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Our approach is generic and does not assume specific details of the system, suggesting wide applications.","lang":"eng"}],"external_id":{"arxiv":["2105.15193"]},"language":[{"iso":"eng"}],"title":"Artificial neural network states for non-additive systems","author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","orcid":"0000-0002-1106-4419"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail"},{"last_name":"Mentink","full_name":"Mentink, Johan H.","first_name":"Johan H."}],"month":"05","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","related_material":{"record":[{"status":"public","id":"10759","relation":"dissertation_contains"}]},"date_created":"2022-02-17T11:18:57Z","arxiv":1,"publication":"arXiv","doi":"10.48550/arXiv.2105.15193","corr_author":"1","year":"2021","project":[{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"acknowledgement":"We acknowledge fruitful discussions with Giacomo Bighin, Giammarco Fabiani, Areg Ghazaryan, Christoph\r\nLampert, and Artem Volosniev at various stages of this work. W.R. is a recipient of a DOC Fellowship of the\r\nAustrian Academy of Sciences and has received funding from the EU Horizon 2020 programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 665385. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). This work is part of the Shell-NWO/FOM-initiative “Computational sciences for energy research” of Shell and Chemical Sciences, Earth and Life Sciences, Physical Sciences, FOM and STW.","status":"public","publication_status":"draft","department":[{"_id":"MiLe"}],"citation":{"mla":"Rzadkowski, Wojciech, et al. “Artificial Neural Network States for Non-Additive Systems.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2105.15193\">10.48550/arXiv.2105.15193</a>.","short":"W. Rzadkowski, M. Lemeshko, J.H. Mentink, ArXiv (n.d.).","ama":"Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for non-additive systems. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2105.15193\">10.48550/arXiv.2105.15193</a>","apa":"Rzadkowski, W., Lemeshko, M., &#38; Mentink, J. H. (n.d.). Artificial neural network states for non-additive systems. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2105.15193\">https://doi.org/10.48550/arXiv.2105.15193</a>","chicago":"Rzadkowski, Wojciech, Mikhail Lemeshko, and Johan H. Mentink. “Artificial Neural Network States for Non-Additive Systems.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2105.15193\">https://doi.org/10.48550/arXiv.2105.15193</a>.","ista":"Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for non-additive systems. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2105.15193\">10.48550/arXiv.2105.15193</a>.","ieee":"W. Rzadkowski, M. Lemeshko, and J. H. Mentink, “Artificial neural network states for non-additive systems,” <i>arXiv</i>. ."},"page":"2105.15193","article_processing_charge":"No","date_published":"2021-05-31T00:00:00Z","day":"31","date_updated":"2026-04-07T14:20:12Z"},{"status":"public","publication_status":"published","intvolume":"        35","publication_identifier":{"isbn":["978-1-57735-866-4"],"eissn":["2374-3468"],"issn":["2159-5399"]},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein\r\nAward), ERC CoG 863818 (FoRM-SMArt), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","year":"2021","corr_author":"1","file":[{"access_level":"open_access","date_updated":"2022-01-26T07:41:16Z","success":1,"content_type":"application/pdf","checksum":"2bc8155b2526a70fba5b7301bc89dbd1","file_size":137235,"creator":"mlechner","relation":"main_file","date_created":"2022-01-26T07:41:16Z","file_id":"10684","file_name":"16496-Article Text-19990-1-2-20210518 (1).pdf"}],"publication":"Proceedings of the AAAI Conference on Artificial Intelligence","arxiv":1,"date_created":"2022-01-25T15:15:02Z","volume":35,"date_updated":"2026-04-07T14:21:58Z","day":"28","conference":{"location":"Virtual","name":"AAAI: Association for the Advancement of Artificial Intelligence","start_date":"2021-02-02","end_date":"2021-02-09"},"date_published":"2021-05-28T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","page":"3787-3795","citation":{"ieee":"T. A. Henzinger, M. Lechner, and D. Zikelic, “Scalable verification of quantized neural networks,” in <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, Virtual, 2021, vol. 35, no. 5A, pp. 3787–3795.","ista":"Henzinger TA, Lechner M, Zikelic D. 2021. Scalable verification of quantized neural networks. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI: Association for the Advancement of Artificial Intelligence, Technical Tracks, vol. 35, 3787–3795.","apa":"Henzinger, T. A., Lechner, M., &#38; Zikelic, D. (2021). Scalable verification of quantized neural networks. In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i> (Vol. 35, pp. 3787–3795). Virtual: AAAI Press.","chicago":"Henzinger, Thomas A, Mathias Lechner, and Dorde Zikelic. “Scalable Verification of Quantized Neural Networks.” In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, 35:3787–95. AAAI Press, 2021.","ama":"Henzinger TA, Lechner M, Zikelic D. Scalable verification of quantized neural networks. In: <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>. Vol 35. AAAI Press; 2021:3787-3795.","short":"T.A. Henzinger, M. Lechner, D. Zikelic, in:, Proceedings of the AAAI Conference on Artificial Intelligence, AAAI Press, 2021, pp. 3787–3795.","mla":"Henzinger, Thomas A., et al. “Scalable Verification of Quantized Neural Networks.” <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, vol. 35, no. 5A, AAAI Press, 2021, pp. 3787–95."},"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"title":"Scalable verification of quantized neural networks","issue":"5A","language":[{"iso":"eng"}],"external_id":{"arxiv":["2012.08185"]},"abstract":[{"text":"Formal verification of neural networks is an active topic of research, and recent advances have significantly increased the size of the networks that verification tools can handle. However, most methods are designed for verification of an idealized model of the actual network which works over real arithmetic and ignores rounding imprecisions. This idealization is in stark contrast to network quantization, which is a technique that trades numerical precision for computational efficiency and is, therefore, often applied in practice. Neglecting rounding errors of such low-bit quantized neural networks has been shown to lead to wrong conclusions about the network’s correctness. Thus, the desired approach for verifying quantized neural networks would be one that takes these rounding errors\r\ninto account. In this paper, we show that verifying the bitexact implementation of quantized neural networks with bitvector specifications is PSPACE-hard, even though verifying idealized real-valued networks and satisfiability of bit-vector specifications alone are each in NP. Furthermore, we explore several practical heuristics toward closing the complexity gap between idealized and bit-exact verification. In particular, we propose three techniques for making SMT-based verification of quantized neural networks more scalable. Our experiments demonstrate that our proposed methods allow a speedup of up to three orders of magnitude over existing approaches.","lang":"eng"}],"ec_funded":1,"file_date_updated":"2022-01-26T07:41:16Z","_id":"10665","main_file_link":[{"open_access":"1","url":"https://ojs.aaai.org/index.php/AAAI/article/view/16496"}],"oa":1,"ddc":["000"],"publisher":"AAAI Press","related_material":{"record":[{"id":"11362","status":"public","relation":"dissertation_contains"}]},"quality_controlled":"1","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","alternative_title":["Technical Tracks"],"month":"05","author":[{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias"},{"full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde"}],"scopus_import":"1"},{"publication_status":"published","status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)"},"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), ERC CoG 863818 (FoRM-SMArt), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"year":"2021","corr_author":"1","file":[{"file_size":452492,"creator":"mlechner","relation":"main_file","date_created":"2022-01-26T07:39:59Z","file_name":"infinite_time_horizon_safety_o.pdf","file_id":"10682","access_level":"open_access","date_updated":"2022-01-26T07:39:59Z","success":1,"content_type":"application/pdf","checksum":"0fc0f852525c10dda9cc9ffea07fb4e4"}],"doi":"10.48550/arXiv.2111.03165","publication":"35th Conference on Neural Information Processing Systems","arxiv":1,"date_created":"2022-01-25T15:45:58Z","date_updated":"2026-04-07T14:21:58Z","day":"01","conference":{"end_date":"2021-12-10","start_date":"2021-12-06","name":"NeurIPS: Neural Information Processing Systems","location":"Virtual"},"has_accepted_license":"1","date_published":"2021-12-01T00:00:00Z","article_processing_charge":"No","citation":{"ieee":"M. Lechner, Ð. Žikelić, K. Chatterjee, and T. A. Henzinger, “Infinite time horizon safety of Bayesian neural networks,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, 2021.","ista":"Lechner M, Žikelić Ð, Chatterjee K, Henzinger TA. 2021. Infinite time horizon safety of Bayesian neural networks. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems,  Advances in Neural Information Processing Systems, .","chicago":"Lechner, Mathias, Ðorđe Žikelić, Krishnendu Chatterjee, and Thomas A Henzinger. “Infinite Time Horizon Safety of Bayesian Neural Networks.” In <i>35th Conference on Neural Information Processing Systems</i>, 2021. <a href=\"https://doi.org/10.48550/arXiv.2111.03165\">https://doi.org/10.48550/arXiv.2111.03165</a>.","apa":"Lechner, M., Žikelić, Ð., Chatterjee, K., &#38; Henzinger, T. A. (2021). Infinite time horizon safety of Bayesian neural networks. In <i>35th Conference on Neural Information Processing Systems</i>. Virtual. <a href=\"https://doi.org/10.48550/arXiv.2111.03165\">https://doi.org/10.48550/arXiv.2111.03165</a>","ama":"Lechner M, Žikelić Ð, Chatterjee K, Henzinger TA. Infinite time horizon safety of Bayesian neural networks. In: <i>35th Conference on Neural Information Processing Systems</i>. ; 2021. doi:<a href=\"https://doi.org/10.48550/arXiv.2111.03165\">10.48550/arXiv.2111.03165</a>","short":"M. Lechner, Ð. Žikelić, K. Chatterjee, T.A. Henzinger, in:, 35th Conference on Neural Information Processing Systems, 2021.","mla":"Lechner, Mathias, et al. “Infinite Time Horizon Safety of Bayesian Neural Networks.” <i>35th Conference on Neural Information Processing Systems</i>, 2021, doi:<a href=\"https://doi.org/10.48550/arXiv.2111.03165\">10.48550/arXiv.2111.03165</a>."},"department":[{"_id":"GradSch"},{"_id":"ToHe"},{"_id":"KrCh"}],"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","title":"Infinite time horizon safety of Bayesian neural networks","language":[{"iso":"eng"}],"external_id":{"arxiv":["2111.03165"]},"abstract":[{"lang":"eng","text":"Bayesian neural networks (BNNs) place distributions over the weights of a neural network to model uncertainty in the data and the network's prediction. We consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with infinite time horizon systems. Compared to the existing sampling-based approaches, which are inapplicable to the infinite time horizon setting, we train a separate deterministic neural network that serves as an infinite time horizon safety certificate. In particular, we show that the certificate network guarantees the safety of the system over a subset of the BNN weight posterior's support. Our method first computes a safe weight set and then alters the BNN's weight posterior to reject samples outside this set. Moreover, we show how to extend our approach to a safe-exploration reinforcement learning setting, in order to avoid unsafe trajectories during the training of the policy. We evaluate our approach on a series of reinforcement learning benchmarks, including non-Lyapunovian safety specifications."}],"file_date_updated":"2022-01-26T07:39:59Z","ec_funded":1,"main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2021/hash/544defa9fddff50c53b71c43e0da72be-Abstract.html","open_access":"1"}],"_id":"10667","oa":1,"ddc":["000"],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11362"}]},"quality_controlled":"1","type":"conference","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","alternative_title":[" Advances in Neural Information Processing Systems"],"month":"12","author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias"},{"last_name":"Žikelić","full_name":"Žikelić, Ðorđe","first_name":"Ðorđe"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}]},{"ddc":["000"],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.08187"}],"_id":"10666","abstract":[{"text":"Adversarial training is an effective method to train deep learning models that are resilient to norm-bounded perturbations, with the cost of nominal performance drop. While adversarial training appears to enhance the robustness and safety of a deep model deployed in open-world decision-critical applications, counterintuitively, it induces undesired behaviors in robot learning settings. In this paper, we show theoretically and experimentally that neural controllers obtained via adversarial training are subjected to three types of defects, namely transient, systematic, and conditional errors. We first generalize adversarial training to a safety-domain optimization scheme allowing for more generic specifications. We then prove that such a learning process tends to cause certain error profiles. We support our theoretical results by a thorough experimental safety analysis in a robot-learning task. Our results suggest that adversarial training is not yet ready for robot learning.","lang":"eng"}],"external_id":{"arxiv":["2103.08187"],"isi":["000765738803040"]},"language":[{"iso":"eng"}],"title":"Adversarial training is not ready for robot learning","isi":1,"scopus_import":"1","author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"last_name":"Hasani","full_name":"Hasani, Ramin","first_name":"Ramin"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"OA_type":"green","month":"06","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","quality_controlled":"1","related_material":{"record":[{"id":"11362","status":"public","relation":"dissertation_contains"}]},"date_created":"2022-01-25T15:44:54Z","arxiv":1,"publication":"2021 IEEE International Conference on Robotics and Automation","series_title":"ICRA","doi":"10.1109/ICRA48506.2021.9561036","year":"2021","project":[{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)"},"acknowledgement":"M.L. and T.A.H. are supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H. and D.R. are supported by Boeing and R.G. by Horizon-2020 ECSEL Project grant no. 783163 (iDev40).","publication_identifier":{"isbn":["978-1-7281-9078-5"],"eisbn":["978-1-7281-9077-8"],"issn":["1050-4729"],"eissn":["2577-087X"]},"publication_status":"published","status":"public","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"citation":{"chicago":"Lechner, Mathias, Ramin Hasani, Radu Grosu, Daniela Rus, and Thomas A Henzinger. “Adversarial Training Is Not Ready for Robot Learning.” In <i>2021 IEEE International Conference on Robotics and Automation</i>, 4140–47. ICRA, 2021. <a href=\"https://doi.org/10.1109/ICRA48506.2021.9561036\">https://doi.org/10.1109/ICRA48506.2021.9561036</a>.","apa":"Lechner, M., Hasani, R., Grosu, R., Rus, D., &#38; Henzinger, T. A. (2021). Adversarial training is not ready for robot learning. In <i>2021 IEEE International Conference on Robotics and Automation</i> (pp. 4140–4147). Xi’an, China. <a href=\"https://doi.org/10.1109/ICRA48506.2021.9561036\">https://doi.org/10.1109/ICRA48506.2021.9561036</a>","ista":"Lechner M, Hasani R, Grosu R, Rus D, Henzinger TA. 2021. Adversarial training is not ready for robot learning. 2021 IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and AutomationICRA, 4140–4147.","ieee":"M. Lechner, R. Hasani, R. Grosu, D. Rus, and T. A. Henzinger, “Adversarial training is not ready for robot learning,” in <i>2021 IEEE International Conference on Robotics and Automation</i>, Xi’an, China, 2021, pp. 4140–4147.","mla":"Lechner, Mathias, et al. “Adversarial Training Is Not Ready for Robot Learning.” <i>2021 IEEE International Conference on Robotics and Automation</i>, 2021, pp. 4140–47, doi:<a href=\"https://doi.org/10.1109/ICRA48506.2021.9561036\">10.1109/ICRA48506.2021.9561036</a>.","short":"M. Lechner, R. Hasani, R. Grosu, D. Rus, T.A. Henzinger, in:, 2021 IEEE International Conference on Robotics and Automation, 2021, pp. 4140–4147.","ama":"Lechner M, Hasani R, Grosu R, Rus D, Henzinger TA. Adversarial training is not ready for robot learning. In: <i>2021 IEEE International Conference on Robotics and Automation</i>. ICRA. ; 2021:4140-4147. doi:<a href=\"https://doi.org/10.1109/ICRA48506.2021.9561036\">10.1109/ICRA48506.2021.9561036</a>"},"page":"4140-4147","article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-06-01T00:00:00Z","conference":{"name":"ICRA: International Conference on Robotics and Automation","location":"Xi'an, China","end_date":"2021-06-05","start_date":"2021-05-30"},"day":"01","date_updated":"2026-04-07T14:21:58Z","OA_place":"repository"},{"publication":"ACM Transactions on Graphics","volume":40,"date_created":"2021-08-08T22:01:26Z","doi":"10.1145/3450626.3459800","file":[{"checksum":"7e5d08ce46b0451b3102eacd3d00f85f","content_type":"application/pdf","success":1,"date_updated":"2021-10-18T10:42:15Z","access_level":"open_access","file_id":"10150","file_name":"elastic-curves-paper.pdf","date_created":"2021-10-18T10:42:15Z","relation":"main_file","creator":"chafner","file_size":17064290},{"content_type":"application/pdf","checksum":"0088643478be7c01a703b5b10767348f","access_level":"open_access","date_updated":"2021-10-18T10:42:22Z","creator":"chafner","relation":"supplementary_material","date_created":"2021-10-18T10:42:22Z","file_id":"10151","file_name":"elastic-curves-supp.pdf","file_size":547156}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"intvolume":"        40","publication_status":"published","status":"public","year":"2021","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","department":[{"_id":"BeBi"}],"citation":{"mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","ama":"Hafner C, Bickel B. The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>","apa":"Hafner, C., &#38; Bickel, B. (2021). The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. Virtual: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>.","ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126."},"article_number":"126","article_processing_charge":"No","day":"19","conference":{"name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Virtual","end_date":"2021-08-13","start_date":"2021-08-09"},"date_published":"2021-07-19T00:00:00Z","has_accepted_license":"1","date_updated":"2026-04-07T22:30:05Z","publisher":"Association for Computing Machinery","ddc":["516"],"ec_funded":1,"file_date_updated":"2021-10-18T10:42:22Z","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"oa":1,"_id":"9817","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements."}],"external_id":{"isi":["000674930900091"]},"issue":"4","title":"The design space of plane elastic curves","license":"https://creativecommons.org/licenses/by/4.0/","isi":1,"scopus_import":"1","author":[{"full_name":"Hafner, Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd"}],"month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/designing-with-elastic-structures/","description":"News on IST Website"}],"record":[{"relation":"dissertation_contains","status":"public","id":"12897"}]},"article_type":"original","quality_controlled":"1","type":"journal_article"},{"abstract":[{"lang":"eng","text":"During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process."}],"external_id":{"isi":["000639461800008"],"pmid":["33352181"]},"language":[{"iso":"eng"}],"title":"Reassembling gastrulation","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["570"],"publisher":"Elsevier","oa":1,"keyword":["Developmental Biology","Cell Biology","Molecular Biology"],"_id":"8966","ec_funded":1,"file_date_updated":"2021-08-11T10:28:06Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"journal_article","article_type":"original","related_material":{"record":[{"status":"public","id":"12891","relation":"dissertation_contains"}]},"isi":1,"scopus_import":"1","author":[{"full_name":"Schauer, Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","first_name":"Alexandra"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"month":"06","pmid":1,"file":[{"date_updated":"2021-08-11T10:28:06Z","access_level":"open_access","checksum":"fa2a5731fd16ab171b029f32f031c440","content_type":"application/pdf","success":1,"file_size":1440321,"file_id":"9880","file_name":"2021_DevBiology_Schauer.pdf","date_created":"2021-08-11T10:28:06Z","relation":"main_file","creator":"kschuh"}],"year":"2021","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"acknowledgement":"We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient of a DOC Fellowship of the Austrian Academy of Science.","intvolume":"       474","publication_identifier":{"issn":["0012-1606"]},"publication_status":"published","status":"public","volume":474,"date_created":"2020-12-22T09:53:34Z","publication":"Developmental Biology","doi":"10.1016/j.ydbio.2020.12.014","date_published":"2021-06-01T00:00:00Z","has_accepted_license":"1","day":"01","date_updated":"2026-04-07T22:30:06Z","department":[{"_id":"CaHe"}],"citation":{"ista":"Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental Biology. 474, 71–81.","ieee":"A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” <i>Developmental Biology</i>, vol. 474. Elsevier, pp. 71–81, 2021.","chicago":"Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>.","apa":"Schauer, A., &#38; Heisenberg, C.-P. J. (2021). Reassembling gastrulation. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>","ama":"Schauer A, Heisenberg C-PJ. Reassembling gastrulation. <i>Developmental Biology</i>. 2021;474:71-81. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>","mla":"Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>, vol. 474, Elsevier, 2021, pp. 71–81, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>.","short":"A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81."},"page":"71-81","article_processing_charge":"Yes (via OA deal)"},{"quality_controlled":"1","type":"journal_article","related_material":{"link":[{"url":"https://ista.ac.at/en/news/spot-the-difference/","relation":"press_release"}],"record":[{"id":"10110","status":"public","relation":"software"}]},"article_type":"original","oa_version":"Submitted Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"orcid":"0000-0003-2209-5242","first_name":"José","full_name":"Guzmán, José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois"},{"last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","first_name":"Claudia "},{"orcid":"0000-0003-0256-6529","first_name":"Xiaomin","last_name":"Zhang","full_name":"Zhang, Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin","last_name":"Suter"},{"last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M"}],"month":"12","isi":1,"scopus_import":"1","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","issue":"12","abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"external_id":{"isi":["000888567500015"]},"language":[{"iso":"eng"}],"oa":1,"keyword":["general medicine"],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/647800"}],"_id":"10816","ec_funded":1,"file_date_updated":"2022-06-18T22:30:03Z","acknowledged_ssus":[{"_id":"SSU"}],"publisher":"Springer Nature","ddc":["610"],"date_updated":"2025-10-09T22:30:54Z","has_accepted_license":"1","date_published":"2021-12-16T00:00:00Z","day":"16","page":"830-842","article_processing_charge":"No","department":[{"_id":"PeJo"}],"citation":{"chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” <i>Nature Computational Science</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s43588-021-00157-1\">https://doi.org/10.1038/s43588-021-00157-1</a>.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-021-00157-1\">https://doi.org/10.1038/s43588-021-00157-1</a>","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842.","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” <i>Nature Computational Science</i>, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” <i>Nature Computational Science</i>, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:<a href=\"https://doi.org/10.1038/s43588-021-00157-1\">10.1038/s43588-021-00157-1</a>.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. <i>Nature Computational Science</i>. 2021;1(12):830-842. doi:<a href=\"https://doi.org/10.1038/s43588-021-00157-1\">10.1038/s43588-021-00157-1</a>"},"year":"2021","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF"}],"acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. 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, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","intvolume":"         1","publication_identifier":{"issn":["2662-8457"]},"publication_status":"published","status":"public","file":[{"date_created":"2022-06-02T12:51:07Z","file_id":"11430","file_name":"Guzmanetal2021.pdf","creator":"patrickd","relation":"main_file","file_size":1699466,"checksum":"9fec5b667909ef52be96d502e4f8c2ae","content_type":"application/pdf","embargo":"2022-06-17","date_updated":"2022-06-18T22:30:03Z","access_level":"open_access"},{"date_updated":"2022-06-18T22:30:03Z","title":"Supplementary Material","access_level":"open_access","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","content_type":"application/pdf","embargo":"2022-06-17","file_size":3005651,"file_name":"Guzmanetal2021Suppl.pdf","file_id":"11431","date_created":"2022-06-02T12:53:47Z","relation":"supplementary_material","creator":"patrickd"}],"corr_author":"1","doi":"10.1038/s43588-021-00157-1","volume":1,"date_created":"2022-03-04T08:32:36Z","publication":"Nature Computational Science"},{"date_updated":"2026-04-07T22:30:07Z","type":"software","related_material":{"link":[{"url":"https://ist.ac.at/en/news/spot-the-difference/","description":"News on IST Webpage","relation":"press_release"}],"record":[{"id":"10816","status":"public","relation":"used_for_analysis_in"}]},"has_accepted_license":"1","date_published":"2021-12-16T00:00:00Z","day":"16","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"12","author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José","last_name":"Guzmán","first_name":"José","orcid":"0000-0003-2209-5242"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"first_name":"Claudia ","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia "},{"full_name":"Zhang, Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0256-6529","first_name":"Xiaomin"},{"last_name":"Suter","full_name":"Suter, Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936","first_name":"Benjamin"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"citation":{"short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","mla":"Guzmán, José, et al. <i>How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>."},"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"tmp":{"short":"GPL 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html","name":"GNU General Public License 3.0"},"year":"2021","status":"public","license":"https://opensource.org/licenses/GPL-3.0","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"file":[{"access_level":"open_access","date_updated":"2021-10-08T08:46:04Z","content_type":"application/x-zip-compressed","success":1,"checksum":"f92f8931cad0aa7e411c1715337bf408","file_size":332990101,"relation":"main_file","creator":"cchlebak","file_name":"patternseparation-main (1).zip","file_id":"10114","date_created":"2021-10-08T08:46:04Z"}],"doi":"10.15479/AT:ISTA:10110","_id":"10110","oa":1,"file_date_updated":"2021-10-08T08:46:04Z","date_created":"2021-10-08T06:44:22Z","publisher":"IST Austria","ddc":["005"]},{"acknowledged_ssus":[{"_id":"M-Shop"}],"publisher":"Springer Nature","ddc":["570"],"oa":1,"_id":"9438","file_date_updated":"2021-12-02T23:30:05Z","ec_funded":1,"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"}],"external_id":{"isi":["000650528700003"],"pmid":["33990799"]},"language":[{"iso":"eng"}],"title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","issue":"6","isi":1,"scopus_import":"1","author":[{"orcid":"0000-0001-7577-1676","first_name":"David H","last_name":"Vandael","full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuji","orcid":"0000-0003-0408-6094","id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto","full_name":"Okamoto, Yuji"},{"first_name":"Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina"},{"last_name":"Vargas Barroso","full_name":"Vargas Barroso, Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M"},{"first_name":"Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin","last_name":"Suter"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"month":"06","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"journal_article","article_type":"original","volume":16,"date_created":"2021-05-30T22:01:24Z","publication":"Nature Protocols","doi":"10.1038/s41596-021-00526-0","pmid":1,"file":[{"embargo":"2021-12-01","content_type":"application/pdf","checksum":"7eb580abd8893cdb0b410cf41bc8c263","access_level":"open_access","date_updated":"2021-12-02T23:30:05Z","creator":"cziletti","relation":"main_file","date_created":"2021-07-08T12:27:55Z","file_id":"9639","file_name":"VandaeletalAuthorVersion2021.pdf","file_size":38574802}],"corr_author":"1","year":"2021","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits"},{"_id":"2696E7FE-B435-11E9-9278-68D0E5697425","grant_number":"V00739","call_identifier":"FWF","name":"Structural plasticity at mossy fiber-CA3 synapses"}],"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.","intvolume":"        16","publication_identifier":{"issn":["1754-2189"],"eissn":["1750-2799"]},"publication_status":"published","status":"public","department":[{"_id":"PeJo"}],"citation":{"mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","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. <i>Nature Protocols</i>. 2021;16(6):2947–2967. doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., &#38; Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>","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.” <i>Nature Protocols</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>.","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,” <i>Nature Protocols</i>, 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."},"page":"2947–2967","article_processing_charge":"No","date_published":"2021-06-01T00:00:00Z","has_accepted_license":"1","day":"01","date_updated":"2025-04-22T22:30:43Z"},{"scopus_import":"1","isi":1,"month":"03","author":[{"first_name":"Yann K.","last_name":"Petit","full_name":"Petit, Yann K."},{"last_name":"Mourad","full_name":"Mourad, Eléonore","first_name":"Eléonore"},{"full_name":"Prehal, Christian","last_name":"Prehal","first_name":"Christian"},{"first_name":"Christian","last_name":"Leypold","full_name":"Leypold, Christian"},{"last_name":"Windischbacher","full_name":"Windischbacher, Andreas","first_name":"Andreas"},{"full_name":"Mijailovic, Daniel","last_name":"Mijailovic","first_name":"Daniel"},{"first_name":"Christian","full_name":"Slugovc, Christian","last_name":"Slugovc"},{"full_name":"Borisov, Sergey M.","last_name":"Borisov","first_name":"Sergey M."},{"first_name":"Egbert","last_name":"Zojer","full_name":"Zojer, Egbert"},{"full_name":"Brutti, Sergio","last_name":"Brutti","first_name":"Sergio"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","article_type":"original","type":"journal_article","quality_controlled":"1","ddc":["540"],"publisher":"Springer Nature","acknowledged_ssus":[{"_id":"M-Shop"}],"file_date_updated":"2021-09-16T22:30:03Z","_id":"9250","oa":1,"keyword":["General Chemistry","General Chemical Engineering"],"language":[{"iso":"eng"}],"external_id":{"isi":["000629296400001"],"pmid":["33723377"]},"abstract":[{"lang":"eng","text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate."}],"title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","issue":"5","citation":{"ieee":"Y. K. Petit <i>et al.</i>, “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” <i>Nature Chemistry</i>, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>.","apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. 2021;13(5):465-471. doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>."},"department":[{"_id":"StFr"}],"article_processing_charge":"No","page":"465-471","day":"15","date_published":"2021-03-15T00:00:00Z","has_accepted_license":"1","date_updated":"2024-10-09T21:00:28Z","publication":"Nature Chemistry","date_created":"2021-03-16T11:12:20Z","volume":13,"doi":"10.1038/s41557-021-00643-z","corr_author":"1","file":[{"file_size":1811448,"date_created":"2021-03-22T11:46:00Z","file_id":"9276","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","creator":"dernst","relation":"main_file","date_updated":"2021-09-16T22:30:03Z","access_level":"open_access","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","embargo":"2021-09-15","content_type":"application/pdf"}],"pmid":1,"status":"public","publication_status":"published","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"intvolume":"        13","acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","year":"2021"},{"publication_identifier":{"eissn":["1745-2481"]},"intvolume":"        17","publication_status":"published","status":"public","year":"2021","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"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.","file":[{"file_size":10028836,"date_created":"2021-09-20T09:27:43Z","file_name":"RevisedQMBSreview.pdf","file_id":"10026","creator":"patrickd","relation":"main_file","date_updated":"2021-12-02T23:30:03Z","access_level":"open_access","checksum":"316ed42ea1b42b0f1a3025bb476266fc","content_type":"application/pdf","embargo":"2021-12-01"}],"doi":"10.1038/s41567-021-01230-2","arxiv":1,"publication":"Nature Physics","volume":17,"date_created":"2021-05-28T09:03:50Z","date_updated":"2025-04-14T07:52:09Z","day":"01","date_published":"2021-06-01T00:00:00Z","has_accepted_license":"1","page":"675–685","article_processing_charge":"No","department":[{"_id":"MaSe"}],"citation":{"ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” <i>Nature Physics</i>, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>.","apa":"Serbyn, M., Abanin, D. A., &#38; Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. 2021;17(6):675–685. doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685."},"issue":"6","title":"Quantum many-body scars and weak breaking of ergodicity","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"external_id":{"isi":["000655563800002"],"arxiv":["2011.09486"]},"ec_funded":1,"file_date_updated":"2021-12-02T23:30:03Z","oa":1,"_id":"9428","ddc":["539"],"publisher":"Nature Research","article_type":"review","type":"journal_article","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","author":[{"first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A.","first_name":"Dmitry A."},{"last_name":"Papić","full_name":"Papić, Zlatko","first_name":"Zlatko"}],"month":"06","isi":1,"scopus_import":"1"},{"citation":{"ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press , pp. 5345–58, 2021.","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press , 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>."},"department":[{"_id":"BeVi"}],"article_processing_charge":"No","page":"5345-58","has_accepted_license":"1","date_published":"2021-06-19T00:00:00Z","day":"19","date_updated":"2026-04-07T22:30:39Z","date_created":"2021-10-21T07:49:12Z","volume":138,"publication":"Molecular Biology and Evolution","doi":"10.1093/molbev/msab178","pmid":1,"corr_author":"1","file":[{"access_level":"open_access","date_updated":"2022-05-06T09:47:18Z","content_type":"application/pdf","success":1,"checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","file_size":1008594,"relation":"main_file","creator":"dernst","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","file_id":"11352","date_created":"2022-05-06T09:47:18Z"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","year":"2021","publication_status":"published","status":"public","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"intvolume":"       138","scopus_import":"1","isi":1,"month":"06","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231"},{"orcid":"0000-0002-8876-6494","first_name":"Mikhail A.","last_name":"Moldovan","full_name":"Moldovan, Mikhail A.","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0"},{"first_name":"Marion A L","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","full_name":"Picard, Marion A L"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"journal_article","related_material":{"record":[{"status":"public","id":"19386","relation":"dissertation_contains"}]},"article_type":"original","acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"Oxford University Press ","ddc":["610"],"_id":"10167","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"oa":1,"file_date_updated":"2022-05-06T09:47:18Z","external_id":{"isi":["000741368600009"],"pmid":["34146097"]},"abstract":[{"text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.","lang":"eng"}],"language":[{"iso":"eng"}],"title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","issue":"12"},{"corr_author":"1","pmid":1,"intvolume":"       118","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"status":"public","publication_status":"published","year":"2021","project":[{"call_identifier":"FWF","name":"Instabilities in pulsating pipe flow in complex fluids","grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E"}],"acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","arxiv":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","volume":118,"date_created":"2021-11-17T13:24:24Z","doi":"10.1073/pnas.2102350118","day":"03","date_published":"2021-11-03T00:00:00Z","date_updated":"2026-04-07T22:30:47Z","department":[{"_id":"BjHo"}],"citation":{"ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences of the United States of America. 118(45), e2102350118.","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 45. National Academy of Sciences, 2021.","apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., &#38; Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>.","ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(45). doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>."},"article_number":"e2102350118","article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"external_id":{"pmid":[" 34732570"],"isi":["000720926900019"],"arxiv":["2103.00023"]},"issue":"45","title":"Experimental observation of the origin and structure of elastoinertial turbulence","publisher":"National Academy of Sciences","oa":1,"keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"_id":"10299","main_file_link":[{"url":"https://arxiv.org/abs/2103.00023","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_type":"original","related_material":{"record":[{"id":"19906","status":"public","relation":"dissertation_contains"}]},"type":"journal_article","quality_controlled":"1","isi":1,"scopus_import":"1","author":[{"last_name":"Choueiri","full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H"},{"first_name":"Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M"},{"first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","full_name":"Varshney, Atul"},{"full_name":"Sankar, Sarath","last_name":"Sankar","first_name":"Sarath"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"month":"11"},{"article_processing_charge":"No","page":"267-274","citation":{"ama":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. 2021;17:267-274. doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>","mla":"Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>, vol. 17, Springer Nature, 2021, pp. 267–74, doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>.","short":"D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics 17 (2021) 267–274.","ista":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. 17, 267–274.","ieee":"D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory of mechanochemical patterning and optimal migration in cell monolayers,” <i>Nature Physics</i>, vol. 17. Springer Nature, pp. 267–274, 2021.","chicago":"Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>.","apa":"Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., &#38; Hannezo, E. B. (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>"},"department":[{"_id":"EdHa"}],"date_updated":"2026-04-07T22:31:00Z","date_published":"2021-02-01T00:00:00Z","day":"01","doi":"10.1038/s41567-020-01037-7","date_created":"2020-10-04T22:01:37Z","volume":17,"publication":"Nature Physics","project":[{"name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"},{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"acknowledgement":"We would like to thank G. Tkacik and all of the members of the Hannezo and Hirashima groups for useful discussions, X. Trepat for help on traction force microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants from the Austrian Science Fund (FWF) (P 31639) and the European Research Council (851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.), from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto University (to E.H. and T.H.).","year":"2021","status":"public","publication_status":"published","intvolume":"        17","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"corr_author":"1","month":"02","author":[{"first_name":"Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","last_name":"Boocock","full_name":"Boocock, Daniel R"},{"first_name":"Naoya","full_name":"Hino, Naoya","last_name":"Hino"},{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia","last_name":"Ruzickova","first_name":"Natalia"},{"last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo"}],"scopus_import":"1","isi":1,"type":"journal_article","quality_controlled":"1","article_type":"original","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/wound-healing-waves/"}],"record":[{"relation":"dissertation_contains","id":"12964","status":"public"}]},"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8602","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.05.15.096479"}],"oa":1,"ec_funded":1,"publisher":"Springer Nature","title":"Theory of mechanochemical patterning and optimal migration in cell monolayers","external_id":{"isi":["000573519500002"]},"abstract":[{"text":"Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration.","lang":"eng"}],"language":[{"iso":"eng"}]},{"arxiv":1,"publication":"Quantum","volume":5,"date_created":"2021-08-01T22:01:21Z","doi":"10.22331/Q-2021-07-01-491","file":[{"content_type":"application/pdf","checksum":"9706c2bb8e748e9b5b138381995a7f6f","access_level":"open_access","date_updated":"2021-08-06T06:44:31Z","creator":"cchlebak","relation":"main_file","date_created":"2021-08-06T06:44:31Z","file_name":"2021_Quantum_Sack.pdf","file_id":"9774","file_size":2312482}],"corr_author":"1","intvolume":"         5","publication_identifier":{"eissn":["2521-327X"]},"publication_status":"published","status":"public","year":"2021","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"article_number":"491","citation":{"mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>.","short":"S. Sack, M. Serbyn, Quantum 5 (2021).","ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. 2021;5. doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>","chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>.","apa":"Sack, S., &#38; Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” <i>Quantum</i>, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021."},"article_processing_charge":"Yes","day":"01","has_accepted_license":"1","date_published":"2021-07-01T00:00:00Z","date_updated":"2026-04-07T22:31:01Z","ddc":["530"],"publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","file_date_updated":"2021-08-06T06:44:31Z","ec_funded":1,"oa":1,"_id":"9760","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing."}],"external_id":{"arxiv":["2101.05742"],"isi":["000669830600001"]},"title":"Quantum annealing initialization of the quantum approximate optimization algorithm","isi":1,"scopus_import":"1","author":[{"orcid":"0000-0001-5400-8508","first_name":"Stefan","last_name":"Sack","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827"}],"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","id":"14622","status":"public"}]},"quality_controlled":"1","type":"journal_article"},{"type":"journal_article","quality_controlled":"1","related_material":{"record":[{"relation":"research_data","status":"public","id":"14988"},{"status":"public","id":"14510","relation":"dissertation_contains"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}]},"article_type":"original","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"last_name":"Dahhan","full_name":"Dahhan, Dana A","first_name":"Dana A"},{"first_name":"Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh"},{"first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","last_name":"Zheden","first_name":"Vanessa","orcid":"0000-0002-9438-4783"},{"orcid":"0000-0001-9732-3815","first_name":"Tommaso","last_name":"Costanzo","full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"first_name":"Pierre","last_name":"Mahou","full_name":"Mahou, Pierre"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika","last_name":"Hrtyan","first_name":"Mónika"},{"last_name":"Wang","full_name":"Wang, Jie","first_name":"Jie"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin","full_name":"Aguilera Servin, Juan L","first_name":"Juan L","orcid":"0000-0002-2862-8372"},{"first_name":"Daniël","last_name":"van Damme","full_name":"van Damme, Daniël"},{"first_name":"Emmanuel","full_name":"Beaurepaire, Emmanuel","last_name":"Beaurepaire"},{"first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin"},{"first_name":"Sebastian Y","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"month":"12","isi":1,"scopus_import":"1","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","issue":"51","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"external_id":{"pmid":["34907016"],"isi":["000736417600043"]},"language":[{"iso":"eng"}],"oa":1,"_id":"9887","file_date_updated":"2021-12-15T08:59:40Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"ddc":["580"],"publisher":"National Academy of Sciences","date_updated":"2026-04-07T22:31:04Z","has_accepted_license":"1","date_published":"2021-12-14T00:00:00Z","day":"14","article_processing_charge":"No","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"article_number":"e2113046118","citation":{"ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences of the United States of America. 118(51), e2113046118.","ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51. National Academy of Sciences, 2021.","chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 118 (2021)."},"year":"2021","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","intvolume":"       118","publication_identifier":{"eissn":["1091-6490"]},"status":"public","publication_status":"published","pmid":1,"file":[{"date_updated":"2021-12-15T08:59:40Z","access_level":"open_access","checksum":"8d01e72e22c4fb1584e72d8601947069","content_type":"application/pdf","success":1,"file_size":2757340,"file_id":"10546","file_name":"2021_PNAS_Johnson.pdf","date_created":"2021-12-15T08:59:40Z","relation":"main_file","creator":"cchlebak"}],"corr_author":"1","doi":"10.1073/pnas.2113046118","volume":118,"date_created":"2021-08-11T14:11:43Z","publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"doi":"10.1002/wdev.383","publication":"Wiley Interdisciplinary Reviews: Developmental Biology","date_created":"2020-05-24T22:01:00Z","status":"public","publication_status":"published","publication_identifier":{"eissn":["1759-7692"],"issn":["1759-7684"]},"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"}],"year":"2021","corr_author":"1","file":[{"relation":"main_file","creator":"dernst","file_id":"8800","file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","date_created":"2020-11-24T13:11:39Z","file_size":2527276,"content_type":"application/pdf","success":1,"checksum":"f0a7745d48afa09ea7025e876a0145a8","access_level":"open_access","date_updated":"2020-11-24T13:11:39Z"}],"pmid":1,"article_processing_charge":"Yes (via OA deal)","citation":{"ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. 2021. doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>","mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>, e383, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021).","ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021.","apa":"Kuzmicz-Kowalska, K., &#38; Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>."},"article_number":"e383","department":[{"_id":"AnKi"}],"OA_place":"publisher","date_updated":"2026-04-07T22:31:06Z","day":"15","date_published":"2021-04-15T00:00:00Z","has_accepted_license":"1","ec_funded":1,"file_date_updated":"2020-11-24T13:11:39Z","_id":"7883","oa":1,"publisher":"Wiley","ddc":["570"],"title":"Regulation of size and scale in vertebrate spinal cord development","language":[{"iso":"eng"}],"external_id":{"isi":["000531419400001"],"pmid":["32391980"]},"abstract":[{"text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern.","lang":"eng"}],"month":"04","OA_type":"hybrid","author":[{"last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","first_name":"Katarzyna"},{"orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","isi":1,"article_type":"original","related_material":{"record":[{"status":"public","id":"14323","relation":"dissertation_contains"}]},"quality_controlled":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"},{"scopus_import":"1","isi":1,"month":"04","author":[{"full_name":"Lenne, Pierre François","last_name":"Lenne","first_name":"Pierre François"},{"first_name":"Edwin","full_name":"Munro, Edwin","last_name":"Munro"},{"first_name":"Idse","last_name":"Heemskerk","full_name":"Heemskerk, Idse"},{"last_name":"Warmflash","full_name":"Warmflash, Aryeh","first_name":"Aryeh"},{"first_name":"Laura","last_name":"Bocanegra","full_name":"Bocanegra, Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","last_name":"Kishi","first_name":"Kasumi","orcid":"0000-0001-6060-4795"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998"},{"first_name":"Yuchen","last_name":"Long","full_name":"Long, Yuchen"},{"full_name":"Fruleux, Antoine","last_name":"Fruleux","first_name":"Antoine"},{"full_name":"Boudaoud, Arezki","last_name":"Boudaoud","first_name":"Arezki"},{"first_name":"Timothy E.","full_name":"Saunders, Timothy E.","last_name":"Saunders"},{"first_name":"Paolo","last_name":"Caldarelli","full_name":"Caldarelli, Paolo"},{"first_name":"Arthur","last_name":"Michaut","full_name":"Michaut, Arthur"},{"first_name":"Jerome","full_name":"Gros, Jerome","last_name":"Gros"},{"full_name":"Maroudas-Sacks, Yonit","last_name":"Maroudas-Sacks","first_name":"Yonit"},{"full_name":"Keren, Kinneret","last_name":"Keren","first_name":"Kinneret"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"first_name":"Zev J.","last_name":"Gartner","full_name":"Gartner, Zev J."},{"first_name":"Benjamin","full_name":"Stormo, Benjamin","last_name":"Stormo"},{"first_name":"Amy","full_name":"Gladfelter, Amy","last_name":"Gladfelter"},{"full_name":"Rodrigues, Alan","last_name":"Rodrigues","first_name":"Alan"},{"first_name":"Amy","last_name":"Shyer","full_name":"Shyer, Amy"},{"last_name":"Minc","full_name":"Minc, Nicolas","first_name":"Nicolas"},{"first_name":"Jean Léon","last_name":"Maître","full_name":"Maître, Jean Léon"},{"full_name":"Di Talia, Stefano","last_name":"Di Talia","first_name":"Stefano"},{"first_name":"Bassma","last_name":"Khamaisi","full_name":"Khamaisi, Bassma"},{"first_name":"David","full_name":"Sprinzak, David","last_name":"Sprinzak"},{"first_name":"Sham","full_name":"Tlili, Sham","last_name":"Tlili"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","type":"journal_article","related_material":{"record":[{"id":"13081","status":"public","relation":"dissertation_contains"}]},"article_type":"original","publisher":"IOP Publishing","ddc":["570"],"_id":"9349","oa":1,"file_date_updated":"2021-04-27T08:38:35Z","ec_funded":1,"external_id":{"pmid":["33276350"],"isi":["000640396400001"]},"abstract":[{"text":"The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development.","lang":"eng"}],"language":[{"iso":"eng"}],"issue":"4","title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","citation":{"ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical biology</i>. 2021;18(4). doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>","mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>.","short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).","ieee":"P. F. Lenne <i>et al.</i>, “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” <i>Physical biology</i>, vol. 18, no. 4. IOP Publishing, 2021.","ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501.","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>."},"article_number":"041501","department":[{"_id":"AnKi"},{"_id":"EdHa"}],"article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-04-14T00:00:00Z","day":"14","date_updated":"2026-04-07T22:31:08Z","date_created":"2021-04-25T22:01:29Z","volume":18,"publication":"Physical biology","doi":"10.1088/1478-3975/abd0db","pmid":1,"file":[{"access_level":"open_access","date_updated":"2021-04-27T08:38:35Z","success":1,"content_type":"application/pdf","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","file_size":6296324,"creator":"cziletti","relation":"main_file","date_created":"2021-04-27T08:38:35Z","file_name":"2021_PhysBio_Lenne.pdf","file_id":"9355"}],"acknowledgement":"The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037"},{"name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"}],"year":"2021","publication_status":"published","status":"public","intvolume":"        18","publication_identifier":{"eissn":["1478-3975"]}},{"date_updated":"2026-04-07T22:31:10Z","type":"preprint","related_material":{"record":[{"id":"14656","status":"public","relation":"later_version"},{"relation":"dissertation_contains","id":"11932","status":"public"}]},"oa_version":"Preprint","date_published":"2021-09-29T00:00:00Z","day":"29","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","article_processing_charge":"No","author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","full_name":"Nardin, Michele","first_name":"Michele","orcid":"0000-0001-8849-6570"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","full_name":"Savin, Cristina","first_name":"Cristina"}],"citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, <a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>"},"department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism"}],"year":"2021","status":"public","publication_status":"draft","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"language":[{"iso":"eng"}],"doi":"10.1101/2021.09.28.460602","_id":"10077","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602","open_access":"1"}],"oa":1,"ec_funded":1,"date_created":"2021-10-04T06:23:34Z","publication":"bioRxiv","publisher":"Cold Spring Harbor Laboratory"},{"doi":"10.1038/s41467-021-23123-x","date_created":"2021-05-28T11:49:46Z","volume":12,"publication":"Nature Communications","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and epilepsy","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","grant_number":"F7807"},{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"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).","year":"2021","publication_status":"published","status":"public","intvolume":"        12","publication_identifier":{"eissn":["2041-1723"]},"corr_author":"1","file":[{"date_updated":"2021-05-28T12:39:43Z","access_level":"open_access","checksum":"337e0f7959c35ec959984cacdcb472ba","content_type":"application/pdf","success":1,"file_size":9358599,"file_name":"2021_NatureCommunications_Morandell.pdf","file_id":"9430","date_created":"2021-05-28T12:39:43Z","relation":"main_file","creator":"kschuh"}],"article_processing_charge":"No","citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>.","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. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>","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.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>","ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","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."},"article_number":"3058","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_updated":"2026-04-07T22:31:14Z","has_accepted_license":"1","date_published":"2021-05-24T00:00:00Z","day":"24","_id":"9429","oa":1,"keyword":["General Biochemistry","Genetics and Molecular Biology"],"file_date_updated":"2021-05-28T12:39:43Z","ec_funded":1,"acknowledged_ssus":[{"_id":"PreCl"}],"publisher":"Springer Nature","ddc":["572"],"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","issue":"1","external_id":{"isi":["000658769900010"]},"abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"month":"05","author":[{"full_name":"Morandell, Jasmin","last_name":"Morandell","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin"},{"first_name":"Lena A","full_name":"Schwarz, Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1843-3173","first_name":"Bernadette","full_name":"Basilico, Bernadette","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425"},{"first_name":"Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","last_name":"Tasciyan"},{"first_name":"Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","full_name":"Dimchev, Georgi A"},{"last_name":"Nicolas","full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel"},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M"},{"first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger"},{"orcid":"0000-0002-9033-9096","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","last_name":"Knaus","first_name":"Lisa"},{"first_name":"Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","last_name":"Dobler","full_name":"Dobler, Zoe"},{"first_name":"Emanuele","last_name":"Cacci","full_name":"Cacci, Emanuele"},{"orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178"}],"scopus_import":"1","isi":1,"type":"journal_article","quality_controlled":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/","relation":"press_release"}],"record":[{"status":"public","id":"7800","relation":"earlier_version"},{"status":"public","id":"19557","relation":"dissertation_contains"},{"status":"public","id":"12401","relation":"dissertation_contains"}]},"article_type":"original","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"}]