypergraph matchings,” Forum of Mathematics,
Sigma, vol. 13. Cambridge University Press, 2025.
ista: Anastos M, Jin Z, Kwan MA, Sudakov B. 2025. Extremal, enumerative and probabilistic
results on ordered hypergraph matchings. Forum of Mathematics, Sigma. 13, e55.
mla: Anastos, Michael, et al. “Extremal, Enumerative and Probabilistic Results on
Ordered Hypergraph Matchings.” Forum of Mathematics, Sigma, vol. 13, e55,
Cambridge University Press, 2025, doi:10.1017/fms.2024.144.
short: M. Anastos, Z. Jin, M.A. Kwan, B. Sudakov, Forum of Mathematics, Sigma 13
(2025).
corr_author: '1'
date_created: 2025-03-20T12:59:14Z
date_published: 2025-03-14T00:00:00Z
date_updated: 2025-09-30T11:18:57Z
day: '14'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1017/fms.2024.144
ec_funded: 1
external_id:
arxiv:
- '2308.12268'
isi:
- '001444429200001'
file:
- access_level: open_access
checksum: f396270ad78c1ed67095c8e5a66fca26
content_type: application/pdf
creator: dernst
date_created: 2025-04-03T11:24:35Z
date_updated: 2025-04-03T11:24:35Z
file_id: '19468'
file_name: 2025_ForumMathSigma_Anastos.pdf
file_size: 630297
relation: main_file
success: 1
file_date_updated: 2025-04-03T11:24:35Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
language:
- iso: eng
month: '03'
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'
- _id: bd95085b-d553-11ed-ba76-e55d3349be45
grant_number: '101076777'
name: Randomness and structure in combinatorics
publication: Forum of Mathematics, Sigma
publication_identifier:
issn:
- 2050-5094
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extremal, enumerative and probabilistic results on ordered hypergraph matchings
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: 13
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19436'
abstract:
- lang: eng
text: Dynamic DNA methylation represses transposable elements (TEs) and regulates
gene activity, playing a pivotal role in plant development. Although substantial
progress has been made in understanding DNA methylation reprogramming during germline
development in Arabidopsis thaliana, whether similar mechanisms exist in other
dicot plants remains unclear. Here, we analyzed DNA methylation levels in meiocytes,
microspores, and pollens of Brassica Rapa using whole-genome bisulfite sequencing
(WGBS). Global DNA methylation analysis revealed similar CHH methylation reprogramming
compared to Arabidopsis, while distinct patterns were observed in the dynamics
of global CG and CHG methylation in B. rapa. Differentially methylated region
(DMR) analysis identified specifically methylated loci in the male sex cells of
B. Rapa with a stronger tendency to target genes, similar to observations in Arabidopsis.
Additionally, we found that the activity and genomic targeting preference of the
small RNA-directed DNA methylation (RdDM) were altered during B. Rapa male germline
development. A subset of long terminal repeat (LTR) TEs were activated, possibly
due to the dynamic regulation of DNA methylation during male sexual development
in B. Rapa. These findings provided new insights into the evolution of epigenetic
reprogramming mechanisms in plants.
acknowledgement: We thank Prof. Ying Li of Nanjing Agricultural University for her
help in providing seeds of K2 materials. This work was carried out with the support
of National Natural Science Foundation of China (Grant No. 32070608).
article_number: '16'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jun
full_name: Zhang, Jun
last_name: Zhang
- first_name: Di
full_name: Wu, Di
last_name: Wu
- first_name: Yating
full_name: Zhang, Yating
last_name: Zhang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hongbo
full_name: Gao, Hongbo
id: 77c2e73a-eabd-11ef-aee9-8093a2ba7a93
last_name: Gao
citation:
ama: Zhang J, Wu D, Zhang Y, Feng X, Gao H. DNA methylation dynamics in male germline
development in Brassica Rapa. Molecular Horticulture. 2025;5. doi:10.1186/s43897-024-00137-9
apa: Zhang, J., Wu, D., Zhang, Y., Feng, X., & Gao, H. (2025). DNA methylation
dynamics in male germline development in Brassica Rapa. Molecular Horticulture.
Springer Nature. https://doi.org/10.1186/s43897-024-00137-9
chicago: Zhang, Jun, Di Wu, Yating Zhang, Xiaoqi Feng, and Hongbo Gao. “DNA Methylation
Dynamics in Male Germline Development in Brassica Rapa.” Molecular Horticulture.
Springer Nature, 2025. https://doi.org/10.1186/s43897-024-00137-9.
ieee: J. Zhang, D. Wu, Y. Zhang, X. Feng, and H. Gao, “DNA methylation dynamics
in male germline development in Brassica Rapa,” Molecular Horticulture,
vol. 5. Springer Nature, 2025.
ista: Zhang J, Wu D, Zhang Y, Feng X, Gao H. 2025. DNA methylation dynamics in male
germline development in Brassica Rapa. Molecular Horticulture. 5, 16.
mla: Zhang, Jun, et al. “DNA Methylation Dynamics in Male Germline Development in
Brassica Rapa.” Molecular Horticulture, vol. 5, 16, Springer Nature, 2025,
doi:10.1186/s43897-024-00137-9.
short: J. Zhang, D. Wu, Y. Zhang, X. Feng, H. Gao, Molecular Horticulture 5 (2025).
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-04T00:00:00Z
date_updated: 2025-09-30T11:17:08Z
day: '04'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1186/s43897-024-00137-9
external_id:
isi:
- '001436233900001'
pmid:
- '40033451'
file:
- access_level: open_access
checksum: 6d1e0e9b0e1902e4a711f81c5c17a070
content_type: application/pdf
creator: dernst
date_created: 2025-03-25T12:15:32Z
date_updated: 2025-03-25T12:15:32Z
file_id: '19460'
file_name: 2025_MolecularHorticulture_Zhang.pdf
file_size: 3014980
relation: main_file
success: 1
file_date_updated: 2025-03-25T12:15:32Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Horticulture
publication_identifier:
eissn:
- 2730-9401
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation dynamics in male germline development in Brassica Rapa
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: 5
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19437'
abstract:
- lang: eng
text: We demonstrate the formation of ferroelectric domain-wall polarons in a minimal
two-dimensional lattice model of electrons interacting with rotating dipoles.
Along the domain wall, the rotors polarize in opposite directions, causing the
electron to localize along a particular lattice direction. The rotor-electron
coupling is identified as the origin of a structural instability in the crystal
that leads to the domain-wall formation via a symmetry-breaking process. Our results
provide the first theoretical description of ferroelectric polarons, as discussed
in the context of soft semiconductors.
acknowledgement: We thank, in alphabetical order, Zhanybek Alpichshev, Cesare Franchini,
Areg Ghazaryan, Sebastian Maehrlein, and Artem Volosniev for fruitful discussions
and comments. G. M. K. received funding from the European Union’s Horizon 2020 research
and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.
R. A. received funding from the Austrian Academy of Science ÖWA Grant No. PR1029OEAW03.
M. L. acknowledges support by the European Research Council (ERC) Starting Grant
No. 801770 (ANGULON).
article_number: '096302'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Florian
full_name: Kluibenschedl, Florian
id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9
last_name: Kluibenschedl
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: Ragheed
full_name: Al Hyder, Ragheed
id: d1c405be-ae15-11ed-8510-ccf53278162e
last_name: Al Hyder
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Kluibenschedl F, Koutentakis G, Al Hyder R, Lemeshko M. Domain-wall ferroelectric
polarons in a two-dimensional rotor lattice model. Physical Review Letters.
2025;134(9). doi:10.1103/PhysRevLett.134.096302
apa: Kluibenschedl, F., Koutentakis, G., Al Hyder, R., & Lemeshko, M. (2025).
Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.134.096302
chicago: Kluibenschedl, Florian, Georgios Koutentakis, Ragheed Al Hyder, and Mikhail
Lemeshko. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional Rotor Lattice
Model.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/PhysRevLett.134.096302.
ieee: F. Kluibenschedl, G. Koutentakis, R. Al Hyder, and M. Lemeshko, “Domain-wall
ferroelectric polarons in a two-dimensional rotor lattice model,” Physical
Review Letters, vol. 134, no. 9. American Physical Society, 2025.
ista: Kluibenschedl F, Koutentakis G, Al Hyder R, Lemeshko M. 2025. Domain-wall
ferroelectric polarons in a two-dimensional rotor lattice model. Physical Review
Letters. 134(9), 096302.
mla: Kluibenschedl, Florian, et al. “Domain-Wall Ferroelectric Polarons in a Two-Dimensional
Rotor Lattice Model.” Physical Review Letters, vol. 134, no. 9, 096302,
American Physical Society, 2025, doi:10.1103/PhysRevLett.134.096302.
short: F. Kluibenschedl, G. Koutentakis, R. Al Hyder, M. Lemeshko, Physical Review
Letters 134 (2025).
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-07T00:00:00Z
date_updated: 2025-09-30T11:17:58Z
day: '07'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/PhysRevLett.134.096302
ec_funded: 1
external_id:
arxiv:
- '2407.19993'
isi:
- '001492808800010'
pmid:
- '40131090'
file:
- access_level: open_access
checksum: 1901efd7f95e8fe70cac412f91ea4da3
content_type: application/pdf
creator: dernst
date_created: 2025-03-25T12:37:07Z
date_updated: 2025-03-25T12:37:07Z
file_id: '19461'
file_name: 2025_PhysReviewLetters_Kluibenschedl.pdf
file_size: 708750
relation: main_file
success: 1
file_date_updated: 2025-03-25T12:37:07Z
has_accepted_license: '1'
intvolume: ' 134'
isi: 1
issue: '9'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
- _id: 8fa7db46-16d5-11f0-9cad-917600954daf
grant_number: '12078'
name: Polarons in Lead Halide Perovskites
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Domain-wall ferroelectric polarons in a two-dimensional rotor lattice model
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: 134
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19438'
abstract:
- lang: eng
text: "Polymorphic short insertions and deletions (INDELs \r\n 50 bp) are abundant,
although less common than single nucleotide polymorphisms (SNPs). Evidence from
model organisms shows INDELs to be more strongly influenced by purifying selection
than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic
processes or to detect divergent selection. Here, we compared INDELs and SNPs
in the intertidal snail Littorina saxatilis, focussing on hybrid zones between
ecotypes, in order to test the utility of INDELs in the detection of divergent
selection. We computed INDEL and SNP site frequency spectra using capture sequencing
data. We assessed the impact of divergent selection by analyzing allele frequency
clines across habitat boundaries. We also examined the influence of GC-biased
gene conversion because it may be confounded with signatures of selection. We
show evidence that short INDELs are affected more by purifying selection than
SNPs, but part of the observed site frequency spectra difference can be attributed
to GC-biased gene conversion. We did not find a difference in the impact of divergent
selection between short INDELs and SNPs. Short INDELs and SNPs were similarly
distributed across the genome and so are likely to respond to indirect selection
in the same way. A few regions likely affected by divergent selection were revealed
by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers
helping to identify genomic regions important for adaptation and population divergence."
acknowledgement: "This work was supported by the Natural Environment Research Council
(NE/K014021/1), European Research Council (ERC-2015-AdG-693030- BARRIERS) and Swedish
Research Council VR (2018-03695) and we are also very grateful for the support of
the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg.\r\nWe
thank the Swedish Bioinformatics Advisory Program organized by SciLifeLab for feedback
and assistance on the variant calling pipeline and Alan Le Moan for helpful discussions.
R.K.B. and A.M.W. contributed equally to this work. We are also very grateful to
Tomas Larsson and Marina Panova for their bioinformatic analyses on the genome and
the annotation. The bioinformatic analyses were performed on resources at the University
of Sheffield’s High Performance Computing cluster, ShARC. We thank two anonymous
reviewers for helpful comments on a previous version."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Samuel
full_name: Perini, Samuel
last_name: Perini
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: Perini S, Johannesson K, Butlin RK, Westram AM. Short INDELs and SNPs as markers
of evolutionary processes in hybrid zones. Journal of Evolutionary Biology.
2025;38(3):367-378. doi:10.1093/jeb/voaf002
apa: Perini, S., Johannesson, K., Butlin, R. K., & Westram, A. M. (2025). Short
INDELs and SNPs as markers of evolutionary processes in hybrid zones. Journal
of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voaf002
chicago: Perini, Samuel, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram.
“Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.”
Journal of Evolutionary Biology. Oxford University Press, 2025. https://doi.org/10.1093/jeb/voaf002.
ieee: S. Perini, K. Johannesson, R. K. Butlin, and A. M. Westram, “Short INDELs
and SNPs as markers of evolutionary processes in hybrid zones,” Journal of
Evolutionary Biology, vol. 38, no. 3. Oxford University Press, pp. 367–378,
2025.
ista: Perini S, Johannesson K, Butlin RK, Westram AM. 2025. Short INDELs and SNPs
as markers of evolutionary processes in hybrid zones. Journal of Evolutionary
Biology. 38(3), 367–378.
mla: Perini, Samuel, et al. “Short INDELs and SNPs as Markers of Evolutionary Processes
in Hybrid Zones.” Journal of Evolutionary Biology, vol. 38, no. 3, Oxford
University Press, 2025, pp. 367–78, doi:10.1093/jeb/voaf002.
short: S. Perini, K. Johannesson, R.K. Butlin, A.M. Westram, Journal of Evolutionary
Biology 38 (2025) 367–378.
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-09-30T11:19:56Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/jeb/voaf002
external_id:
isi:
- '001415267900001'
pmid:
- '39803902'
file:
- access_level: open_access
checksum: 01408e626a4131bfec5ffc70b0af9129
content_type: application/pdf
creator: dernst
date_created: 2025-04-03T11:53:06Z
date_updated: 2025-04-03T11:53:06Z
file_id: '19469'
file_name: 2025_JourEvolBiology_Perini.pdf
file_size: 12826085
relation: main_file
success: 1
file_date_updated: 2025-04-03T11:53:06Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 367-378
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Short INDELs and SNPs as markers of evolutionary processes in hybrid zones
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 38
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19439'
abstract:
- lang: eng
text: "White dwarfs (WDs) are the most abundant compact objects, and recent surveys
have suggested that over a third of WDs in accreting binaries host a strong (B
\ ≳ 1 MG) magnetic field. However, the origin and evolution of WD magnetism remain
under debate. Two WD pulsars, AR Sco and J191213.72–441045.1 (J1912), have been
found, which are non-accreting binaries hosting rapidly spinning (1.97 minutes
and 5.30 minutes, respectively) magnetic WDs. The WD in AR Sco is slowing down
on a (math formular) yr timescale. It is believed they will eventually become
polars, accreting systems in which a magnetic WD (B ≈ 10−240 MG) accretes from
a Roche lobe-filling donor spinning in sync with the orbit (≳78 minutes). Here,
we present multiwavelength data and analysis of Gaia22ayj, which outbursted in
2022 March. We find that Gaia22ayj is a magnetic accreting WD that is rapidly
spinning down (math formular\r\n yr) like WD pulsars, but shows clear evidence
of accretion, like polars. Strong linear polarization (40%) is detected in Gaia22ayj;
such high levels have only been seen in the WD pulsar AR Sco and demonstrate the
WD is magnetic. High speed photometry reveals a 9.36 minutes period accompanying
a high amplitude (∼2 mag) modulation. We associate this with a WD spin or spin–orbit
beat period, not an orbital period as was previously suggested. Fast (60 s) optical
spectroscopy reveals a broad \"hump,\" reminiscent of cyclotron emission in polars,
between 4000 and 8000 Å. We find an X-ray luminosity of (math formular) in the
0.3–8 keV energy range, while two very large array radio campaigns resulted in
a non-detection with a Fr < 15.8 μJy 3σ upper limit. The shared properties of
both WD pulsars and polars suggest that Gaia22ayj is a missing link between the
two classes of magnetic WD binaries."
acknowledgement: "We wish to dedicate this work to the memory of our colleague and
friend Tom Marsh. Tom's enthusiasm to work on this object and rapid efforts to facilitate
data collection truly made this project possible.\r\n\r\nA.C.R. acknowledges support
from an NSF Graduate Fellowship. A.C.R. thanks the LSST-DA Data Science Fellowship
Program, which is funded by LSST-DA, the Brinson Foundation, and the Moore Foundation;
his participation in the program has benefited this work. P.R.-G. acknowledges support
by the Spanish Agencia Estatal de Investigación del Ministerio de Ciencia e Innovación
(MCIN/AEI) and the European Regional Development Fund (ERDF) under grant PID2021–124879NB–I00.
M.R.S. is supported by FONDECYT (grant No. 1221059) and eRO-STEP (SA 2131/15-2 project
number 414059771). I.P. acknowledges support from a Royal Society University Research
Fellowship (URF/R1/231496). We thank the referee for feedback that improved the
clarity of this paper.\r\n\r\nBased on observations made with the Gran Telescopio
Canarias (GTC), installed at the Spanish Observatorio del Roque de los Muchachos
of the Instituto de Astrofìsica de Canarias, on the island of La Palma. Based on
observations obtained with the Samuel Oschin Telescope 48 inch and the 60 inch Telescope
at the Palomar Observatory as part of the ZTF project. ZTF is supported by the National
Science Foundation under grants No. AST-1440341 and AST-2034437 and a collaboration
including current partners Caltech, IPAC, the Weizmann Institute of Science, the
Oskar Klein Center at Stockholm University, the University of Maryland, Deutsches
Elektronen-Synchrotron and Humboldt University, the TANGO Consortium of Taiwan,
the University of Wisconsin at Milwaukee, Trinity College Dublin, Lawrence Livermore
National Laboratories, IN2P3, University of Warwick, Ruhr University Bochum, Northwestern
University and former partners the University of Washington, Los Alamos National
Laboratories, and Lawrence Berkeley National Laboratories. Operations are conducted
by COO, IPAC, and UW.\r\n\r\nSome of the data presented herein were obtained at
Keck Observatory, which is a private 501(c)3 non-profit organization operated as
a scientific partnership among the California Institute of Technology, the University
of California, and the National Aeronautics and Space Administration. The Observatory
was made possible by the generous financial support of the W. M. Keck Foundation.
The authors wish to recognize and acknowledge the very significant cultural role
and reverence that the summit of Maunakea has always had within the Native Hawaiian
community. We are most fortunate to have the opportunity to conduct observations
from this mountain. We are also grateful to the staff of Palomar Observatory for
their assistance in carrying out observations used in this work.\r\n\r\nPartly based
on observations made with the NOT, owned in collaboration by the University of Turku
and Aarhus University, and operated jointly by Aarhus University, the University
of Turku and the University of Oslo, representing Denmark, Finland and Norway, the
University of Iceland and Stockholm University at the Observatorio del Roque de
los Muchachos, La Palma, Spain, of the Instituto de Astrofisica de Canarias. The
data presented here were obtained with ALFOSC, which is provided by the Instituto
de Astrofisica de Andalucia (IAA) under a joint agreement with the University of
Copenhagen and NOT. The observation with the SALT was obtained under program 2021-2-LSP-001
(PI: D. Buckley). Polish participation in SALT is funded by grant No. MEiN nr 2021/WK/01.
D.A.H.B. acknowledges support from the National Research Foundation.\r\n\r\nThis
work presents results from the European Space Agency (ESA) space mission Gaia. Gaia
data are being processed by the Gaia Data Processing and Analysis Consortium (DPAC).
Funding for the DPAC is provided by national institutions, in particular the institutions
participating in the Gaia MultiLateral Agreement (MLA). The Gaia mission website
is https://www.cosmos.esa.int/gaia. The Gaia archive website is https://archives.esac.esa.int/gaia.
This work made use of data supplied by the UK Swift Science Data Centre at the University
of Leicester\r\n\r\nE.C.B. and J.K. acknowledge support from the DIRAC Institute
in the Department of Astronomy at the University of Washington. The DIRAC Institute
is supported through generous gifts from the Charles and Lisa Simonyi Fund for Arts
and Sciences, and the Washington Research Foundation."
article_number: '024202'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Antonio C.
full_name: Rodriguez, Antonio C.
last_name: Rodriguez
- first_name: Kareem
full_name: El-Badry, Kareem
last_name: El-Badry
- first_name: Pasi
full_name: Hakala, Pasi
last_name: Hakala
- first_name: Pablo
full_name: Rodríguez-Gil, Pablo
last_name: Rodríguez-Gil
- first_name: Tong
full_name: Bao, Tong
last_name: Bao
- first_name: Ilkham
full_name: Galiullin, Ilkham
last_name: Galiullin
- first_name: Jacob A.
full_name: Kurlander, Jacob A.
last_name: Kurlander
- first_name: Casey J.
full_name: Law, Casey J.
last_name: Law
- first_name: Ingrid
full_name: Pelisoli, Ingrid
last_name: Pelisoli
- first_name: Matthias R.
full_name: Schreiber, Matthias R.
last_name: Schreiber
- first_name: Kevin
full_name: Burdge, Kevin
last_name: Burdge
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Jan Van
full_name: Roestel, Jan Van
last_name: Roestel
- first_name: Paula
full_name: Szkody, Paula
last_name: Szkody
- first_name: Andrew J.
full_name: Drake, Andrew J.
last_name: Drake
- first_name: David A.H.
full_name: Buckley, David A.H.
last_name: Buckley
- first_name: Stephen B.
full_name: Potter, Stephen B.
last_name: Potter
- first_name: Boris
full_name: Gaensicke, Boris
last_name: Gaensicke
- first_name: Kaya
full_name: Mori, Kaya
last_name: Mori
- first_name: Eric C.
full_name: Bellm, Eric C.
last_name: Bellm
- first_name: Shrinivas R.
full_name: Kulkarni, Shrinivas R.
last_name: Kulkarni
- first_name: Thomas A.
full_name: Prince, Thomas A.
last_name: Prince
- first_name: Matthew
full_name: Graham, Matthew
last_name: Graham
- first_name: Mansi M.
full_name: Kasliwal, Mansi M.
last_name: Kasliwal
- first_name: Sam
full_name: Rose, Sam
last_name: Rose
- first_name: Yashvi
full_name: Sharma, Yashvi
last_name: Sharma
- first_name: Tomás
full_name: Ahumada, Tomás
last_name: Ahumada
- first_name: Shreya
full_name: Anand, Shreya
last_name: Anand
- first_name: Akke
full_name: Viitanen, Akke
last_name: Viitanen
- first_name: Avery
full_name: Wold, Avery
last_name: Wold
- first_name: Tracy X.
full_name: Chen, Tracy X.
last_name: Chen
- first_name: Reed
full_name: Riddle, Reed
last_name: Riddle
- first_name: Roger
full_name: Smith, Roger
last_name: Smith
citation:
ama: 'Rodriguez AC, El-Badry K, Hakala P, et al. A link between White Dwarf pulsars
and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj.
Publications of the Astronomical Society of the Pacific. 2025;137(2). doi:10.1088/1538-3873/adb0f1'
apa: 'Rodriguez, A. C., El-Badry, K., Hakala, P., Rodríguez-Gil, P., Bao, T., Galiullin,
I., … Smith, R. (2025). A link between White Dwarf pulsars and polars: Multiwavelength
observations of the 9.36-minute period variable Gaia22ayj. Publications of
the Astronomical Society of the Pacific. IOP Publishing. https://doi.org/10.1088/1538-3873/adb0f1'
chicago: 'Rodriguez, Antonio C., Kareem El-Badry, Pasi Hakala, Pablo Rodríguez-Gil,
Tong Bao, Ilkham Galiullin, Jacob A. Kurlander, et al. “A Link between White Dwarf
Pulsars and Polars: Multiwavelength Observations of the 9.36-Minute Period Variable
Gaia22ayj.” Publications of the Astronomical Society of the Pacific. IOP
Publishing, 2025. https://doi.org/10.1088/1538-3873/adb0f1.'
ieee: 'A. C. Rodriguez et al., “A link between White Dwarf pulsars and polars:
Multiwavelength observations of the 9.36-minute period variable Gaia22ayj,” Publications
of the Astronomical Society of the Pacific, vol. 137, no. 2. IOP Publishing,
2025.'
ista: 'Rodriguez AC, El-Badry K, Hakala P, Rodríguez-Gil P, Bao T, Galiullin I,
Kurlander JA, Law CJ, Pelisoli I, Schreiber MR, Burdge K, Caiazzo I, Roestel JV,
Szkody P, Drake AJ, Buckley DAH, Potter SB, Gaensicke B, Mori K, Bellm EC, Kulkarni
SR, Prince TA, Graham M, Kasliwal MM, Rose S, Sharma Y, Ahumada T, Anand S, Viitanen
A, Wold A, Chen TX, Riddle R, Smith R. 2025. A link between White Dwarf pulsars
and polars: Multiwavelength observations of the 9.36-minute period variable Gaia22ayj.
Publications of the Astronomical Society of the Pacific. 137(2), 024202.'
mla: 'Rodriguez, Antonio C., et al. “A Link between White Dwarf Pulsars and Polars:
Multiwavelength Observations of the 9.36-Minute Period Variable Gaia22ayj.” Publications
of the Astronomical Society of the Pacific, vol. 137, no. 2, 024202, IOP Publishing,
2025, doi:10.1088/1538-3873/adb0f1.'
short: A.C. Rodriguez, K. El-Badry, P. Hakala, P. Rodríguez-Gil, T. Bao, I. Galiullin,
J.A. Kurlander, C.J. Law, I. Pelisoli, M.R. Schreiber, K. Burdge, I. Caiazzo,
J.V. Roestel, P. Szkody, A.J. Drake, D.A.H. Buckley, S.B. Potter, B. Gaensicke,
K. Mori, E.C. Bellm, S.R. Kulkarni, T.A. Prince, M. Graham, M.M. Kasliwal, S.
Rose, Y. Sharma, T. Ahumada, S. Anand, A. Viitanen, A. Wold, T.X. Chen, R. Riddle,
R. Smith, Publications of the Astronomical Society of the Pacific 137 (2025).
date_created: 2025-03-23T23:01:26Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-09-30T11:15:10Z
day: '01'
ddc:
- '520'
department:
- _id: IlCa
doi: 10.1088/1538-3873/adb0f1
external_id:
arxiv:
- '2501.01490'
isi:
- '001427877700001'
file:
- access_level: open_access
checksum: 42d5aa504479c3fdf2a10165a9e3319f
content_type: application/pdf
creator: dernst
date_created: 2025-03-25T10:01:24Z
date_updated: 2025-03-25T10:01:24Z
file_id: '19455'
file_name: 2025_PubAstronomSocPacific_Rodriguez.pdf
file_size: 3291933
relation: main_file
success: 1
file_date_updated: 2025-03-25T10:01:24Z
has_accepted_license: '1'
intvolume: ' 137'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Publications of the Astronomical Society of the Pacific
publication_identifier:
issn:
- 0004-6280
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A link between White Dwarf pulsars and polars: Multiwavelength observations
of the 9.36-minute period variable Gaia22ayj'
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: 137
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19440'
abstract:
- lang: eng
text: Let μ(G) denote the minimum number of edges whose addition to G results in
a Hamiltonian graph, and let μ^(G) denote the minimum number of edges whose addition
to G results in a pancyclic graph. We study the distributions of μ(G),μ^(G) in
the context of binomial random graphs. Letting d=d(n):=n⋅p, we prove that there
exists a function f:R+→[0,1] of order f(d)=12de−d+e−d+O(d6e−3d) such that, if
G∼G(n,p) with 20≤d(n)≤0.4logn, then with high probability μ(G)=(1+o(1))⋅f(d)⋅n.
Let ni(G) denote the number of degree i vertices in G. A trivial lower bound on
μ(G) is given by the expression n0(G)+⌈12n1(G)⌉. In the denser regime of random
graphs, we show that if np−13logn−2loglogn→∞ and G∼G(n,p) then, with high probability,
μ(G)=n0(G)+⌈12n1(G)⌉. For completion to pancyclicity, we show that if G∼G(n,p)
and np≥20 then, with high probability, μ^(G)=μ(G). Finally, we present a polynomial
time algorithm such that, if G∼G(n,p) and np≥20, then, with high probability,
the algorithm returns a set of edges of size μ(G) whose addition to G results
in a pancyclic (and therefore also Hamiltonian) graph.
acknowledgement: The authors would like to express their thanks to the referees of
the article for their valuable input towards improving the presentation of our result.
This project has received funding from the European Union's Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.
article_number: e21286
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Yahav
full_name: Alon, Yahav
last_name: Alon
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
citation:
ama: Alon Y, Anastos M. The completion numbers of hamiltonicity and pancyclicity
in random graphs. Random Structures and Algorithms. 2025;66(2). doi:10.1002/rsa.21286
apa: Alon, Y., & Anastos, M. (2025). The completion numbers of hamiltonicity
and pancyclicity in random graphs. Random Structures and Algorithms. Wiley.
https://doi.org/10.1002/rsa.21286
chicago: Alon, Yahav, and Michael Anastos. “The Completion Numbers of Hamiltonicity
and Pancyclicity in Random Graphs.” Random Structures and Algorithms. Wiley,
2025. https://doi.org/10.1002/rsa.21286.
ieee: Y. Alon and M. Anastos, “The completion numbers of hamiltonicity and pancyclicity
in random graphs,” Random Structures and Algorithms, vol. 66, no. 2. Wiley,
2025.
ista: Alon Y, Anastos M. 2025. The completion numbers of hamiltonicity and pancyclicity
in random graphs. Random Structures and Algorithms. 66(2), e21286.
mla: Alon, Yahav, and Michael Anastos. “The Completion Numbers of Hamiltonicity
and Pancyclicity in Random Graphs.” Random Structures and Algorithms, vol.
66, no. 2, e21286, Wiley, 2025, doi:10.1002/rsa.21286.
short: Y. Alon, M. Anastos, Random Structures and Algorithms 66 (2025).
date_created: 2025-03-23T23:01:26Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-09-30T11:15:41Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1002/rsa.21286
ec_funded: 1
external_id:
arxiv:
- '2304.03710'
isi:
- '001420226800001'
file:
- access_level: open_access
checksum: 6067747e805fa356d560dc45f2a89918
content_type: application/pdf
creator: dernst
date_created: 2025-03-25T11:46:27Z
date_updated: 2025-03-25T11:46:27Z
file_id: '19459'
file_name: 2025_RandomStruc_Alon.pdf
file_size: 549236
relation: main_file
success: 1
file_date_updated: 2025-03-25T11:46:27Z
has_accepted_license: '1'
intvolume: ' 66'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
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: Random Structures and Algorithms
publication_identifier:
eissn:
- 1098-2418
issn:
- 1042-9832
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: The completion numbers of hamiltonicity and pancyclicity in random graphs
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 66
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19441'
abstract:
- lang: eng
text: Catalytic microswimmers convert the chemical energy from fuel into motion.
They sustain chemical gradients and fluid flows that propel them by phoresis.
This leads to unconventional behavior and collective dynamics, such as self-organization
into complex structures. Characterizing the nonequilibrium interactions of microswimmers
is crucial for advancing our understanding of active systems. However, this remains
a challenge owing to the importance of fluctuations at the microscale and the
difficulty in disentangling the different contributions to the interactions. Here,
we show a massive dependence of the nonequilibrium interactions on the shape of
catalytic microswimmers. We perform tracking experiments at high throughput to
map interactions between nanocolloidal tracers and dimeric microswimmers of various
aspect ratios. Our method leverages dual tracers with differing phoretic mobilities
to quantitatively disentangle phoretic motion from hydrodynamic advection. This
approach is validated through experiments on single chemically active sites and
on immobilized catalytic microswimmers. We further investigate the activity-driven
interactions of free microswimmers and directly measure their phoretic interactions.
When compared to standard models, our findings highlight the important role of
osmotic flows for microswimmers near surfaces and reveal an enhanced contribution
of hydrodynamic advection relative to phoretic motion as the size of the microswimmer
increases. Our study provides robust measurements of the nonequilibrium interactions
from catalytic microswimmers and lays the groundwork for a realistic description
of active systems.
acknowledgement: The authors thank M. Perrin and A. Allard for enlightening discussions.
This research was funded in whole or in part by the Austrian Science Fund (FWF)
[10.55776/P35206]. This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Sklodowska Curie grant agreement
No. 886024.
article_processing_charge: No
article_type: original
author:
- first_name: Celso
full_name: Carrasco, Celso
last_name: Carrasco
- first_name: Quentin
full_name: Martinet, Quentin
id: b37485a8-d343-11eb-a0e9-df8c484ef8ab
last_name: Martinet
orcid: 0000-0002-2916-6632
- first_name: Zaiyi
full_name: Shen, Zaiyi
last_name: Shen
- first_name: Juho
full_name: Lintuvuori, Juho
last_name: Lintuvuori
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Antoine
full_name: Aubret, Antoine
last_name: Aubret
citation:
ama: Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. Characterization
of nonequilibrium interactions of catalytic microswimmers using phoretically responsive
nanotracers. ACS Nano. 2025;19(11):11133-11145. doi:10.1021/acsnano.4c18078
apa: Carrasco, C., Martinet, Q., Shen, Z., Lintuvuori, J., Palacci, J. A., &
Aubret, A. (2025). Characterization of nonequilibrium interactions of catalytic
microswimmers using phoretically responsive nanotracers. ACS Nano. American
Chemical Society. https://doi.org/10.1021/acsnano.4c18078
chicago: Carrasco, Celso, Quentin Martinet, Zaiyi Shen, Juho Lintuvuori, Jérémie
A Palacci, and Antoine Aubret. “Characterization of Nonequilibrium Interactions
of Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” ACS
Nano. American Chemical Society, 2025. https://doi.org/10.1021/acsnano.4c18078.
ieee: C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J. A. Palacci, and A. Aubret,
“Characterization of nonequilibrium interactions of catalytic microswimmers using
phoretically responsive nanotracers,” ACS Nano, vol. 19, no. 11. American
Chemical Society, pp. 11133–11145, 2025.
ista: Carrasco C, Martinet Q, Shen Z, Lintuvuori J, Palacci JA, Aubret A. 2025.
Characterization of nonequilibrium interactions of catalytic microswimmers using
phoretically responsive nanotracers. ACS Nano. 19(11), 11133–11145.
mla: Carrasco, Celso, et al. “Characterization of Nonequilibrium Interactions of
Catalytic Microswimmers Using Phoretically Responsive Nanotracers.” ACS Nano,
vol. 19, no. 11, American Chemical Society, 2025, pp. 11133–45, doi:10.1021/acsnano.4c18078.
short: C. Carrasco, Q. Martinet, Z. Shen, J. Lintuvuori, J.A. Palacci, A. Aubret,
ACS Nano 19 (2025) 11133–11145.
date_created: 2025-03-23T23:01:26Z
date_published: 2025-03-11T00:00:00Z
date_updated: 2025-10-16T10:26:59Z
day: '11'
department:
- _id: JePa
doi: 10.1021/acsnano.4c18078
external_id:
isi:
- '001443359300001'
pmid:
- '40069094'
intvolume: ' 19'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.science/hal-04682818v2
month: '03'
oa: 1
oa_version: Submitted Version
page: 11133-11145
pmid: 1
project:
- _id: eb99c9bb-77a9-11ec-83b8-9f8cffa20a35
grant_number: P35206
name: Emergent Behavior in Spinning Active Matter
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Characterization of nonequilibrium interactions of catalytic microswimmers
using phoretically responsive nanotracers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19442'
abstract:
- lang: eng
text: "1. Climate change is expected to induce shifts in the composition, structure
and functioning of Arctic tundra ecosystems. Increases in the frequency and severity
of tundra fires have the potential to catalyse vegetation transitions with far-reaching
local, regional and global consequences.\r\n2. We propose that post-fire tundra
recovery, coupled with climate change, may not necessarily lead to pre-fire conditions.
Our hypothesis, based on surveys and literature, suggests two climate–fire driven
trajectories. One trajectory results in increased woody vegetation under low fire
frequency; the other results in grass dominance under high frequency.\r\n3. Future
research should address uncertainties regarding possible tundra ecosystem shifts
linked to fires, using methods that encompass greater temporal and spatial scales
than previously addressed. More case studies, especially in underrepresented regions
and ecosystem types, are essential to broaden the empirical basis for forecasts
and potential fire management strategies.\r\n4. Synthesis. Our review synthesises
current knowledge on post-fire vegetation trajectories in Arctic tundra ecosystems,
highlighting potential transitions and alternative ecosystem states and their
implications. We discuss challenges in defining and predicting these trajectories
as well as future directions."
acknowledgement: We would like to express our sincere gratitude to all the data providers
who carried out fieldwork in different regions of the Arctic and published their
data, which we used for our meta-analysis. We recognise the hard work and dedication
of these individuals, without whom this paper would not have been possible. We are
grateful to the editor and the anonymous reviewer for their time and valuable feedback
on this manuscript. We particularly appreciate the detailed and constructive comments
provided by reviewer Mara Baudena, which significantly strengthened our work. We
also acknowledge the Indigenous peoples and rural communities of the Arctic, whose
traditional knowledge, rights, and interests are integral to the stewardship and
study of these ecosystems. This work was funded in part by the U.S. National Aeronautics
and Space Administration (NASA) grant 80NSSC22K1256 (GVF). Open Access funding enabled
and organized by Projekt DEAL.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Ramona Julia
full_name: Heim, Ramona Julia
last_name: Heim
- first_name: Adrian V.
full_name: Rocha, Adrian V.
last_name: Rocha
- first_name: Vitalii
full_name: Zemlianskii, Vitalii
last_name: Zemlianskii
- first_name: Kirsten
full_name: Barrett, Kirsten
last_name: Barrett
- first_name: Helga
full_name: Bültmann, Helga
last_name: Bültmann
- first_name: Amy
full_name: Breen, Amy
last_name: Breen
- first_name: Gerald Verner
full_name: Frost, Gerald Verner
last_name: Frost
- first_name: Teresa Nettleton
full_name: Hollingsworth, Teresa Nettleton
last_name: Hollingsworth
- first_name: Randi
full_name: Jandt, Randi
last_name: Jandt
- first_name: Maria
full_name: Kozlova, Maria
last_name: Kozlova
- first_name: Anastasiya
full_name: Kurka, Anastasiya
last_name: Kurka
- first_name: Mark Torre
full_name: Jorgenson, Mark Torre
last_name: Jorgenson
- first_name: Simon M.
full_name: Landhäusser, Simon M.
last_name: Landhäusser
- first_name: Michael Mark
full_name: Loranty, Michael Mark
last_name: Loranty
- first_name: Eric A.
full_name: Miller, Eric A.
last_name: Miller
- first_name: Kenji
full_name: Narita, Kenji
last_name: Narita
- first_name: Evgeniya
full_name: Pravdolyubova, Evgeniya
id: 0b30719b-13f0-11ed-ab2a-94498bc6a278
last_name: Pravdolyubova
- first_name: Norbert
full_name: Hölzel, Norbert
last_name: Hölzel
- first_name: Gabriela
full_name: Schaepman-Strub, Gabriela
last_name: Schaepman-Strub
citation:
ama: Heim RJ, Rocha AV, Zemlianskii V, et al. Arctic tundra ecosystems under fire—Alternative
ecosystem states in a changing climate? Journal of Ecology. 2025;113(5):1042-1056.
doi:10.1111/1365-2745.70022
apa: Heim, R. J., Rocha, A. V., Zemlianskii, V., Barrett, K., Bültmann, H., Breen,
A., … Schaepman-Strub, G. (2025). Arctic tundra ecosystems under fire—Alternative
ecosystem states in a changing climate? Journal of Ecology. Wiley. https://doi.org/10.1111/1365-2745.70022
chicago: Heim, Ramona Julia, Adrian V. Rocha, Vitalii Zemlianskii, Kirsten Barrett,
Helga Bültmann, Amy Breen, Gerald Verner Frost, et al. “Arctic Tundra Ecosystems
under Fire—Alternative Ecosystem States in a Changing Climate?” Journal of
Ecology. Wiley, 2025. https://doi.org/10.1111/1365-2745.70022.
ieee: R. J. Heim et al., “Arctic tundra ecosystems under fire—Alternative
ecosystem states in a changing climate?,” Journal of Ecology, vol. 113,
no. 5. Wiley, pp. 1042–1056, 2025.
ista: Heim RJ, Rocha AV, Zemlianskii V, Barrett K, Bültmann H, Breen A, Frost GV,
Hollingsworth TN, Jandt R, Kozlova M, Kurka A, Jorgenson MT, Landhäusser SM, Loranty
MM, Miller EA, Narita K, Pravdolyubova E, Hölzel N, Schaepman-Strub G. 2025. Arctic
tundra ecosystems under fire—Alternative ecosystem states in a changing climate?
Journal of Ecology. 113(5), 1042–1056.
mla: Heim, Ramona Julia, et al. “Arctic Tundra Ecosystems under Fire—Alternative
Ecosystem States in a Changing Climate?” Journal of Ecology, vol. 113,
no. 5, Wiley, 2025, pp. 1042–56, doi:10.1111/1365-2745.70022.
short: R.J. Heim, A.V. Rocha, V. Zemlianskii, K. Barrett, H. Bültmann, A. Breen,
G.V. Frost, T.N. Hollingsworth, R. Jandt, M. Kozlova, A. Kurka, M.T. Jorgenson,
S.M. Landhäusser, M.M. Loranty, E.A. Miller, K. Narita, E. Pravdolyubova, N. Hölzel,
G. Schaepman-Strub, Journal of Ecology 113 (2025) 1042–1056.
date_created: 2025-03-23T23:01:27Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2025-12-30T08:09:47Z
day: '01'
ddc:
- '550'
- '570'
department:
- _id: NiBa
doi: 10.1111/1365-2745.70022
external_id:
isi:
- '001443422900001'
file:
- access_level: open_access
checksum: e2785ae265e211b4dc7fc9c5b7744948
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T08:08:18Z
date_updated: 2025-12-30T08:08:18Z
file_id: '20890'
file_name: 2025_JournEcology_Heim.pdf
file_size: 2662766
relation: main_file
success: 1
file_date_updated: 2025-12-30T08:08:18Z
has_accepted_license: '1'
intvolume: ' 113'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1042-1056
publication: Journal of Ecology
publication_identifier:
eissn:
- 1365-2745
issn:
- 0022-0477
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing
climate?
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: 113
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19443'
abstract:
- lang: eng
text: In cryo-electron microscopy, accurate particle localization and classification
are imperative. Recent deep learning solutions, though successful, require extensive
training datasets. The protracted generation time of physics-based models, often
employed to produce these datasets, limits their broad applicability. We introduce
FakET, a method based on neural style transfer, capable of simulating the forward
operator of any cryo transmission electron microscope. It can be used to adapt
a synthetic training dataset according to reference data producing high-quality
simulated micrographs or tilt-series. To assess the quality of our generated data,
we used it to train a state-of-the-art localization and classification architecture
and compared its performance with a counterpart trained on benchmark data. Remarkably,
our technique matches the performance, boosts data generation speed 750x, uses
33x less memory, and scales well to typical transmission electron microscope detector
sizes. It leverages GPU acceleration and parallel processing. The source code
is available at https://github.com/paloha/faket/.
acknowledgement: The IMP and D.H. are generously funded by Boehringer Ingelheim. We
thank Julius Berner from the Mathematical Data Science group @ UniVie, Ilja Gubins
and Marten Chaillet from the SHREC team, and the members of the Haselbach lab for
helpful discussions.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Pavol
full_name: Harar, Pavol
id: e03d953a-6e8c-11ef-99e4-f0717d385cd5
last_name: Harar
orcid: 0000-0001-5206-1794
- first_name: Lukas
full_name: Herrmann, Lukas
last_name: Herrmann
- first_name: Philipp
full_name: Grohs, Philipp
last_name: Grohs
- first_name: David
full_name: Haselbach, David
last_name: Haselbach
citation:
ama: 'Harar P, Herrmann L, Grohs P, Haselbach D. FakET: Simulating cryo-electron
tomograms with neural style transfer. Structure. 2025;33(4):820-827.e4.
doi:10.1016/j.str.2025.01.020'
apa: 'Harar, P., Herrmann, L., Grohs, P., & Haselbach, D. (2025). FakET: Simulating
cryo-electron tomograms with neural style transfer. Structure. Elsevier.
https://doi.org/10.1016/j.str.2025.01.020'
chicago: 'Harar, Pavol, Lukas Herrmann, Philipp Grohs, and David Haselbach. “FakET:
Simulating Cryo-Electron Tomograms with Neural Style Transfer.” Structure.
Elsevier, 2025. https://doi.org/10.1016/j.str.2025.01.020.'
ieee: 'P. Harar, L. Herrmann, P. Grohs, and D. Haselbach, “FakET: Simulating cryo-electron
tomograms with neural style transfer,” Structure, vol. 33, no. 4. Elsevier,
p. 820–827.e4, 2025.'
ista: 'Harar P, Herrmann L, Grohs P, Haselbach D. 2025. FakET: Simulating cryo-electron
tomograms with neural style transfer. Structure. 33(4), 820–827.e4.'
mla: 'Harar, Pavol, et al. “FakET: Simulating Cryo-Electron Tomograms with Neural
Style Transfer.” Structure, vol. 33, no. 4, Elsevier, 2025, p. 820–827.e4,
doi:10.1016/j.str.2025.01.020.'
short: P. Harar, L. Herrmann, P. Grohs, D. Haselbach, Structure 33 (2025) 820–827.e4.
corr_author: '1'
date_created: 2025-03-23T23:01:27Z
date_published: 2025-04-03T00:00:00Z
date_updated: 2025-09-30T11:13:02Z
day: '03'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.str.2025.01.020
external_id:
isi:
- '001463196100001'
pmid:
- '39947174'
file:
- access_level: open_access
checksum: f346bc357a66a88cca3d0eb95793fb73
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T12:15:13Z
date_updated: 2025-08-05T12:15:13Z
file_id: '20130'
file_name: 2025_Structure_Harar.pdf
file_size: 4367530
relation: main_file
success: 1
file_date_updated: 2025-08-05T12:15:13Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 820-827.e4
pmid: 1
publication: Structure
publication_identifier:
eissn:
- 1878-4186
issn:
- 0969-2126
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/paloha/faket/
scopus_import: '1'
status: public
title: 'FakET: Simulating cryo-electron tomograms with neural style transfer'
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: 33
year: '2025'
...
---
OA_type: closed access
_id: '19444'
abstract:
- lang: eng
text: As the field of neural organoids and assembloids expands, there is an emergent
need for guidance and advice on designing, conducting and reporting experiments
to increase the reproducibility and utility of these models. In this Perspective,
we present a framework for the experimental process that encompasses ensuring
the quality and integrity of human pluripotent stem cells, characterizing and
manipulating neural cells in vitro, transplantation techniques and considerations
for modelling human development, evolution and disease. As with all scientific
endeavours, we advocate for rigorous experimental designs tailored to explicit
scientific questions as well as transparent methodologies and data sharing to
provide useful knowledge for current research practices and for developing regulatory
standards.
acknowledgement: The authors thank members of their laboratories who provided feedback
on earlier versions of this manuscript, including A. Jourdon, V. Mariano, T. L.
Li, N. Caporale, E. Villa and M. Sutcliffe.
article_processing_charge: No
article_type: original
author:
- first_name: Sergiu P.
full_name: Pașca, Sergiu P.
last_name: Pașca
- first_name: Paola
full_name: Arlotta, Paola
last_name: Arlotta
- first_name: Helen S.
full_name: Bateup, Helen S.
last_name: Bateup
- first_name: J. Gray
full_name: Camp, J. Gray
last_name: Camp
- first_name: Silvia
full_name: Cappello, Silvia
last_name: Cappello
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
- first_name: Jürgen A.
full_name: Knoblich, Jürgen A.
last_name: Knoblich
- first_name: Arnold R.
full_name: Kriegstein, Arnold R.
last_name: Kriegstein
- first_name: Madeline A.
full_name: Lancaster, Madeline A.
last_name: Lancaster
- first_name: Guo Li
full_name: Ming, Guo Li
last_name: Ming
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Hideyuki
full_name: Okano, Hideyuki
last_name: Okano
- first_name: Malin
full_name: Parmar, Malin
last_name: Parmar
- first_name: In Hyun
full_name: Park, In Hyun
last_name: Park
- first_name: Orly
full_name: Reiner, Orly
last_name: Reiner
- first_name: Hongjun
full_name: Song, Hongjun
last_name: Song
- first_name: Lorenz
full_name: Studer, Lorenz
last_name: Studer
- first_name: Jun
full_name: Takahashi, Jun
last_name: Takahashi
- first_name: Sally
full_name: Temple, Sally
last_name: Temple
- first_name: Giuseppe
full_name: Testa, Giuseppe
last_name: Testa
- first_name: Barbara
full_name: Treutlein, Barbara
last_name: Treutlein
- first_name: Flora M.
full_name: Vaccarino, Flora M.
last_name: Vaccarino
- first_name: Pierre
full_name: Vanderhaeghen, Pierre
last_name: Vanderhaeghen
- first_name: Tracy
full_name: Young-Pearse, Tracy
last_name: Young-Pearse
citation:
ama: Pașca SP, Arlotta P, Bateup HS, et al. A framework for neural organoids, assembloids
and transplantation studies. Nature. 2025;639(8054):315-320. doi:10.1038/s41586-024-08487-6
apa: Pașca, S. P., Arlotta, P., Bateup, H. S., Camp, J. G., Cappello, S., Gage,
F. H., … Young-Pearse, T. (2025). A framework for neural organoids, assembloids
and transplantation studies. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-08487-6
chicago: Pașca, Sergiu P., Paola Arlotta, Helen S. Bateup, J. Gray Camp, Silvia
Cappello, Fred H. Gage, Jürgen A. Knoblich, et al. “A Framework for Neural Organoids,
Assembloids and Transplantation Studies.” Nature. Springer Nature, 2025.
https://doi.org/10.1038/s41586-024-08487-6.
ieee: S. P. Pașca et al., “A framework for neural organoids, assembloids
and transplantation studies,” Nature, vol. 639, no. 8054. Springer Nature,
pp. 315–320, 2025.
ista: Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA,
Kriegstein AR, Lancaster MA, Ming GL, Novarino G, Okano H, Parmar M, Park IH,
Reiner O, Song H, Studer L, Takahashi J, Temple S, Testa G, Treutlein B, Vaccarino
FM, Vanderhaeghen P, Young-Pearse T. 2025. A framework for neural organoids, assembloids
and transplantation studies. Nature. 639(8054), 315–320.
mla: Pașca, Sergiu P., et al. “A Framework for Neural Organoids, Assembloids and
Transplantation Studies.” Nature, vol. 639, no. 8054, Springer Nature,
2025, pp. 315–20, doi:10.1038/s41586-024-08487-6.
short: S.P. Pașca, P. Arlotta, H.S. Bateup, J.G. Camp, S. Cappello, F.H. Gage, J.A.
Knoblich, A.R. Kriegstein, M.A. Lancaster, G.L. Ming, G. Novarino, H. Okano, M.
Parmar, I.H. Park, O. Reiner, H. Song, L. Studer, J. Takahashi, S. Temple, G.
Testa, B. Treutlein, F.M. Vaccarino, P. Vanderhaeghen, T. Young-Pearse, Nature
639 (2025) 315–320.
date_created: 2025-03-23T23:01:27Z
date_published: 2025-03-13T00:00:00Z
date_updated: 2025-09-30T11:13:47Z
day: '13'
department:
- _id: GaNo
doi: 10.1038/s41586-024-08487-6
external_id:
isi:
- '001437461900001'
pmid:
- '39653126'
intvolume: ' 639'
isi: 1
issue: '8054'
language:
- iso: eng
month: '03'
oa_version: None
page: 315-320
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A framework for neural organoids, assembloids and transplantation studies
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 639
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '19445'
abstract:
- lang: eng
text: "In reconfiguration, we are given two solutions to a graph problem, such as
Vertex Cover or Dominating Set, with each solution represented by a placement
of tokens on vertices of the graph. Our task is to reconfigure one into the other
using small steps while ensuring the intermediate configurations of tokens are
also valid solutions. The two commonly studied settings are Token Jumping and
Token Sliding, which allows moving a single token to an arbitrary or an adjacent
vertex, respectively.\r\n\r\nWe introduce new rules that generalize Token Jumping,
parameterized by the number of tokens allowed to move at once and by the maximum
distance of each move. Our main contribution is identifying minimal rules that
allow reconfiguring any possible given solution into any other for Independent
Set, Vertex Cover, and Dominating Set. For each minimal rule, we also provide
an efficient algorithm that finds a corresponding reconfiguration sequence.\r\n\r\nWe
further focus on the rule that allows each token to move to an adjacent vertex
in a single step. This natural variant turns out to be the minimal rule that guarantees
reconfigurability for Vertex Cover. We determine the computational complexity
of deciding whether a (shortest) reconfiguration sequence exists under this rule
for the three studied problems. While reachability for Vertex Cover is shown to
be in P, finding a shortest sequence is shown to be NP-complete. For Independent
Set and Dominating Set, even reachability is shown to be PSPACE-complete."
acknowledgement: J. M. Křišťan acknowledges the support of the Czech Science Foundation
Grant No. 24-12046S. This work was supported by the Grant Agency of the Czech Technical
University in Prague, grant No. SGS23/205/OHK3/3T/18. J. Svoboda acknowledges the
support of the ERC CoG 863818 (ForM-SMArt) grant.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Jan Matyáš
full_name: Křišťan, Jan Matyáš
last_name: Křišťan
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
citation:
ama: 'Křišťan JM, Svoboda J. Reconfiguration using generalized token jumping. In:
19th International Conference and Workshops on Algorithms and Computation.
Vol 15411. Springer Nature; 2025:244-265. doi:10.1007/978-981-96-2845-2_16'
apa: 'Křišťan, J. M., & Svoboda, J. (2025). Reconfiguration using generalized
token jumping. In 19th International Conference and Workshops on Algorithms
and Computation (Vol. 15411, pp. 244–265). Chengdu, China: Springer Nature.
https://doi.org/10.1007/978-981-96-2845-2_16'
chicago: Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized
Token Jumping.” In 19th International Conference and Workshops on Algorithms
and Computation, 15411:244–65. Springer Nature, 2025. https://doi.org/10.1007/978-981-96-2845-2_16.
ieee: J. M. Křišťan and J. Svoboda, “Reconfiguration using generalized token jumping,”
in 19th International Conference and Workshops on Algorithms and Computation,
Chengdu, China, 2025, vol. 15411, pp. 244–265.
ista: 'Křišťan JM, Svoboda J. 2025. Reconfiguration using generalized token jumping.
19th International Conference and Workshops on Algorithms and Computation. WALCOM:
International Conference and Workshops on Algorithms and Computation, LNCS, vol.
15411, 244–265.'
mla: Křišťan, Jan Matyáš, and Jakub Svoboda. “Reconfiguration Using Generalized
Token Jumping.” 19th International Conference and Workshops on Algorithms and
Computation, vol. 15411, Springer Nature, 2025, pp. 244–65, doi:10.1007/978-981-96-2845-2_16.
short: J.M. Křišťan, J. Svoboda, in:, 19th International Conference and Workshops
on Algorithms and Computation, Springer Nature, 2025, pp. 244–265.
conference:
end_date: 2025-03-02
location: Chengdu, China
name: 'WALCOM: International Conference and Workshops on Algorithms and Computation'
start_date: 2025-02-28
date_created: 2025-03-23T23:01:27Z
date_published: 2025-02-20T00:00:00Z
date_updated: 2025-09-30T11:14:33Z
day: '20'
department:
- _id: KrCh
doi: 10.1007/978-981-96-2845-2_16
ec_funded: 1
external_id:
arxiv:
- '2411.12582'
isi:
- '001537885900016'
intvolume: ' 15411'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2411.12582
month: '02'
oa: 1
oa_version: Preprint
page: 244-265
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 19th International Conference and Workshops on Algorithms and Computation
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9789819628445'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconfiguration using generalized token jumping
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15411
year: '2025'
...