---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18630'
abstract:
- lang: eng
text: 'Markov chains are the de facto finite-state model for stochastic dynamical
systems, and Markov decision processes (MDPs) extend Markov chains by incorporating
non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization
criterion is the maximal expected total reward where the MDP stops after T steps,
which can be computed by a simple dynamic programming algorithm. We consider a
natural generalization of the problem where the stopping times can be chosen according
to a probability distribution, such that the expected stopping time is T, to optimize
the expected total reward. Quite surprisingly we establish inter-reducibility
of the expected stopping-time problem for Markov chains with the Positivity problem
(which is related to the well-known Skolem problem), for which establishing either
decidability or undecidability would be a major breakthrough. Given the hardness
of the exact problem, we consider the approximate version of the problem: we show
that it can be solved in exponential time for Markov chains and in exponential
space for MDPs.'
acknowledgement: The authors are grateful to the anonymous reviewers of LICS 2021
and of a previous version of this paper for insightful comments that helped improving
the presentation. The research presented in this paper was partially supported by
the grant ERC CoG 863818 (ForM-SMArt).
alternative_title:
- LMCS
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: Chatterjee K, Doyen L. Stochastic processes with expected stopping time. Logical
Methods in Computer Science. 2024;20(4):11:1-11:34. doi:10.46298/lmcs-20(4:11)2024
apa: Chatterjee, K., & Doyen, L. (2024). Stochastic processes with expected
stopping time. Logical Methods in Computer Science. EPI Sciences. https://doi.org/10.46298/lmcs-20(4:11)2024
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected
Stopping Time.” Logical Methods in Computer Science. EPI Sciences, 2024.
https://doi.org/10.46298/lmcs-20(4:11)2024.
ieee: K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,”
Logical Methods in Computer Science, vol. 20, no. 4. EPI Sciences, p. 11:1-11:34,
2024.
ista: Chatterjee K, Doyen L. 2024. Stochastic processes with expected stopping time.
Logical Methods in Computer Science. 20(4), 11:1-11:34.
mla: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected
Stopping Time.” Logical Methods in Computer Science, vol. 20, no. 4, EPI
Sciences, 2024, p. 11:1-11:34, doi:10.46298/lmcs-20(4:11)2024.
short: K. Chatterjee, L. Doyen, Logical Methods in Computer Science 20 (2024) 11:1-11:34.
corr_author: '1'
date_created: 2024-12-08T23:01:56Z
date_published: 2024-11-12T00:00:00Z
date_updated: 2026-08-12T06:39:26Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.46298/lmcs-20(4:11)2024
ec_funded: 1
external_id:
arxiv:
- '2104.07278'
isi:
- '001367316400002'
file:
- access_level: open_access
checksum: b3315c74ce18ce0a30ed33d8c9972992
content_type: application/pdf
creator: dernst
date_created: 2024-12-09T08:38:48Z
date_updated: 2024-12-09T08:38:48Z
file_id: '18633'
file_name: 2024_LMCS_Chatterjee.pdf
file_size: 416814
relation: main_file
success: 1
file_date_updated: 2024-12-09T08:38:48Z
fulldoi: https://doi.org/10.46298/lmcs-20(4:11)2024
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 11:1-11:34
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Logical Methods in Computer Science
publication_identifier:
eissn:
- 1860-5974
publication_status: published
publisher: EPI Sciences
quality_controlled: '1'
related_material:
record:
- id: '10004'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Stochastic processes with expected stopping time
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: 20
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18923'
abstract:
- lang: eng
text: 'Combinatorial optimization is a challenging problem applicable in a wide
range of fields from logistics to finance. Recently, quantum computing has been
used to attempt to solve these problems using a range of algorithms, including
parameterized quantum circuits, adiabatic protocols, and quantum annealing. These
solutions typically have several challenges: 1) there is little to no performance
gain over classical methods; 2) not all constraints and objectives may be efficiently
encoded in the quantum ansatz; and 3) the solution domain of the objective function
may not be the same as the bit strings of measurement outcomes. This work presents
“nonnative hybrid algorithms”: a framework to overcome these challenges by integrating
quantum and classical resources with a hybrid approach. By designing nonnative
quantum variational anosatzes that inherit some but not all problem structure,
measurement outcomes from the quantum computer can act as a resource to be used
by classical routines to indirectly compute optimal solutions, partially overcoming
the challenges of contemporary quantum optimization approaches. These methods
are demonstrated using a publicly available neutral-atom quantum computer on two
simple problems of Max k-Cut and maximum independent set. We find improvements
in solution quality when comparing the hybrid algorithm to its “no quantum” version,
a demonstration of a “comparative advantage.”'
acknowledgement: "The authors would like to thank Alexander Keesling, Maddie Cain,
Nate Gemelke, and Phillip Weinberg for helpful discussions and Danylo Lykov who
had early contributions to this work.\r\n10.13039/100000185-Defense Advanced Research
Projects Agency Noisy Intermediate-Scale Quantum Devices (Grant Number: W911NF2010021),
DARPA Small Business Technology Transfer program (Grant Number: 140D0422C0035)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jonathan
full_name: Wurtz, Jonathan
last_name: Wurtz
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Sheng-Tao
full_name: Wang, Sheng-Tao
last_name: Wang
citation:
ama: Wurtz J, Sack S, Wang S-T. Solving nonnative combinatorial optimization problems
using hybrid quantum–classical algorithms. IEEE Transactions on Quantum Engineering.
2024;5:1-14. doi:10.1109/tqe.2024.3443660
apa: Wurtz, J., Sack, S., & Wang, S.-T. (2024). Solving nonnative combinatorial
optimization problems using hybrid quantum–classical algorithms. IEEE Transactions
on Quantum Engineering. IEEE. https://doi.org/10.1109/tqe.2024.3443660
chicago: Wurtz, Jonathan, Stefan Sack, and Sheng-Tao Wang. “Solving Nonnative Combinatorial
Optimization Problems Using Hybrid Quantum–Classical Algorithms.” IEEE Transactions
on Quantum Engineering. IEEE, 2024. https://doi.org/10.1109/tqe.2024.3443660.
ieee: J. Wurtz, S. Sack, and S.-T. Wang, “Solving nonnative combinatorial optimization
problems using hybrid quantum–classical algorithms,” IEEE Transactions on Quantum
Engineering, vol. 5. IEEE, pp. 1–14, 2024.
ista: Wurtz J, Sack S, Wang S-T. 2024. Solving nonnative combinatorial optimization
problems using hybrid quantum–classical algorithms. IEEE Transactions on Quantum
Engineering. 5, 1–14.
mla: Wurtz, Jonathan, et al. “Solving Nonnative Combinatorial Optimization Problems
Using Hybrid Quantum–Classical Algorithms.” IEEE Transactions on Quantum Engineering,
vol. 5, IEEE, 2024, pp. 1–14, doi:10.1109/tqe.2024.3443660.
short: J. Wurtz, S. Sack, S.-T. Wang, IEEE Transactions on Quantum Engineering 5
(2024) 1–14.
das_tickbox: '1'
date_created: 2025-01-27T15:00:44Z
date_published: 2024-08-14T00:00:00Z
date_updated: 2026-08-12T06:42:26Z
day: '14'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1109/tqe.2024.3443660
file:
- access_level: open_access
checksum: 19b84e35cba05bde72bfe7e0b54c3e6c
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T15:03:09Z
date_updated: 2025-01-27T15:03:09Z
file_id: '18924'
file_name: 2024_IEEEQuantumComputing_Wurtz.pdf
file_size: 1753095
relation: main_file
success: 1
file_date_updated: 2025-01-27T15:03:09Z
fulldoi: https://doi.org/10.1109/tqe.2024.3443660
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1-14
publication: IEEE Transactions on Quantum Engineering
publication_identifier:
issn:
- 2689-1808
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solving nonnative combinatorial optimization problems using hybrid quantum–classical
algorithms
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: 5
year: '2024'
...
---
_id: '17481'
abstract:
- lang: eng
text: "Phase-field models such as the Allen–Cahn equation may give rise to the formation
and evolution of geometric shapes, a phenomenon that may be analyzed rigorously
in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen–Cahn
equation with a potential with N≥3 distinct minima has been conjectured to describe
the evolution of branched interfaces by multiphase mean curvature flow. In the
present work, we give a rigorous proof for this statement in two and three ambient
dimensions and for a suitable class of potentials: as long as a strong solution
to multiphase mean curvature flow exists, solutions to the vectorial Allen–Cahn
equation with well-prepared initial data converge towards multiphase mean curvature
flow in the limit of vanishing interface width parameter ε↘0. We even establish
the rate of convergence O(ε \r\n1/2\r\n ). Our approach is based on the gradient-flow
structure of the Allen–Cahn equation and its limiting motion: building on the
recent concept of “gradient-flow calibrations” for multiphase mean curvature flow,
we introduce a notion of relative entropy for the vectorial Allen–Cahn equation
with multi-well potential. This enables us to overcome the limitations of other
approaches, e.g. avoiding the need for a stability analysis of the Allen–Cahn
operator or additional convergence hypotheses for the energy at positive times."
acknowledgement: "The authors thank Sebastian Hensel for useful and helpful commentson
the first draft of this work.\r\nThis project has received funding from the European
Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation
programme (grant\r\nagreement no. 948819."
article_processing_charge: Yes
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
- first_name: Alice
full_name: Marveggio, Alice
id: 25647992-AA84-11E9-9D75-8427E6697425
last_name: Marveggio
citation:
ama: Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen–Cahn
equation towards multiphase mean curvature flow. Annales de l’Institut Henri
Poincaré C. 2024;41(5):1117-1178. doi:10.4171/AIHPC/109
apa: Fischer, J. L., & Marveggio, A. (2024). Quantitative convergence of the
vectorial Allen–Cahn equation towards multiphase mean curvature flow. Annales
de l’Institut Henri Poincaré C. EMS Press. https://doi.org/10.4171/AIHPC/109
chicago: Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the
Vectorial Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” Annales
de l’Institut Henri Poincaré C. EMS Press, 2024. https://doi.org/10.4171/AIHPC/109.
ieee: J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial
Allen–Cahn equation towards multiphase mean curvature flow,” Annales de l’Institut
Henri Poincaré C, vol. 41, no. 5. EMS Press, pp. 1117–1178, 2024.
ista: Fischer JL, Marveggio A. 2024. Quantitative convergence of the vectorial Allen–Cahn
equation towards multiphase mean curvature flow. Annales de l’Institut Henri Poincaré
C. 41(5), 1117–1178.
mla: Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial
Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” Annales de l’Institut
Henri Poincaré C, vol. 41, no. 5, EMS Press, 2024, pp. 1117–78, doi:10.4171/AIHPC/109.
short: J.L. Fischer, A. Marveggio, Annales de l’Institut Henri Poincaré C 41 (2024)
1117–1178.
corr_author: '1'
date_created: 2024-09-01T22:01:09Z
date_published: 2024-01-24T00:00:00Z
date_updated: 2026-08-12T09:15:49Z
day: '24'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.4171/AIHPC/109
ec_funded: 1
external_id:
isi:
- '001293853900003'
file:
- access_level: open_access
checksum: b5ad02d9abd5b4701269cd1ad0a1cc8f
content_type: application/pdf
creator: dernst
date_created: 2024-09-09T07:46:42Z
date_updated: 2024-09-09T07:46:42Z
file_id: '17923'
file_name: 2024_AnnInstHPoincare_Fischer.pdf
file_size: 1348896
relation: main_file
success: 1
file_date_updated: 2024-09-09T07:46:42Z
fulldoi: https://doi.org/10.4171/AIHPC/109
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '5'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1117-1178
project:
- _id: 0aa76401-070f-11eb-9043-b5bb049fa26d
call_identifier: H2020
grant_number: '948819'
name: Bridging Scales in Random Materials
publication: Annales de l'Institut Henri Poincaré C
publication_identifier:
eissn:
- 1873-1430
issn:
- 0294-1449
publication_status: published
publisher: EMS Press
quality_controlled: '1'
related_material:
record:
- id: '14597'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase
mean curvature flow
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: 41
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '22234'
abstract:
- lang: eng
text: Lists of nontrivial integral points on some (families of) cubic surfaces.
(2024-07-18)
article_processing_charge: No
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Andrew
full_name: Sutherland, Andrew
last_name: Sutherland
citation:
ama: 'Browning TD, Sutherland A. Data and code for: Integral points on cubic surfaces:
heuristics and numerics. 2024. doi:10.25625/4FLFH8'
apa: 'Browning, T. D., & Sutherland, A. (2024). Data and code for: Integral
points on cubic surfaces: heuristics and numerics. Göttingen Research Online Data.
https://doi.org/10.25625/4FLFH8'
chicago: 'Browning, Timothy D, and Andrew Sutherland. “Data and Code for: Integral
Points on Cubic Surfaces: Heuristics and Numerics.” Göttingen Research Online
Data, 2024. https://doi.org/10.25625/4FLFH8.'
ieee: 'T. D. Browning and A. Sutherland, “Data and code for: Integral points on
cubic surfaces: heuristics and numerics.” Göttingen Research Online Data, 2024.'
ista: 'Browning TD, Sutherland A. 2024. Data and code for: Integral points on cubic
surfaces: heuristics and numerics, Göttingen Research Online Data, 10.25625/4FLFH8.'
mla: 'Browning, Timothy D., and Andrew Sutherland. Data and Code for: Integral
Points on Cubic Surfaces: Heuristics and Numerics. Göttingen Research Online
Data, 2024, doi:10.25625/4FLFH8.'
short: T.D. Browning, A. Sutherland, (2024).
contributor:
- first_name: Florian Alexander
id: 560601DA-8D36-11E9-A136-7AC1E5697425
last_name: Wilsch
orcid: 0000-0001-7302-8256
corr_author: '1'
date_created: 2026-07-02T10:38:53Z
date_published: 2024-07-22T00:00:00Z
date_updated: 2026-08-12T12:15:33Z
day: '22'
ddc:
- '500'
department:
- _id: TiBr
doi: 10.25625/4FLFH8
fulldoi: https://doi.org/10.25625/4FLFH8
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.25625/4FLFH8
month: '07'
oa: 1
oa_version: Published Version
publisher: Göttingen Research Online Data
related_material:
record:
- id: '20249'
relation: used_in_publication
status: public
status: public
title: 'Data and code for: Integral points on cubic surfaces: heuristics and numerics'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '19063'
abstract:
- lang: eng
text: "Instruction-tuned Large Language Models (LLMs) show impressive results in
numerous practical applications, but they lack essential safety features that
are common in other areas of computer science, particularly an explicit separation
of instructions and data. This makes them vulnerable to manipulations such as
indirect prompt injections and generally unsuitable for safety-critical tasks.
Surprisingly, there is currently no established definition or benchmark to quantify
this phenomenon. In this work, we close this gap by introducing a formal measure
for instruction-data separation and an empirical variant that is calculable from
a model's outputs. We also present a new dataset, SEP, that allows estimating
the measure for real-world models. Our results on various LLMs show that the problem
of instruction-data separation is real: all models fail to achieve high separation,
and canonical mitigation techniques, such as prompt engineering and fine-tuning,
either fail to substantially improve separation or reduce model utility. The source
code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed.\r\n"
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors would like to sincerely thank Juan Rocamonde for valuable
feedback to our manuscript. We acknowledge the support from the Scientific Service
Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).
We thank Dan Alistarh for providing us with computational resources. This work was
partially funded by the German Federal Ministry of Education and Research (BMBF)
under the grant AIgenCY (16KIS2012) and ELSA – European Lighthouse on Secure and
Safe AI funded by the European Union under grant agreement No. 101070617. Views
and opinions expressed are however those of the authors only and do not necessarily
reflect those of the European Union or European Commission. Neither the European
Union nor the European Commission can be held responsible for them.
article_number: '2403.06833'
article_processing_charge: No
arxiv: 1
author:
- first_name: Egor
full_name: Zverev, Egor
id: 05162b19-1340-11ed-8f02-fa94e0e8c3bc
last_name: Zverev
- first_name: Sahar
full_name: Abdelnabi, Sahar
last_name: Abdelnabi
- first_name: Soroush
full_name: Tabesh, Soroush
id: 06000900-6068-11ef-8d61-c2472ef2e752
last_name: Tabesh
orcid: 0009-0003-4119-6281
- first_name: Mario
full_name: Fritz, Mario
last_name: Fritz
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions
from data? And what do we even mean by that? arXiv. doi:10.48550/arXiv.2403.06833
apa: Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., & Lampert, C. (n.d.).
Can LLMs separate instructions from data? And what do we even mean by that? arXiv.
https://doi.org/10.48550/arXiv.2403.06833
chicago: Zverev, Egor, Sahar Abdelnabi, Soroush Tabesh, Mario Fritz, and Christoph
Lampert. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by
That?” ArXiv, n.d. https://doi.org/10.48550/arXiv.2403.06833.
ieee: E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, and C. Lampert, “Can LLMs separate
instructions from data? And what do we even mean by that?,” arXiv. .
ista: Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions
from data? And what do we even mean by that? arXiv, 2403.06833.
mla: Zverev, Egor, et al. “Can LLMs Separate Instructions from Data? And What Do
We Even Mean by That?” ArXiv, 2403.06833, doi:10.48550/arXiv.2403.06833.
short: E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (n.d.).
corr_author: '1'
date_created: 2025-02-20T10:13:42Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2026-08-13T07:26:54Z
day: '01'
ddc:
- '000'
department:
- _id: GradSch
- _id: ChLa
doi: 10.48550/arXiv.2403.06833
external_id:
arxiv:
- '2403.06833'
file:
- access_level: open_access
checksum: 35eb43968684b87be59144603ef10af0
content_type: application/pdf
creator: ezverev
date_created: 2025-02-20T10:11:45Z
date_updated: 2025-02-20T10:11:45Z
file_id: '19064'
file_name: 2403.06833v3.pdf
file_size: 530972
relation: main_file
success: 1
file_date_updated: 2025-02-20T10:11:45Z
fulldoi: https://doi.org/10.48550/arXiv.2403.06833
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
link:
- relation: software
url: ' https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed'
status: public
title: Can LLMs separate instructions from data? And what do we even mean by that?
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '14826'
abstract:
- lang: eng
text: The plant-signaling molecule auxin triggers fast and slow cellular responses
across land plants and algae. The nuclear auxin pathway mediates gene expression
and controls growth and development in land plants, but this pathway is absent
from algal sister groups. Several components of rapid responses have been identified
in Arabidopsis, but it is unknown if these are part of a conserved mechanism.
We recently identified a fast, proteome-wide phosphorylation response to auxin.
Here, we show that this response occurs across 5 land plant and algal species
and converges on a core group of shared targets. We found conserved rapid physiological
responses to auxin in the same species and identified rapidly accelerated fibrosarcoma
(RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation
across species. Genetic analysis connects this kinase to both auxin-triggered
protein phosphorylation and rapid cellular response, thus identifying an ancient
mechanism for fast auxin responses in the green lineage.
acknowledgement: 'We are grateful to Asuka Shitaku and Eri Koide for generating and
sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis
raf mutant. We are grateful to our team members for discussions and helpful advice.
This work was supported by funding from the Netherlands Organization for Scientific
Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.;
VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract
number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.;
and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to
T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to
R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Andre
full_name: Kuhn, Andre
last_name: Kuhn
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Sumanth
full_name: Mutte, Sumanth
last_name: Mutte
- first_name: Shiv Mani
full_name: Dubey, Shiv Mani
last_name: Dubey
- first_name: Vanessa Polet
full_name: Carrillo Carrasco, Vanessa Polet
last_name: Carrillo Carrasco
- first_name: Sjef
full_name: Boeren, Sjef
last_name: Boeren
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Jasper
full_name: Koehorst, Jasper
last_name: Koehorst
- first_name: Takayuki
full_name: Kohchi, Takayuki
last_name: Kohchi
- first_name: Ryuichi
full_name: Nishihama, Ryuichi
last_name: Nishihama
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Joris
full_name: Sprakel, Joris
last_name: Sprakel
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
citation:
ama: Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply
conserved, rapid auxin response. Cell. 2024;187(1):130-148.e17. doi:10.1016/j.cell.2023.11.021
apa: Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren,
S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved,
rapid auxin response. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.11.021
chicago: Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet
Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases
Mediate a Deeply Conserved, Rapid Auxin Response.” Cell. Elsevier, 2024.
https://doi.org/10.1016/j.cell.2023.11.021.
ieee: A. Kuhn et al., “RAF-like protein kinases mediate a deeply conserved,
rapid auxin response,” Cell, vol. 187, no. 1. Elsevier, p. 130–148.e17,
2024.
ista: Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer
A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers
D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response.
Cell. 187(1), 130–148.e17.
mla: Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid
Auxin Response.” Cell, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17,
doi:10.1016/j.cell.2023.11.021.
short: A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren,
A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml,
D. Weijers, Cell 187 (2024) 130–148.e17.
date_created: 2024-01-17T12:45:40Z
date_published: 2024-01-04T00:00:00Z
date_updated: 2026-08-14T09:33:45Z
day: '04'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.cell.2023.11.021
ec_funded: 1
external_id:
isi:
- '001152705700001'
pmid:
- '38128538'
file:
- access_level: open_access
checksum: 06fd236a9ee0b46ccb05f44695bfc34b
content_type: application/pdf
creator: dernst
date_created: 2024-01-22T13:41:41Z
date_updated: 2024-01-22T13:41:41Z
file_id: '14874'
file_name: 2024_Cell_Kuhn.pdf
file_size: 13194060
relation: main_file
success: 1
file_date_updated: 2024-01-22T13:41:41Z
fulldoi: https://doi.org/10.1016/j.cell.2023.11.021
has_accepted_license: '1'
intvolume: ' 187'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 130-148.e17
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
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '19395'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: RAF-like protein kinases mediate a deeply conserved, rapid auxin response
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: 187
year: '2024'
...
---
_id: '17373'
abstract:
- lang: eng
text: Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating
the electrostatic properties of material surfaces, enabling the imaging of variations
in work function, topology, surface charge density, or combinations thereof. Regardless
of the underlying signal source, SKPM results in a voltage image, which is spatially
distorted due to the finite size of the probe, long-range electrostatic interactions,
mechanical and electrical noise, and the finite response time of the electronics.
In order to recover the underlying signal, it is necessary to deconvolve the measurement
with an appropriate point spread function (PSF) that accounts the aforementioned
distortions, but determining this PSF is difficult. Here, we describe how such
PSFs can be determined experimentally and show how they can be used to recover
the underlying information of interest. We first consider the physical principles
that enable SKPM and discuss how these affect the system PSF. We then show how
one can experimentally measure PSFs by looking at well-defined features, and that
these compare well to simulated PSFs, provided scans are performed extremely slowly
and carefully. Next, we work at realistic scan speeds and show that the idealized
PSFs fail to capture temporal distortions in the scan direction. While simulating
PSFs for these situations would be quite challenging, we show that measuring PSFs
with similar scan conditions works well. Our approach clarifies the basic principles
and inherent challenges to SKPM measurements and gives practical methods to improve
results.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
- _id: LifeSc
- _id: ScienComp
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant
Agreement No. 949120). This research was supported by the Scientific Service Units
of the Institute of Science and Technology Austria (ISTA) through resources provided
by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility,
and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo
for letting us use their equipment. The authors wish to thank the contributions
of the whole Waitukaitis Group for useful discussions and feedback.
article_number: '045305'
article_processing_charge: No
article_type: original
author:
- first_name: Isaac C
full_name: Lenton, Isaac C
id: a550210f-223c-11ec-8182-e2d45e817efb
last_name: Lenton
orcid: 0000-0002-5010-6984
- first_name: Felix
full_name: Pertl, Felix
id: 6313aec0-15b2-11ec-abd3-ed67d16139af
last_name: Pertl
orcid: 0000-0003-0463-5794
- first_name: Lubuna B
full_name: Shafeek, Lubuna B
id: 3CD37A82-F248-11E8-B48F-1D18A9856A87
last_name: Shafeek
orcid: 0000-0001-7180-6050
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: 'Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. Beyond the blur: Using experimentally
determined point spread functions to improve scanning Kelvin probe imaging. Journal
of Applied Physics. 2024;136(4). doi:10.1063/5.0215151'
apa: 'Lenton, I. C., Pertl, F., Shafeek, L. B., & Waitukaitis, S. R. (2024).
Beyond the blur: Using experimentally determined point spread functions to improve
scanning Kelvin probe imaging. Journal of Applied Physics. AIP Publishing.
https://doi.org/10.1063/5.0215151'
chicago: 'Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis.
“Beyond the Blur: Using Experimentally Determined Point Spread Functions to Improve
Scanning Kelvin Probe Imaging.” Journal of Applied Physics. AIP Publishing,
2024. https://doi.org/10.1063/5.0215151.'
ieee: 'I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “Beyond the
blur: Using experimentally determined point spread functions to improve scanning
Kelvin probe imaging,” Journal of Applied Physics, vol. 136, no. 4. AIP
Publishing, 2024.'
ista: 'Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2024. Beyond the blur: Using
experimentally determined point spread functions to improve scanning Kelvin probe
imaging. Journal of Applied Physics. 136(4), 045305.'
mla: 'Lenton, Isaac C., et al. “Beyond the Blur: Using Experimentally Determined
Point Spread Functions to Improve Scanning Kelvin Probe Imaging.” Journal of
Applied Physics, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:10.1063/5.0215151.'
short: I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied
Physics 136 (2024).
corr_author: '1'
date_created: 2024-08-04T22:01:21Z
date_published: 2024-07-28T00:00:00Z
date_updated: 2026-08-27T11:42:44Z
day: '28'
ddc:
- '530'
department:
- _id: ScWa
- _id: NanoFab
doi: 10.1063/5.0215151
ec_funded: 1
external_id:
isi:
- '001281681100003'
file:
- access_level: open_access
checksum: 6141d05cd68d540a7446dce9490975db
content_type: application/pdf
creator: dernst
date_created: 2024-08-05T08:19:58Z
date_updated: 2024-08-05T08:19:58Z
file_id: '17386'
file_name: 2024_JourApplPhysics_Lenton.pdf
file_size: 2537502
relation: main_file
success: 1
file_date_updated: 2024-08-05T08:19:58Z
fulldoi: https://doi.org/10.1063/5.0215151
has_accepted_license: '1'
intvolume: ' 136'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: Journal of Applied Physics
publication_identifier:
eissn:
- 1089-7550
issn:
- 0021-8979
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '22684'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Beyond the blur: Using experimentally determined point spread functions to
improve scanning Kelvin probe imaging'
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: 136
year: '2024'
...
---
_id: '18155'
abstract:
- lang: eng
text: We study the classical problem of verifying programs with respect to formal
specifications given in the linear temporal logic (LTL). We first present novel
sound and complete witnesses for LTL verification over imperative programs. Our
witnesses are applicable to both verification (proving) and refutation (finding
bugs) settings. We then consider LTL formulas in which atomic propositions can
be polynomial constraints and turn our focus to polynomial arithmetic programs,
i.e. programs in which every assignment and guard consists only of polynomial
expressions. For this setting, we provide an efficient algorithm to automatically
synthesize such LTL witnesses. Our synthesis procedure is both sound and semi-complete.
Finally, we present experimental results demonstrating the effectiveness of our
approach and that it can handle programs which were beyond the reach of previous
state-of-the-art tools.
acknowledgement: This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt)
and the Hong Kong Research Grants Council ECS Project Number 26208122.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Ehsan
full_name: Goharshady, Ehsan
last_name: Goharshady
- first_name: Mehrdad
full_name: Karrabi, Mehrdad
id: 67638922-f394-11eb-9cf6-f20423e08757
last_name: Karrabi
orcid: 0009-0007-5253-9170
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Chatterjee K, Goharshady AK, Goharshady E, Karrabi M, Zikelic D. Sound and complete
witnesses for template-based verification of LTL properties on polynomial programs.
In: Lecture Notes in Computer Science (Including Subseries Lecture Notes in
Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 14933. Springer
Nature; 2024:600-619. doi:10.1007/978-3-031-71162-6_31'
apa: 'Chatterjee, K., Goharshady, A. K., Goharshady, E., Karrabi, M., & Zikelic,
D. (2024). Sound and complete witnesses for template-based verification of LTL
properties on polynomial programs. In Lecture Notes in Computer Science (including
subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
(Vol. 14933, pp. 600–619). Milan, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-71162-6_31'
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Ehsan Goharshady, Mehrdad
Karrabi, and Dorde Zikelic. “Sound and Complete Witnesses for Template-Based Verification
of LTL Properties on Polynomial Programs.” In Lecture Notes in Computer Science
(Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics), 14933:600–619. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-71162-6_31.
ieee: K. Chatterjee, A. K. Goharshady, E. Goharshady, M. Karrabi, and D. Zikelic,
“Sound and complete witnesses for template-based verification of LTL properties
on polynomial programs,” in Lecture Notes in Computer Science (including subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
Milan, Italy, 2024, vol. 14933, pp. 600–619.
ista: 'Chatterjee K, Goharshady AK, Goharshady E, Karrabi M, Zikelic D. 2024. Sound
and complete witnesses for template-based verification of LTL properties on polynomial
programs. Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics). FM: Formal Methods,
LNCS, vol. 14933, 600–619.'
mla: Chatterjee, Krishnendu, et al. “Sound and Complete Witnesses for Template-Based
Verification of LTL Properties on Polynomial Programs.” Lecture Notes in Computer
Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics), vol. 14933, Springer Nature, 2024, pp. 600–19, doi:10.1007/978-3-031-71162-6_31.
short: K. Chatterjee, A.K. Goharshady, E. Goharshady, M. Karrabi, D. Zikelic, in:,
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2024, pp.
600–619.
conference:
end_date: 2024-09-13
location: Milan, Italy
name: 'FM: Formal Methods'
start_date: 2024-09-09
corr_author: '1'
date_created: 2024-09-29T22:01:37Z
date_published: 2024-09-11T00:00:00Z
date_updated: 2026-09-03T11:51:22Z
day: '11'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-71162-6_31
ec_funded: 1
external_id:
arxiv:
- '2403.05386'
isi:
- '001336893300031'
file:
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checksum: 223845be9e754681ee218866827c95e7
content_type: application/pdf
creator: dernst
date_created: 2024-10-01T09:56:54Z
date_updated: 2024-10-01T09:56:54Z
file_id: '18165'
file_name: 2024_LNCS_Chatterjee.pdf
file_size: 650495
relation: main_file
success: 1
file_date_updated: 2024-10-01T09:56:54Z
fulldoi: https://doi.org/10.1007/978-3-031-71162-6_31
has_accepted_license: '1'
intvolume: ' 14933'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 600-619
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031711619'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '22798'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Sound and complete witnesses for template-based verification of LTL properties
on polynomial programs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14933
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '22798'
abstract:
- lang: eng
text: "This repository contains the artifact of the paper titled \"Sound and Complete
Witnesses for Template-based Verification of LTL Properties on Polynomial Programs\"
accepted at FM 2024.\r\n\r\nThe task of verifying an LTL formula on a program
can be reduced to verifying a Büchi specification on the product transition system.
This tool takes a non-deterministic transition system together with a Büchi specification
as input and based on user preferences tries to either (i) prove the existence
of a run in the program that satisfies the Büchi condition or (ii) demonstrate
that every run of the program satisfies the Büchi condition.\r\n \r\nThe tool
is written in Java and works well with openjdk 11 on Ubuntu 22.04. Running all
the experiments can take weeks to finish. We have provided a script for running
the strongest configuration of our tool which solves most of the benchmarks and
takes less than 48 hours. Detailed guidance is given in the readme file."
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
last_name: Chatterjee
- first_name: Amir
full_name: ' Kafshdar Goharshady, Amir'
last_name: ' Kafshdar Goharshady'
- first_name: Ehsan
full_name: Kafshdar Goharshady, Ehsan
last_name: Kafshdar Goharshady
- first_name: Mehrdad
full_name: Karrabi, Mehrdad
last_name: Karrabi
- first_name: Ðorđe
full_name: Žikelić, Ðorđe
last_name: Žikelić
citation:
ama: Chatterjee K, Kafshdar Goharshady A, Kafshdar Goharshady E, Karrabi M, Žikelić
Ð. Data for Sound and Complete Witnesses for Template-based Verification of LTL
Properties on Polynomial Programs. 2024. doi:10.5281/zenodo.12518216
apa: Chatterjee, K., Kafshdar Goharshady, A., Kafshdar Goharshady, E., Karrabi,
M., & Žikelić, Ð. (2024). Data for Sound and Complete Witnesses for Template-based
Verification of LTL Properties on Polynomial Programs. Repository. https://doi.org/10.5281/zenodo.12518216
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Ehsan Kafshdar Goharshady,
Mehrdad Karrabi, and Ðorđe Žikelić. “Data for Sound and Complete Witnesses for
Template-Based Verification of LTL Properties on Polynomial Programs.” Repository,
2024. https://doi.org/10.5281/zenodo.12518216.
ieee: K. Chatterjee, A. Kafshdar Goharshady, E. Kafshdar Goharshady, M. Karrabi,
and Ð. Žikelić, “Data for Sound and Complete Witnesses for Template-based Verification
of LTL Properties on Polynomial Programs.” Repository, 2024.
ista: Chatterjee K, Kafshdar Goharshady A, Kafshdar Goharshady E, Karrabi M, Žikelić
Ð. 2024. Data for Sound and Complete Witnesses for Template-based Verification
of LTL Properties on Polynomial Programs, Repository, 10.5281/zenodo.12518216.
mla: Chatterjee, Krishnendu, et al. Data for Sound and Complete Witnesses for
Template-Based Verification of LTL Properties on Polynomial Programs. Repository,
2024, doi:10.5281/zenodo.12518216.
short: K. Chatterjee, A. Kafshdar Goharshady, E. Kafshdar Goharshady, M. Karrabi,
Ð. Žikelić, (2024).
date_created: 2026-09-03T11:50:15Z
date_published: 2024-06-24T00:00:00Z
date_updated: 2026-09-03T11:51:23Z
day: '24'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.5281/zenodo.12518216
fulldoi: https://doi.org/10.5281/zenodo.12518216
main_file_link:
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url: https://doi.org/10.5281/zenodo.12518216
month: '06'
oa: 1
oa_version: None
publisher: Repository
related_material:
record:
- id: '18155'
relation: used_in_publication
status: public
status: public
title: Data for Sound and Complete Witnesses for Template-based Verification of LTL
Properties on Polynomial Programs
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18528'
abstract:
- lang: eng
text: The recent measurement of magnetic field strength inside the radiative interior
of red giant stars has opened the way toward full 3D characterization of the geometry
of stable large-scale magnetic fields. However, current measurements, which are
limited to dipolar (ℓ = 1) mixed modes, do not properly constrain the topology
of magnetic fields due to degeneracies on the observed magnetic field signature
on such ℓ = 1 mode frequencies. Efforts focused toward unambiguous detections
of magnetic field configurations are now key to better understand angular momentum
transport in stars. We investigated the detectability of complex magnetic field
topologies (such as the ones observed at the surface of stars with a radiative
envelope with spectropolarimetry) inside the radiative interior of red giants.
We focused on a field composed of a combination of a dipole and a quadrupole (quadrudipole)
and on an offset field. We explored the potential of probing such magnetic field
topologies from a combined measurement of magnetic signatures on ℓ = 1 and quadrupolar
(ℓ = 2) mixed mode oscillation frequencies. We first derived the asymptotic theoretical
formalism for computing the asymmetric signature in the frequency pattern for
ℓ = 2 modes due to a quadrudipole magnetic field. To access asymmetry parameters
for more complex magnetic field topologies, we numerically performed a grid search
over the parameter space to map the degeneracy of the signatures of given topologies.
We demonstrate the crucial role played by ℓ = 2 mixed modes in accessing internal
magnetic fields with a quadrupolar component. The degeneracy of the quadrudipole
compared to pure dipolar fields is lifted when considering magnetic asymmetries
in both ℓ = 1 and ℓ = 2 mode frequencies. In addition to the analytical derivation
for the quadrudipole, we present the prospect for complex magnetic field inversions
using magnetic sensitivity kernels from standard perturbation analysis for forward
modeling. Using this method, we explored the detectability of offset magnetic
fields from ℓ = 1 and ℓ = 2 frequencies and demonstrate that offset fields may
be mistaken for weak and centered magnetic fields, resulting in underestimating
the magnetic field strength in stellar cores. We emphasize the need to characterize
ℓ = 2 mixed-mode frequencies, (along with the currently characterized ℓ = 1 mixed
modes), to unveil the higher-order components of the geometry of buried magnetic
fields and to better constrain angular momentum transport inside stars.
acknowledgement: The authors thank S. Mathis, L. Barrault, S. Torres, A. Cristea,
and K. M. Smith for very useful discussions. This project has received funding from
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curíe grant agreement No 101034413. The authors thank the anonymous referee
for valuable comments and suggestions to improve the manuscript.
article_number: A217
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Srijan B
full_name: Das, Srijan B
id: 9ce7c423-dacf-11ed-8942-e09c6cb27149
last_name: Das
orcid: 0000-0003-0896-7972
- first_name: Lukas
full_name: Einramhof, Lukas
id: f1497a1a-72ef-11ef-b75a-fd877bbf6e8c
last_name: Einramhof
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
citation:
ama: Das SB, Einramhof L, Bugnet LA. Unveiling complex magnetic field configurations
in red giant stars. Astronomy & Astrophysics. 2024;690. doi:10.1051/0004-6361/202450918
apa: Das, S. B., Einramhof, L., & Bugnet, L. A. (2024). Unveiling complex magnetic
field configurations in red giant stars. Astronomy & Astrophysics.
EDP Sciences. https://doi.org/10.1051/0004-6361/202450918
chicago: Das, Srijan B, Lukas Einramhof, and Lisa Annabelle Bugnet. “Unveiling Complex
Magnetic Field Configurations in Red Giant Stars.” Astronomy & Astrophysics.
EDP Sciences, 2024. https://doi.org/10.1051/0004-6361/202450918.
ieee: S. B. Das, L. Einramhof, and L. A. Bugnet, “Unveiling complex magnetic field
configurations in red giant stars,” Astronomy & Astrophysics, vol.
690. EDP Sciences, 2024.
ista: Das SB, Einramhof L, Bugnet LA. 2024. Unveiling complex magnetic field configurations
in red giant stars. Astronomy & Astrophysics. 690, A217.
mla: Das, Srijan B., et al. “Unveiling Complex Magnetic Field Configurations in
Red Giant Stars.” Astronomy & Astrophysics, vol. 690, A217, EDP Sciences,
2024, doi:10.1051/0004-6361/202450918.
short: S.B. Das, L. Einramhof, L.A. Bugnet, Astronomy & Astrophysics 690 (2024).
corr_author: '1'
das_tickbox: '1'
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date_published: 2024-10-01T00:00:00Z
date_updated: 2026-09-04T09:43:52Z
day: '01'
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department:
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doi: 10.1051/0004-6361/202450918
ec_funded: 1
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text: MESA inlist file for the paper "Unveiling complex magnetic field configurations
in red giant stars" (10.1051/0004-6361/202450918)
article_processing_charge: No
author:
- first_name: Srijan B
full_name: Das, Srijan B
last_name: Das
- first_name: Lukas
full_name: Einramhof, Lukas
last_name: Einramhof
- first_name: Lisa
full_name: Bugnet, Lisa
last_name: Bugnet
citation:
ama: Das SB, Einramhof L, Bugnet L. MESA inlist file. 2024. doi:10.5281/zenodo.12804810
apa: Das, S. B., Einramhof, L., & Bugnet, L. (2024). MESA inlist file. Institute
of Science and Technology Austria. https://doi.org/10.5281/zenodo.12804810
chicago: Das, Srijan B, Lukas Einramhof, and Lisa Bugnet. “MESA Inlist File.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.5281/zenodo.12804810.
ieee: S. B. Das, L. Einramhof, and L. Bugnet, “MESA inlist file.” Institute of Science
and Technology Austria, 2024.
ista: Das SB, Einramhof L, Bugnet L. 2024. MESA inlist file, Institute of Science
and Technology Austria, 10.5281/zenodo.12804810.
mla: Das, Srijan B., et al. MESA Inlist File. Institute of Science and Technology
Austria, 2024, doi:10.5281/zenodo.12804810.
short: S.B. Das, L. Einramhof, L. Bugnet, (2024).
date_created: 2026-09-04T09:42:23Z
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text: 'In this work we prove lower bounds on the (communication) cost of maintaining
a shared key among a dynamic group of users. Being “dynamic” means one can add
and remove users from the group. This captures important protocols like multicast
encryption (ME) and continuous group-key agreement (CGKA), which is the primitive
underlying many group messaging applications. We prove our bounds in a combinatorial
setting where the state of the protocol progresses in rounds. The state of the
protocol in each round is captured by a set system, with each of its elements
specifying a set of users who share a secret key. We show this combinatorial model
implies bounds in symbolic models for ME and CGKA that capture, as building blocks,
PRGs, PRFs, dual PRFs, secret sharing, and symmetric encryption in the setting
of ME, and PRGs, PRFs, dual PRFs, secret sharing, public-key encryption, and key-updatable
public-key encryption in the setting of CGKA. The models are related to the ones
used by Micciancio and Panjwani (Eurocrypt’04) and Bienstock et al. (TCC’20) to
analyze ME and CGKA, respectively. We prove – using the Bollobás’ Set Pairs Inequality
– that the cost (number of uploaded ciphertexts) for replacing a set of d users
in a group of size n is Ω(dln(n/d)). Our lower bound is asymptotically tight and
both improves on a bound of Ω(d) by Bienstock et al. (TCC’20), and generalizes
a result by Micciancio and Panjwani (Eurocrypt’04), who proved a lower bound of
Ω(log(n)) for d=1. '
alternative_title:
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author:
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full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Mirza Ahad
full_name: Baig, Mirza Ahad
id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
last_name: Baig
- first_name: Miguel
full_name: Cueto Noval, Miguel
id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
last_name: Cueto Noval
orcid: 0000-0002-2505-4246
- 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: Guillermo
full_name: Pascual Perez, Guillermo
id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
last_name: Pascual Perez
orcid: 0000-0001-8630-415X
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Anastos M, Auerbach B, Baig MA, et al. The cost of maintaining keys in dynamic
groups with applications to multicast encryption and group messaging. In: 22nd
International Conference on Theory of Cryptography. Vol 15364. Springer Nature;
2024:413-443. doi:10.1007/978-3-031-78011-0_14'
apa: 'Anastos, M., Auerbach, B., Baig, M. A., Cueto Noval, M., Kwan, M. A., Pascual
Perez, G., & Pietrzak, K. Z. (2024). The cost of maintaining keys in dynamic
groups with applications to multicast encryption and group messaging. In 22nd
International Conference on Theory of Cryptography (Vol. 15364, pp. 413–443).
Milan, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-78011-0_14'
chicago: Anastos, Michael, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval,
Matthew Alan Kwan, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “The Cost
of Maintaining Keys in Dynamic Groups with Applications to Multicast Encryption
and Group Messaging.” In 22nd International Conference on Theory of Cryptography,
15364:413–43. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-78011-0_14.
ieee: M. Anastos et al., “The cost of maintaining keys in dynamic groups
with applications to multicast encryption and group messaging,” in 22nd International
Conference on Theory of Cryptography, Milan, Italy, 2024, vol. 15364, pp.
413–443.
ista: 'Anastos M, Auerbach B, Baig MA, Cueto Noval M, Kwan MA, Pascual Perez G,
Pietrzak KZ. 2024. The cost of maintaining keys in dynamic groups with applications
to multicast encryption and group messaging. 22nd International Conference on
Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 15364, 413–443.'
mla: Anastos, Michael, et al. “The Cost of Maintaining Keys in Dynamic Groups with Applications
to Multicast Encryption and Group Messaging.” 22nd International Conference
on Theory of Cryptography, vol. 15364, Springer Nature, 2024, pp. 413–43,
doi:10.1007/978-3-031-78011-0_14.
short: M. Anastos, B. Auerbach, M.A. Baig, M. Cueto Noval, M.A. Kwan, G. Pascual
Perez, K.Z. Pietrzak, in:, 22nd International Conference on Theory of Cryptography,
Springer Nature, 2024, pp. 413–443.
conference:
end_date: 2024-12-06
location: Milan, Italy
name: 'TCC: Theory of Cryptography'
start_date: 2024-12-02
corr_author: '1'
date_created: 2024-12-22T23:01:47Z
date_published: 2024-12-02T00:00:00Z
date_updated: 2026-09-07T11:37:57Z
day: '02'
department:
- _id: MaKw
- _id: KrPi
doi: 10.1007/978-3-031-78011-0_14
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publication: 22nd International Conference on Theory of Cryptography
publication_identifier:
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title: The cost of maintaining keys in dynamic groups with applications to multicast
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abstract:
- lang: eng
text: Caloric restriction (CR) can extend the organism life- and health-span by
improving glucose homeostasis. How CR affects the structure-function of pancreatic
beta cells remains unknown. We used single nucleus transcriptomics to show that
CR increases the expression of genes for beta cell identity, protein processing,
and organelle homeostasis. Gene regulatory network analysis reveal that CR activates
transcription factors important for beta cell identity and homeostasis, while
imaging metabolomics demonstrates that beta cells upon CR are more energetically
competent. In fact, high-resolution microscopy show that CR reduces beta cell
mitophagy to increase mitochondria mass and the potential for ATP generation.
However, CR beta cells have impaired adaptive proliferation in response to high
fat diet feeding. Finally, we show that long-term CR delays the onset of beta
cell aging hallmarks and promotes cell longevity by reducing beta cell turnover.
Therefore, CR could be a feasible approach to preserve compromised beta cell structure-function
during aging and diabetes.
acknowledgement: We are thankful to Michelle Reyzer from the Vanderbilt Mass Spectrometry
Research Center for assistance with MALDI-MS imaging and analysis, to the outstanding
team at the Vanderbilt Mouse Metabolic Phenotyping Center for all the assistance
with in vivo glucose homeostasis tests (DK135073, 1S10RR028101-01). We also thank
the University of Michigan Animal Phenotyping Core for conducting the bomb calorimetry
experiments (1U2CDK110768, DK020575, and DK089503). This research was supported
by recruitment funds from the Vanderbilt’s Department of Molecular Physiology and
Biophysics and NIH grants 1R03DK127484, 5U24DK097771, and 1R01DK138141 to RAeD,
by a grant from the Canadian Institutes of Health Research (CIHR; 487188) to PEM,
by and NIH DK132669 to D.D. PEM holds the Canada Research Chair in Islet Biology.
article_number: '9063'
article_processing_charge: Yes
article_type: original
author:
- first_name: Cristiane
full_name: Dos Santos, Cristiane
last_name: Dos Santos
- first_name: Amanda
full_name: Cambraia, Amanda
last_name: Cambraia
- first_name: Shristi
full_name: Shrestha, Shristi
last_name: Shrestha
- first_name: Melanie
full_name: Cutler, Melanie
last_name: Cutler
- first_name: Matthew
full_name: Cottam, Matthew
last_name: Cottam
- first_name: Guy
full_name: Perkins, Guy
last_name: Perkins
- first_name: Varda
full_name: Lev-Ram, Varda
last_name: Lev-Ram
- first_name: Birbickram
full_name: Roy, Birbickram
last_name: Roy
- first_name: Christopher
full_name: Acree, Christopher
last_name: Acree
- first_name: Keun Young
full_name: Kim, Keun Young
last_name: Kim
- first_name: Thomas
full_name: Deerinck, Thomas
last_name: Deerinck
- first_name: Danielle
full_name: Dean, Danielle
last_name: Dean
- first_name: Jean Philippe
full_name: Cartailler, Jean Philippe
last_name: Cartailler
- first_name: Patrick E.
full_name: Macdonald, Patrick E.
last_name: Macdonald
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
- first_name: Mark
full_name: Ellisman, Mark
last_name: Ellisman
- first_name: Rafael
full_name: Arrojo E Drigo, Rafael
last_name: Arrojo E Drigo
citation:
ama: Dos Santos C, Cambraia A, Shrestha S, et al. Calorie restriction increases
insulin sensitivity to promote beta cell homeostasis and longevity in mice. Nature
Communications. 2024;15. doi:10.1038/s41467-024-53127-2
apa: Dos Santos, C., Cambraia, A., Shrestha, S., Cutler, M., Cottam, M., Perkins,
G., … Arrojo E Drigo, R. (2024). Calorie restriction increases insulin sensitivity
to promote beta cell homeostasis and longevity in mice. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-024-53127-2
chicago: Dos Santos, Cristiane, Amanda Cambraia, Shristi Shrestha, Melanie Cutler,
Matthew Cottam, Guy Perkins, Varda Lev-Ram, et al. “Calorie Restriction Increases
Insulin Sensitivity to Promote Beta Cell Homeostasis and Longevity in Mice.” Nature
Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53127-2.
ieee: C. Dos Santos et al., “Calorie restriction increases insulin sensitivity
to promote beta cell homeostasis and longevity in mice,” Nature Communications,
vol. 15. Springer Nature, 2024.
ista: Dos Santos C, Cambraia A, Shrestha S, Cutler M, Cottam M, Perkins G, Lev-Ram
V, Roy B, Acree C, Kim KY, Deerinck T, Dean D, Cartailler JP, Macdonald PE, Hetzer
M, Ellisman M, Arrojo E Drigo R. 2024. Calorie restriction increases insulin sensitivity
to promote beta cell homeostasis and longevity in mice. Nature Communications.
15, 9063.
mla: Dos Santos, Cristiane, et al. “Calorie Restriction Increases Insulin Sensitivity
to Promote Beta Cell Homeostasis and Longevity in Mice.” Nature Communications,
vol. 15, 9063, Springer Nature, 2024, doi:10.1038/s41467-024-53127-2.
short: C. Dos Santos, A. Cambraia, S. Shrestha, M. Cutler, M. Cottam, G. Perkins,
V. Lev-Ram, B. Roy, C. Acree, K.Y. Kim, T. Deerinck, D. Dean, J.P. Cartailler,
P.E. Macdonald, M. Hetzer, M. Ellisman, R. Arrojo E Drigo, Nature Communications
15 (2024).
date_created: 2024-10-27T23:01:44Z
date_published: 2024-10-21T00:00:00Z
date_updated: 2026-09-09T08:44:31Z
day: '21'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.1038/s41467-024-53127-2
external_id:
isi:
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pmid:
- '39433757'
file:
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checksum: b936b1c047f41cd427f00e3dc79327d3
content_type: application/pdf
creator: dernst
date_created: 2024-11-04T10:37:56Z
date_updated: 2024-11-04T10:37:56Z
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file_name: 2024_NatureComm_dosSantos.pdf
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title: Calorie restriction increases insulin sensitivity to promote beta cell homeostasis
and longevity in mice
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
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abstract:
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text: Dataset for Dos Santos et al, 2024
article_processing_charge: No
author:
- first_name: Rafael
full_name: Arrojo e Drigo, Rafael
last_name: Arrojo e Drigo
citation:
ama: Arrojo e Drigo R. Calorie restriction increases insulin sensitivity to promote
beta cell homeostasis and longevity. 2024. doi:10.5281/zenodo.6491943
apa: Arrojo e Drigo, R. (2024). Calorie restriction increases insulin sensitivity
to promote beta cell homeostasis and longevity. Repository. https://doi.org/10.5281/zenodo.6491943
chicago: Arrojo e Drigo, Rafael. “Calorie Restriction Increases Insulin Sensitivity
to Promote Beta Cell Homeostasis and Longevity.” Repository, 2024. https://doi.org/10.5281/zenodo.6491943.
ieee: R. Arrojo e Drigo, “Calorie restriction increases insulin sensitivity to promote
beta cell homeostasis and longevity.” Repository, 2024.
ista: Arrojo e Drigo R. 2024. Calorie restriction increases insulin sensitivity
to promote beta cell homeostasis and longevity, Repository, 10.5281/zenodo.6491943.
mla: Arrojo e Drigo, Rafael. Calorie Restriction Increases Insulin Sensitivity
to Promote Beta Cell Homeostasis and Longevity. Repository, 2024, doi:10.5281/zenodo.6491943.
short: R. Arrojo e Drigo, (2024).
date_created: 2026-09-09T08:43:34Z
date_published: 2024-10-21T00:00:00Z
date_updated: 2026-09-09T08:44:32Z
day: '21'
ddc:
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author:
- first_name: Mateja
full_name: Hrast, Mateja
last_name: Hrast
citation:
ama: 'Hrast M. Data for: Ab initio Auger spectrum of the ultrafast dissociating
2p3/2−1σ* resonance in HCl. 2024. doi:10.5281/zenodo.13833474'
apa: 'Hrast, M. (2024). Data for: Ab initio Auger spectrum of the ultrafast dissociating
2p3/2−1σ* resonance in HCl. Repository. https://doi.org/10.5281/zenodo.13833474'
chicago: 'Hrast, Mateja. “Data for: Ab Initio Auger Spectrum of the Ultrafast Dissociating
2p3/2−1σ* Resonance in HCl.” Repository, 2024. https://doi.org/10.5281/zenodo.13833474.'
ieee: 'M. Hrast, “Data for: Ab initio Auger spectrum of the ultrafast dissociating
2p3/2−1σ* resonance in HCl.” Repository, 2024.'
ista: 'Hrast M. 2024. Data for: Ab initio Auger spectrum of the ultrafast dissociating
2p3/2−1σ* resonance in HCl, Repository, 10.5281/zenodo.13833474.'
mla: 'Hrast, Mateja. Data for: Ab Initio Auger Spectrum of the Ultrafast Dissociating
2p3/2−1σ* Resonance in HCl. Repository, 2024, doi:10.5281/zenodo.13833474.'
short: M. Hrast, (2024).
date_created: 2026-09-09T09:20:36Z
date_published: 2024-09-24T00:00:00Z
date_updated: 2026-09-09T09:20:40Z
day: '24'
ddc:
- '530'
department:
- _id: MiLe
- _id: MaSe
doi: 10.5281/zenodo.13833474
fulldoi: https://doi.org/10.5281/zenodo.13833474
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.13833475
month: '09'
oa: 1
oa_version: None
publisher: Repository
related_material:
record:
- id: '18710'
relation: used_in_publication
status: public
status: public
title: 'Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ*
resonance in HCl'
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '14850'
abstract:
- lang: eng
text: Elaborate sexual signals are thought to have evolved and be maintained to
serve as honest indicators of signaller quality. One measure of quality is health,
which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal
gecko that is often infested with ectoparasites in the wild, and males of this
species express visual (coloured gular patches) and chemical (femoral gland secretions)
traits that receivers could assess during social interactions. In this paper,
we tested whether ectoparasites affect individual health, and whether signal quality
is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite
level was negatively correlated with body condition in both sexes. Moreover, some
characteristics of both visual and chemical traits in males were strongly associated
with ectoparasite levels. Specifically, males with higher ectoparasite levels
had yellow gular patches with lower brightness and chroma, and chemical secretions
with a lower proportion of aromatic compounds. We then determined whether ectoparasite
levels in males influence female behaviour. Using sequential choice trials, wherein
females were provided with either the visual or the chemical signals of wild-caught
males that varied in ectoparasite level, we found that only chemical secretions
evoked an elevated female response towards less parasitised males. Simultaneous
choice trials in which females were exposed to the chemical secretions from males
that varied in parasite level further confirmed a preference for males with lower
parasites loads. Overall, we find that although health (body condition) or ectoparasite
load can be honestly advertised through multiple modalities, the parasite-mediated
female response is exclusively driven by chemical signals.
acknowledgement: "We thank Anuradha Batabyal and Shakilur Kabir for scientific discussions,
and help with sampling and colour analyses. We thank Muralidhar and the central
LCMS facility of the IISc for their technical support with the GCMS.\r\nResearch
funding was provided by the Department of Science and Technology Fund for Improvement
of S&T Infrastructure (DST-FIST), the Department of Biotechnology-Indian Institute
of Science (DBT-IISc) partnership program and a Science and Engineering Research
Board (SERB) grant to M.T. (EMR/2017/002228). Open Access funding provided by Indian
Institute of Science. Deposited in PMC for immediate release."
article_number: jeb246217
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Mihir
full_name: Joshi, Mihir
last_name: Joshi
- first_name: Maria
full_name: Thaker, Maria
last_name: Thaker
citation:
ama: Pal A, Joshi M, Thaker M. Too much information? Males convey parasite levels
using more signal modalities than females utilise. Journal of Experimental
Biology. 2024;227(1). doi:10.1242/jeb.246217
apa: Pal, A., Joshi, M., & Thaker, M. (2024). Too much information? Males convey
parasite levels using more signal modalities than females utilise. Journal
of Experimental Biology. The Company of Biologists. https://doi.org/10.1242/jeb.246217
chicago: Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males
Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Journal
of Experimental Biology. The Company of Biologists, 2024. https://doi.org/10.1242/jeb.246217.
ieee: A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite
levels using more signal modalities than females utilise,” Journal of Experimental
Biology, vol. 227, no. 1. The Company of Biologists, 2024.
ista: Pal A, Joshi M, Thaker M. 2024. Too much information? Males convey parasite
levels using more signal modalities than females utilise. Journal of Experimental
Biology. 227(1), jeb246217.
mla: Pal, Arka, et al. “Too Much Information? Males Convey Parasite Levels Using
More Signal Modalities than Females Utilise.” Journal of Experimental Biology,
vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:10.1242/jeb.246217.
short: A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).
corr_author: '1'
date_created: 2024-01-22T08:14:49Z
date_published: 2024-01-10T00:00:00Z
date_updated: 2026-09-09T09:54:41Z
day: '10'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1242/jeb.246217
external_id:
isi:
- '001214515700016'
pmid:
- '38054353'
file:
- access_level: open_access
checksum: 136325372f6f45abaa62a71e2d23bfb6
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T12:08:24Z
date_updated: 2024-01-23T12:08:24Z
file_id: '14877'
file_name: 2024_JourExperimBiology_Pal.pdf
file_size: 594128
relation: main_file
success: 1
file_date_updated: 2024-01-23T12:08:24Z
fulldoi: https://doi.org/10.1242/jeb.246217
has_accepted_license: '1'
intvolume: ' 227'
isi: 1
issue: '1'
keyword:
- Insect Science
- Molecular Biology
- Animal Science and Zoology
- Aquatic Science
- Physiology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Experimental Biology
publication_identifier:
eissn:
- 0022-0949
issn:
- 1477-9145
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/arka-pal/Cnemaspis-SexualSignaling
record:
- id: '22868'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Too much information? Males convey parasite levels using more signal modalities
than females utilise
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: 227
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18908'
abstract:
- lang: eng
text: Chromosomal rearrangements can lead to the coupling of reproductive barriers,
but whether and how they contribute to the completion of speciation remains unclear.
Marine snails of the genus Littorina repeatedly form hybrid zones between populations
segregating for multiple inversion arrangements, providing opportunities to study
their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones
between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different
wave exposure conditions on a Swedish island. Applying whole-genome sequencing,
we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions
reached near differential fixation between the 2 ecotypes, and all were in strong
linkage disequilibrium. These inversions cover 20% of the genome and carry 93%
of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both
transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic
and phenotypic integrity following contact. The bimodality reflects the strong
coupling between inversion clines and the extension of the barrier effect across
the whole genome. Demographic inference suggests that coupling arose during a
period of allopatry and has been maintained for > 1,000 generations after
secondary contact. Overall, this study shows that the coupling of multiple chromosomal
inversions contributes to strong reproductive isolation. Notably, 2 of the putative
inversions overlap with inverted genomic regions associated with ecotype differences
in a closely related species (Littorina saxatilis), suggesting the same regions,
with similar structural variants, repeatedly contribute to ecotype evolution in
distinct species.
acknowledgement: The computations and data handling were enabled by resources provided
by the Swedish National Infrastructure for Computing at UPPMAX partially funded
by the Swedish Research Council through grant agreement no. 2018-05973. We thank
all the member of the Littorina team for the stimulating discussions about the manuscripts,
James Reeves for his help the implementation of Hsplit, and Thomas Broquet for his
useful comments in the latter stage of manuscript revisions.
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Olga
full_name: Ortega-Martinez, Olga
last_name: Ortega-Martinez
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Roger K
full_name: Butlin, Roger K
last_name: Butlin
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
citation:
ama: Le Moan A, Stankowski S, Rafajlović M, et al. Coupling of twelve putative chromosomal
inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution
Letters. 2024;8(4):575-586. doi:10.1093/evlett/qrae014
apa: Le Moan, A., Stankowski, S., Rafajlović, M., Ortega-Martinez, O., Faria, R.,
Butlin, R. K., & Johannesson, K. (2024). Coupling of twelve putative chromosomal
inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution
Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrae014
chicago: Le Moan, Alan, Sean Stankowski, Marina Rafajlović, Olga Ortega-Martinez,
Rui Faria, Roger K Butlin, and Kerstin Johannesson. “Coupling of Twelve Putative
Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.”
Evolution Letters. Oxford University Press, 2024. https://doi.org/10.1093/evlett/qrae014.
ieee: A. Le Moan et al., “Coupling of twelve putative chromosomal inversions
maintains a strong barrier to gene flow between snail ecotypes,” Evolution
Letters, vol. 8, no. 4. Oxford University Press, pp. 575–586, 2024.
ista: Le Moan A, Stankowski S, Rafajlović M, Ortega-Martinez O, Faria R, Butlin
RK, Johannesson K. 2024. Coupling of twelve putative chromosomal inversions maintains
a strong barrier to gene flow between snail ecotypes. Evolution Letters. 8(4),
575–586.
mla: Le Moan, Alan, et al. “Coupling of Twelve Putative Chromosomal Inversions Maintains
a Strong Barrier to Gene Flow between Snail Ecotypes.” Evolution Letters,
vol. 8, no. 4, Oxford University Press, 2024, pp. 575–86, doi:10.1093/evlett/qrae014.
short: A. Le Moan, S. Stankowski, M. Rafajlović, O. Ortega-Martinez, R. Faria, R.K.
Butlin, K. Johannesson, Evolution Letters 8 (2024) 575–586.
date_created: 2025-01-27T13:30:27Z
date_published: 2024-04-23T00:00:00Z
date_updated: 2026-09-09T10:39:13Z
day: '23'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evlett/qrae014
external_id:
isi:
- '001206532900001'
pmid:
- '39479507'
file:
- access_level: open_access
checksum: 2f7780b7b6b3489755f1815f476639c6
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T13:33:14Z
date_updated: 2025-01-27T13:33:14Z
file_id: '18909'
file_name: 2024_EvolutionLetter_Moan.pdf
file_size: 24356661
relation: main_file
success: 1
file_date_updated: 2025-01-27T13:33:14Z
fulldoi: https://doi.org/10.1093/evlett/qrae014
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 575-586
pmid: 1
publication: Evolution Letters
publication_identifier:
issn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '22870'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Coupling of twelve putative chromosomal inversions maintains a strong barrier
to gene flow between snail ecotypes
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: 8
year: '2024'
...
---
APC_amount: 4569,23 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '18491'
abstract:
- lang: eng
text: Predicting the outcomes of adaptation is a major goal of evolutionary biology.
When temporal changes in the environment mirror spatial gradients, it opens up
the potential for predicting the course of adaptive evolution over time based
on patterns of spatial genetic and phenotypic variation. We assessed this approach
in a 30-year transplant experiment in the intertidal snail Littorina saxatilis.
In 1992, snails were transplanted from a predation-dominated environment to one
dominated by wave action. On the basis of spatial patterns, we predicted transitions
in shell size and morphology, allele frequencies at positions throughout the genome,
and chromosomal rearrangement frequencies. Observed changes closely agreed with
predictions and transformation was both dramatic and rapid. Hence, adaptation
can be predicted from knowledge of the phenotypic and genetic variation among
populations.
acknowledgement: 'This work was received funding from the following: Norwegian Research
Council RCN project 315287 (A.M.W.), Swedish Research Council 2021-04191 (K.J.),
European Research Council grant 101055327 HaplotypeStructure (N.B.), Austrian Science
Fund FWF; P 32166-B32 Snapdragon Speciation (N.B.), European Research Council (R.B.),
and Portuguese Foundation for Science and Technology FCT: 2020.00275.CEECIND and
PTDC/BIA-EVL/1614/2021 (R.F.).'
article_number: eadp2102
article_processing_charge: Yes
article_type: original
author:
- first_name: Diego Fernando
full_name: Garcia Castillo, Diego Fernando
id: ae681a14-dc74-11ea-a0a7-c6ef18161701
last_name: Garcia Castillo
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Jenny
full_name: Larsson, Jenny
last_name: Larsson
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- 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: 'Garcia Castillo DF, Barton NH, Faria R, et al. Predicting rapid adaptation
in time from adaptation in space: A 30-year field experiment in marine snails.
Science Advances. 2024;10(41). doi:10.1126/sciadv.adp2102'
apa: 'Garcia Castillo, D. F., Barton, N. H., Faria, R., Larsson, J., Stankowski,
S., Butlin, R., … Westram, A. M. (2024). Predicting rapid adaptation in time from
adaptation in space: A 30-year field experiment in marine snails. Science Advances.
AAAS. https://doi.org/10.1126/sciadv.adp2102'
chicago: 'Garcia Castillo, Diego Fernando, Nicholas H Barton, Rui Faria, Jenny Larsson,
Sean Stankowski, Roger Butlin, Kerstin Johannesson, and Anja M Westram. “Predicting
Rapid Adaptation in Time from Adaptation in Space: A 30-Year Field Experiment
in Marine Snails.” Science Advances. AAAS, 2024. https://doi.org/10.1126/sciadv.adp2102.'
ieee: 'D. F. Garcia Castillo et al., “Predicting rapid adaptation in time
from adaptation in space: A 30-year field experiment in marine snails,” Science
Advances, vol. 10, no. 41. AAAS, 2024.'
ista: 'Garcia Castillo DF, Barton NH, Faria R, Larsson J, Stankowski S, Butlin R,
Johannesson K, Westram AM. 2024. Predicting rapid adaptation in time from adaptation
in space: A 30-year field experiment in marine snails. Science Advances. 10(41),
eadp2102.'
mla: 'Garcia Castillo, Diego Fernando, et al. “Predicting Rapid Adaptation in Time
from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” Science
Advances, vol. 10, no. 41, eadp2102, AAAS, 2024, doi:10.1126/sciadv.adp2102.'
short: D.F. Garcia Castillo, N.H. Barton, R. Faria, J. Larsson, S. Stankowski, R.
Butlin, K. Johannesson, A.M. Westram, Science Advances 10 (2024).
corr_author: '1'
date_created: 2024-11-03T23:01:44Z
date_published: 2024-10-11T00:00:00Z
date_updated: 2026-09-09T10:10:02Z
day: '11'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1126/sciadv.adp2102
external_id:
isi:
- '001354405400018'
file:
- access_level: open_access
checksum: 96aa0d3640fa9401975138e59054f84e
content_type: application/pdf
creator: dernst
date_created: 2024-11-04T09:35:49Z
date_updated: 2024-11-04T09:35:49Z
file_id: '18499'
file_name: 2024_ScienceAdv_Castillo.pdf
file_size: 1154107
relation: main_file
success: 1
file_date_updated: 2024-11-04T09:35:49Z
fulldoi: https://doi.org/10.1126/sciadv.adp2102
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '41'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
- _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1
call_identifier: FWF
name: FWF Open Access Fund
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/fernandoGarcia21/littorina_saxatilis_skerry
record:
- id: '18498'
relation: research_data
status: public
- id: '20991'
relation: dissertation_contains
status: public
- id: '22869'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Predicting rapid adaptation in time from adaptation in space: A 30-year field
experiment in marine snails'
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: 10
year: '2024'
...
---
_id: '17237'
abstract:
- lang: eng
text: 'The impact of climate change on populations will be contingent upon their
contemporary adaptive evolution. In this study, we investigated the contemporary
evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing
their spatial and temporal genomic variations using ddRAD-sequencing. These populations
were sampled from the center to the southern margin of its north-eastern Atlantic
distribution at 2 time points, spanning at least 2 generations. Through genome
scans for local adaptation at a single time point, we identified candidate loci
that showed clinal variation correlated with changes in sea surface temperature
(SST) along latitudinal gradients. This finding suggests that SST may drive the
adaptive response of these kelp populations, although factors such as species’
demographic history should also be considered. Additionally, we performed a simulation
approach to distinguish the effect of selection from genetic drift in allele frequency
changes over time. This enabled the detection of loci in the southernmost population
that exhibited temporal differentiation beyond what would be expected from genetic
drift alone: these are candidate loci which could have evolved under selection
over time. In contrast, we did not detect any outlier locus based on temporal
differentiation in the population from the North Sea, which also displayed low
and decreasing levels of genetic diversity. The diverse evolutionary scenarios
observed among populations can be attributed to variations in the prevalence of
selection relative to genetic drift across different environments. Therefore,
our study highlights the potential of temporal genomics to offer valuable insights
into the contemporary evolution of marine foundation species facing climate change.'
acknowledgement: "This work was funded by the EU project MARFOR Biodiversa/004/2015.
L.F. was additionally funded by the Region Bretagne (ARED 2017 REEALG) and the NOMIS
Foundation. The project leading to this publication has received funding from the
EC2CO (CNRS) fund and from the European FEDER Fund under project 1166-39417.\r\nThis
work is especially dedicated to the memory of Gernot Glöckner who contributed to
the sequencing of Laminaria digitata genome and passed away in very recent time.
The authors thank the ABiMS platform of the Roscoff biological station (http://abims.sb-roscoff.fr)
for providing the HPC resources that contributed to the search results reported
in this document. We also acknowledge the staff of the “Cluster de calcul intensif
HPC” Platform of the OSU Institut Pythéas (Aix-Marseille Université, INSU-CNRS)
for providing the computing facilities."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lauric
full_name: Reynes, Lauric
last_name: Reynes
- first_name: Louise
full_name: Fouqueau, Louise
id: 1676e173-8143-11ed-8927-fe165216a93f
last_name: Fouqueau
orcid: 0000-0003-0371-9339
- first_name: Didier
full_name: Aurelle, Didier
last_name: Aurelle
- first_name: Stephane
full_name: Mauger, Stephane
last_name: Mauger
- first_name: Christophe
full_name: Destombe, Christophe
last_name: Destombe
- first_name: Myriam
full_name: Valero, Myriam
last_name: Valero
citation:
ama: Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. Temporal genomics
help in deciphering neutral and adaptive patterns in the contemporary evolution
of kelp populations. Journal of Evolutionary Biology. 2024;37(6):677-692.
doi:10.1093/jeb/voae048
apa: Reynes, L., Fouqueau, L., Aurelle, D., Mauger, S., Destombe, C., & Valero,
M. (2024). Temporal genomics help in deciphering neutral and adaptive patterns
in the contemporary evolution of kelp populations. Journal of Evolutionary
Biology. Oxford University Press. https://doi.org/10.1093/jeb/voae048
chicago: Reynes, Lauric, Louise Fouqueau, Didier Aurelle, Stephane Mauger, Christophe
Destombe, and Myriam Valero. “Temporal Genomics Help in Deciphering Neutral and
Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” Journal
of Evolutionary Biology. Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae048.
ieee: L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, and M. Valero,
“Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary
evolution of kelp populations,” Journal of Evolutionary Biology, vol. 37,
no. 6. Oxford University Press, pp. 677–692, 2024.
ista: Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. 2024. Temporal
genomics help in deciphering neutral and adaptive patterns in the contemporary
evolution of kelp populations. Journal of Evolutionary Biology. 37(6), 677–692.
mla: Reynes, Lauric, et al. “Temporal Genomics Help in Deciphering Neutral and Adaptive
Patterns in the Contemporary Evolution of Kelp Populations.” Journal of Evolutionary
Biology, vol. 37, no. 6, Oxford University Press, 2024, pp. 677–92, doi:10.1093/jeb/voae048.
short: L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, M. Valero, Journal
of Evolutionary Biology 37 (2024) 677–692.
date_created: 2024-07-14T22:01:12Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2026-09-09T09:33:37Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/jeb/voae048
external_id:
arxiv:
- '2404.14003'
pmid:
- '38629140'
fulldoi: https://doi.org/10.1093/jeb/voae048
intvolume: ' 37'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2404.14003
month: '06'
oa: 1
oa_version: Preprint
page: 677-692
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'
related_material:
record:
- id: '22867'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Temporal genomics help in deciphering neutral and adaptive patterns in the
contemporary evolution of kelp populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '22870'
abstract:
- lang: eng
text: 'Abstract: Chromosomal rearrangements can lead to the coupling of reproductive
barriers, but whether and how they contribute to completion of speciation remains
unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between
populations segregating for multiple inversion arrangements, providing opportunities
to study their barrier effects. Here, we analysed two adjacent transects across
hybrid zones between two ecotypes of Littorina fabalis (‘large’ and ‘dwarf’) adapted
to different wave exposure conditions on a Swedish island. Applying whole-genome
sequencing, we found 12 putative inversions on nine of 17 chromosomes. Nine of
the putative inversions reached near differential fixation between the two ecotypes,
and all were in strong linkage disequilibrium. These inversions cover 20% of the
genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal
hybrid zones in both transects indicated that the two ecotypes of Littorina fabalis
maintain their genetic and phenotypic integrity following contact. The bimodality
reflects the strong coupling between inversion clines and the extension of the
barrier effect across the whole genome. Demographic inference suggests that coupling
arose during a period of allopatry and has been maintained for >1000 generations
after secondary contact. Overall, this study shows that the coupling of multiple
chromosomal inversions contributes to strong reproductive isolation. Notably,
two of the putative inversions overlap with inverted genomic regions associated
with ecotype differences in a closely-related species (Littorina saxatilis), suggesting
the same regions, with similar structural variants, repeatedly contribute to ecotype
evolution in distinct species.'
article_processing_charge: No
author:
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
citation:
ama: Le Moan A. Coupling of twelve putative chromosomal inversions maintains a strong
barrier to gene flow between snail ecotypes. 2024. doi:10.5281/zenodo.10790257
apa: Le Moan, A. (2024). Coupling of twelve putative chromosomal inversions maintains
a strong barrier to gene flow between snail ecotypes. Repository. https://doi.org/10.5281/zenodo.10790257
chicago: Le Moan, Alan. “Coupling of Twelve Putative Chromosomal Inversions Maintains
a Strong Barrier to Gene Flow between Snail Ecotypes.” Repository, 2024. https://doi.org/10.5281/zenodo.10790257.
ieee: A. Le Moan, “Coupling of twelve putative chromosomal inversions maintains
a strong barrier to gene flow between snail ecotypes.” Repository, 2024.
ista: Le Moan A. 2024. Coupling of twelve putative chromosomal inversions maintains
a strong barrier to gene flow between snail ecotypes, Repository, 10.5281/zenodo.10790257.
mla: Le Moan, Alan. Coupling of Twelve Putative Chromosomal Inversions Maintains
a Strong Barrier to Gene Flow between Snail Ecotypes. Repository, 2024, doi:10.5281/zenodo.10790257.
short: A. Le Moan, (2024).
contributor:
- contributor_type: contact_person
first_name: Alan
last_name: Le Moan
date_created: 2026-09-09T10:39:08Z
date_published: 2024-03-06T00:00:00Z
date_updated: 2026-09-09T10:39:13Z
day: '06'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/zenodo.10790257
fulldoi: https://doi.org/10.5281/zenodo.10790257
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.10790257
month: '03'
oa: 1
oa_version: None
publisher: Repository
related_material:
record:
- id: '18908'
relation: used_in_publication
status: public
status: public
title: Coupling of twelve putative chromosomal inversions maintains a strong barrier
to gene flow between snail ecotypes
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...