---
OA_place: repository
_id: '19551'
abstract:
- lang: eng
  text: "We introduce a notion of a \\emph{local gap} for interacting many-body quantum
    lattice systems and prove the validity of response theory and Kubo's formula for
    localized perturbations in such settings.\r\nOn a high level, our result shows
    that the usual spectral gap condition, concerning the system as a whole, is not
    a necessary condition for understanding local properties of the system.\r\nMore
    precisely, we say that an equilibrium state ρ0 of a Hamiltonian H0 is locally
    gapped in Λgap⊂Λ, whenever the Liouvillian −i[H0,⋅] is almost invertible on local
    observables supported in Λgap when tested in ρ0.\r\nTo put this into context,
    we provide other alternative notions of a local gap and discuss their relations.\r\nThe
    validity of response theory is based on the construction of \\emph{non-equilibrium
    almost stationary states} (NEASSs).\r\nBy controlling locality properties of the
    NEASS construction, we show that response theory holds to any order, whenever
    the perturbation \\(\\epsilon V\\) acts in a region which is further than |logϵ|
    away from the non-gapped region Λ∖Λgap."
article_processing_charge: No
arxiv: 1
author:
- first_name: Sven Joscha
  full_name: Henheik, Sven Joscha
  id: 31d731d7-d235-11ea-ad11-b50331c8d7fb
  last_name: Henheik
  orcid: 0000-0003-1106-327X
- first_name: Tom
  full_name: Wessel, Tom
  last_name: Wessel
citation:
  ama: Henheik SJ, Wessel T. Response theory for locally gapped systems. <i>arXiv</i>.
    doi:<a href="https://doi.org/10.48550/arXiv.2410.10809">10.48550/arXiv.2410.10809</a>
  apa: Henheik, S. J., &#38; Wessel, T. (n.d.). Response theory for locally gapped
    systems. <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.2410.10809">https://doi.org/10.48550/arXiv.2410.10809</a>
  chicago: Henheik, Sven Joscha, and Tom Wessel. “Response Theory for Locally Gapped
    Systems.” <i>ArXiv</i>, n.d. <a href="https://doi.org/10.48550/arXiv.2410.10809">https://doi.org/10.48550/arXiv.2410.10809</a>.
  ieee: S. J. Henheik and T. Wessel, “Response theory for locally gapped systems,”
    <i>arXiv</i>. .
  ista: Henheik SJ, Wessel T. Response theory for locally gapped systems. arXiv, <a
    href="https://doi.org/10.48550/arXiv.2410.10809">10.48550/arXiv.2410.10809</a>.
  mla: Henheik, Sven Joscha, and Tom Wessel. “Response Theory for Locally Gapped Systems.”
    <i>ArXiv</i>, doi:<a href="https://doi.org/10.48550/arXiv.2410.10809">10.48550/arXiv.2410.10809</a>.
  short: S.J. Henheik, T. Wessel, ArXiv (n.d.).
corr_author: '1'
date_created: 2025-04-11T11:54:56Z
date_published: 2024-10-14T00:00:00Z
date_updated: 2026-07-29T13:18:16Z
day: '14'
department:
- _id: LaEr
doi: 10.48550/arXiv.2410.10809
external_id:
  arxiv:
  - '2410.10809'
fulldoi: https://doi.org/10.48550/arXiv.2410.10809
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2410.10809
month: '10'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
  record:
  - id: '19540'
    relation: dissertation_contains
    status: public
status: public
title: Response theory for locally gapped systems
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
_id: '15359'
abstract:
- lang: eng
  text: Molecular dynamics (MD) simulations play an important role in understanding
    and engineering heat transport properties of complex materials. An essential requirement
    for reliably predicting heat transport properties is the use of accurate and efficient
    interatomic potentials. Recently, machine-learned potentials (MLPs) have shown
    great promise in providing the required accuracy for a broad range of materials.
    In this mini-review and tutorial, we delve into the fundamentals of heat transport,
    explore pertinent MD simulation methods, and survey the applications of MLPs in
    MD simulations of heat transport. Furthermore, we provide a step-by-step tutorial
    on developing MLPs for highly efficient and predictive heat transport simulations,
    utilizing the neuroevolution potentials as implemented in the GPUMD package. Our
    aim with this mini-review and tutorial is to empower researchers with valuable
    insights into cutting-edge methodologies that can significantly enhance the accuracy
    and efficiency of MD simulations for heat transport studies.
acknowledgement: H.D. is supported by the Science Foundation from the Education Department
  of Liaoning Province (No. JYTMS20231613) and the Doctoral start-up Fund of Bohai
  University (No. 0523bs008). P.Y. is supported by the Israel Academy of Sciences
  and Humanities & Council for Higher Education Excellence Fellowship Program for
  International Postdoctoral Researchers. K.X. and T.L. acknowledge support from the
  National Key R&D Project from Ministry of Science and Technology of China (No. 2022YFA1203100),
  the Research Grants Council of Hong Kong (No. AoE/P-701/20), and RGC GRF (No. 14220022).
  Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation programme
  under the Marie Skłodowska-Curie Grant Agreement No. 101034413. S.X. acknowledges
  financial support from the National Natural Science Foundation of China (NNSFC)
  (Grant No. 12174276).
article_number: '161101'
article_processing_charge: Yes (in subscription journal)
article_type: review
arxiv: 1
author:
- first_name: Haikuan
  full_name: Dong, Haikuan
  last_name: Dong
- first_name: Yongbo
  full_name: Shi, Yongbo
  last_name: Shi
- first_name: Penghua
  full_name: Ying, Penghua
  last_name: Ying
- first_name: Ke
  full_name: Xu, Ke
  last_name: Xu
- first_name: Ting
  full_name: Liang, Ting
  last_name: Liang
- first_name: Yanzhou
  full_name: Wang, Yanzhou
  last_name: Wang
- first_name: Zezhu
  full_name: Zeng, Zezhu
  id: 54a2c730-803f-11ed-ab7e-95b29d2680e7
  last_name: Zeng
  orcid: 0000-0001-5126-4928
- first_name: Xin
  full_name: Wu, Xin
  last_name: Wu
- first_name: Wenjiang
  full_name: Zhou, Wenjiang
  last_name: Zhou
- first_name: Shiyun
  full_name: Xiong, Shiyun
  last_name: Xiong
- first_name: Shunda
  full_name: Chen, Shunda
  last_name: Chen
- first_name: Zheyong
  full_name: Fan, Zheyong
  last_name: Fan
citation:
  ama: 'Dong H, Shi Y, Ying P, et al. Molecular dynamics simulations of heat transport
    using machine-learned potentials: A mini-review and tutorial on GPUMD with neuroevolution
    potentials. <i>Journal of Applied Physics</i>. 2024;135(16). doi:<a href="https://doi.org/10.1063/5.0200833">10.1063/5.0200833</a>'
  apa: 'Dong, H., Shi, Y., Ying, P., Xu, K., Liang, T., Wang, Y., … Fan, Z. (2024).
    Molecular dynamics simulations of heat transport using machine-learned potentials:
    A mini-review and tutorial on GPUMD with neuroevolution potentials. <i>Journal
    of Applied Physics</i>. AIP Publishing. <a href="https://doi.org/10.1063/5.0200833">https://doi.org/10.1063/5.0200833</a>'
  chicago: 'Dong, Haikuan, Yongbo Shi, Penghua Ying, Ke Xu, Ting Liang, Yanzhou Wang,
    Zezhu Zeng, et al. “Molecular Dynamics Simulations of Heat Transport Using Machine-Learned
    Potentials: A Mini-Review and Tutorial on GPUMD with Neuroevolution Potentials.”
    <i>Journal of Applied Physics</i>. AIP Publishing, 2024. <a href="https://doi.org/10.1063/5.0200833">https://doi.org/10.1063/5.0200833</a>.'
  ieee: 'H. Dong <i>et al.</i>, “Molecular dynamics simulations of heat transport
    using machine-learned potentials: A mini-review and tutorial on GPUMD with neuroevolution
    potentials,” <i>Journal of Applied Physics</i>, vol. 135, no. 16. AIP Publishing,
    2024.'
  ista: 'Dong H, Shi Y, Ying P, Xu K, Liang T, Wang Y, Zeng Z, Wu X, Zhou W, Xiong
    S, Chen S, Fan Z. 2024. Molecular dynamics simulations of heat transport using
    machine-learned potentials: A mini-review and tutorial on GPUMD with neuroevolution
    potentials. Journal of Applied Physics. 135(16), 161101.'
  mla: 'Dong, Haikuan, et al. “Molecular Dynamics Simulations of Heat Transport Using
    Machine-Learned Potentials: A Mini-Review and Tutorial on GPUMD with Neuroevolution
    Potentials.” <i>Journal of Applied Physics</i>, vol. 135, no. 16, 161101, AIP
    Publishing, 2024, doi:<a href="https://doi.org/10.1063/5.0200833">10.1063/5.0200833</a>.'
  short: H. Dong, Y. Shi, P. Ying, K. Xu, T. Liang, Y. Wang, Z. Zeng, X. Wu, W. Zhou,
    S. Xiong, S. Chen, Z. Fan, Journal of Applied Physics 135 (2024).
das_tickbox: '1'
dataavailabilitystatement: All the training and test datasets and the trained NEP
  models for crystalline silicon are freely available at https://gitlab.com/brucefan1983/nep-data.
  The training datasets, trained NEP, DP, and MTP models for graphene and MD input
  files for reproducing Fig. 3 are freely available at https://github.com/hityingph/supporting-info/tree/main/Dong_GPUMD_Tutorial_2024.
date_created: 2024-05-05T22:01:03Z
date_published: 2024-04-28T00:00:00Z
date_updated: 2026-08-07T10:35:13Z
day: '28'
ddc:
- '530'
department:
- _id: BiCh
doi: 10.1063/5.0200833
ec_funded: 1
external_id:
  arxiv:
  - '2401.16249'
  isi:
  - '001215967400009'
file:
- access_level: open_access
  checksum: 4d6abb3ebe058ce8eebf4fc7e9cdda0d
  content_type: application/pdf
  creator: dernst
  date_created: 2024-05-13T08:07:44Z
  date_updated: 2024-05-13T08:07:44Z
  file_id: '15382'
  file_name: 2024_JourApplPhysics_Dong.pdf
  file_size: 3240613
  relation: main_file
  success: 1
file_date_updated: 2024-05-13T08:07:44Z
fulldoi: https://doi.org/10.1063/5.0200833
has_accepted_license: '1'
intvolume: '       135'
isi: 1
issue: '16'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Journal of Applied Physics
publication_identifier:
  eissn:
  - 1089-7550
  issn:
  - 0021-8979
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://gitlab.com/brucefan1983/nep-data
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'Molecular dynamics simulations of heat transport using machine-learned potentials:
  A mini-review and tutorial on GPUMD with neuroevolution potentials'
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: 135
year: '2024'
...
---
_id: '17278'
abstract:
- lang: eng
  text: An azeotrope is a constant boiling point mixture, and its behavior is important
    for fluid separation processes. Predicting azeotropes from atomistic simulations
    is difficult due to the complexities and convergence problems of Monte Carlo and
    free-energy perturbation techniques. Here, we present a methodology for predicting
    the azeotropes of binary mixtures, which computes the compositional dependence
    of chemical potentials from molecular dynamics simulations using the S0 method
    and employs experimental boiling point and vaporization enthalpy data. Using this
    methodology, we reproduce the azeotropes, or lack thereof, in five case studies,
    including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and
    acetone/chloroform mixtures. We find that it is crucial to use the experimental
    boiling point and vaporization enthalpy for reliable azeotrope predictions, as
    empirical force fields are not accurate enough for these quantities. Finally,
    we use regular solution models to rationalize the azeotropes and reveal that they
    tend to form when the mixture components have similar boiling points and strong
    interactions.
acknowledgement: B.C. thanks Alessandro Laio, who introduced the phenomenon of azeotrope
  and suggested using the S0 method to compute it. B.C. and X.W. thank Felix Wodaczek
  for the insightful comments and suggestions on the manuscript. B.C. and X.W. acknowledge
  the resources provided by the Cambridge Tier-2 system operated by the University
  of Cambridge Research Computing Service, funded by EPSRC Tier-2 capital (Grant No.
  EP/P020259/1).
article_number: '034111'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Xiaoyu
  full_name: Wang, Xiaoyu
  id: 8dff9c62-32b0-11ee-9fa8-fc73025e10f3
  last_name: Wang
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
citation:
  ama: Wang X, Cheng B. Integrating molecular dynamics simulations and experimental
    data for azeotrope predictions in binary mixtures. <i>Journal of Chemical Physics</i>.
    2024;161(3). doi:<a href="https://doi.org/10.1063/5.0217232">10.1063/5.0217232</a>
  apa: Wang, X., &#38; Cheng, B. (2024). Integrating molecular dynamics simulations
    and experimental data for azeotrope predictions in binary mixtures. <i>Journal
    of Chemical Physics</i>. AIP Publishing. <a href="https://doi.org/10.1063/5.0217232">https://doi.org/10.1063/5.0217232</a>
  chicago: Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations
    and Experimental Data for Azeotrope Predictions in Binary Mixtures.” <i>Journal
    of Chemical Physics</i>. AIP Publishing, 2024. <a href="https://doi.org/10.1063/5.0217232">https://doi.org/10.1063/5.0217232</a>.
  ieee: X. Wang and B. Cheng, “Integrating molecular dynamics simulations and experimental
    data for azeotrope predictions in binary mixtures,” <i>Journal of Chemical Physics</i>,
    vol. 161, no. 3. AIP Publishing, 2024.
  ista: Wang X, Cheng B. 2024. Integrating molecular dynamics simulations and experimental
    data for azeotrope predictions in binary mixtures. Journal of Chemical Physics.
    161(3), 034111.
  mla: Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations
    and Experimental Data for Azeotrope Predictions in Binary Mixtures.” <i>Journal
    of Chemical Physics</i>, vol. 161, no. 3, 034111, AIP Publishing, 2024, doi:<a
    href="https://doi.org/10.1063/5.0217232">10.1063/5.0217232</a>.
  short: X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: All simulation setups, analysis scripts, and raw data in
  the study are available in the SI repository https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0.
date_created: 2024-07-21T22:01:00Z
date_published: 2024-07-14T00:00:00Z
date_updated: 2026-08-07T10:38:59Z
day: '14'
department:
- _id: BiCh
- _id: GradSch
doi: 10.1063/5.0217232
external_id:
  arxiv:
  - '2405.02216'
  isi:
  - '001281819100016'
  pmid:
  - '39007379'
fulldoi: https://doi.org/10.1063/5.0217232
intvolume: '       161'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2405.02216
month: '07'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Chemical Physics
publication_identifier:
  eissn:
  - 1089-7690
  issn:
  - 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Integrating molecular dynamics simulations and experimental data for azeotrope
  predictions in binary mixtures
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 161
year: '2024'
...
---
OA_type: free access
_id: '17231'
abstract:
- lang: eng
  text: In the class of projective billiards, which contains the usual billiards,
    we exhibit counter-examples to Ivrii's conjecture, which states that in any planar
    billiard with smooth boundary the set of periodic orbits has zero measure. The
    counter-examples are polygons admitting a 2-parameters family of n-periodic orbits,
    with n being either 3 or any even integer greater than 4.
article_processing_charge: No
article_type: original
author:
- first_name: Corentin
  full_name: Fiorebe, Corentin
  id: 06619f18-9070-11eb-847d-d1ee780bd88b
  last_name: Fiorebe
citation:
  ama: Fiorebe C. Examples of projective billiards with open sets of periodic orbits.
    <i>Discrete and Continuous Dynamical Systems- Series A</i>. 2024;44(11):3287-3301.
    doi:<a href="https://doi.org/10.3934/dcds.2024059">10.3934/dcds.2024059</a>
  apa: Fiorebe, C. (2024). Examples of projective billiards with open sets of periodic
    orbits. <i>Discrete and Continuous Dynamical Systems- Series A</i>. AIMS. <a href="https://doi.org/10.3934/dcds.2024059">https://doi.org/10.3934/dcds.2024059</a>
  chicago: Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of
    Periodic Orbits.” <i>Discrete and Continuous Dynamical Systems- Series A</i>.
    AIMS, 2024. <a href="https://doi.org/10.3934/dcds.2024059">https://doi.org/10.3934/dcds.2024059</a>.
  ieee: C. Fiorebe, “Examples of projective billiards with open sets of periodic orbits,”
    <i>Discrete and Continuous Dynamical Systems- Series A</i>, vol. 44, no. 11. AIMS,
    pp. 3287–3301, 2024.
  ista: Fiorebe C. 2024. Examples of projective billiards with open sets of periodic
    orbits. Discrete and Continuous Dynamical Systems- Series A. 44(11), 3287–3301.
  mla: Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic
    Orbits.” <i>Discrete and Continuous Dynamical Systems- Series A</i>, vol. 44,
    no. 11, AIMS, 2024, pp. 3287–301, doi:<a href="https://doi.org/10.3934/dcds.2024059">10.3934/dcds.2024059</a>.
  short: C. Fiorebe, Discrete and Continuous Dynamical Systems- Series A 44 (2024)
    3287–3301.
corr_author: '1'
date_created: 2024-07-14T22:01:10Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2026-08-12T06:19:26Z
day: '01'
ddc:
- '500'
department:
- _id: VaKa
doi: 10.3934/dcds.2024059
external_id:
  isi:
  - '001230091000001'
fulldoi: https://doi.org/10.3934/dcds.2024059
intvolume: '        44'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.3934/dcds.2024059
month: '11'
oa: 1
oa_version: Published Version
page: 3287-3301
publication: Discrete and Continuous Dynamical Systems- Series A
publication_identifier:
  eissn:
  - 1553-5231
  issn:
  - 1078-0947
publication_status: published
publisher: AIMS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Examples of projective billiards with open sets of periodic orbits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2024'
...
---
_id: '17898'
abstract:
- lang: eng
  text: 'There is an ever-growing zoo of modern neural network models that can efficiently
    learn end-to-end control from visual observations. These advanced deep models,
    ranging from convolutional to Vision Transformers, from small to gigantic networks,
    have been extensively tested on offline image classification tasks. In this paper,
    we study these vision models with respect to the open-loop training to closed-loop
    generalization abilities, i.e., deployment realizes a causal feedback loop that
    is not present during training. This causality gap typically emerges in robotics
    applications such as autonomous driving, where a network is trained to imitate
    the control commands of a human. In this setting, two situations arise: 1) Closed-loop
    testing in-distribution, where the test environment shares properties with those
    of offline training data. 2) Closed-loop testing under distribution shifts and
    out-of-distribution. Contrary to recently reported results, we show that under
    proper training guidelines, all vision architectures perform indistinguishably
    well on in-distribution deployment, resolving the causality gap. In situation
    2, We observe that scale is the strongest factor in improving closed-loop generalization
    regardless of the choice of the model architecture. Our results predict the trend
    that in the future we will see larger and larger models being used in offline-training-online-deployment
    imitation learning tasks in robotic applications.'
acknowledgement: This work was partially supported in parts by the ERC-2020-AdG 101020093.
  Additionally, it was partially sponsored by the United States Air Force Research
  Laboratory and the United States Air Force Artificial Intelligence Accelerator and
  was accomplished under Cooperative Agreement Number FA8750-19-2-1000. The views
  and conclusions contained in this document are those of the authors and should not
  be interpreted as representing the official policies, either expressed or implied,
  of the United States Air Force or the U.S. Government. The U.S. Government is authorized
  to reproduce and distribute reprints for Government purposes notwithstanding any
  copyright notation herein. This work was further supported by The Boeing Company
  and the Office of Naval Research (ONR) Grant N00014-18-1-2830.
article_processing_charge: No
author:
- first_name: Mathias
  full_name: Lechner, Mathias
  id: 3DC22916-F248-11E8-B48F-1D18A9856A87
  last_name: Lechner
- first_name: Ramin
  full_name: Hasani, Ramin
  last_name: Hasani
- first_name: Alexander
  full_name: Amini, Alexander
  last_name: Amini
- first_name: Tsun Hsuan
  full_name: Wang, Tsun Hsuan
  last_name: Wang
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000-0002-2985-7724
- first_name: Daniela
  full_name: Rus, Daniela
  last_name: Rus
citation:
  ama: 'Lechner M, Hasani R, Amini A, Wang TH, Henzinger TA, Rus D. Overparametrization
    helps offline-to-online generalization of closed-loop control from pixels. In:
    <i>Proceedings of the 2024 IEEE International Conference on Robotics and Automation</i>.
    IEEE; 2024:2774-2782. doi:<a href="https://doi.org/10.1109/ICRA57147.2024.10610284">10.1109/ICRA57147.2024.10610284</a>'
  apa: 'Lechner, M., Hasani, R., Amini, A., Wang, T. H., Henzinger, T. A., &#38; Rus,
    D. (2024). Overparametrization helps offline-to-online generalization of closed-loop
    control from pixels. In <i>Proceedings of the 2024 IEEE International Conference
    on Robotics and Automation</i> (pp. 2774–2782). Yokohama, Japan: IEEE. <a href="https://doi.org/10.1109/ICRA57147.2024.10610284">https://doi.org/10.1109/ICRA57147.2024.10610284</a>'
  chicago: Lechner, Mathias, Ramin Hasani, Alexander Amini, Tsun Hsuan Wang, Thomas
    A Henzinger, and Daniela Rus. “Overparametrization Helps Offline-to-Online Generalization
    of Closed-Loop Control from Pixels.” In <i>Proceedings of the 2024 IEEE International
    Conference on Robotics and Automation</i>, 2774–82. IEEE, 2024. <a href="https://doi.org/10.1109/ICRA57147.2024.10610284">https://doi.org/10.1109/ICRA57147.2024.10610284</a>.
  ieee: M. Lechner, R. Hasani, A. Amini, T. H. Wang, T. A. Henzinger, and D. Rus,
    “Overparametrization helps offline-to-online generalization of closed-loop control
    from pixels,” in <i>Proceedings of the 2024 IEEE International Conference on Robotics
    and Automation</i>, Yokohama, Japan, 2024, pp. 2774–2782.
  ista: 'Lechner M, Hasani R, Amini A, Wang TH, Henzinger TA, Rus D. 2024. Overparametrization
    helps offline-to-online generalization of closed-loop control from pixels. Proceedings
    of the 2024 IEEE International Conference on Robotics and Automation. ICRA: International
    Conference on Robotics and Automation, 2774–2782.'
  mla: Lechner, Mathias, et al. “Overparametrization Helps Offline-to-Online Generalization
    of Closed-Loop Control from Pixels.” <i>Proceedings of the 2024 IEEE International
    Conference on Robotics and Automation</i>, IEEE, 2024, pp. 2774–82, doi:<a href="https://doi.org/10.1109/ICRA57147.2024.10610284">10.1109/ICRA57147.2024.10610284</a>.
  short: M. Lechner, R. Hasani, A. Amini, T.H. Wang, T.A. Henzinger, D. Rus, in:,
    Proceedings of the 2024 IEEE International Conference on Robotics and Automation,
    IEEE, 2024, pp. 2774–2782.
conference:
  end_date: 2024-05-17
  location: Yokohama, Japan
  name: 'ICRA: International Conference on Robotics and Automation'
  start_date: 2024-05-13
date_created: 2024-09-08T22:01:13Z
date_published: 2024-08-08T00:00:00Z
date_updated: 2026-08-12T06:35:50Z
day: '08'
department:
- _id: ToHe
doi: 10.1109/ICRA57147.2024.10610284
ec_funded: 1
external_id:
  isi:
  - '001294576202044'
fulldoi: https://doi.org/10.1109/ICRA57147.2024.10610284
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 2774-2782
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
  call_identifier: H2020
  grant_number: '101020093'
  name: Vigilant Algorithmic Monitoring of Software
publication: Proceedings of the 2024 IEEE International Conference on Robotics and
  Automation
publication_identifier:
  isbn:
  - '9798350384574'
  issn:
  - 1050-4729
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overparametrization helps offline-to-online generalization of closed-loop control
  from pixels
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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:<a href="https://doi.org/10.25625/4FLFH8">10.25625/4FLFH8</a>'
  apa: 'Browning, T. D., &#38; Sutherland, A. (2024). Data and code for: Integral
    points on cubic surfaces: heuristics and numerics. Göttingen Research Online Data.
    <a href="https://doi.org/10.25625/4FLFH8">https://doi.org/10.25625/4FLFH8</a>'
  chicago: 'Browning, Timothy D, and Andrew Sutherland. “Data and Code for: Integral
    Points on Cubic Surfaces: Heuristics and Numerics.” Göttingen Research Online
    Data, 2024. <a href="https://doi.org/10.25625/4FLFH8">https://doi.org/10.25625/4FLFH8</a>.'
  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, <a href="https://doi.org/10.25625/4FLFH8">10.25625/4FLFH8</a>.'
  mla: 'Browning, Timothy D., and Andrew Sutherland. <i>Data and Code for: Integral
    Points on Cubic Surfaces: Heuristics and Numerics</i>. Göttingen Research Online
    Data, 2024, doi:<a href="https://doi.org/10.25625/4FLFH8">10.25625/4FLFH8</a>.'
  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? <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.2403.06833">10.48550/arXiv.2403.06833</a>
  apa: Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., &#38; Lampert, C. (n.d.).
    Can LLMs separate instructions from data? And what do we even mean by that? <i>arXiv</i>.
    <a href="https://doi.org/10.48550/arXiv.2403.06833">https://doi.org/10.48550/arXiv.2403.06833</a>
  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?” <i>ArXiv</i>, n.d. <a href="https://doi.org/10.48550/arXiv.2403.06833">https://doi.org/10.48550/arXiv.2403.06833</a>.
  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?,” <i>arXiv</i>. .
  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?” <i>ArXiv</i>, 2403.06833, doi:<a href="https://doi.org/10.48550/arXiv.2403.06833">10.48550/arXiv.2403.06833</a>.
  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: '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. <i>Journal
    of Applied Physics</i>. 2024;136(4). doi:<a href="https://doi.org/10.1063/5.0215151">10.1063/5.0215151</a>'
  apa: 'Lenton, I. C., Pertl, F., Shafeek, L. B., &#38; Waitukaitis, S. R. (2024).
    Beyond the blur: Using experimentally determined point spread functions to improve
    scanning Kelvin probe imaging. <i>Journal of Applied Physics</i>. AIP Publishing.
    <a href="https://doi.org/10.1063/5.0215151">https://doi.org/10.1063/5.0215151</a>'
  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.” <i>Journal of Applied Physics</i>. AIP Publishing,
    2024. <a href="https://doi.org/10.1063/5.0215151">https://doi.org/10.1063/5.0215151</a>.'
  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,” <i>Journal of Applied Physics</i>, 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.” <i>Journal of
    Applied Physics</i>, vol. 136, no. 4, 045305, AIP Publishing, 2024, doi:<a href="https://doi.org/10.1063/5.0215151">10.1063/5.0215151</a>.'
  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
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
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'
...
---
OA_place: repository
OA_type: green
_id: '22866'
article_processing_charge: No
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:<a href="https://doi.org/10.5281/zenodo.13833474">10.5281/zenodo.13833474</a>'
  apa: 'Hrast, M. (2024). Data for: Ab initio Auger spectrum of the ultrafast dissociating
    2p3/2−1σ* resonance in HCl. Repository. <a href="https://doi.org/10.5281/zenodo.13833474">https://doi.org/10.5281/zenodo.13833474</a>'
  chicago: 'Hrast, Mateja. “Data for: Ab Initio Auger Spectrum of the Ultrafast Dissociating
    2p3/2−1σ* Resonance in HCl.” Repository, 2024. <a href="https://doi.org/10.5281/zenodo.13833474">https://doi.org/10.5281/zenodo.13833474</a>.'
  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, <a href="https://doi.org/10.5281/zenodo.13833474">10.5281/zenodo.13833474</a>.'
  mla: 'Hrast, Mateja. <i>Data for: Ab Initio Auger Spectrum of the Ultrafast Dissociating
    2p3/2−1σ* Resonance in HCl</i>. Repository, 2024, doi:<a href="https://doi.org/10.5281/zenodo.13833474">10.5281/zenodo.13833474</a>.'
  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.</jats:p>
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. <i>Journal of Experimental
    Biology</i>. 2024;227(1). doi:<a href="https://doi.org/10.1242/jeb.246217">10.1242/jeb.246217</a>
  apa: Pal, A., Joshi, M., &#38; Thaker, M. (2024). Too much information? Males convey
    parasite levels using more signal modalities than females utilise. <i>Journal
    of Experimental Biology</i>. The Company of Biologists. <a href="https://doi.org/10.1242/jeb.246217">https://doi.org/10.1242/jeb.246217</a>
  chicago: Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males
    Convey Parasite Levels Using More Signal Modalities than Females Utilise.” <i>Journal
    of Experimental Biology</i>. The Company of Biologists, 2024. <a href="https://doi.org/10.1242/jeb.246217">https://doi.org/10.1242/jeb.246217</a>.
  ieee: A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite
    levels using more signal modalities than females utilise,” <i>Journal of Experimental
    Biology</i>, 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.” <i>Journal of Experimental Biology</i>,
    vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:<a href="https://doi.org/10.1242/jeb.246217">10.1242/jeb.246217</a>.
  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 &amp;gt; 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. <i>Evolution
    Letters</i>. 2024;8(4):575-586. doi:<a href="https://doi.org/10.1093/evlett/qrae014">10.1093/evlett/qrae014</a>
  apa: Le Moan, A., Stankowski, S., Rafajlović, M., Ortega-Martinez, O., Faria, R.,
    Butlin, R. K., &#38; Johannesson, K. (2024). Coupling of twelve putative chromosomal
    inversions maintains a strong barrier to gene flow between snail ecotypes. <i>Evolution
    Letters</i>. Oxford University Press. <a href="https://doi.org/10.1093/evlett/qrae014">https://doi.org/10.1093/evlett/qrae014</a>
  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.”
    <i>Evolution Letters</i>. Oxford University Press, 2024. <a href="https://doi.org/10.1093/evlett/qrae014">https://doi.org/10.1093/evlett/qrae014</a>.
  ieee: A. Le Moan <i>et al.</i>, “Coupling of twelve putative chromosomal inversions
    maintains a strong barrier to gene flow between snail ecotypes,” <i>Evolution
    Letters</i>, 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.” <i>Evolution Letters</i>,
    vol. 8, no. 4, Oxford University Press, 2024, pp. 575–86, doi:<a href="https://doi.org/10.1093/evlett/qrae014">10.1093/evlett/qrae014</a>.
  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
license: https://creativecommons.org/licenses/by-nc/4.0/
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.
    <i>Science Advances</i>. 2024;10(41). doi:<a href="https://doi.org/10.1126/sciadv.adp2102">10.1126/sciadv.adp2102</a>'
  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. <i>Science Advances</i>.
    AAAS. <a href="https://doi.org/10.1126/sciadv.adp2102">https://doi.org/10.1126/sciadv.adp2102</a>'
  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.” <i>Science Advances</i>. AAAS, 2024. <a href="https://doi.org/10.1126/sciadv.adp2102">https://doi.org/10.1126/sciadv.adp2102</a>.'
  ieee: 'D. F. Garcia Castillo <i>et al.</i>, “Predicting rapid adaptation in time
    from adaptation in space: A 30-year field experiment in marine snails,” <i>Science
    Advances</i>, 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.” <i>Science
    Advances</i>, vol. 10, no. 41, eadp2102, AAAS, 2024, doi:<a href="https://doi.org/10.1126/sciadv.adp2102">10.1126/sciadv.adp2102</a>.'
  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. <i>Journal of Evolutionary Biology</i>. 2024;37(6):677-692.
    doi:<a href="https://doi.org/10.1093/jeb/voae048">10.1093/jeb/voae048</a>
  apa: Reynes, L., Fouqueau, L., Aurelle, D., Mauger, S., Destombe, C., &#38; Valero,
    M. (2024). Temporal genomics help in deciphering neutral and adaptive patterns
    in the contemporary evolution of kelp populations. <i>Journal of Evolutionary
    Biology</i>. Oxford University Press. <a href="https://doi.org/10.1093/jeb/voae048">https://doi.org/10.1093/jeb/voae048</a>
  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.” <i>Journal
    of Evolutionary Biology</i>. Oxford University Press, 2024. <a href="https://doi.org/10.1093/jeb/voae048">https://doi.org/10.1093/jeb/voae048</a>.
  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,” <i>Journal of Evolutionary Biology</i>, 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.” <i>Journal of Evolutionary
    Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 677–92, doi:<a
    href="https://doi.org/10.1093/jeb/voae048">10.1093/jeb/voae048</a>.
  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:<a href="https://doi.org/10.5281/zenodo.10790257">10.5281/zenodo.10790257</a>
  apa: Le Moan, A. (2024). Coupling of twelve putative chromosomal inversions maintains
    a strong barrier to gene flow between snail ecotypes. Repository. <a href="https://doi.org/10.5281/zenodo.10790257">https://doi.org/10.5281/zenodo.10790257</a>
  chicago: Le Moan, Alan. “Coupling of Twelve Putative Chromosomal Inversions Maintains
    a Strong Barrier to Gene Flow between Snail Ecotypes.” Repository, 2024. <a href="https://doi.org/10.5281/zenodo.10790257">https://doi.org/10.5281/zenodo.10790257</a>.
  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, <a href="https://doi.org/10.5281/zenodo.10790257">10.5281/zenodo.10790257</a>.
  mla: Le Moan, Alan. <i>Coupling of Twelve Putative Chromosomal Inversions Maintains
    a Strong Barrier to Gene Flow between Snail Ecotypes</i>. Repository, 2024, doi:<a
    href="https://doi.org/10.5281/zenodo.10790257">10.5281/zenodo.10790257</a>.
  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'
...
---
OA_place: repository
OA_type: green
_id: '22869'
abstract:
- lang: eng
  text: 'Scripts and data used in the research study Predicting rapid adaptation in
    time from adaptation in space: a 30-year field experiment in marine snails.'
article_processing_charge: No
author:
- first_name: Nicholas
  full_name: Barton, Nicholas
  last_name: Barton
citation:
  ama: 'Barton N. Data and code for: Predicting rapid adaptation in time from adaptation
    in space: a 30-year field experiment in marine snails. 2024. doi:<a href="https://doi.org/10.5281/zenodo.12159343">10.5281/zenodo.12159343</a>'
  apa: 'Barton, N. (2024). Data and code for: Predicting rapid adaptation in time
    from adaptation in space: a 30-year field experiment in marine snails. Repository.
    <a href="https://doi.org/10.5281/zenodo.12159343">https://doi.org/10.5281/zenodo.12159343</a>'
  chicago: 'Barton, Nicholas. “Data and Code for: Predicting Rapid Adaptation in Time
    from Adaptation in Space: A 30-Year Field Experiment in Marine Snails.” Repository,
    2024. <a href="https://doi.org/10.5281/zenodo.12159343">https://doi.org/10.5281/zenodo.12159343</a>.'
  ieee: 'N. Barton, “Data and code for: Predicting rapid adaptation in time from adaptation
    in space: a 30-year field experiment in marine snails.” Repository, 2024.'
  ista: 'Barton N. 2024. Data and code for: Predicting rapid adaptation in time from
    adaptation in space: a 30-year field experiment in marine snails, Repository,
    <a href="https://doi.org/10.5281/zenodo.12159343">10.5281/zenodo.12159343</a>.'
  mla: 'Barton, Nicholas. <i>Data and Code for: Predicting Rapid Adaptation in Time
    from Adaptation in Space: A 30-Year Field Experiment in Marine Snails</i>. Repository,
    2024, doi:<a href="https://doi.org/10.5281/zenodo.12159343">10.5281/zenodo.12159343</a>.'
  short: N. Barton, (2024).
contributor:
- contributor_type: researcher
  first_name: Diego
  last_name: Garcia Castillo
- contributor_type: researcher
  first_name: Nicholas
  last_name: Barton
- contributor_type: researcher
  first_name: Rui
  last_name: Faria
- contributor_type: researcher
  first_name: Jenny
  last_name: Larsson
- contributor_type: researcher
  first_name: Sean
  last_name: Stankowski
- contributor_type: researcher
  first_name: Roger
  last_name: Butlin
- contributor_type: researcher
  first_name: Kerstin
  last_name: Johannesson
- contributor_type: researcher
  first_name: Anja Marie
  last_name: Westram
date_created: 2026-09-09T10:09:57Z
date_published: 2024-06-19T00:00:00Z
date_updated: 2026-09-09T10:10:02Z
day: '19'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/zenodo.12159343
fulldoi: https://doi.org/10.5281/zenodo.12159343
main_file_link:
- open_access: '1'
  url: https://doi.org/10.5281/zenodo.12159343
month: '06'
oa: 1
oa_version: None
publisher: Repository
related_material:
  record:
  - id: '18491'
    relation: used_in_publication
    status: public
status: public
title: 'Data and code for: Predicting rapid adaptation in time from adaptation in
  space: a 30-year field experiment in marine snails'
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '17161'
abstract:
- lang: eng
  text: Dynamic processes in molecules can occur on a wide range of timescales, and
    it is important to understand which timescales of motion contribute to different
    parameters used in dynamics measurements. For spin relaxation, this can easily
    be understood from the sampling frequencies of the spectral-density function by
    different relaxation-rate constants. In addition to data from relaxation measurements,
    determining dynamically averaged anisotropic interactions in magic-angle spinning
    (MAS) solid-state NMR allows for better quantification of the amplitude of molecular
    motion. For partially averaged anisotropic interactions, the relevant timescales
    of motion are not so clearly defined. Whether the averaging depends on the experimental
    methods (e.g., pulse sequences) or conditions (e.g., MAS frequency, magnitude
    of anisotropic interaction, radio-frequency field amplitudes) is not fully understood.
    To investigate these questions, we performed numerical simulations of dynamic
    systems based on the stochastic Liouville equation using several experiments for
    recoupling the dipolar coupling, chemical-shift anisotropy or quadrupolar coupling.
    As described in the literature, the transition between slow motion, where parameters
    characterizing the anisotropic interaction are not averaged, and fast motion,
    where the tensors are averaged leading to a scaled anisotropic quantity, occurs
    over a window of motional rate constants that depends mainly on the strength of
    the interaction. This transition region can span 2 orders of magnitude in exchange-rate
    constants (typically in the microsecond range) but depends only marginally on
    the employed recoupling scheme or sample spinning frequency. The transition region
    often coincides with a fast relaxation of coherences, making precise quantitative
    measurements difficult. Residual couplings in off-magic-angle experiments, however,
    average over longer timescales of motion. While in principle one may gain information
    on the timescales of motion from the transition area, extracting such information
    is hampered by low signal-to-noise ratio in experimental spectra due to fast relaxation
    that occurs in the same region.
acknowledgement: "We would like to thank Kay Saalwächter for pointing out important
  aspects of the intermediate regime during the open review process. Lea Marie Becker
  is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute
  of Science and Technology Austria.\r\nThis research has been supported by the Österreichischen
  Akademie der Wissenschaften (grant no. PR10660EAW01) and the Schweizerischer Nationalfonds
  zur Förderung der Wissenschaftlichen Forschung (grant nos. 200020_188988 and 200020_219375)."
article_processing_charge: Yes
article_type: original
author:
- first_name: Kathrin
  full_name: Aebischer, Kathrin
  last_name: Aebischer
- first_name: Lea Marie
  full_name: Becker, Lea Marie
  id: 36336939-eb97-11eb-a6c2-c83f1214ca79
  last_name: Becker
  orcid: 0000-0002-6401-5151
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Matthias
  full_name: Ernst, Matthias
  last_name: Ernst
citation:
  ama: Aebischer K, Becker LM, Schanda P, Ernst M. Evaluating the motional timescales
    contributing to averaged anisotropic interactions in MAS solid-state NMR. <i>Magnetic
    Resonance</i>. 2024;5(1):69-86. doi:<a href="https://doi.org/10.5194/mr-5-69-2024">10.5194/mr-5-69-2024</a>
  apa: Aebischer, K., Becker, L. M., Schanda, P., &#38; Ernst, M. (2024). Evaluating
    the motional timescales contributing to averaged anisotropic interactions in MAS
    solid-state NMR. <i>Magnetic Resonance</i>. Copernicus Publications. <a href="https://doi.org/10.5194/mr-5-69-2024">https://doi.org/10.5194/mr-5-69-2024</a>
  chicago: Aebischer, Kathrin, Lea Marie Becker, Paul Schanda, and Matthias Ernst.
    “Evaluating the Motional Timescales Contributing to Averaged Anisotropic Interactions
    in MAS Solid-State NMR.” <i>Magnetic Resonance</i>. Copernicus Publications, 2024.
    <a href="https://doi.org/10.5194/mr-5-69-2024">https://doi.org/10.5194/mr-5-69-2024</a>.
  ieee: K. Aebischer, L. M. Becker, P. Schanda, and M. Ernst, “Evaluating the motional
    timescales contributing to averaged anisotropic interactions in MAS solid-state
    NMR,” <i>Magnetic Resonance</i>, vol. 5, no. 1. Copernicus Publications, pp. 69–86,
    2024.
  ista: Aebischer K, Becker LM, Schanda P, Ernst M. 2024. Evaluating the motional
    timescales contributing to averaged anisotropic interactions in MAS solid-state
    NMR. Magnetic Resonance. 5(1), 69–86.
  mla: Aebischer, Kathrin, et al. “Evaluating the Motional Timescales Contributing
    to Averaged Anisotropic Interactions in MAS Solid-State NMR.” <i>Magnetic Resonance</i>,
    vol. 5, no. 1, Copernicus Publications, 2024, pp. 69–86, doi:<a href="https://doi.org/10.5194/mr-5-69-2024">10.5194/mr-5-69-2024</a>.
  short: K. Aebischer, L.M. Becker, P. Schanda, M. Ernst, Magnetic Resonance 5 (2024)
    69–86.
date_created: 2024-06-23T22:01:02Z
date_published: 2024-06-11T00:00:00Z
date_updated: 2026-09-11T08:49:55Z
day: '11'
ddc:
- '530'
department:
- _id: PaSc
doi: 10.5194/mr-5-69-2024
external_id:
  pmid:
  - '40384772'
file:
- access_level: open_access
  checksum: d01074f6919387fcaf8c9ebed320ccae
  content_type: application/pdf
  creator: dernst
  date_created: 2024-06-27T06:42:55Z
  date_updated: 2024-06-27T06:42:55Z
  file_id: '17181'
  file_name: 2024_MagneticResonance_Aebischer.pdf
  file_size: 6736194
  relation: main_file
  success: 1
file_date_updated: 2024-06-27T06:42:55Z
fulldoi: https://doi.org/10.5194/mr-5-69-2024
has_accepted_license: '1'
intvolume: '         5'
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 69-86
pmid: 1
project:
- _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0
  grant_number: '26777'
  name: Exploring protein dynamics by solid-state MAS NMR through specific labeling
    approaches
publication: Magnetic Resonance
publication_identifier:
  eissn:
  - 2699-0016
publication_status: published
publisher: Copernicus Publications
quality_controlled: '1'
related_material:
  record:
  - id: '22906'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Evaluating the motional timescales contributing to averaged anisotropic interactions
  in MAS solid-state NMR
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'
...
---
OA_place: repository
OA_type: green
_id: '22906'
article_processing_charge: No
author:
- first_name: Kathrin
  full_name: Aebischer, Kathrin
  last_name: Aebischer
citation:
  ama: Aebischer K. Evaluating the motional time scales contributing to averaged anisotropic
    interactions in MAS solid-state NMR. 2024. doi:<a href="https://doi.org/10.3929/ethz-b-000666765">10.3929/ethz-b-000666765</a>
  apa: Aebischer, K. (2024). Evaluating the motional time scales contributing to averaged
    anisotropic interactions in MAS solid-state NMR. Repository. <a href="https://doi.org/10.3929/ethz-b-000666765">https://doi.org/10.3929/ethz-b-000666765</a>
  chicago: Aebischer, Kathrin. “Evaluating the Motional Time Scales Contributing to
    Averaged Anisotropic Interactions in MAS Solid-State NMR.” Repository, 2024. <a
    href="https://doi.org/10.3929/ethz-b-000666765">https://doi.org/10.3929/ethz-b-000666765</a>.
  ieee: K. Aebischer, “Evaluating the motional time scales contributing to averaged
    anisotropic interactions in MAS solid-state NMR.” Repository, 2024.
  ista: Aebischer K. 2024. Evaluating the motional time scales contributing to averaged
    anisotropic interactions in MAS solid-state NMR, Repository, <a href="https://doi.org/10.3929/ethz-b-000666765">10.3929/ethz-b-000666765</a>.
  mla: Aebischer, Kathrin. <i>Evaluating the Motional Time Scales Contributing to
    Averaged Anisotropic Interactions in MAS Solid-State NMR</i>. Repository, 2024,
    doi:<a href="https://doi.org/10.3929/ethz-b-000666765">10.3929/ethz-b-000666765</a>.
  short: K. Aebischer, (2024).
contributor:
- contributor_type: contact_person
  first_name: Matthias
  last_name: Ernst
- contributor_type: data_collector
  first_name: Kathrin
  last_name: Aebischer
- contributor_type: data_collector
  first_name: Matthias
  last_name: Ernst
- contributor_type: data_collector
  first_name: Paul
  last_name: Schanda
- contributor_type: data_collector
  first_name: Lea Marie
  last_name: Becker
- contributor_type: producer
  first_name: Matthias
  last_name: ' Ernst'
- contributor_type: producer
  first_name: Kathrin
  last_name: ' Aebischer'
- contributor_type: producer
  first_name: 'Paul '
  last_name: Schanda
- contributor_type: producer
  first_name: Lea Marie
  last_name: Becker
date_created: 2026-09-11T08:49:48Z
date_published: 2024-04-03T00:00:00Z
date_updated: 2026-09-11T08:49:55Z
day: '03'
ddc:
- '530'
department:
- _id: PaSc
doi: 10.3929/ethz-b-000666765
fulldoi: https://doi.org/10.3929/ethz-b-000666765
main_file_link:
- open_access: '1'
  url: https://doi.org/10.3929/ethz-b-000666765
month: '04'
oa: 1
oa_version: None
publisher: Repository
related_material:
  record:
  - id: '17161'
    relation: used_in_publication
    status: public
status: public
title: Evaluating the motional time scales contributing to averaged anisotropic interactions
  in MAS solid-state NMR
type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
APC_amount: 6248,82 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18603'
abstract:
- lang: eng
  text: It is widely believed that information storage in neuronal circuits involves
    nanoscopic structural changes at synapses, resulting in the formation of synaptic
    engrams. However, direct evidence for this hypothesis is lacking. To test this
    conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic
    recordings, and structural analysis by electron microscopy (EM) and freeze-fracture
    replica labeling (FRL) at the rodent hippocampal mossy fiber synapse, a key synapse
    in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic
    transmission revealed that forskolin-induced chemical potentiation increased the
    readily releasable vesicle pool size and vesicular release probability by 146%
    and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL
    demonstrated an increase in the number of vesicles close to the plasma membrane
    and the number of clusters of the priming protein Munc13-1, indicating an increase
    in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed
    a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels,
    suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our
    results indicate that presynaptic plasticity is associated with structural reorganization
    of active zones. We propose that changes in potential nanoscopic organization
    at synaptic vesicle release sites may be correlates of learning and memory at
    a plastic central synapse.
acknowledged_ssus:
- _id: EM-Fac
- _id: PreCl
acknowledgement: "We thank Carolina Borges-Merjane, Jing-Jing Chen, Katharina Lichter,
  and Samuel Young for critically reading the manuscript; the Electron Microscopy
  Facility of ISTA, in particular Vanessa Zheden, for extensive support, advice, and
  experimental assistance; the Preclinical Facility of ISTA, in particular Victoria
  Wimmer and Michael Schunn, for experimental assistance; Florian Marr and Christina
  Altmutter for technical support; Alois Schlögl for help with analysis; and Eleftheria
  Kralli-Beller for manuscript editing. We also thank Cordelia Imig for providing
  Munc13-1cKO-Munc13-2/3(−/−) mutant mice. Part of the work has been published in
  O.K.’s thesis in partial fulfillment of the requirements for the degree of Doctor
  of Philosophy.\r\nThis project received funding from the European Research Council
  and European Union’s Horizon 2020 research and innovation programme (ERC 692692
  to P.J.; https://cordis.europa.eu/project/id/692692/de) and from the Fond zur Förderung
  der Wissenschaftlichen Forschung (Z312-B27 Wittgenstein award to P.J., https://www.fwf.ac.at/en/funding/portfolio/projects/fwf-wittgenstein-award;
  W1205-B09 and P36232-B to P.J., https://www.fwf.ac.at/en/funding; I6166-B to R.S.;
  https://www.fwf.ac.at/en/funding). The funders had no role in study design, data
  collection and analysis, decision to publish, or preparation of the manuscript."
article_number: e3002879
article_processing_charge: Yes
article_type: original
author:
- first_name: Olena
  full_name: Kim, Olena
  id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
  last_name: Kim
  orcid: 0000-0003-2344-1039
- first_name: Yuji
  full_name: Okamoto, Yuji
  id: 3337E116-F248-11E8-B48F-1D18A9856A87
  last_name: Okamoto
  orcid: 0000-0003-0408-6094
- first_name: Walter
  full_name: Kaufmann, Walter
  id: 3F99E422-F248-11E8-B48F-1D18A9856A87
  last_name: Kaufmann
  orcid: 0000-0001-9735-5315
- first_name: Nils
  full_name: Brose, Nils
  last_name: Brose
- first_name: Ryuichi
  full_name: Shigemoto, Ryuichi
  id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
  last_name: Shigemoto
  orcid: 0000-0001-8761-9444
- first_name: Peter M
  full_name: Jonas, Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
citation:
  ama: Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. Presynaptic cAMP-PKA-mediated
    potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle
    coupling at hippocampal mossy fiber boutons. <i>PLoS Biology</i>. 2024;22(11).
    doi:<a href="https://doi.org/10.1371/journal.pbio.3002879">10.1371/journal.pbio.3002879</a>
  apa: Kim, O., Okamoto, Y., Kaufmann, W., Brose, N., Shigemoto, R., &#38; Jonas,
    P. M. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration
    of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber
    boutons. <i>PLoS Biology</i>. Public Library of Science. <a href="https://doi.org/10.1371/journal.pbio.3002879">https://doi.org/10.1371/journal.pbio.3002879</a>
  chicago: Kim, Olena, Yuji Okamoto, Walter Kaufmann, Nils Brose, Ryuichi Shigemoto,
    and Peter M Jonas. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration
    of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber
    Boutons.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href="https://doi.org/10.1371/journal.pbio.3002879">https://doi.org/10.1371/journal.pbio.3002879</a>.
  ieee: O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, and P. M. Jonas,
    “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic
    vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons,”
    <i>PLoS Biology</i>, vol. 22, no. 11. Public Library of Science, 2024.
  ista: Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. 2024. Presynaptic
    cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools
    and channel-vesicle coupling at hippocampal mossy fiber boutons. PLoS Biology.
    22(11), e3002879.
  mla: Kim, Olena, et al. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration
    of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber
    Boutons.” <i>PLoS Biology</i>, vol. 22, no. 11, e3002879, Public Library of Science,
    2024, doi:<a href="https://doi.org/10.1371/journal.pbio.3002879">10.1371/journal.pbio.3002879</a>.
  short: O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, P.M. Jonas, PLoS
    Biology 22 (2024).
corr_author: '1'
date_created: 2024-12-01T23:01:54Z
date_published: 2024-11-18T00:00:00Z
date_updated: 2026-04-16T12:20:34Z
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related_material:
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status: public
title: Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic
  vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons
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: 22
year: '2024'
...
---
_id: '18296'
abstract:
- lang: eng
  text: It is widely believed that information storage in neuronal circuits involves
    nanoscopic structural changes at synapses, resulting in the formation of synaptic
    engrams. However, direct evidence for this hypothesis is lacking. To test this
    conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic
    recordings, and structural analysis by electron microscopy (EM) and freeze-fracture
    replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse
    in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic
    transmission revealed that forskolin-induced chemical potentiation increased the
    readily releasable vesicle pool size and vesicular release probability by 146%
    and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL
    demonstrated an increase in the number of vesicles close to the plasma membrane
    and the number of clusters of the priming protein Munc13-1, indicating an increase
    in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed
    a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels,
    suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our
    results indicate that presynaptic plasticity is associated with structural reorganization
    of active zones. We propose that changes in potential nanoscopic organization
    at synaptic vesicle release sites may be correlates of learning and memory at
    a plastic central synapse.
article_processing_charge: No
author:
- first_name: Olena
  full_name: Kim, Olena
  id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
  last_name: Kim
  orcid: 0000-0003-2344-1039
citation:
  ama: Kim O. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of
    synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber
    boutons. 2024. doi:<a href="https://doi.org/10.15479/AT:ISTA:18296">10.15479/AT:ISTA:18296</a>
  apa: Kim, O. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration
    of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber
    boutons. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:18296">https://doi.org/10.15479/AT:ISTA:18296</a>
  chicago: Kim, Olena. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration
    of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber
    Boutons.” Institute of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/AT:ISTA:18296">https://doi.org/10.15479/AT:ISTA:18296</a>.
  ieee: O. Kim, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration
    of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber
    boutons.” Institute of Science and Technology Austria, 2024.
  ista: Kim O. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration
    of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber
    boutons, Institute of Science and Technology Austria, <a href="https://doi.org/10.15479/AT:ISTA:18296">10.15479/AT:ISTA:18296</a>.
  mla: Kim, Olena. <i>Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration
    of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber
    Boutons</i>. Institute of Science and Technology Austria, 2024, doi:<a href="https://doi.org/10.15479/AT:ISTA:18296">10.15479/AT:ISTA:18296</a>.
  short: O. Kim, (2024).
contributor:
- contributor_type: researcher
  first_name: Olena
  id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
  last_name: Kim
- contributor_type: researcher
  first_name: Yuji
  id: 3337E116-F248-11E8-B48F-1D18A9856A87
  last_name: Okamoto
  orcid: 0000-0003-0408-6094
- contributor_type: researcher
  first_name: Walter
  id: 3F99E422-F248-11E8-B48F-1D18A9856A87
  last_name: Kaufmann
  orcid: 0000-0001-9735-5315
- contributor_type: researcher
  first_name: 'Nils '
  last_name: Brose
- contributor_type: researcher
  first_name: Ryuichi
  id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
  last_name: Shigemoto
  orcid: 0000-0001-8761-9444
- contributor_type: supervisor
  first_name: Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
corr_author: '1'
date_created: 2024-10-11T10:12:17Z
date_published: 2024-10-11T00:00:00Z
date_updated: 2026-09-14T08:48:01Z
day: '11'
ddc:
- '570'
department:
- _id: PeJo
- _id: RySh
- _id: EM-Fac
doi: 10.15479/AT:ISTA:18296
ec_funded: 1
file:
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  creator: okim
  date_created: 2024-10-11T10:04:19Z
  date_updated: 2024-10-11T10:04:19Z
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fulldoi: https://doi.org/10.15479/AT:ISTA:18296
has_accepted_license: '1'
keyword:
- Hippocampal mossy fiber synapses
- short-term potentiation
- long-term potentiation
- presynaptic plasticity
- electron microscopy
- freeze-fracture replica labeling
- paired recordings
- forskolin
- cyclic adenosine monophosphate (cAMP)
- protein kinase A (PKA)
- neuromodulation
- synaptic vesicle pools
- presynaptic Ca2+ channels
- Munc13
- docking
- priming
- active zone
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '692692'
  name: Biophysics and circuit function of a giant cortical glutamatergic synapse
publisher: Institute of Science and Technology Austria
related_material:
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status: public
title: Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic
  vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons
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
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2024'
...
---
_id: '14687'
abstract:
- lang: eng
  text: The short history of research on Li-O2 batteries has seen a remarkable number
    of mechanistic U-turns over the years. From the initial use of carbonate electrolytes,
    that were then found to be entirely unsuitable, to the belief that (su)peroxide
    was solely responsible for degradation, before the more reactive singlet oxygen
    was found to form, to the hypothesis that capacity depends on a competing surface/solution
    mechanism before a practically exclusive solution mechanism was identified. Herein,
    we argue for an ever-fresh look at the reported data without bias towards supposedly
    established explanations. We explain how the latest findings on rate and capacity
    limits, as well as the origin of side reactions, are connected via the disproportionation
    (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the
    design of electrolytes and mediators on how to suppress side reactions and to
    enable high rate and high reversible capacity.
acknowledgement: S.A.F. is indebted to ISTA for support. R.B.J. thanks the European
  Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
  grant agreement No 101034413 for funding. B.P. thanks Alistore ERI for providing
  a PhD scholarship.
article_number: e202316476
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Rajesh B
  full_name: Jethwa, Rajesh B
  id: 4cc538d5-803f-11ed-ab7e-8139573aad8f
  last_name: Jethwa
  orcid: 0000-0002-0404-4356
- first_name: Soumyadip
  full_name: Mondal, Soumyadip
  id: d25d21ef-dc8d-11ea-abe3-ec4576307f48
  last_name: Mondal
- first_name: Bhargavi
  full_name: Pant, Bhargavi
  id: 50c64d4d-eb97-11eb-a6c2-d33e5e14f112
  last_name: Pant
- first_name: Stefan Alexander
  full_name: Freunberger, Stefan Alexander
  id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
  last_name: Freunberger
  orcid: 0000-0003-2902-5319
citation:
  ama: Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching
    reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International
    Edition</i>. 2024;63(28). doi:<a href="https://doi.org/10.1002/anie.202316476">10.1002/anie.202316476</a>
  apa: Jethwa, R. B., Mondal, S., Pant, B., &#38; Freunberger, S. A. (2024). To DISP
    or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries.
    <i>Angewandte Chemie International Edition</i>. Wiley. <a href="https://doi.org/10.1002/anie.202316476">https://doi.org/10.1002/anie.202316476</a>
  chicago: Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander
    Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning
    Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>. Wiley,
    2024. <a href="https://doi.org/10.1002/anie.202316476">https://doi.org/10.1002/anie.202316476</a>.
  ieee: R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not?
    The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” <i>Angewandte
    Chemie International Edition</i>, vol. 63, no. 28. Wiley, 2024.
  ista: Jethwa RB, Mondal S, Pant B, Freunberger SA. 2024. To DISP or not? The far‐reaching
    reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International
    Edition. 63(28), e202316476.
  mla: Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms
    Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>,
    vol. 63, no. 28, e202316476, Wiley, 2024, doi:<a href="https://doi.org/10.1002/anie.202316476">10.1002/anie.202316476</a>.
  short: R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International
    Edition 63 (2024).
corr_author: '1'
date_created: 2023-12-15T16:10:13Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2026-09-16T07:07:04Z
day: '08'
ddc:
- '540'
department:
- _id: StFr
- _id: GradSch
doi: 10.1002/anie.202316476
ec_funded: 1
external_id:
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  - '001241932700001'
  pmid:
  - '38095355'
file:
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  success: 1
file_date_updated: 2024-07-16T11:54:46Z
fulldoi: https://doi.org/10.1002/anie.202316476
has_accepted_license: '1'
intvolume: '        63'
isi: 1
issue: '28'
keyword:
- General Chemistry
- Catalysis
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Angewandte Chemie International Edition
publication_identifier:
  eissn:
  - 1521-3773
  issn:
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publication_status: published
publisher: Wiley
quality_controlled: '1'
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scopus_import: '1'
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title: To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air
  batteries
tmp:
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    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 63
year: '2024'
...
