[{"department":[{"_id":"LaEr"}],"year":"2024","arxiv":1,"status":"public","license":"https://creativecommons.org/licenses/by/4.0/","type":"preprint","fulldoi":"https://doi.org/10.48550/arXiv.2410.10809","day":"14","date_updated":"2026-07-29T13:18:16Z","publication_status":"draft","date_created":"2025-04-11T11:54:56Z","article_processing_charge":"No","doi":"10.48550/arXiv.2410.10809","oa_version":"Preprint","author":[{"full_name":"Henheik, Sven Joscha","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","orcid":"0000-0003-1106-327X","last_name":"Henheik"},{"last_name":"Wessel","full_name":"Wessel, Tom","first_name":"Tom"}],"abstract":[{"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.","lang":"eng"}],"external_id":{"arxiv":["2410.10809"]},"related_material":{"record":[{"id":"19540","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"corr_author":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"S.J. Henheik, T. Wessel, ArXiv (n.d.).","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>","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>.","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>.","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>","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>."},"publication":"arXiv","date_published":"2024-10-14T00:00:00Z","OA_place":"repository","oa":1,"month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Response theory for locally gapped systems","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2410.10809"}],"_id":"19551"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":135,"month":"04","date_published":"2024-04-28T00:00:00Z","das_tickbox":"1","oa":1,"_id":"15359","supplementarymaterial":"no","publisher":"AIP Publishing","article_type":"review","title":"Molecular dynamics simulations of heat transport using machine-learned potentials: A mini-review and tutorial on GPUMD with neuroevolution potentials","author":[{"full_name":"Dong, Haikuan","first_name":"Haikuan","last_name":"Dong"},{"first_name":"Yongbo","full_name":"Shi, Yongbo","last_name":"Shi"},{"full_name":"Ying, Penghua","first_name":"Penghua","last_name":"Ying"},{"first_name":"Ke","full_name":"Xu, Ke","last_name":"Xu"},{"last_name":"Liang","full_name":"Liang, Ting","first_name":"Ting"},{"last_name":"Wang","full_name":"Wang, Yanzhou","first_name":"Yanzhou"},{"last_name":"Zeng","orcid":"0000-0001-5126-4928","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","full_name":"Zeng, Zezhu"},{"full_name":"Wu, Xin","first_name":"Xin","last_name":"Wu"},{"full_name":"Zhou, Wenjiang","first_name":"Wenjiang","last_name":"Zhou"},{"full_name":"Xiong, Shiyun","first_name":"Shiyun","last_name":"Xiong"},{"last_name":"Chen","first_name":"Shunda","full_name":"Chen, Shunda"},{"full_name":"Fan, Zheyong","first_name":"Zheyong","last_name":"Fan"}],"abstract":[{"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.","lang":"eng"}],"external_id":{"arxiv":["2401.16249"],"isi":["001215967400009"]},"article_number":"161101","file_date_updated":"2024-05-13T08:07:44Z","publication_identifier":{"eissn":["1089-7550"],"issn":["0021-8979"]},"oa_version":"Preprint","date_created":"2024-05-05T22:01:03Z","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","doi":"10.1063/5.0200833","citation":{"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>.","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.","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.","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).","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>","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>.","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>"},"intvolume":"       135","publication":"Journal of Applied Physics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"related_material":{"link":[{"relation":"software","url":"https://gitlab.com/brucefan1983/nep-data"}]},"language":[{"iso":"eng"}],"type":"journal_article","has_accepted_license":"1","status":"public","ec_funded":1,"issue":"16","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"fulldoi":"https://doi.org/10.1063/5.0200833","date_updated":"2026-08-07T10:35:13Z","day":"28","scopus_import":"1","ddc":["530"],"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).","researchdata_availability":"no","quality_controlled":"1","arxiv":1,"file":[{"creator":"dernst","relation":"main_file","file_name":"2024_JourApplPhysics_Dong.pdf","content_type":"application/pdf","date_updated":"2024-05-13T08:07:44Z","checksum":"4d6abb3ebe058ce8eebf4fc7e9cdda0d","file_id":"15382","access_level":"open_access","date_created":"2024-05-13T08:07:44Z","file_size":3240613,"success":1}],"year":"2024","department":[{"_id":"BiCh"}],"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."},{"oa":1,"das_tickbox":"1","date_published":"2024-07-14T00:00:00Z","volume":161,"month":"07","publisher":"AIP Publishing","_id":"17278","supplementarymaterial":"no","title":"Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures","article_type":"original","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.02216","open_access":"1"}],"article_number":"034111","external_id":{"pmid":["39007379"],"arxiv":["2405.02216"],"isi":["001281819100016"]},"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."}],"author":[{"first_name":"Xiaoyu","full_name":"Wang, Xiaoyu","id":"8dff9c62-32b0-11ee-9fa8-fc73025e10f3","last_name":"Wang"},{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","full_name":"Cheng, Bingqing"}],"publication_status":"published","article_processing_charge":"No","date_created":"2024-07-21T22:01:00Z","doi":"10.1063/5.0217232","oa_version":"Preprint","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"publication":"Journal of Chemical Physics","citation":{"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>","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>.","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>","short":"X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).","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."},"intvolume":"       161","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0"}]},"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","status":"public","type":"journal_article","issue":"3","day":"14","date_updated":"2026-08-07T10:38:59Z","fulldoi":"https://doi.org/10.1063/5.0217232","pmid":1,"scopus_import":"1","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).","quality_controlled":"1","researchdata_availability":"no","arxiv":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.","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"year":"2024"},{"quality_controlled":"1","OA_type":"free access","year":"2024","department":[{"_id":"VaKa"}],"page":"3287-3301","issue":"11","type":"journal_article","status":"public","scopus_import":"1","ddc":["500"],"day":"01","date_updated":"2026-08-12T06:19:26Z","fulldoi":"https://doi.org/10.3934/dcds.2024059","publication_identifier":{"issn":["1078-0947"],"eissn":["1553-5231"]},"oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","doi":"10.3934/dcds.2024059","date_created":"2024-07-14T22:01:10Z","external_id":{"isi":["001230091000001"]},"abstract":[{"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.","lang":"eng"}],"author":[{"id":"06619f18-9070-11eb-847d-d1ee780bd88b","first_name":"Corentin","full_name":"Fiorebe, Corentin","last_name":"Fiorebe"}],"isi":1,"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Discrete and Continuous Dynamical Systems- Series A","citation":{"short":"C. Fiorebe, Discrete and Continuous Dynamical Systems- Series A 44 (2024) 3287–3301.","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>","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.","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.","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>.","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>.","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>"},"intvolume":"        44","month":"11","volume":44,"oa":1,"date_published":"2024-11-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3934/dcds.2024059"}],"article_type":"original","title":"Examples of projective billiards with open sets of periodic orbits","_id":"17231","publisher":"AIMS"},{"fulldoi":"https://doi.org/10.1109/ICRA57147.2024.10610284","day":"08","date_updated":"2026-08-12T06:35:50Z","scopus_import":"1","type":"conference","status":"public","ec_funded":1,"page":"2774-2782","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"year":"2024","department":[{"_id":"ToHe"}],"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.","conference":{"start_date":"2024-05-13","name":"ICRA: International Conference on Robotics and Automation","location":"Yokohama, Japan","end_date":"2024-05-17"},"quality_controlled":"1","_id":"17898","publisher":"IEEE","title":"Overparametrization helps offline-to-online generalization of closed-loop control from pixels","month":"08","date_published":"2024-08-08T00:00:00Z","citation":{"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.","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>","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>.","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>"},"publication":"Proceedings of the 2024 IEEE International Conference on Robotics and Automation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"author":[{"full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner"},{"last_name":"Hasani","first_name":"Ramin","full_name":"Hasani, Ramin"},{"last_name":"Amini","full_name":"Amini, Alexander","first_name":"Alexander"},{"last_name":"Wang","first_name":"Tsun Hsuan","full_name":"Wang, Tsun Hsuan"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"full_name":"Rus, Daniela","first_name":"Daniela","last_name":"Rus"}],"external_id":{"isi":["001294576202044"]},"publication_identifier":{"isbn":["9798350384574"],"issn":["1050-4729"]},"oa_version":"None","doi":"10.1109/ICRA57147.2024.10610284","article_processing_charge":"No","publication_status":"published","date_created":"2024-09-08T22:01:13Z"},{"month":"07","OA_place":"repository","date_published":"2024-07-22T00:00:00Z","oa":1,"type":"research_data_reference","has_accepted_license":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.25625/4FLFH8","open_access":"1"}],"title":"Data and code for: Integral points on cubic surfaces: heuristics and numerics","ddc":["500"],"contributor":[{"last_name":"Wilsch","first_name":"Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425","orcid":"0000-0001-7302-8256"}],"fulldoi":"https://doi.org/10.25625/4FLFH8","day":"22","_id":"22234","date_updated":"2026-08-12T12:15:33Z","publisher":"Göttingen Research Online Data","oa_version":"Published Version","OA_type":"green","date_created":"2026-07-02T10:38:53Z","article_processing_charge":"No","doi":"10.25625/4FLFH8","abstract":[{"lang":"eng","text":"Lists of nontrivial integral points on some (families of) cubic surfaces. (2024-07-18)"}],"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","full_name":"Browning, Timothy D","last_name":"Browning"},{"full_name":"Sutherland, Andrew","first_name":"Andrew","last_name":"Sutherland"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","year":"2024","department":[{"_id":"TiBr"}],"related_material":{"record":[{"id":"20249","status":"public","relation":"used_in_publication"}]},"citation":{"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>.","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>","short":"T.D. Browning, A. Sutherland, (2024).","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>","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>.","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>.","ieee":"T. D. Browning and A. Sutherland, “Data and code for: Integral points on cubic surfaces: heuristics and numerics.” Göttingen Research Online Data, 2024."}},{"related_material":{"link":[{"url":" https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed","relation":"software"}]},"language":[{"iso":"eng"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>","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>.","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.","short":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (n.d.).","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>"},"publication":"arXiv","doi":"10.48550/arXiv.2403.06833","publication_status":"submitted","date_created":"2025-02-20T10:13:42Z","article_processing_charge":"No","oa_version":"Preprint","article_number":"2403.06833","file_date_updated":"2025-02-20T10:11:45Z","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"}],"author":[{"full_name":"Zverev, Egor","first_name":"Egor","id":"05162b19-1340-11ed-8f02-fa94e0e8c3bc","last_name":"Zverev"},{"last_name":"Abdelnabi","full_name":"Abdelnabi, Sahar","first_name":"Sahar"},{"full_name":"Tabesh, Soroush","first_name":"Soroush","id":"06000900-6068-11ef-8d61-c2472ef2e752","orcid":"0009-0003-4119-6281","last_name":"Tabesh"},{"last_name":"Fritz","first_name":"Mario","full_name":"Fritz, Mario"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert"}],"external_id":{"arxiv":["2403.06833"]},"title":"Can LLMs separate instructions from data? And what do we even mean by that?","_id":"19063","date_published":"2024-03-01T00:00:00Z","OA_place":"repository","oa":1,"month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"file":[{"creator":"ezverev","relation":"main_file","file_name":"2403.06833v3.pdf","content_type":"application/pdf","date_updated":"2025-02-20T10:11:45Z","checksum":"35eb43968684b87be59144603ef10af0","access_level":"open_access","file_id":"19064","date_created":"2025-02-20T10:11:45Z","file_size":530972,"success":1}],"year":"2024","arxiv":1,"OA_type":"green","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.","ddc":["000"],"fulldoi":"https://doi.org/10.48550/arXiv.2403.06833","date_updated":"2026-08-13T07:26:54Z","day":"01","has_accepted_license":"1","status":"public","type":"preprint"},{"publisher":"AIP Publishing","_id":"17373","title":"Beyond the blur: Using experimentally determined point spread functions to improve scanning Kelvin probe imaging","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"date_published":"2024-07-28T00:00:00Z","oa":1,"month":"07","volume":136,"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>","short":"I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Journal of Applied Physics 136 (2024).","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.","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>","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>."},"intvolume":"       136","publication":"Journal of Applied Physics","related_material":{"record":[{"status":"public","id":"22684","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","isi":1,"article_number":"045305","file_date_updated":"2024-08-05T08:19:58Z","abstract":[{"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.","lang":"eng"}],"author":[{"full_name":"Lenton, Isaac C","first_name":"Isaac C","orcid":"0000-0002-5010-6984","id":"a550210f-223c-11ec-8182-e2d45e817efb","last_name":"Lenton"},{"last_name":"Pertl","orcid":"0000-0003-0463-5794","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","full_name":"Pertl, Felix","first_name":"Felix"},{"full_name":"Shafeek, Lubuna B","first_name":"Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7180-6050","last_name":"Shafeek"},{"last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}],"external_id":{"isi":["001281681100003"]},"publication_status":"published","doi":"10.1063/5.0215151","date_created":"2024-08-04T22:01:21Z","article_processing_charge":"No","oa_version":"Published Version","publication_identifier":{"issn":["0021-8979"],"eissn":["1089-7550"]},"fulldoi":"https://doi.org/10.1063/5.0215151","date_updated":"2026-08-27T11:42:44Z","day":"28","ddc":["530"],"scopus_import":"1","has_accepted_license":"1","status":"public","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"journal_article","issue":"4","ec_funded":1,"project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"}],"department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"file":[{"file_size":2537502,"date_created":"2024-08-05T08:19:58Z","access_level":"open_access","file_id":"17386","checksum":"6141d05cd68d540a7446dce9490975db","success":1,"content_type":"application/pdf","relation":"main_file","file_name":"2024_JourApplPhysics_Lenton.pdf","creator":"dernst","date_updated":"2024-08-05T08:19:58Z"}],"year":"2024","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.","quality_controlled":"1"},{"author":[{"first_name":"Mateja","full_name":"Hrast, Mateja","last_name":"Hrast"}],"oa_version":"None","OA_type":"green","article_processing_charge":"No","date_created":"2026-09-09T09:20:36Z","doi":"10.5281/zenodo.13833474","citation":{"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>","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).","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>","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>."},"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MiLe"},{"_id":"MaSe"}],"related_material":{"record":[{"relation":"used_in_publication","id":"18710","status":"public"}]},"type":"research_data_reference","status":"public","month":"09","oa":1,"OA_place":"repository","date_published":"2024-09-24T00:00:00Z","day":"24","_id":"22866","date_updated":"2026-09-09T09:20:40Z","fulldoi":"https://doi.org/10.5281/zenodo.13833474","publisher":"Repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.13833475"}],"ddc":["530"],"title":"Data for: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl"},{"quality_controlled":"1","keyword":["Insect Science","Molecular Biology","Animal Science and Zoology","Aquatic Science","Physiology","Ecology","Evolution","Behavior and Systematics"],"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.","department":[{"_id":"NiBa"}],"year":"2024","file":[{"access_level":"open_access","date_created":"2024-01-23T12:08:24Z","file_id":"14877","checksum":"136325372f6f45abaa62a71e2d23bfb6","file_size":594128,"success":1,"creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2024_JourExperimBiology_Pal.pdf","date_updated":"2024-01-23T12:08:24Z"}],"issue":"1","status":"public","has_accepted_license":"1","type":"journal_article","ddc":["570"],"scopus_import":"1","date_updated":"2026-09-09T09:54:41Z","day":"10","pmid":1,"fulldoi":"https://doi.org/10.1242/jeb.246217","doi":"10.1242/jeb.246217","article_processing_charge":"Yes (via OA deal)","publication_status":"published","date_created":"2024-01-22T08:14:49Z","publication_identifier":{"eissn":["0022-0949"],"issn":["1477-9145"]},"oa_version":"Published Version","file_date_updated":"2024-01-23T12:08:24Z","article_number":"jeb246217","external_id":{"pmid":["38054353"],"isi":["001214515700016"]},"author":[{"last_name":"Pal","full_name":"Pal, Arka","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469"},{"first_name":"Mihir","full_name":"Joshi, Mihir","last_name":"Joshi"},{"last_name":"Thaker","full_name":"Thaker, Maria","first_name":"Maria"}],"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>"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"22868","status":"public","relation":"research_data"}],"link":[{"url":"https://github.com/arka-pal/Cnemaspis-SexualSignaling","relation":"software"}]},"isi":1,"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Journal of Experimental Biology","citation":{"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.","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>.","short":"A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).","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>","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>."},"intvolume":"       227","oa":1,"date_published":"2024-01-10T00:00:00Z","month":"01","volume":227,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Too much information? Males convey parasite levels using more signal modalities than females utilise","article_type":"original","publisher":"The Company of Biologists","_id":"14850"},{"issue":"4","page":"575-586","has_accepted_license":"1","status":"public","license":"https://creativecommons.org/licenses/by-nc/4.0/","type":"journal_article","ddc":["570"],"scopus_import":"1","fulldoi":"https://doi.org/10.1093/evlett/qrae014","pmid":1,"day":"23","date_updated":"2026-09-09T10:39:13Z","OA_type":"gold","quality_controlled":"1","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.","department":[{"_id":"NiBa"}],"file":[{"checksum":"2f7780b7b6b3489755f1815f476639c6","access_level":"open_access","file_id":"18909","date_created":"2025-01-27T13:33:14Z","file_size":24356661,"success":1,"creator":"dernst","file_name":"2024_EvolutionLetter_Moan.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2025-01-27T13:33:14Z"}],"year":"2024","date_published":"2024-04-23T00:00:00Z","OA_place":"publisher","oa":1,"month":"04","volume":8,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"title":"Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes","article_type":"letter_note","publisher":"Oxford University Press","_id":"18908","article_processing_charge":"Yes","publication_status":"published","doi":"10.1093/evlett/qrae014","date_created":"2025-01-27T13:30:27Z","oa_version":"Published Version","publication_identifier":{"issn":["2056-3744"]},"file_date_updated":"2025-01-27T13:33:14Z","author":[{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"full_name":"Ortega-Martinez, Olga","first_name":"Olga","last_name":"Ortega-Martinez"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Roger K","full_name":"Butlin, Roger K","last_name":"Butlin"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"}],"abstract":[{"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.","lang":"eng"}],"external_id":{"pmid":["39479507"],"isi":["001206532900001"]},"related_material":{"record":[{"status":"public","id":"22870","relation":"research_data"}]},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"intvolume":"         8","citation":{"short":"A. Le Moan, S. Stankowski, M. Rafajlović, O. Ortega-Martinez, R. Faria, R.K. Butlin, K. Johannesson, Evolution Letters 8 (2024) 575–586.","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>","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.","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>.","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.","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>","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>."},"publication":"Evolution Letters"},{"publication_identifier":{"eissn":["2375-2548"]},"oa_version":"Published Version","article_processing_charge":"Yes","publication_status":"published","date_created":"2024-11-03T23:01:44Z","doi":"10.1126/sciadv.adp2102","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."}],"author":[{"last_name":"Garcia Castillo","first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Larsson","full_name":"Larsson, Jenny","first_name":"Jenny"},{"first_name":"Sean","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001354405400018"]},"article_number":"eadp2102","file_date_updated":"2024-11-04T09:35:49Z","DOAJ_listed":"1","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"related_material":{"link":[{"url":"https://github.com/fernandoGarcia21/littorina_saxatilis_skerry","relation":"software"}],"record":[{"relation":"research_data","status":"public","id":"18498"},{"relation":"dissertation_contains","status":"public","id":"20991"},{"id":"22869","status":"public","relation":"research_data"}]},"language":[{"iso":"eng"}],"intvolume":"        10","citation":{"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.","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.","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).","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>","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>."},"publication":"Science Advances","month":"10","volume":10,"date_published":"2024-10-11T00:00:00Z","OA_place":"publisher","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","title":"Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails","_id":"18491","publisher":"AAAS","OA_type":"gold","quality_controlled":"1","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.).","PlanS_conform":"1","file":[{"file_name":"2024_ScienceAdv_Castillo.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst","date_updated":"2024-11-04T09:35:49Z","file_size":1154107,"checksum":"96aa0d3640fa9401975138e59054f84e","date_created":"2024-11-04T09:35:49Z","file_id":"18499","access_level":"open_access","success":1}],"year":"2024","department":[{"_id":"NiBa"}],"issue":"41","project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"},{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"type":"journal_article","APC_amount":"4569,23 EUR","has_accepted_license":"1","status":"public","scopus_import":"1","ddc":["570"],"fulldoi":"https://doi.org/10.1126/sciadv.adp2102","day":"11","date_updated":"2026-09-09T10:10:02Z"},{"scopus_import":"1","fulldoi":"https://doi.org/10.1093/jeb/voae048","pmid":1,"day":"01","date_updated":"2026-09-09T09:33:37Z","issue":"6","page":"677-692","status":"public","type":"journal_article","department":[{"_id":"NiBa"}],"year":"2024","arxiv":1,"quality_controlled":"1","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.","title":"Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2404.14003"}],"publisher":"Oxford University Press","_id":"17237","date_published":"2024-06-01T00:00:00Z","oa":1,"month":"06","volume":37,"related_material":{"record":[{"id":"22867","status":"public","relation":"research_data"}]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, M. Valero, Journal of Evolutionary Biology 37 (2024) 677–692.","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>","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.","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>.","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>","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>."},"intvolume":"        37","publication":"Journal of Evolutionary Biology","doi":"10.1093/jeb/voae048","date_created":"2024-07-14T22:01:12Z","publication_status":"published","article_processing_charge":"No","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"oa_version":"Preprint","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."}],"author":[{"first_name":"Lauric","full_name":"Reynes, Lauric","last_name":"Reynes"},{"full_name":"Fouqueau, Louise","first_name":"Louise","id":"1676e173-8143-11ed-8927-fe165216a93f","orcid":"0000-0003-0371-9339","last_name":"Fouqueau"},{"last_name":"Aurelle","first_name":"Didier","full_name":"Aurelle, Didier"},{"full_name":"Mauger, Stephane","first_name":"Stephane","last_name":"Mauger"},{"last_name":"Destombe","first_name":"Christophe","full_name":"Destombe, Christophe"},{"first_name":"Myriam","full_name":"Valero, Myriam","last_name":"Valero"}],"external_id":{"pmid":["38629140"],"arxiv":["2404.14003"]}},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"18908","status":"public","relation":"used_in_publication"}]},"citation":{"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>.","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>.","short":"A. Le Moan, (2024).","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>","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>.","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>"},"OA_type":"green","oa_version":"None","date_created":"2026-09-09T10:39:08Z","doi":"10.5281/zenodo.10790257","article_processing_charge":"No","author":[{"last_name":"Le Moan","full_name":"Le Moan, Alan","first_name":"Alan"}],"abstract":[{"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.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.10790257","open_access":"1"}],"title":"Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes","ddc":["570"],"contributor":[{"last_name":"Le Moan","contributor_type":"contact_person","first_name":"Alan"}],"fulldoi":"https://doi.org/10.5281/zenodo.10790257","_id":"22870","date_updated":"2026-09-09T10:39:13Z","day":"06","publisher":"Repository","month":"03","date_published":"2024-03-06T00:00:00Z","OA_place":"repository","oa":1,"type":"research_data_reference","status":"public"},{"citation":{"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>","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>.","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>","short":"N. Barton, (2024).","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>.","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>."},"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"status":"public","id":"18491","relation":"used_in_publication"}]},"department":[{"_id":"NiBa"}],"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."}],"author":[{"first_name":"Nicholas","full_name":"Barton, Nicholas","last_name":"Barton"}],"oa_version":"None","OA_type":"green","doi":"10.5281/zenodo.12159343","date_created":"2026-09-09T10:09:57Z","article_processing_charge":"No","_id":"22869","day":"19","date_updated":"2026-09-09T10:10:02Z","contributor":[{"first_name":"Diego","last_name":"Garcia Castillo","contributor_type":"researcher"},{"first_name":"Nicholas","last_name":"Barton","contributor_type":"researcher"},{"last_name":"Faria","contributor_type":"researcher","first_name":"Rui"},{"last_name":"Larsson","contributor_type":"researcher","first_name":"Jenny"},{"first_name":"Sean","contributor_type":"researcher","last_name":"Stankowski"},{"last_name":"Butlin","contributor_type":"researcher","first_name":"Roger"},{"last_name":"Johannesson","contributor_type":"researcher","first_name":"Kerstin"},{"first_name":"Anja Marie","contributor_type":"researcher","last_name":"Westram"}],"fulldoi":"https://doi.org/10.5281/zenodo.12159343","publisher":"Repository","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.12159343","open_access":"1"}],"ddc":["570"],"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","status":"public","month":"06","oa":1,"date_published":"2024-06-19T00:00:00Z","OA_place":"repository"},{"type":"journal_article","status":"public","has_accepted_license":"1","project":[{"_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0","grant_number":"26777","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches"}],"issue":"1","page":"69-86","day":"11","date_updated":"2026-09-11T08:49:55Z","pmid":1,"fulldoi":"https://doi.org/10.5194/mr-5-69-2024","scopus_import":"1","ddc":["530"],"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).","quality_controlled":"1","year":"2024","file":[{"success":1,"file_size":6736194,"checksum":"d01074f6919387fcaf8c9ebed320ccae","date_created":"2024-06-27T06:42:55Z","access_level":"open_access","file_id":"17181","date_updated":"2024-06-27T06:42:55Z","file_name":"2024_MagneticResonance_Aebischer.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst"}],"department":[{"_id":"PaSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":5,"month":"06","oa":1,"date_published":"2024-06-11T00:00:00Z","_id":"17161","publisher":"Copernicus Publications","article_type":"original","title":"Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR","external_id":{"pmid":["40384772"]},"author":[{"full_name":"Aebischer, Kathrin","first_name":"Kathrin","last_name":"Aebischer"},{"orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","full_name":"Becker, Lea Marie","last_name":"Becker"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul"},{"full_name":"Ernst, Matthias","first_name":"Matthias","last_name":"Ernst"}],"abstract":[{"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.","lang":"eng"}],"file_date_updated":"2024-06-27T06:42:55Z","publication_identifier":{"eissn":["2699-0016"]},"oa_version":"Published Version","publication_status":"published","date_created":"2024-06-23T22:01:02Z","article_processing_charge":"Yes","doi":"10.5194/mr-5-69-2024","publication":"Magnetic Resonance","citation":{"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>.","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>","short":"K. Aebischer, L.M. Becker, P. Schanda, M. Ernst, Magnetic Resonance 5 (2024) 69–86.","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>","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.","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."},"intvolume":"         5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"22906","status":"public","relation":"research_data"}]}},{"oa_version":"None","OA_type":"green","doi":"10.3929/ethz-b-000666765","date_created":"2026-09-11T08:49:48Z","article_processing_charge":"No","author":[{"first_name":"Kathrin","full_name":"Aebischer, Kathrin","last_name":"Aebischer"}],"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"relation":"used_in_publication","id":"17161","status":"public"}]},"department":[{"_id":"PaSc"}],"citation":{"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>","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>.","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>.","ieee":"K. Aebischer, “Evaluating the motional time scales contributing to averaged anisotropic interactions in MAS solid-state NMR.” Repository, 2024.","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>.","short":"K. Aebischer, (2024).","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>"},"month":"04","oa":1,"date_published":"2024-04-03T00:00:00Z","OA_place":"repository","type":"research_data_reference","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3929/ethz-b-000666765"}],"ddc":["530"],"title":"Evaluating the motional time scales contributing to averaged anisotropic interactions in MAS solid-state NMR","date_updated":"2026-09-11T08:49:55Z","_id":"22906","day":"03","fulldoi":"https://doi.org/10.3929/ethz-b-000666765","contributor":[{"last_name":"Ernst","contributor_type":"contact_person","first_name":"Matthias"},{"last_name":"Aebischer","contributor_type":"data_collector","first_name":"Kathrin"},{"first_name":"Matthias","last_name":"Ernst","contributor_type":"data_collector"},{"first_name":"Paul","last_name":"Schanda","contributor_type":"data_collector"},{"contributor_type":"data_collector","last_name":"Becker","first_name":"Lea Marie"},{"contributor_type":"producer","last_name":" Ernst","first_name":"Matthias"},{"contributor_type":"producer","last_name":" Aebischer","first_name":"Kathrin"},{"first_name":"Paul ","last_name":"Schanda","contributor_type":"producer"},{"last_name":"Becker","contributor_type":"producer","first_name":"Lea Marie"}],"publisher":"Repository"},{"title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","article_type":"original","publisher":"Public Library of Science","_id":"18603","oa":1,"OA_place":"publisher","date_published":"2024-11-18T00:00:00Z","volume":22,"month":"11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"18296","status":"public"}]},"isi":1,"DOAJ_listed":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","publication":"PLoS Biology","intvolume":"        22","citation":{"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>.","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.","short":"O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, P.M. Jonas, PLoS Biology 22 (2024).","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>"},"article_processing_charge":"Yes","doi":"10.1371/journal.pbio.3002879","date_created":"2024-12-01T23:01:54Z","publication_status":"published","oa_version":"Published Version","publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"file_date_updated":"2024-12-03T08:56:53Z","article_number":"e3002879","external_id":{"isi":["001358568700003"],"pmid":["39556620"]},"author":[{"last_name":"Kim","full_name":"Kim, Olena","first_name":"Olena","orcid":"0000-0003-2344-1039","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0408-6094","id":"3337E116-F248-11E8-B48F-1D18A9856A87","first_name":"Yuji","full_name":"Okamoto, Yuji","last_name":"Okamoto"},{"last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brose","full_name":"Brose, Nils","first_name":"Nils"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","last_name":"Jonas"}],"abstract":[{"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.","lang":"eng"}],"ddc":["570"],"scopus_import":"1","day":"18","date_updated":"2026-04-16T12:20:34Z","fulldoi":"https://doi.org/10.1371/journal.pbio.3002879","pmid":1,"project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits"},{"name":"Structural & functional basis of presynaptic plasticity","grant_number":"I06166","_id":"b1b85715-d554-11ed-a5ad-84a07fc9f18e"},{"_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","name":"Zellkommunikation in Gesundheit und Krankheit","grant_number":"W01205","call_identifier":"FWF"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"ec_funded":1,"issue":"11","status":"public","APC_amount":"6248,82 EUR","has_accepted_license":"1","type":"journal_article","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"year":"2024","file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2024_PloSBio_Kim.pdf","date_updated":"2024-12-03T08:56:53Z","file_id":"18608","access_level":"open_access","date_created":"2024-12-03T08:56:53Z","checksum":"7de2dcb50deb65dde05c80082bb85a82","file_size":3057631,"success":1}],"quality_controlled":"1","OA_type":"gold","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."},{"title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","publisher":"Institute of Science and Technology Austria","_id":"18296","oa":1,"date_published":"2024-10-11T00:00:00Z","month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"relation":"used_in_publication","id":"18603","status":"public"}]},"corr_author":"1","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","citation":{"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>.","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>.","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>.","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.","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>","short":"O. Kim, (2024)."},"article_processing_charge":"No","doi":"10.15479/AT:ISTA:18296","date_created":"2024-10-11T10:12:17Z","oa_version":"Submitted Version","file_date_updated":"2024-10-11T10:04:23Z","author":[{"last_name":"Kim","orcid":"0000-0003-2344-1039","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena","first_name":"Olena"}],"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."}],"ddc":["570"],"date_updated":"2026-09-14T08:48:01Z","day":"11","fulldoi":"https://doi.org/10.15479/AT:ISTA:18296","contributor":[{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","contributor_type":"researcher","last_name":"Kim"},{"id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094","first_name":"Yuji","contributor_type":"researcher","last_name":"Okamoto"},{"last_name":"Kaufmann","contributor_type":"researcher","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"contributor_type":"researcher","last_name":"Brose","first_name":"Nils "},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","contributor_type":"researcher","last_name":"Shigemoto"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","contributor_type":"supervisor"}],"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"status":"public","has_accepted_license":"1","type":"research_data","department":[{"_id":"PeJo"},{"_id":"RySh"},{"_id":"EM-Fac"}],"year":"2024","file":[{"date_updated":"2024-10-11T10:04:19Z","content_type":"application/zip","file_name":"Kim_et_al_2024_PlosBio_Source_data.zip","relation":"main_file","creator":"okim","success":1,"file_size":164382,"date_created":"2024-10-11T10:04:19Z","file_id":"18297","access_level":"open_access","checksum":"0a977e7df54c418251b10dfd3f8a015c"},{"creator":"okim","content_type":"text/plain","relation":"main_file","file_name":"info.txt","date_updated":"2024-10-11T10:04:23Z","date_created":"2024-10-11T10:04:23Z","access_level":"open_access","file_id":"18298","checksum":"5b9343d6b2035ac3185e390fad4d3830","file_size":654,"success":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"]},{"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.","keyword":["General Chemistry","Catalysis"],"quality_controlled":"1","department":[{"_id":"StFr"},{"_id":"GradSch"}],"file":[{"success":1,"checksum":"fe2c23454279eb9d76ed6ca9970c21c7","file_id":"17261","date_created":"2024-07-16T11:54:46Z","access_level":"open_access","file_size":4766445,"date_updated":"2024-07-16T11:54:46Z","creator":"dernst","file_name":"2024_AngChemieInt_Jethwa.pdf","relation":"main_file","content_type":"application/pdf"}],"year":"2024","has_accepted_license":"1","status":"public","type":"journal_article","ec_funded":1,"issue":"28","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"pmid":1,"fulldoi":"https://doi.org/10.1002/anie.202316476","date_updated":"2026-09-16T07:07:04Z","day":"08","ddc":["540"],"scopus_import":"1","article_number":"e202316476","file_date_updated":"2024-07-16T11:54:46Z","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."}],"author":[{"last_name":"Jethwa","orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","first_name":"Rajesh B","full_name":"Jethwa, Rajesh B"},{"first_name":"Soumyadip","full_name":"Mondal, Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal"},{"last_name":"Pant","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","first_name":"Bhargavi","full_name":"Pant, Bhargavi"},{"last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander"}],"external_id":{"pmid":["38095355"],"isi":["001241932700001"]},"doi":"10.1002/anie.202316476","article_processing_charge":"Yes (via OA deal)","date_created":"2023-12-15T16:10:13Z","publication_status":"published","oa_version":"Published Version","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"intvolume":"        63","citation":{"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>","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).","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>","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.","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.","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>."},"publication":"Angewandte Chemie International Edition","related_material":{"record":[{"relation":"dissertation_contains","id":"20607","status":"public"}]},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2024-07-08T00:00:00Z","oa":1,"month":"07","volume":63,"publisher":"Wiley","_id":"14687","title":"To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries","article_type":"review"}]