[{"file_date_updated":"2021-05-25T15:08:49Z","publication_identifier":{"eissn":["10772626"],"issn":["19410506"]},"publication_status":"published","intvolume":" 27","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype."}],"has_accepted_license":"1","date_created":"2021-05-23T22:01:42Z","volume":27,"title":"Computational design of skinned Quad-Robots","oa_version":"Published Version","scopus_import":"1","day":"01","author":[{"first_name":"Xudong","full_name":"Feng, Xudong","last_name":"Feng"},{"first_name":"Jiafeng","last_name":"Liu","full_name":"Liu, Jiafeng"},{"first_name":"Huamin","full_name":"Wang, Huamin","last_name":"Wang"},{"last_name":"Yang","full_name":"Yang, Yin","first_name":"Yin"},{"full_name":"Bao, Hujun","last_name":"Bao","first_name":"Hujun"},{"first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"first_name":"Weiwei","last_name":"Xu","full_name":"Xu, Weiwei"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"X. Feng et al., “Computational design of skinned Quad-Robots,” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6. IEEE, 2021.","short":"X. Feng, J. Liu, H. Wang, Y. Yang, H. Bao, B. Bickel, W. Xu, IEEE Transactions on Visualization and Computer Graphics 27 (2021).","ama":"Feng X, Liu J, Wang H, et al. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 2021;27(6). doi:10.1109/TVCG.2019.2957218","apa":"Feng, X., Liu, J., Wang, H., Yang, Y., Bao, H., Bickel, B., & Xu, W. (2021). Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2019.2957218","mla":"Feng, Xudong, et al. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics, vol. 27, no. 6, 2881–2895, IEEE, 2021, doi:10.1109/TVCG.2019.2957218.","chicago":"Feng, Xudong, Jiafeng Liu, Huamin Wang, Yin Yang, Hujun Bao, Bernd Bickel, and Weiwei Xu. “Computational Design of Skinned Quad-Robots.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021. https://doi.org/10.1109/TVCG.2019.2957218.","ista":"Feng X, Liu J, Wang H, Yang Y, Bao H, Bickel B, Xu W. 2021. Computational design of skinned Quad-Robots. IEEE Transactions on Visualization and Computer Graphics. 27(6), 2881–2895."},"issue":"6","language":[{"iso":"eng"}],"oa":1,"article_number":"2881-2895","file":[{"creator":"kschuh","date_updated":"2021-05-25T15:08:49Z","file_size":6183002,"date_created":"2021-05-25T15:08:49Z","file_id":"9427","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2021_TVCG_Feng.pdf","checksum":"a78e6ac94e33ade4ffaea66943d5f7dc","relation":"main_file"}],"department":[{"_id":"BeBi"}],"month":"06","quality_controlled":"1","ddc":["000"],"type":"journal_article","_id":"9408","date_updated":"2023-08-08T13:45:46Z","publisher":"IEEE","article_processing_charge":"No","doi":"10.1109/TVCG.2019.2957218","acknowledgement":"The authors would like to thank anonymous reviewers for their constructive comments. Weiwei Xu is partially supported by Zhejiang Lab. Yin Yang is partially spported by NSF under Grant Nos. CHS 1845024 and 1717972. Weiwei Xu and Hujun Bao are supported by Fundamental Research Funds for the Central Universities. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant agreement No 715767).","date_published":"2021-06-01T00:00:00Z","ec_funded":1,"pmid":1,"status":"public","publication":"IEEE Transactions on Visualization and Computer Graphics","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["31804937"],"isi":["000649620700009"]},"isi":1,"year":"2021"},{"quality_controlled":"1","ddc":["570"],"_id":"9410","date_updated":"2025-05-28T11:42:50Z","type":"journal_article","article_processing_charge":"No","doi":"10.1098/rsbl.2020.0913","publisher":"Royal Society of London","ec_funded":1,"pmid":1,"acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","date_published":"2021-05-12T00:00:00Z","status":"public","publication":"Biology letters","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"}],"isi":1,"year":"2021","external_id":{"isi":["000651501400001"],"pmid":[" 33975485"]},"file_date_updated":"2021-05-25T14:09:03Z","publication_status":"published","publication_identifier":{"eissn":["1744957X"]},"has_accepted_license":"1","intvolume":" 17","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.","lang":"eng"}],"volume":17,"date_created":"2021-05-23T22:01:43Z","scopus_import":"1","day":"12","author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator"},{"last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","full_name":"Uecker, Hildegard","first_name":"Hildegard","orcid":"0000-0001-9435-2813"},{"last_name":"Neve","full_name":"Neve, Paul","first_name":"Paul"}],"oa_version":"Published Version","title":"Adaptation at different points along antibiotic concentration gradients","citation":{"ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021.","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913.","apa":"Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913"},"issue":"5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"file":[{"success":1,"file_name":"2021_BiologyLetters_Lagator.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"9c13c1f5af7609c97c741f11d293188a","file_size":726759,"date_created":"2021-05-25T14:09:03Z","creator":"kschuh","date_updated":"2021-05-25T14:09:03Z","file_id":"9425"}],"article_number":"20200913","month":"05"},{"publication":"European Physical Journal E","status":"public","date_published":"2021-04-24T00:00:00Z","acknowledgement":"This work was financially supported by the DFG Priority Programme SPP 1726 “Microswimmers–From Single Particle Motion to Collective Behaviour” (HA 4382/5-1). We further acknowledge the Jülich Supercomputing Centre (JSC) and the High Performance Computing Centre Stuttgart (HLRS) for the allocation of computing time.","year":"2021","isi":1,"external_id":{"isi":["000643251300001"]},"ddc":["530"],"quality_controlled":"1","doi":"10.1140/epje/s10189-021-00065-2","article_processing_charge":"No","publisher":"Springer","date_updated":"2023-08-08T13:36:28Z","_id":"9411","type":"journal_article","oa":1,"language":[{"iso":"eng"}],"issue":"4","citation":{"ama":"Sukhov A, Hubert M, Grosjean GM, et al. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 2021;44(4). doi:10.1140/epje/s10189-021-00065-2","ieee":"A. Sukhov et al., “Regimes of motion of magnetocapillary swimmers,” European Physical Journal E, vol. 44, no. 4. Springer, 2021.","short":"A. Sukhov, M. Hubert, G.M. Grosjean, O. Trosman, S. Ziegler, Y. Collard, N. Vandewalle, A.S. Smith, J. Harting, European Physical Journal E 44 (2021).","ista":"Sukhov A, Hubert M, Grosjean GM, Trosman O, Ziegler S, Collard Y, Vandewalle N, Smith AS, Harting J. 2021. Regimes of motion of magnetocapillary swimmers. European Physical Journal E. 44(4), 59.","chicago":"Sukhov, Alexander, Maxime Hubert, Galien M Grosjean, Oleg Trosman, Sebastian Ziegler, Ylona Collard, Nicolas Vandewalle, Ana Sunčana Smith, and Jens Harting. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E. Springer, 2021. https://doi.org/10.1140/epje/s10189-021-00065-2.","apa":"Sukhov, A., Hubert, M., Grosjean, G. M., Trosman, O., Ziegler, S., Collard, Y., … Harting, J. (2021). Regimes of motion of magnetocapillary swimmers. European Physical Journal E. Springer. https://doi.org/10.1140/epje/s10189-021-00065-2","mla":"Sukhov, Alexander, et al. “Regimes of Motion of Magnetocapillary Swimmers.” European Physical Journal E, vol. 44, no. 4, 59, Springer, 2021, doi:10.1140/epje/s10189-021-00065-2."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","department":[{"_id":"ScWa"}],"article_number":"59","file":[{"file_name":"2021_EPJE_Sukhov.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0ef342d011afbe3c5cb058fda9a3f395","file_size":2507870,"date_created":"2021-05-25T11:32:14Z","date_updated":"2021-05-25T11:32:14Z","creator":"kschuh","file_id":"9422"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 44","abstract":[{"text":"The dynamics of a triangular magnetocapillary swimmer is studied using the lattice Boltzmann method. We extend on our previous work, which deals with the self-assembly and a specific type of the swimmer motion characterized by the swimmer’s maximum velocity centred around the particle’s inverse viscous time. Here, we identify additional regimes of motion. First, modifying the ratio of surface tension and magnetic forces allows to study the swimmer propagation in the regime of significantly lower frequencies mainly defined by the strength of the magnetocapillary potential. Second, introducing a constant magnetic contribution in each of the particles in addition to their magnetic moment induced by external fields leads to another regime characterized by strong in-plane swimmer reorientations that resemble experimental observations.","lang":"eng"}],"publication_identifier":{"eissn":["1292895X"],"issn":["12928941"]},"publication_status":"published","file_date_updated":"2021-05-25T11:32:14Z","author":[{"full_name":"Sukhov, Alexander","last_name":"Sukhov","first_name":"Alexander"},{"first_name":"Maxime","last_name":"Hubert","full_name":"Hubert, Maxime"},{"id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M","last_name":"Grosjean","orcid":"0000-0001-5154-417X","first_name":"Galien M"},{"full_name":"Trosman, Oleg","last_name":"Trosman","first_name":"Oleg"},{"full_name":"Ziegler, Sebastian","last_name":"Ziegler","first_name":"Sebastian"},{"last_name":"Collard","full_name":"Collard, Ylona","first_name":"Ylona"},{"full_name":"Vandewalle, Nicolas","last_name":"Vandewalle","first_name":"Nicolas"},{"first_name":"Ana Sunčana","last_name":"Smith","full_name":"Smith, Ana Sunčana"},{"first_name":"Jens","full_name":"Harting, Jens","last_name":"Harting"}],"scopus_import":"1","day":"24","title":"Regimes of motion of magnetocapillary swimmers","oa_version":"Published Version","volume":44,"date_created":"2021-05-23T22:01:44Z"},{"ddc":["510"],"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","article_processing_charge":"No","doi":"10.1214/21-EJP591","type":"journal_article","_id":"9412","date_updated":"2023-08-08T13:39:19Z","status":"public","publication":"Electronic Journal of Probability","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"date_published":"2021-03-23T00:00:00Z","ec_funded":1,"external_id":{"arxiv":["2002.02438"],"isi":["000641855600001"]},"year":"2021","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness.","lang":"eng"}],"intvolume":" 26","has_accepted_license":"1","file_date_updated":"2021-05-25T13:24:19Z","publication_identifier":{"eissn":["10836489"]},"publication_status":"published","oa_version":"Published Version","title":"Fluctuation around the circular law for random matrices with real entries","day":"23","scopus_import":"1","author":[{"orcid":"0000-0002-4901-7992","first_name":"Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-2904-1856","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"date_created":"2021-05-23T22:01:44Z","volume":26,"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/21-EJP591","mla":"Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:10.1214/21-EJP591.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2021. https://doi.org/10.1214/21-EJP591.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” Electronic Journal of Probability, vol. 26. Institute of Mathematical Statistics, 2021.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021).","ama":"Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 2021;26. doi:10.1214/21-EJP591"},"arxiv":1,"month":"03","article_number":"24","file":[{"file_id":"9423","creator":"kschuh","date_updated":"2021-05-25T13:24:19Z","date_created":"2021-05-25T13:24:19Z","file_size":865148,"checksum":"864ab003ad4cffea783f65aa8c2ba69f","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2021_EJP_Cipolloni.pdf"}],"department":[{"_id":"LaEr"}]},{"type":"journal_article","_id":"9414","date_updated":"2023-08-08T13:36:02Z","publisher":"American Society for Cell Biology","article_processing_charge":"No","doi":"10.1091/MBC.E20-11-0723","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723"}],"page":"869-879","external_id":{"isi":["000641574700005"]},"isi":1,"year":"2021","acknowledgement":"The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753.","date_published":"2021-04-19T00:00:00Z","ec_funded":1,"status":"public","publication":"Molecular Biology of the Cell","project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"date_created":"2021-05-23T22:01:45Z","article_type":"original","volume":32,"oa_version":"Published Version","title":"Spatial variation of microtubule depolymerization in large asters","scopus_import":"1","day":"19","author":[{"first_name":"Keisuke","full_name":"Ishihara, Keisuke","last_name":"Ishihara"},{"first_name":"Franziska","last_name":"Decker","full_name":"Decker, Franziska"},{"orcid":"0000-0001-6730-4461","first_name":"Paulo R","last_name":"Dos Santos Caldas","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","full_name":"Dos Santos Caldas, Paulo R"},{"full_name":"Pelletier, James F.","last_name":"Pelletier","first_name":"James F."},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"first_name":"Jan","last_name":"Brugués","full_name":"Brugués, Jan"},{"last_name":"Mitchison","full_name":"Mitchison, Timothy J.","first_name":"Timothy J."}],"publication_status":"published","publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","tmp":{"short":"CC BY-NC-SA (3.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","image":"/images/cc_by_nc_sa.png"},"intvolume":" 32","abstract":[{"text":"Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.","lang":"eng"}],"department":[{"_id":"MaLo"}],"month":"04","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879. doi:10.1091/MBC.E20-11-0723","short":"K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose, J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.","ieee":"K. Ishihara et al., “Spatial variation of microtubule depolymerization in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","chicago":"Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.","ista":"Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 32(9), 869–879.","mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723"},"issue":"9","language":[{"iso":"eng"}],"oa":1},{"file":[{"creator":"bphuong","date_updated":"2021-05-24T11:15:57Z","file_size":502356,"date_created":"2021-05-24T11:15:57Z","file_id":"9417","access_level":"open_access","content_type":"application/pdf","file_name":"iclr2021_conference.pdf","checksum":"f34ff17017527db5ba6927f817bdd125","relation":"main_file"}],"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"month":"05","related_material":{"record":[{"id":"9418","status":"public","relation":"dissertation_contains"}]},"year":"2021","date_published":"2021-05-01T00:00:00Z","conference":{"name":" ICLR: International Conference on Learning Representations","end_date":"2021-05-07","start_date":"2021-05-03","location":"Virtual"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Phuong, C. Lampert, in:, 9th International Conference on Learning Representations, 2021.","ieee":"M. Phuong and C. Lampert, “The inductive bias of ReLU networks on orthogonally separable data,” in 9th International Conference on Learning Representations, Virtual, 2021.","ama":"Phuong M, Lampert C. The inductive bias of ReLU networks on orthogonally separable data. In: 9th International Conference on Learning Representations. ; 2021.","mla":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” 9th International Conference on Learning Representations, 2021.","apa":"Phuong, M., & Lampert, C. (2021). The inductive bias of ReLU networks on orthogonally separable data. In 9th International Conference on Learning Representations. Virtual.","ista":"Phuong M, Lampert C. 2021. The inductive bias of ReLU networks on orthogonally separable data. 9th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” In 9th International Conference on Learning Representations, 2021."},"status":"public","language":[{"iso":"eng"}],"publication":"9th International Conference on Learning Representations","oa":1,"type":"conference","date_created":"2021-05-24T11:16:46Z","date_updated":"2023-09-07T13:29:50Z","_id":"9416","title":"The inductive bias of ReLU networks on orthogonally separable data","oa_version":"Published Version","author":[{"last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","full_name":"Bui Thi Mai, Phuong","first_name":"Phuong"},{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"article_processing_charge":"No","day":"01","scopus_import":"1","publication_status":"published","quality_controlled":"1","file_date_updated":"2021-05-24T11:15:57Z","main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=krz7T0xU9Z_"}],"abstract":[{"text":"We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks.","lang":"eng"}],"ddc":["000"],"has_accepted_license":"1"},{"ddc":["000"],"page":"125","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:9418","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","type":"dissertation","date_updated":"2023-09-08T11:11:12Z","_id":"9418","status":"public","degree_awarded":"PhD","date_published":"2021-05-30T00:00:00Z","related_material":{"record":[{"id":"7435","relation":"part_of_dissertation","status":"deleted"},{"status":"public","relation":"part_of_dissertation","id":"7481"},{"status":"public","relation":"part_of_dissertation","id":"9416"},{"id":"7479","status":"public","relation":"part_of_dissertation"}]},"year":"2021","abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file_date_updated":"2021-05-24T11:56:02Z","oa_version":"Published Version","title":"Underspecification in deep learning","author":[{"full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","last_name":"Bui Thi Mai","first_name":"Phuong"}],"day":"30","date_created":"2021-05-24T13:06:23Z","language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418.","mla":"Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418.","apa":"Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418"},"month":"05","supervisor":[{"last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"file":[{"file_size":2673905,"date_created":"2021-05-24T11:22:29Z","date_updated":"2021-05-24T11:22:29Z","creator":"bphuong","file_id":"9419","file_name":"mph-thesis-v519-pdfimages.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"4f0abe64114cfed264f9d36e8d1197e3"},{"relation":"source_file","checksum":"f5699e876bc770a9b0df8345a77720a2","file_name":"thesis.zip","access_level":"closed","content_type":"application/zip","file_id":"9420","file_size":92995100,"date_created":"2021-05-24T11:56:02Z","creator":"bphuong","date_updated":"2021-05-24T11:56:02Z"}],"department":[{"_id":"GradSch"},{"_id":"ChLa"}]},{"ec_funded":1,"acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","date_published":"2021-06-01T00:00:00Z","project":[{"call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"status":"public","publication":"Nature Physics","isi":1,"year":"2021","external_id":{"arxiv":["2011.09486"],"isi":["000655563800002"]},"quality_controlled":"1","page":"675–685","ddc":["539"],"date_updated":"2023-10-18T08:20:59Z","_id":"9428","type":"journal_article","doi":"10.1038/s41567-021-01230-2","article_processing_charge":"No","publisher":"Nature Research","issue":"6","citation":{"short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.","apa":"Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research, 2021. https://doi.org/10.1038/s41567-021-01230-2."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"file":[{"file_id":"10026","creator":"patrickd","date_updated":"2021-12-02T23:30:03Z","embargo":"2021-12-01","date_created":"2021-09-20T09:27:43Z","file_size":10028836,"checksum":"316ed42ea1b42b0f1a3025bb476266fc","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"RevisedQMBSreview.pdf"}],"arxiv":1,"month":"06","publication_identifier":{"eissn":["1745-2481"]},"publication_status":"published","file_date_updated":"2021-12-02T23:30:03Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology."}],"intvolume":" 17","volume":17,"article_type":"review","date_created":"2021-05-28T09:03:50Z","author":[{"first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."},{"first_name":"Zlatko","full_name":"Papić, Zlatko","last_name":"Papić"}],"day":"01","oa_version":"Preprint","title":"Quantum many-body scars and weak breaking of ergodicity"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058."},"issue":"1","language":[{"iso":"eng"}],"oa":1,"article_number":"3058","file":[{"date_created":"2021-05-28T12:39:43Z","file_size":9358599,"creator":"kschuh","date_updated":"2021-05-28T12:39:43Z","file_id":"9430","file_name":"2021_NatureCommunications_Morandell.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"337e0f7959c35ec959984cacdcb472ba"}],"department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"month":"05","file_date_updated":"2021-05-28T12:39:43Z","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","acknowledged_ssus":[{"_id":"PreCl"}],"intvolume":" 12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.","lang":"eng"}],"has_accepted_license":"1","date_created":"2021-05-28T11:49:46Z","article_type":"original","volume":12,"oa_version":"Published Version","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","day":"24","author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin"},{"last_name":"Schwarz","full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A"},{"last_name":"Basilico","full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","orcid":"0000-0003-1843-3173"},{"orcid":"0000-0003-1671-393X","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","last_name":"Tasciyan"},{"first_name":"Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev","full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105"},{"last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","first_name":"Caroline"},{"orcid":"0000-0002-9033-9096","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","first_name":"Lisa"},{"id":"D23090A2-9057-11EA-883A-A8396FC7A38F","full_name":"Dobler, Zoe","last_name":"Dobler","first_name":"Zoe"},{"first_name":"Emanuele","last_name":"Cacci","full_name":"Cacci, Emanuele"},{"first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973"},{"first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","date_published":"2021-05-24T00:00:00Z","ec_funded":1,"status":"public","publication":"Nature Communications","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","grant_number":"F07807","name":"Neural stem cells in autism and epilepsy"},{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"related_material":{"record":[{"id":"7800","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"12401"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}]},"external_id":{"isi":["000658769900010"]},"year":"2021","isi":1,"quality_controlled":"1","ddc":["572"],"type":"journal_article","_id":"9429","date_updated":"2024-09-10T12:04:26Z","publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1038/s41467-021-23123-x"},{"ddc":["570"],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1038/s41467-021-23506-0","publisher":"Nature Research","_id":"9431","date_updated":"2023-08-08T13:53:53Z","type":"journal_article","publication":"Nature Communications","status":"public","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"date_published":"2021-05-28T00:00:00Z","acknowledgement":"This work was funded by the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D., R01AI150454 to V.M.V, R35GM136258 in support of J-P.R.F, and the Austrian Science Fund (FWF) grant P31445 to F.K.M.S. Access to high-resolution cryo-ET data acquisition at EMBL Heidelberg was supported by iNEXT (grant no. 653706), funded by the Horizon 2020 program of the European Union (PID 4246). We thank Wim Hagen and Felix Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This work made use of the Cornell Center for Materials Research Shared Facilities, which are supported through the NSF MRSEC program (DMR-179875). This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF).","isi":1,"year":"2021","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-retroviruses-become-infectious/","relation":"press_release"}]},"external_id":{"isi":["000659145000011"]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"intvolume":" 12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles."}],"file_date_updated":"2021-06-09T15:21:14Z","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"scopus_import":"1","day":"28","author":[{"full_name":"Obr, Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","first_name":"Martin"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"full_name":"Nikulin, Nadia","last_name":"Nikulin","first_name":"Nadia"},{"last_name":"Feathers","full_name":"Feathers, Jon-Philip R.","first_name":"Jon-Philip R."},{"full_name":"Klanschnig, Marco","last_name":"Klanschnig","first_name":"Marco"},{"first_name":"Andreas","last_name":"Thader","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marc C.","last_name":"Johnson","full_name":"Johnson, Marc C."},{"first_name":"Volker M.","last_name":"Vogt","full_name":"Vogt, Volker M."},{"orcid":"0000-0003-4790-8078","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur"},{"first_name":"Robert A.","full_name":"Dick, Robert A.","last_name":"Dick"}],"oa_version":"Published Version","title":"Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer","volume":12,"date_created":"2021-05-28T14:25:50Z","article_type":"original","oa":1,"language":[{"iso":"eng"}],"citation":{"mla":"Obr, Martin, et al. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications, vol. 12, no. 1, 3226, Nature Research, 2021, doi:10.1038/s41467-021-23506-0.","apa":"Obr, M., Ricana, C. L., Nikulin, N., Feathers, J.-P. R., Klanschnig, M., Thader, A., … Dick, R. A. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-021-23506-0","ista":"Obr M, Ricana CL, Nikulin N, Feathers J-PR, Klanschnig M, Thader A, Johnson MC, Vogt VM, Schur FK, Dick RA. 2021. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 12(1), 3226.","chicago":"Obr, Martin, Clifton L. Ricana, Nadia Nikulin, Jon-Philip R. Feathers, Marco Klanschnig, Andreas Thader, Marc C. Johnson, Volker M. Vogt, Florian KM Schur, and Robert A. Dick. “Structure of the Mature Rous Sarcoma Virus Lattice Reveals a Role for IP6 in the Formation of the Capsid Hexamer.” Nature Communications. Nature Research, 2021. https://doi.org/10.1038/s41467-021-23506-0.","short":"M. Obr, C.L. Ricana, N. Nikulin, J.-P.R. Feathers, M. Klanschnig, A. Thader, M.C. Johnson, V.M. Vogt, F.K. Schur, R.A. Dick, Nature Communications 12 (2021).","ieee":"M. Obr et al., “Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer,” Nature Communications, vol. 12, no. 1. Nature Research, 2021.","ama":"Obr M, Ricana CL, Nikulin N, et al. Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23506-0"},"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"05","department":[{"_id":"FlSc"}],"file":[{"success":1,"file_name":"2021_NatureCommunications_Obr.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"53ccc53d09a9111143839dbe7784e663","date_created":"2021-06-09T15:21:14Z","file_size":6166295,"date_updated":"2021-06-09T15:21:14Z","creator":"kschuh","file_id":"9538"}],"article_number":"3226"},{"department":[{"_id":"VaKa"}],"file":[{"file_id":"9436","file_size":353431,"date_created":"2021-05-30T13:57:37Z","date_updated":"2021-05-30T13:57:37Z","creator":"ekoudjin","relation":"main_file","checksum":"b281b5c2e3e90de0646c3eafcb2c6c25","file_name":"CoExistence 2&3 caustics 3_17_6_2_3.pdf","content_type":"application/pdf","access_level":"open_access"}],"year":"2021","citation":{"ista":"Kaloshin V, Koudjinan E. 2021. Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles.","chicago":"Kaloshin, Vadim, and Edmond Koudjinan. “Non Co-Preservation of the 1/2 and 1/(2l+1)-Rational Caustics along Deformations of Circles,” 2021.","mla":"Kaloshin, Vadim, and Edmond Koudjinan. Non Co-Preservation of the 1/2 and 1/(2l+1)-Rational Caustics along Deformations of Circles. 2021.","apa":"Kaloshin, V., & Koudjinan, E. (2021). Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles.","ama":"Kaloshin V, Koudjinan E. Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles. 2021.","short":"V. Kaloshin, E. Koudjinan, (2021).","ieee":"V. Kaloshin and E. Koudjinan, “Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles.” 2021."},"date_published":"2021-01-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"status":"public","language":[{"iso":"eng"}],"date_updated":"2021-06-01T09:10:22Z","_id":"9435","type":"preprint","date_created":"2021-05-30T13:58:13Z","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","first_name":"Vadim"},{"last_name":"Koudjinan","full_name":"Koudjinan, Edmond","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","orcid":"0000-0003-2640-4049","first_name":"Edmond"}],"article_processing_charge":"No","title":"Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles","oa_version":"Submitted Version","file_date_updated":"2021-05-30T13:57:37Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"For any given positive integer l, we prove that every plane deformation of a circlewhich preserves the 1/2and 1/ (2l + 1) -rational caustics is trivial i.e. the deformationconsists only of similarities (rescalings and isometries)."}],"ddc":["500"]},{"ddc":["570"],"quality_controlled":"1","publisher":"eLife Sciences Publications","doi":"10.7554/ELIFE.68274","article_processing_charge":"No","type":"journal_article","date_updated":"2024-03-25T23:30:16Z","_id":"9437","project":[{"call_identifier":"H2020","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"eLife","date_published":"2021-04-29T00:00:00Z","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","ec_funded":1,"external_id":{"isi":["000651761700001"]},"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.04.16.045112"}],"record":[{"id":"9562","relation":"dissertation_contains","status":"public"}]},"year":"2021","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 10","abstract":[{"text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation.","lang":"eng"}],"has_accepted_license":"1","publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","file_date_updated":"2021-05-31T09:43:09Z","title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","oa_version":"Published Version","author":[{"full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","orcid":"0000-0003-0863-4481","first_name":"Pradeep"},{"orcid":"0000-0001-7577-1676","first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"first_name":"Diego","last_name":"Fernández-Fernández","full_name":"Fernández-Fernández, Diego"},{"last_name":"Fritzius","full_name":"Fritzius, Thorsten","first_name":"Thorsten"},{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David"},{"id":"4659D740-F248-11E8-B48F-1D18A9856A87","full_name":"Önal, Hüseyin C","last_name":"Önal","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011"},{"first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gassmann, Martin","last_name":"Gassmann","first_name":"Martin"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"},{"full_name":"Kulik, Akos","last_name":"Kulik","first_name":"Akos"},{"last_name":"Bettler","full_name":"Bettler, Bernhard","first_name":"Bernhard"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"}],"day":"29","scopus_import":"1","article_type":"original","date_created":"2021-05-30T22:01:23Z","volume":10,"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274.","ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife Sciences Publications, 2021, doi:10.7554/ELIFE.68274.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 2021;10. doi:10.7554/ELIFE.68274","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).","ieee":"P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” eLife, vol. 10. eLife Sciences Publications, 2021."},"month":"04","article_number":"e68274","file":[{"success":1,"file_name":"2021_eLife_Bhandari.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"6ebcb79999f889766f7cd79ee134ad28","file_size":8174719,"date_created":"2021-05-31T09:43:09Z","date_updated":"2021-05-31T09:43:09Z","creator":"cziletti","file_id":"9440"}],"department":[{"_id":"RySh"},{"_id":"PeJo"}]},{"department":[{"_id":"PeJo"}],"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"VandaeletalAuthorVersion2021.pdf","checksum":"7eb580abd8893cdb0b410cf41bc8c263","relation":"main_file","creator":"cziletti","embargo":"2021-12-01","date_updated":"2021-12-02T23:30:05Z","file_size":38574802,"date_created":"2021-07-08T12:27:55Z","file_id":"9639"}],"month":"06","citation":{"ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0.","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:10.1038/s41596-021-00526-0.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0"},"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"volume":16,"date_created":"2021-05-30T22:01:24Z","article_type":"original","scopus_import":"1","day":"01","author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676"},{"first_name":"Yuji","orcid":"0000-0003-0408-6094","last_name":"Okamoto","full_name":"Okamoto, Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0005-401X","first_name":"Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina"},{"first_name":"Victor M","last_name":"Vargas Barroso","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M"},{"orcid":"0000-0002-9885-6936","first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin","last_name":"Suter"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas"}],"title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","oa_version":"Submitted Version","file_date_updated":"2021-12-02T23:30:05Z","publication_status":"published","publication_identifier":{"eissn":["17502799"],"issn":["17542189"]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"}],"intvolume":" 16","abstract":[{"text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system.","lang":"eng"}],"year":"2021","isi":1,"external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"ec_funded":1,"pmid":1,"date_published":"2021-06-01T00:00:00Z","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","publication":"Nature Protocols","status":"public","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312"},{"_id":"2696E7FE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"V00739","name":"Structural plasticity at mossy fiber-CA3 synapses"}],"_id":"9438","date_updated":"2023-08-10T22:30:51Z","type":"journal_article","article_processing_charge":"No","doi":"10.1038/s41596-021-00526-0","publisher":"Springer Nature","quality_controlled":"1","page":"2947–2967","ddc":["570"]},{"oa":1,"language":[{"iso":"eng"}],"citation":{"short":"W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.","ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0","mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0.","apa":"Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0","chicago":"Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.","ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"05","department":[{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks."}],"intvolume":" 24","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"publication_status":"published","day":"20","scopus_import":"1","author":[{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski","first_name":"Wiktor F"},{"first_name":"Ann M.","last_name":"Hermundstad","full_name":"Hermundstad, Ann M."}],"oa_version":"Preprint","title":"Efficient and adaptive sensory codes","volume":24,"date_created":"2021-05-30T22:01:24Z","article_type":"original","publication":"Nature Neuroscience","status":"public","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"acknowledgement":"We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.","date_published":"2021-05-20T00:00:00Z","year":"2021","isi":1,"external_id":{"isi":["000652577300003"]},"page":"998-1009","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/669200 "}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1038/s41593-021-00846-0","publisher":"Springer Nature","_id":"9439","date_updated":"2023-08-08T13:51:14Z","type":"journal_article"},{"date_created":"2021-06-02T10:10:55Z","volume":189,"title":"Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations","oa_version":"Published Version","day":"02","author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"last_name":"Kachanovich","full_name":"Kachanovich, Siargey","first_name":"Siargey"},{"orcid":"0000-0002-7472-2220","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"file_date_updated":"2021-06-02T10:22:33Z","publication_identifier":{"isbn":["978-3-95977-184-9"],"issn":["1868-8969"]},"publication_status":"published","intvolume":" 189","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. "}],"has_accepted_license":"1","file":[{"checksum":"c322aa48d5d35a35877896cc565705b6","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"LIPIcs-SoCG-2021-17.pdf","file_id":"9442","date_updated":"2021-06-02T10:22:33Z","creator":"mwintrae","date_created":"2021-06-02T10:22:33Z","file_size":1972902}],"department":[{"_id":"HeEd"}],"month":"06","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations,” in 37th International Symposium on Computational Geometry (SoCG 2021), Virtual, 2021, vol. 189, p. 17:1-17:16.","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, in:, 37th International Symposium on Computational Geometry (SoCG 2021), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2021, p. 17:1-17:16.","ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In: 37th International Symposium on Computational Geometry (SoCG 2021). Vol 189. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021:17:1-17:16. doi:10.4230/LIPIcs.SoCG.2021.17","apa":"Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. In 37th International Symposium on Computational Geometry (SoCG 2021) (Vol. 189, p. 17:1-17:16). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2021.17","mla":"Boissonnat, Jean-Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” 37th International Symposium on Computational Geometry (SoCG 2021), vol. 189, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, p. 17:1-17:16, doi:10.4230/LIPIcs.SoCG.2021.17.","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter-Freudenthal-Kuhn Triangulations.” In 37th International Symposium on Computational Geometry (SoCG 2021), 189:17:1-17:16. Leibniz International Proceedings in Informatics (LIPIcs). Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. https://doi.org/10.4230/LIPIcs.SoCG.2021.17.","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations. 37th International Symposium on Computational Geometry (SoCG 2021). SoCG: Symposium on Computational GeometryLeibniz International Proceedings in Informatics (LIPIcs), LIPIcs, vol. 189, 17:1-17:16."},"place":"Dagstuhl, Germany","language":[{"iso":"eng"}],"oa":1,"series_title":"Leibniz International Proceedings in Informatics (LIPIcs)","type":"conference","_id":"9441","date_updated":"2023-10-10T07:34:34Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"No","alternative_title":["LIPIcs"],"doi":"10.4230/LIPIcs.SoCG.2021.17","quality_controlled":"1","ddc":["005","516","514"],"page":"17:1-17:16","related_material":{"record":[{"id":"12960","relation":"later_version","status":"public"}]},"year":"2021","conference":{"location":"Virtual","name":"SoCG: Symposium on Computational Geometry","end_date":"2021-06-11","start_date":"2021-06-07"},"date_published":"2021-06-02T00:00:00Z","acknowledgement":"We thank Dominique Attali, Guilherme de Fonseca, Arijit Ghosh, Vincent Pilaud and Aurélien Alvarez for their comments and suggestions. We also acknowledge the reviewers.","ec_funded":1,"publication":"37th International Symposium on Computational Geometry (SoCG 2021)","status":"public","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}]},{"publisher":"American Society of Plant Biologists","article_processing_charge":"No","doi":"10.1093/plcell/koab122","type":"journal_article","_id":"9443","date_updated":"2023-08-08T13:54:32Z","ddc":["580"],"page":"2431-2453","quality_controlled":"1","external_id":{"pmid":["33944955"],"isi":["000703938100026"]},"isi":1,"year":"2021","status":"public","publication":"Plant Cell","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"}],"date_published":"2021-07-01T00:00:00Z","acknowledgement":"We would also like to thank Lothar Willmitzer for the lipidomic analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany). We thank Manuela Vega from SCI for her technical assistance in image analysis. We thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1 clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga, Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom (Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1 construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University). We thank Plan Propio from the University of Málaga for financial support.\r\nFunding","ec_funded":1,"pmid":1,"oa_version":"Published Version","title":"Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress","scopus_import":"1","day":"01","author":[{"first_name":"N","last_name":"Ruiz-Lopez","full_name":"Ruiz-Lopez, N"},{"first_name":"J","full_name":"Pérez-Sancho, J","last_name":"Pérez-Sancho"},{"full_name":"Esteban Del Valle, A","last_name":"Esteban Del Valle","first_name":"A"},{"last_name":"Haslam","full_name":"Haslam, RP","first_name":"RP"},{"first_name":"S","full_name":"Vanneste, S","last_name":"Vanneste"},{"last_name":"Catalá","full_name":"Catalá, R","first_name":"R"},{"first_name":"C","last_name":"Perea-Resa","full_name":"Perea-Resa, C"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"first_name":"S","full_name":"García-Hernández, S","last_name":"García-Hernández"},{"first_name":"A","full_name":"Albert, A","last_name":"Albert"},{"last_name":"Vallarino","full_name":"Vallarino, J","first_name":"J"},{"last_name":"Lin","full_name":"Lin, J","first_name":"J"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"AP","full_name":"Macho, AP","last_name":"Macho"},{"full_name":"Salinas, J","last_name":"Salinas","first_name":"J"},{"first_name":"A","last_name":"Rosado","full_name":"Rosado, A"},{"full_name":"Napier, JA","last_name":"Napier","first_name":"JA"},{"full_name":"Amorim-Silva, V","last_name":"Amorim-Silva","first_name":"V"},{"full_name":"Botella, MA","last_name":"Botella","first_name":"MA"}],"date_created":"2021-06-02T13:13:58Z","article_type":"original","volume":33,"intvolume":" 33","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"abstract":[{"text":"Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress.","lang":"eng"}],"has_accepted_license":"1","file_date_updated":"2021-10-14T13:36:38Z","publication_status":"published","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"month":"07","file":[{"checksum":"22d596678d00310d793611864a6d0fcd","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2021_PlantCell_RuizLopez.pdf","success":1,"file_id":"10141","date_updated":"2021-10-14T13:36:38Z","creator":"cchlebak","file_size":2952028,"date_created":"2021-10-14T13:36:38Z"}],"department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122","ieee":"N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021.","short":"N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste, R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino, J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva, M. Botella, Plant Cell 33 (2021) 2431–2453.","chicago":"Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste, R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.","ista":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J, Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453.","apa":"Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste, S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122","mla":"Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:10.1093/plcell/koab122."},"issue":"7"},{"oa_version":"None","title":"Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes","day":"01","author":[{"first_name":"Marion","full_name":"Maffre, Marion","last_name":"Maffre"},{"first_name":"Roza","full_name":"Bouchal, Roza","last_name":"Bouchal"},{"first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger"},{"full_name":"Lindahl, Niklas","last_name":"Lindahl","first_name":"Niklas"},{"last_name":"Johansson","full_name":"Johansson, Patrik","first_name":"Patrik"},{"last_name":"Favier","full_name":"Favier, Frédéric","first_name":"Frédéric"},{"full_name":"Fontaine, Olivier","last_name":"Fontaine","first_name":"Olivier"},{"last_name":"Bélanger","full_name":"Bélanger, Daniel","first_name":"Daniel"}],"date_created":"2021-06-03T09:58:38Z","volume":168,"intvolume":" 168","abstract":[{"lang":"eng","text":"Lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) based water-in-salt electrolytes (WiSEs) has recently emerged as a new promising class of electrolytes, primarily owing to their wide electrochemical stability windows (~3–4 V), that by far exceed the thermodynamic stability window of water (1.23 V). Upon increasing the salt concentration towards superconcentration the onset of the oxygen evolution reaction (OER) shifts more significantly than the hydrogen evolution reaction (HER) does. The OER shift has been explained by the accumulation of hydrophobic anions blocking water access to the electrode surface, hence by double layer theory. Here we demonstrate that the processes during oxidation are much more complex, involving OER, carbon and salt decomposition by OER intermediates, and salt precipitation upon local oversaturation. The positive shift in the onset potential of oxidation currents was elucidated by combining several advanced analysis techniques: rotating ring-disk electrode voltammetry, online electrochemical mass spectrometry, and X-ray photoelectron spectroscopy, using both dilute and superconcentrated electrolytes. The results demonstrate the importance of reactive OER intermediates and surface films for electrolyte and electrode stability and motivate further studies of the nature of the electrode."}],"publication_identifier":{"issn":["0013-4651"],"eissn":["1945-7111"]},"publication_status":"published","month":"05","article_number":"050550","department":[{"_id":"StFr"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Maffre M, Bouchal R, Freunberger SA, et al. Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. Journal of The Electrochemical Society. 2021;168(5). doi:10.1149/1945-7111/ac0300","short":"M. Maffre, R. Bouchal, S.A. Freunberger, N. Lindahl, P. Johansson, F. Favier, O. Fontaine, D. Bélanger, Journal of The Electrochemical Society 168 (2021).","ieee":"M. Maffre et al., “Investigation of electrochemical and chemical processes occurring at positive potentials in ‘Water-in-Salt’ electrolytes,” Journal of The Electrochemical Society, vol. 168, no. 5. IOP Publishing, 2021.","chicago":"Maffre, Marion, Roza Bouchal, Stefan Alexander Freunberger, Niklas Lindahl, Patrik Johansson, Frédéric Favier, Olivier Fontaine, and Daniel Bélanger. “Investigation of Electrochemical and Chemical Processes Occurring at Positive Potentials in ‘Water-in-Salt’ Electrolytes.” Journal of The Electrochemical Society. IOP Publishing, 2021. https://doi.org/10.1149/1945-7111/ac0300.","ista":"Maffre M, Bouchal R, Freunberger SA, Lindahl N, Johansson P, Favier F, Fontaine O, Bélanger D. 2021. Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. Journal of The Electrochemical Society. 168(5), 050550.","mla":"Maffre, Marion, et al. “Investigation of Electrochemical and Chemical Processes Occurring at Positive Potentials in ‘Water-in-Salt’ Electrolytes.” Journal of The Electrochemical Society, vol. 168, no. 5, 050550, IOP Publishing, 2021, doi:10.1149/1945-7111/ac0300.","apa":"Maffre, M., Bouchal, R., Freunberger, S. A., Lindahl, N., Johansson, P., Favier, F., … Bélanger, D. (2021). Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes. Journal of The Electrochemical Society. IOP Publishing. https://doi.org/10.1149/1945-7111/ac0300"},"issue":"5","publisher":"IOP Publishing","article_processing_charge":"No","doi":"10.1149/1945-7111/ac0300","type":"journal_article","_id":"9447","date_updated":"2023-09-05T13:25:30Z","quality_controlled":"1","external_id":{"isi":["000657724200001"]},"year":"2021","isi":1,"keyword":["Renewable Energy","Sustainability and the Environment","Electrochemistry","Materials Chemistry","Electronic","Optical and Magnetic Materials","Surfaces","Coatings and Films","Condensed Matter Physics"],"publication":"Journal of The Electrochemical Society","status":"public","date_published":"2021-05-01T00:00:00Z"},{"publisher":"Elsevier","doi":"10.1016/j.jfa.2021.109096","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-08T13:56:27Z","_id":"9462","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2009.00992","open_access":"1"}],"external_id":{"arxiv":["2009.00992"],"isi":["000656508600008"]},"year":"2021","isi":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"status":"public","publication":"Journal of Functional Analysis","date_published":"2021-09-15T00:00:00Z","acknowledgement":"Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 (R.S.) and under the Marie Sklodowska-Curie grant agreement No 836146 (A.D.) is gratefully acknowledged. A.D. acknowledges support of the Swiss National Science Foundation through the Ambizione grant PZ00P2 185851.","ec_funded":1,"oa_version":"Preprint","title":"Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons","author":[{"full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas"},{"orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"scopus_import":"1","day":"15","article_type":"original","date_created":"2021-06-06T22:01:28Z","volume":281,"intvolume":" 281","abstract":[{"text":"We consider a system of N trapped bosons with repulsive interactions in a combined semiclassical mean-field limit at positive temperature. We show that the free energy is well approximated by the minimum of the Hartree free energy functional – a natural extension of the Hartree energy functional to positive temperatures. The Hartree free energy functional converges in the same limit to a semiclassical free energy functional, and we show that the system displays Bose–Einstein condensation if and only if it occurs in the semiclassical free energy functional. This allows us to show that for weak coupling the critical temperature decreases due to the repulsive interactions.","lang":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"month":"09","arxiv":1,"article_number":"109096","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"6","citation":{"ista":"Deuchert A, Seiringer R. 2021. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 281(6), 109096.","chicago":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis. Elsevier, 2021. https://doi.org/10.1016/j.jfa.2021.109096.","apa":"Deuchert, A., & Seiringer, R. (2021). Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2021.109096","mla":"Deuchert, Andreas, and Robert Seiringer. “Semiclassical Approximation and Critical Temperature Shift for Weakly Interacting Trapped Bosons.” Journal of Functional Analysis, vol. 281, no. 6, 109096, Elsevier, 2021, doi:10.1016/j.jfa.2021.109096.","ama":"Deuchert A, Seiringer R. Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons. Journal of Functional Analysis. 2021;281(6). doi:10.1016/j.jfa.2021.109096","ieee":"A. Deuchert and R. Seiringer, “Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons,” Journal of Functional Analysis, vol. 281, no. 6. Elsevier, 2021.","short":"A. Deuchert, R. Seiringer, Journal of Functional Analysis 281 (2021)."}},{"quality_controlled":"1","doi":"10.1109/EDTM50988.2021.9420817","article_processing_charge":"No","publisher":"IEEE","date_updated":"2023-10-03T12:51:59Z","_id":"9464","type":"conference","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","call_identifier":"FP7"}],"status":"public","publication":"2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021","ec_funded":1,"acknowledgement":"This work was supported by the National Key R&D Program of China (Grant No. 2016YFA0301700) and the ERC Starting Grant no. 335497.","date_published":"2021-04-08T00:00:00Z","conference":{"location":"Virtual, Online","end_date":"2021-04-11","start_date":"2021-04-08","name":"EDTM: IEEE Electron Devices Technology and Manufacturing Conference"},"isi":1,"year":"2021","external_id":{"isi":["000675595800006"]},"abstract":[{"text":"We firstly introduce the self-assembled growth of highly uniform Ge quantum wires with controllable position, distance and length on patterned Si (001) substrates. We then present the electrically tunable strong spin-orbit coupling, the first Ge hole spin qubit and ultrafast operation of hole spin qubit in the Ge/Si quantum wires.","lang":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781728181769"]},"author":[{"full_name":"Gao, Fei","last_name":"Gao","first_name":"Fei"},{"last_name":"Zhang","full_name":"Zhang, Jie Yin","first_name":"Jie Yin"},{"last_name":"Wang","full_name":"Wang, Jian Huan","first_name":"Jian Huan"},{"first_name":"Ming","last_name":"Ming","full_name":"Ming, Ming"},{"last_name":"Wang","full_name":"Wang, Tina","first_name":"Tina"},{"full_name":"Zhang, Jian Jun","last_name":"Zhang","first_name":"Jian Jun"},{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes","last_name":"Watzinger","first_name":"Hannes"},{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"last_name":"Vukušić","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","full_name":"Vukušić, Lada","orcid":"0000-0003-2424-8636","first_name":"Lada"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","first_name":"Georgios"},{"last_name":"Wang","full_name":"Wang, Ke","first_name":"Ke"},{"full_name":"Xu, Gang","last_name":"Xu","first_name":"Gang"},{"last_name":"Li","full_name":"Li, Hai Ou","first_name":"Hai Ou"},{"first_name":"Guo Ping","last_name":"Guo","full_name":"Guo, Guo Ping"}],"day":"08","scopus_import":"1","title":"Ge/Si quantum wires for quantum computing","oa_version":"None","date_created":"2021-06-06T22:01:29Z","language":[{"iso":"eng"}],"citation":{"short":"F. Gao, J.Y. Zhang, J.H. Wang, M. Ming, T. Wang, J.J. Zhang, H. Watzinger, J. Kukucka, L. Vukušić, G. Katsaros, K. Wang, G. Xu, H.O. Li, G.P. Guo, in:, 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021, IEEE, 2021.","ieee":"F. Gao et al., “Ge/Si quantum wires for quantum computing,” in 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021, Virtual, Online, 2021.","ama":"Gao F, Zhang JY, Wang JH, et al. Ge/Si quantum wires for quantum computing. In: 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. IEEE; 2021. doi:10.1109/EDTM50988.2021.9420817","mla":"Gao, Fei, et al. “Ge/Si Quantum Wires for Quantum Computing.” 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021, 9420817, IEEE, 2021, doi:10.1109/EDTM50988.2021.9420817.","apa":"Gao, F., Zhang, J. Y., Wang, J. H., Ming, M., Wang, T., Zhang, J. J., … Guo, G. P. (2021). Ge/Si quantum wires for quantum computing. In 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. Virtual, Online: IEEE. https://doi.org/10.1109/EDTM50988.2021.9420817","chicago":"Gao, Fei, Jie Yin Zhang, Jian Huan Wang, Ming Ming, Tina Wang, Jian Jun Zhang, Hannes Watzinger, et al. “Ge/Si Quantum Wires for Quantum Computing.” In 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. IEEE, 2021. https://doi.org/10.1109/EDTM50988.2021.9420817.","ista":"Gao F, Zhang JY, Wang JH, Ming M, Wang T, Zhang JJ, Watzinger H, Kukucka J, Vukušić L, Katsaros G, Wang K, Xu G, Li HO, Guo GP. 2021. Ge/Si quantum wires for quantum computing. 2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021. EDTM: IEEE Electron Devices Technology and Manufacturing Conference, 9420817."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","department":[{"_id":"GeKa"}],"article_number":"9420817"},{"year":"2021","date_published":"2021-04-01T00:00:00Z","status":"public","publication":"Journal of Geometry","type":"journal_article","_id":"9465","date_updated":"2022-05-12T11:41:45Z","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00022-021-00577-4","quality_controlled":"1","ddc":["510"],"file":[{"file_id":"9544","date_updated":"2021-06-11T13:16:26Z","creator":"kschuh","date_created":"2021-06-11T13:16:26Z","file_size":694706,"checksum":"e52a832f1def52a2b23d21bcc09e646f","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2021_Geometry_Edelsbrunner.pdf","success":1}],"article_number":"15","department":[{"_id":"HeEd"}],"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Edelsbrunner H, Nikitenko A, Osang GF. 2021. A step in the Delaunay mosaic of order k. Journal of Geometry. 112(1), 15.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, and Georg F Osang. “A Step in the Delaunay Mosaic of Order K.” Journal of Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00022-021-00577-4.","mla":"Edelsbrunner, Herbert, et al. “A Step in the Delaunay Mosaic of Order K.” Journal of Geometry, vol. 112, no. 1, 15, Springer Nature, 2021, doi:10.1007/s00022-021-00577-4.","apa":"Edelsbrunner, H., Nikitenko, A., & Osang, G. F. (2021). A step in the Delaunay mosaic of order k. Journal of Geometry. Springer Nature. https://doi.org/10.1007/s00022-021-00577-4","ama":"Edelsbrunner H, Nikitenko A, Osang GF. A step in the Delaunay mosaic of order k. Journal of Geometry. 2021;112(1). doi:10.1007/s00022-021-00577-4","short":"H. Edelsbrunner, A. Nikitenko, G.F. Osang, Journal of Geometry 112 (2021).","ieee":"H. Edelsbrunner, A. Nikitenko, and G. F. Osang, “A step in the Delaunay mosaic of order k,” Journal of Geometry, vol. 112, no. 1. Springer Nature, 2021."},"issue":"1","language":[{"iso":"eng"}],"oa":1,"date_created":"2021-06-06T22:01:29Z","article_type":"original","volume":112,"title":"A step in the Delaunay mosaic of order k","oa_version":"Published Version","day":"01","scopus_import":"1","author":[{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"Anton","full_name":"Nikitenko, Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko"},{"last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","first_name":"Georg F"}],"file_date_updated":"2021-06-11T13:16:26Z","publication_status":"published","publication_identifier":{"eissn":["14208997"],"issn":["00472468"]},"intvolume":" 112","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Given a locally finite set 𝑋⊆ℝ𝑑 and an integer 𝑘≥0, we consider the function 𝐰𝑘:Del𝑘(𝑋)→ℝ on the dual of the order-k Voronoi tessellation, whose sublevel sets generalize the notion of alpha shapes from order-1 to order-k (Edelsbrunner et al. in IEEE Trans Inf Theory IT-29:551–559, 1983; Krasnoshchekov and Polishchuk in Inf Process Lett 114:76–83, 2014). While this function is not necessarily generalized discrete Morse, in the sense of Forman (Adv Math 134:90–145, 1998) and Freij (Discrete Math 309:3821–3829, 2009), we prove that it satisfies similar properties so that its increments can be meaningfully classified into critical and non-critical steps. This result extends to the case of weighted points and sheds light on k-fold covers with balls in Euclidean space."}],"has_accepted_license":"1"}]