[{"citation":{"mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.","apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., &#38; Tkačik, G. (2021). Statistical analysis and optimality of neural systems. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. <i>Neuron</i>. 2021;109(7):1227-1241.e5. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” <i>Neuron</i>, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.","chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>."},"_id":"7553","status":"public","quality_controlled":"1","scopus_import":"1","publication":"Neuron","day":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"article_processing_charge":"No","oa_version":"Preprint","oa":1,"language":[{"iso":"eng"}],"pmid":1,"date_published":"2021-04-07T00:00:00Z","year":"2021","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"fulldoi":"https://doi.org/10.1016/j.neuron.2021.01.020","type":"journal_article","volume":109,"abstract":[{"lang":"eng","text":"Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems."}],"title":"Statistical analysis and optimality of neural systems","month":"04","related_material":{"link":[{"url":"https://ist.ac.at/en/news/can-evolution-be-predicted/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"status":"public","id":"15020","relation":"dissertation_contains"}]},"issue":"7","external_id":{"pmid":["33592180"],"isi":["000637809600006"]},"corr_author":"1","publication_status":"published","isi":1,"doi":"10.1016/j.neuron.2021.01.020","main_file_link":[{"url":"https://doi.org/10.1101/848374","open_access":"1"}],"acknowledgement":"The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018.","publisher":"Cell Press","page":"1227-1241.e5","intvolume":"       109","date_updated":"2026-10-02T11:40:30Z","department":[{"_id":"GaTk"}],"author":[{"last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Hledik, Michal","last_name":"Hledik"},{"orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","last_name":"Sokolowski"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik"}],"date_created":"2020-02-28T11:00:12Z"},{"publication_status":"published","isi":1,"external_id":{"isi":["000636121800001"],"pmid":["33634751"]},"issue":"1","page":"1-382","publisher":"Taylor & Francis","OA_type":"free access","author":[{"first_name":"Daniel J.","full_name":"Klionsky, Daniel J.","last_name":"Klionsky"},{"last_name":"Abdel-Aziz","first_name":"Amal Kamal","full_name":"Abdel-Aziz, Amal Kamal"},{"full_name":"Abdelfatah, Sara","first_name":"Sara","last_name":"Abdelfatah"},{"full_name":"Abdellatif, Mahmoud","first_name":"Mahmoud","last_name":"Abdellatif"},{"full_name":"Abdoli, Asghar","first_name":"Asghar","last_name":"Abdoli"},{"last_name":"Abel","first_name":"Steffen","full_name":"Abel, Steffen"},{"last_name":"Abeliovich","full_name":"Abeliovich, Hagai","first_name":"Hagai"},{"full_name":"Abildgaard, Marie H.","first_name":"Marie H.","last_name":"Abildgaard"},{"last_name":"Abudu","full_name":"Abudu, Yakubu Princely","first_name":"Yakubu Princely"},{"first_name":"Abraham","full_name":"Acevedo-Arozena, Abraham","last_name":"Acevedo-Arozena"},{"full_name":"Adamopoulos, Iannis E.","first_name":"Iannis E.","last_name":"Adamopoulos"},{"last_name":"Adeli","first_name":"Khosrow","full_name":"Adeli, Khosrow"},{"full_name":"Adolph, Timon E.","first_name":"Timon E.","last_name":"Adolph"},{"full_name":"Adornetto, Annagrazia","first_name":"Annagrazia","last_name":"Adornetto"},{"full_name":"Aflaki, Elma","first_name":"Elma","last_name":"Aflaki"},{"first_name":"Galila","full_name":"Agam, Galila","last_name":"Agam"},{"first_name":"Anupam","full_name":"Agarwal, Anupam","last_name":"Agarwal"},{"last_name":"Aggarwal","full_name":"Aggarwal, Bharat B.","first_name":"Bharat B."},{"last_name":"Agnello","first_name":"Maria","full_name":"Agnello, Maria"},{"last_name":"Agostinis","full_name":"Agostinis, Patrizia","first_name":"Patrizia"},{"last_name":"Agrewala","first_name":"Javed N.","full_name":"Agrewala, Javed N."},{"last_name":"Agrotis","first_name":"Alexander","full_name":"Agrotis, Alexander"},{"last_name":"Aguilar","first_name":"Patricia V.","full_name":"Aguilar, Patricia V."},{"full_name":"Ahmad, S. 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Christine M.","first_name":"Christine M."},{"last_name":"Ziviani","full_name":"Ziviani, Elena","first_name":"Elena"},{"last_name":"Zoladek","first_name":"Teresa","full_name":"Zoladek, Teresa"},{"last_name":"Zong","first_name":"Wei Xing","full_name":"Zong, Wei Xing"},{"first_name":"Dmitry B.","full_name":"Zorov, Dmitry B.","last_name":"Zorov"},{"last_name":"Zorzano","first_name":"Antonio","full_name":"Zorzano, Antonio"},{"last_name":"Zou","full_name":"Zou, Weiping","first_name":"Weiping"},{"last_name":"Zou","full_name":"Zou, Zhen","first_name":"Zhen"},{"first_name":"Zhengzhi","full_name":"Zou, Zhengzhi","last_name":"Zou"},{"first_name":"Steven","full_name":"Zuryn, Steven","last_name":"Zuryn"},{"full_name":"Zwerschke, Werner","first_name":"Werner","last_name":"Zwerschke"},{"last_name":"Brand-Saberi","first_name":"Beate","full_name":"Brand-Saberi, Beate"},{"first_name":"X. Charlie","full_name":"Dong, X. Charlie","last_name":"Dong"},{"full_name":"Kenchappa, Chandra Shekar","first_name":"Chandra Shekar","last_name":"Kenchappa"},{"last_name":"Li","first_name":"Zuguo","full_name":"Li, Zuguo"},{"last_name":"Lin","full_name":"Lin, Yong","first_name":"Yong"},{"full_name":"Oshima, Shigeru","first_name":"Shigeru","last_name":"Oshima"},{"full_name":"Rong, Yueguang","first_name":"Yueguang","last_name":"Rong"},{"first_name":"Judith C.","full_name":"Sluimer, Judith C.","last_name":"Sluimer"},{"first_name":"Christina L.","full_name":"Stallings, Christina L.","last_name":"Stallings"},{"full_name":"Tong, Chun Kit","first_name":"Chun Kit","last_name":"Tong"}],"date_created":"2021-03-28T22:01:44Z","department":[{"_id":"JiFr"}],"intvolume":"        17","date_updated":"2026-10-05T13:54:55Z","doi":"10.1080/15548627.2020.1797280","main_file_link":[{"url":"https://doi.org/10.1080/15548627.2020.1797280","open_access":"1"}],"acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support.","volume":17,"abstract":[{"lang":"eng","text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. "}],"fulldoi":"https://doi.org/10.1080/15548627.2020.1797280","type":"journal_article","ddc":["580","570"],"month":"02","title":"Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)","publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"oa_version":"Published Version","article_processing_charge":"No","date_published":"2021-02-08T00:00:00Z","year":"2021","language":[{"iso":"eng"}],"pmid":1,"oa":1,"scopus_import":"1","_id":"9298","citation":{"short":"D.J. Klionsky, A.K. Abdel-Aziz, S. Abdelfatah, M. Abdellatif, A. Abdoli, S. Abel, H. Abeliovich, M.H. Abildgaard, Y.P. Abudu, A. Acevedo-Arozena, I.E. Adamopoulos, K. Adeli, T.E. Adolph, A. Adornetto, E. Aflaki, G. Agam, A. Agarwal, B.B. Aggarwal, M. Agnello, P. Agostinis, J.N. Agrewala, A. Agrotis, P.V. Aguilar, S.T. Ahmad, Z.M. Ahmed, U. Ahumada-Castro, S. Aits, S. Aizawa, Y. Akkoc, T. Akoumianaki, H.A. Akpinar, A.M. Al-Abd, L. Al-Akra, A. Al-Gharaibeh, M.A. Alaoui-Jamali, S. Alberti, E. Alcocer-Gómez, C. Alessandri, M. Ali, M.A. Alim Al-Bari, S. Aliwaini, J. Alizadeh, E. Almacellas, A. Almasan, A. Alonso, G.D. Alonso, N. Altan-Bonnet, D.C. Altieri, É.M.C. Álvarez, S. Alves, C. Alves Da Costa, M.M. Alzaharna, M. Amadio, C. Amantini, C. Amaral, S. Ambrosio, A.O. Amer, V. Ammanathan, Z. An, S.U. Andersen, S.A. Andrabi, M. Andrade-Silva, A.M. Andres, S. Angelini, D. Ann, U.C. Anozie, M.Y. Ansari, P. Antas, A. Antebi, Z. Antón, T. Anwar, L. Apetoh, N. Apostolova, T. Araki, Y. Araki, K. Arasaki, W.L. Araújo, J. Araya, C. Arden, M.A. Arévalo, S. Arguelles, E. Arias, J. Arikkath, H. Arimoto, A.R. Ariosa, D. Armstrong-James, L. Arnauné-Pelloquin, A. Aroca, D.S. Arroyo, I. Arsov, R. Artero, D.M.L. Asaro, M. Aschner, M. Ashrafizadeh, O. Ashur-Fabian, A.G. Atanasov, A.K. Au, P. Auberger, H.W. Auner, L. Aurelian, R. Autelli, L. Avagliano, Y. Ávalos, S. Aveic, C.A. Aveleira, T. 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Klionsky <i>et al.</i>, “Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition),” <i>Autophagy</i>, vol. 17, no. 1. Taylor &#38; Francis, pp. 1–382, 2021.","chicago":"Klionsky, Daniel J., Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” <i>Autophagy</i>. Taylor &#38; Francis, 2021. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>.","mla":"Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” <i>Autophagy</i>, vol. 17, no. 1, Taylor &#38; Francis, 2021, pp. 1–382, doi:<a href=\"https://doi.org/10.1080/15548627.2020.1797280\">10.1080/15548627.2020.1797280</a>.","ama":"Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). <i>Autophagy</i>. 2021;17(1):1-382. doi:<a href=\"https://doi.org/10.1080/15548627.2020.1797280\">10.1080/15548627.2020.1797280</a>","apa":"Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., … Tong, C. K. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>","ista":"Klionsky DJ et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 17(1), 1–382."},"quality_controlled":"1","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"review","publication":"Autophagy","day":"08"},{"has_accepted_license":"1","day":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"ASHPC21 – Austrian-Slovenian HPC Meeting 2021","citation":{"short":"A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5.","chicago":"Schlögl, Alois, Stefano Elefante, Andrei Hornoiu, and Stephan Stadlbauer. “Managing Software on a Heterogenous HPC Cluster.” In <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>, 5. University of Ljubljana, 2021. <a href=\"https://doi.org/10.3359/2021hpc\">https://doi.org/10.3359/2021hpc</a>.","ieee":"A. Schlögl, S. Elefante, A. Hornoiu, and S. Stadlbauer, “Managing software on a heterogenous HPC cluster,” in <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>, Virtual, 2021, p. 5.","mla":"Schlögl, Alois, et al. “Managing Software on a Heterogenous HPC Cluster.” <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>, University of Ljubljana, 2021, p. 5, doi:<a href=\"https://doi.org/10.3359/2021hpc\">10.3359/2021hpc</a>.","ista":"Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. 2021. Managing software on a heterogenous HPC cluster. ASHPC21 – Austrian-Slovenian HPC Meeting 2021. ASHPC: Austrian-Slovenian HPC Meeting, 5.","apa":"Schlögl, A., Elefante, S., Hornoiu, A., &#38; Stadlbauer, S. (2021). Managing software on a heterogenous HPC cluster. In <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i> (p. 5). Virtual: University of Ljubljana. <a href=\"https://doi.org/10.3359/2021hpc\">https://doi.org/10.3359/2021hpc</a>","ama":"Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous HPC cluster. In: <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>. University of Ljubljana; 2021:5. doi:<a href=\"https://doi.org/10.3359/2021hpc\">10.3359/2021hpc</a>"},"_id":"12909","status":"public","language":[{"iso":"eng"}],"date_published":"2021-06-02T00:00:00Z","year":"2021","oa":1,"article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2023-05-16T07:36:34Z","ddc":["000"],"title":"Managing software on a heterogenous HPC cluster","month":"06","publication_identifier":{"isbn":["978-961-6980-77-7","978-961-6133-48-7"]},"fulldoi":"https://doi.org/10.3359/2021hpc","type":"conference_abstract","file":[{"relation":"main_file","file_name":"2021_ASHPC_Schloegl.pdf","date_created":"2023-05-16T07:36:34Z","success":1,"date_updated":"2023-05-16T07:36:34Z","content_type":"application/pdf","access_level":"open_access","checksum":"ba73f85858fb9d5737ebc7724646dd45","file_id":"12971","file_size":422761,"creator":"dernst"}],"publisher":"University of Ljubljana","page":"5","date_updated":"2026-10-14T09:47:31Z","department":[{"_id":"ScienComp"}],"author":[{"last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","full_name":"Elefante, Stefano"},{"full_name":"Hornoiu, Andrei","id":"77129392-B450-11EA-8745-D4653DDC885E","first_name":"Andrei","last_name":"Hornoiu"},{"full_name":"Stadlbauer, Stephan","first_name":"Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","last_name":"Stadlbauer"}],"date_created":"2023-05-05T13:17:36Z","doi":"10.3359/2021hpc","main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf"}],"publication_status":"published","conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Virtual","end_date":"2021-06-02","start_date":"2021-05-31"},"corr_author":"1"},{"publication_identifier":{"issn":["1043-6871"],"isbn":["978-1-6654-4896-3"],"eisbn":["978-1-6654-4895-6"]},"related_material":{"record":[{"status":"public","id":"18630","relation":"later_version"}]},"month":"07","title":"Stochastic processes with expected stopping time","keyword":["Computer science","Heuristic algorithms","Memory management","Automata","Markov processes","Probability distribution","Complexity theory"],"arxiv":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"abstract":[{"text":"Markov chains are the de facto finite-state model for stochastic dynamical systems, and Markov decision processes (MDPs) extend Markov chains by incorporating non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization criterion is the maximal expected total reward where the MDP stops after T steps, which can be computed by a simple dynamic programming algorithm. We consider a natural generalization of the problem where the stopping times can be chosen according to a probability distribution, such that the expected stopping time is T, to optimize the expected total reward. Quite surprisingly we establish inter-reducibility of the expected stopping-time problem for Markov chains with the Positivity problem (which is related to the well-known Skolem problem), for which establishing either decidability or undecidability would be a major breakthrough. Given the hardness of the exact problem, we consider the approximate version of the problem: we show that it can be solved in exponential time for Markov chains and in exponential space for MDPs.","lang":"eng"}],"fulldoi":"https://doi.org/10.1109/LICS52264.2021.9470595","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.07278"}],"acknowledgement":"We are grateful to the anonymous reviewers of LICS 2021 and of a previous version of this paper for insightful comments that helped improving the presentation. This research was partially supported by the grant ERC CoG 863818 (ForM-SMArt).","doi":"10.1109/LICS52264.2021.9470595","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"date_created":"2021-09-12T22:01:25Z","date_updated":"2026-10-16T07:57:38Z","department":[{"_id":"KrCh"}],"page":"1-13","publisher":"IEEE","external_id":{"isi":["000947350400036"],"arxiv":["2104.07278"]},"conference":{"name":"LICS: Logic in Computer Science","end_date":"2021-07-02","start_date":"2021-06-29","location":"Rome, Italy"},"isi":1,"publication_status":"published","day":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","ec_funded":1,"quality_controlled":"1","status":"public","_id":"10004","citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, IEEE, 2021, pp. 1–13, doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470595\">10.1109/LICS52264.2021.9470595</a>.","ama":"Chatterjee K, Doyen L. Stochastic processes with expected stopping time. In: <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. IEEE; 2021:1-13. doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470595\">10.1109/LICS52264.2021.9470595</a>","ista":"Chatterjee K, Doyen L. 2021. Stochastic processes with expected stopping time. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, 1–13.","apa":"Chatterjee, K., &#38; Doyen, L. (2021). Stochastic processes with expected stopping time. In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 1–13). Rome, Italy: IEEE. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470595\">https://doi.org/10.1109/LICS52264.2021.9470595</a>","short":"K. Chatterjee, L. Doyen, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2021, pp. 1–13.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected Stopping Time.” In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 1–13. IEEE, 2021. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470595\">https://doi.org/10.1109/LICS52264.2021.9470595</a>.","ieee":"K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,” in <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Rome, Italy, 2021, pp. 1–13."},"scopus_import":"1","oa":1,"date_published":"2021-07-07T00:00:00Z","year":"2021","language":[{"iso":"eng"}],"oa_version":"Preprint","article_processing_charge":"No"},{"oa_version":"Preprint","article_processing_charge":"No","oa":1,"year":"2021","date_published":"2021-11-04T00:00:00Z","language":[{"iso":"eng"}],"_id":"10408","citation":{"mla":"Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” <i>19th International Conference</i>, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:<a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">10.1007/978-3-030-90456-2_8</a>.","ama":"Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: <i>19th International Conference</i>. Vol 13044. Springer Nature; 2021:222-253. doi:<a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">10.1007/978-3-030-90456-2_8</a>","apa":"Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for overlapping groups. In <i>19th International Conference</i> (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">https://doi.org/10.1007/978-3-030-90456-2_8</a>","ista":"Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13044, 222–253.","short":"J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 222–253.","chicago":"Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In <i>19th International Conference</i>, 13044:222–53. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">https://doi.org/10.1007/978-3-030-90456-2_8</a>.","ieee":"J. F. Alwen <i>et al.</i>, “Grafting key trees: Efficient key management for overlapping groups,” in <i>19th International Conference</i>, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253."},"quality_controlled":"1","status":"public","scopus_import":"1","publication":"19th International Conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"04","alternative_title":["LNCS"],"ec_funded":1,"external_id":{"isi":["000728363700008"]},"conference":{"name":"TCC: Theory of Cryptography","location":"Raleigh, NC, United States","start_date":"2021-11-08","end_date":"2021-11-11"},"publication_status":"published","isi":1,"doi":"10.1007/978-3-030-90456-2_8","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1158"}],"acknowledgement":"B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","page":"222-253","publisher":"Springer Nature","author":[{"last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","full_name":"Alwen, Joel F"},{"last_name":"Auerbach","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","first_name":"Benedikt","full_name":"Auerbach, Benedikt","orcid":"0000-0002-7553-6606"},{"last_name":"Baig","full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad"},{"id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","first_name":"Miguel","full_name":"Cueto Noval, Miguel","orcid":"0000-0002-2505-4246","last_name":"Cueto Noval"},{"last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"},{"orcid":"0000-0001-8630-415X","full_name":"Pascual Perez, Guillermo","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","last_name":"Pascual Perez"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"},{"orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter"}],"date_created":"2021-12-05T23:01:42Z","department":[{"_id":"KrPi"}],"date_updated":"2026-10-16T08:11:07Z","intvolume":"     13044","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"volume":13044,"abstract":[{"lang":"eng","text":"Key trees are often the best solution in terms of transmission cost and storage requirements for managing keys in a setting where a group needs to share a secret key, while being able to efficiently rotate the key material of users (in order to recover from a potential compromise, or to add or remove users). Applications include multicast encryption protocols like LKH (Logical Key Hierarchies) or group messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced) binary tree, where each node is identified with a key: leaf nodes hold users’ secret keys while the root is the shared group key. For a group of size N, each user just holds   log(N)  keys (the keys on the path from its leaf to the root) and its entire key material can be rotated by broadcasting   2log(N)  ciphertexts (encrypting each fresh key on the path under the keys of its parents). In this work we consider the natural setting where we have many groups with partially overlapping sets of users, and ask if we can find solutions where the cost of rotating a key is better than in the trivial one where we have a separate key tree for each group. We show that in an asymptotic setting (where the number m of groups is fixed while the number N of users grows) there exist more general key graphs whose cost converges to the cost of a single group, thus saving a factor linear in the number of groups over the trivial solution. As our asymptotic “solution” converges very slowly and performs poorly on concrete examples, we propose an algorithm that uses a natural heuristic to compute a key graph for any given group structure. Our algorithm combines two greedy algorithms, and is thus very efficient: it first converts the group structure into a “lattice graph”, which is then turned into a key graph by repeatedly applying the algorithm for constructing a Huffman code. To better understand how far our proposal is from an optimal solution, we prove lower bounds on the update cost of continuous group-key agreement and multicast encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom generators, and secret sharing as building blocks."}],"type":"conference","fulldoi":"https://doi.org/10.1007/978-3-030-90456-2_8","month":"11","title":"Grafting key trees: Efficient key management for overlapping groups","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["978-3-030-90456-2"],"isbn":["9-783-0309-0455-5"]},"related_material":{"record":[{"relation":"dissertation_contains","id":"18088","status":"public"}]}},{"scopus_import":"1","quality_controlled":"1","status":"public","_id":"10049","citation":{"short":"K. Klein, G. Pascual Perez, M. Walter, C. Kamath Hosdurg, M. Capretto, M. Cueto Noval, I. Markov, M.X. Yeo, J.F. Alwen, K.Z. Pietrzak, in:, 2021 IEEE Symposium on Security and Privacy , IEEE, 2021, pp. 268–284.","ieee":"K. Klein <i>et al.</i>, “Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement,” in <i>2021 IEEE Symposium on Security and Privacy </i>, San Francisco, CA, United States, 2021, pp. 268–284.","chicago":"Klein, Karen, Guillermo Pascual Perez, Michael Walter, Chethan Kamath Hosdurg, Margarita Capretto, Miguel Cueto Noval, Ilia Markov, Michelle X Yeo, Joel F Alwen, and Krzysztof Z Pietrzak. “Keep the Dirt: Tainted TreeKEM, Adaptively and Actively Secure Continuous Group Key Agreement.” In <i>2021 IEEE Symposium on Security and Privacy </i>, 268–84. IEEE, 2021. <a href=\"https://doi.org/10.1109/sp40001.2021.00035\">https://doi.org/10.1109/sp40001.2021.00035</a>.","mla":"Klein, Karen, et al. “Keep the Dirt: Tainted TreeKEM, Adaptively and Actively Secure Continuous Group Key Agreement.” <i>2021 IEEE Symposium on Security and Privacy </i>, IEEE, 2021, pp. 268–84, doi:<a href=\"https://doi.org/10.1109/sp40001.2021.00035\">10.1109/sp40001.2021.00035</a>.","ista":"Klein K, Pascual Perez G, Walter M, Kamath Hosdurg C, Capretto M, Cueto Noval M, Markov I, Yeo MX, Alwen JF, Pietrzak KZ. 2021. Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement. 2021 IEEE Symposium on Security and Privacy . SP: Symposium on Security and Privacy, 268–284.","apa":"Klein, K., Pascual Perez, G., Walter, M., Kamath Hosdurg, C., Capretto, M., Cueto Noval, M., … Pietrzak, K. Z. (2021). Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement. In <i>2021 IEEE Symposium on Security and Privacy </i> (pp. 268–284). San Francisco, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/sp40001.2021.00035\">https://doi.org/10.1109/sp40001.2021.00035</a>","ama":"Klein K, Pascual Perez G, Walter M, et al. Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement. In: <i>2021 IEEE Symposium on Security and Privacy </i>. IEEE; 2021:268-284. doi:<a href=\"https://doi.org/10.1109/sp40001.2021.00035\">10.1109/sp40001.2021.00035</a>"},"ec_funded":1,"day":"26","publication":"2021 IEEE Symposium on Security and Privacy ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","article_processing_charge":"No","date_published":"2021-08-26T00:00:00Z","year":"2021","language":[{"iso":"eng"}],"oa":1,"abstract":[{"text":"While messaging systems with strong security guarantees are widely used in practice, designing a protocol that scales efficiently to large groups and enjoys similar security guarantees remains largely open. The two existing proposals to date are ART (Cohn-Gordon et al., CCS18) and TreeKEM (IETF, The Messaging Layer Security Protocol, draft). TreeKEM is the currently considered candidate by the IETF MLS working group, but dynamic group operations (i.e. adding and removing users) can cause efficiency issues. In this paper we formalize and analyze a variant of TreeKEM which we term Tainted TreeKEM (TTKEM for short). The basic idea underlying TTKEM was suggested by Millican (MLS mailing list, February 2018). This version is more efficient than TreeKEM for some natural distributions of group operations, we quantify this through simulations.Our second contribution is two security proofs for TTKEM which establish post compromise and forward secrecy even against adaptive attackers. The security loss (to the underlying PKE) in the Random Oracle Model is a polynomial factor, and a quasipolynomial one in the Standard Model. Our proofs can be adapted to TreeKEM as well. Before our work no security proof for any TreeKEM-like protocol establishing tight security against an adversary who can adaptively choose the sequence of operations was known. We also are the first to prove (or even formalize) active security where the server can arbitrarily deviate from the protocol specification. Proving fully active security – where also the users can arbitrarily deviate – remains open.","lang":"eng"}],"fulldoi":"https://doi.org/10.1109/sp40001.2021.00035","type":"conference","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10035"},{"status":"public","id":"18088","relation":"dissertation_contains"}]},"month":"08","title":"Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement","isi":1,"publication_status":"published","corr_author":"1","external_id":{"isi":["001316065000016"]},"conference":{"name":"SP: Symposium on Security and Privacy","end_date":"2021-05-27","start_date":"2021-05-24","location":"San Francisco, CA, United States"},"author":[{"last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","first_name":"Guillermo","full_name":"Pascual Perez, Guillermo","orcid":"0000-0001-8630-415X","last_name":"Pascual Perez"},{"orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Walter"},{"full_name":"Kamath Hosdurg, Chethan","orcid":"0009-0006-6812-7317","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg"},{"last_name":"Capretto","first_name":"Margarita","full_name":"Capretto, Margarita"},{"last_name":"Cueto Noval","orcid":"0000-0002-2505-4246","full_name":"Cueto Noval, Miguel","first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc"},{"first_name":"Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","full_name":"Markov, Ilia","last_name":"Markov"},{"last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","orcid":"0009-0001-3676-4809","full_name":"Yeo, Michelle X"},{"full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"date_created":"2021-09-27T13:46:27Z","date_updated":"2026-10-16T08:11:07Z","department":[{"_id":"KrPi"},{"_id":"DaAl"}],"page":"268-284","publisher":"IEEE","acknowledgement":"The first three authors contributed equally to this work. Funded by the European Research Council (ERC) under the European Union’s Horizon2020 research and innovation programme (682815-TOCNeT). Funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No.665385.","main_file_link":[{"url":"https://eprint.iacr.org/2019/1489","open_access":"1"}],"doi":"10.1109/sp40001.2021.00035"},{"publication_status":"published","isi":1,"corr_author":"1","external_id":{"isi":["000573519500002"]},"page":"267-274","publisher":"Springer Nature","date_created":"2020-10-04T22:01:37Z","author":[{"id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R","orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","last_name":"Boocock"},{"last_name":"Hino","first_name":"Naoya","full_name":"Hino, Naoya"},{"full_name":"Ruzickova, Natalia","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","last_name":"Ruzickova"},{"last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"}],"intvolume":"        17","date_updated":"2026-11-11T23:30:06Z","department":[{"_id":"EdHa"}],"doi":"10.1038/s41567-020-01037-7","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.).","main_file_link":[{"url":"https://doi.org/10.1101/2020.05.15.096479","open_access":"1"}],"volume":17,"abstract":[{"lang":"eng","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."}],"fulldoi":"https://doi.org/10.1038/s41567-020-01037-7","type":"journal_article","project":[{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"month":"02","title":"Theory of mechanochemical patterning and optimal migration in cell monolayers","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"related_material":{"record":[{"status":"public","id":"12964","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/wound-healing-waves/"}]},"oa_version":"Preprint","article_processing_charge":"No","year":"2021","date_published":"2021-02-01T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","_id":"8602","citation":{"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>.","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>","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.","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>","short":"D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics 17 (2021) 267–274.","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>.","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."},"quality_controlled":"1","status":"public","ec_funded":1,"article_type":"original","publication":"Nature Physics","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Association for Computing Machinery","date_created":"2021-08-08T22:01:26Z","author":[{"last_name":"Hafner","full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BeBi"}],"date_updated":"2026-11-11T23:30:07Z","intvolume":"        40","doi":"10.1145/3450626.3459800","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","publication_status":"published","isi":1,"external_id":{"isi":["000674930900091"]},"conference":{"name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Virtual","end_date":"2021-08-13","start_date":"2021-08-09"},"issue":"4","ddc":["516"],"month":"07","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"title":"The design space of plane elastic curves","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"related_material":{"link":[{"relation":"press_release","description":"News on IST Website","url":"https://ist.ac.at/en/news/designing-with-elastic-structures/"}],"record":[{"status":"public","id":"12897","relation":"dissertation_contains"}]},"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."}],"volume":40,"type":"journal_article","fulldoi":"https://doi.org/10.1145/3450626.3459800","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"file":[{"file_name":"elastic-curves-paper.pdf","relation":"main_file","access_level":"open_access","date_created":"2021-10-18T10:42:15Z","success":1,"date_updated":"2021-10-18T10:42:15Z","content_type":"application/pdf","file_id":"10150","file_size":17064290,"checksum":"7e5d08ce46b0451b3102eacd3d00f85f","creator":"chafner"},{"access_level":"open_access","content_type":"application/pdf","date_updated":"2021-10-18T10:42:22Z","date_created":"2021-10-18T10:42:22Z","file_name":"elastic-curves-supp.pdf","relation":"supplementary_material","creator":"chafner","file_id":"10151","file_size":547156,"checksum":"0088643478be7c01a703b5b10767348f"}],"year":"2021","date_published":"2021-07-19T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-10-18T10:42:22Z","ec_funded":1,"has_accepted_license":"1","article_number":"126","publication":"ACM Transactions on Graphics","article_type":"original","day":"19","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","_id":"9817","citation":{"short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","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.","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>.","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>.","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>","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126."},"quality_controlled":"1","status":"public"},{"ddc":["570"],"month":"06","keyword":["Developmental Biology","Cell Biology","Molecular Biology"],"title":"Reassembling gastrulation","publication_identifier":{"issn":["0012-1606"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12891"}]},"abstract":[{"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.","lang":"eng"}],"volume":474,"fulldoi":"https://doi.org/10.1016/j.ydbio.2020.12.014","type":"journal_article","file":[{"date_created":"2021-08-11T10:28:06Z","success":1,"date_updated":"2021-08-11T10:28:06Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2021_DevBiology_Schauer.pdf","creator":"kschuh","checksum":"fa2a5731fd16ab171b029f32f031c440","file_id":"9880","file_size":1440321}],"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"page":"71-81","publisher":"Elsevier","date_created":"2020-12-22T09:53:34Z","author":[{"first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"intvolume":"       474","date_updated":"2026-11-11T23:30:11Z","department":[{"_id":"CaHe"}],"doi":"10.1016/j.ydbio.2020.12.014","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.","publication_status":"published","isi":1,"external_id":{"pmid":["33352181"],"isi":["000639461800008"]},"ec_funded":1,"has_accepted_license":"1","publication":"Developmental Biology","day":"01","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"scopus_import":"1","_id":"8966","citation":{"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>.","short":"A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81.","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>","ista":"Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental Biology. 474, 71–81.","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>","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>."},"quality_controlled":"1","status":"public","year":"2021","date_published":"2021-06-01T00:00:00Z","language":[{"iso":"eng"}],"pmid":1,"oa":1,"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2021-08-11T10:28:06Z"},{"_id":"9429","citation":{"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>","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.","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>","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>.","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>.","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.","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)."},"quality_controlled":"1","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","day":"24","publication":"Nature Communications","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ec_funded":1,"article_number":"3058","has_accepted_license":"1","acknowledged_ssus":[{"_id":"PreCl"}],"file_date_updated":"2021-05-28T12:39:43Z","oa_version":"Published Version","article_processing_charge":"No","oa":1,"year":"2021","date_published":"2021-05-24T00:00:00Z","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","date_updated":"2021-05-28T12:39:43Z","content_type":"application/pdf","date_created":"2021-05-28T12:39:43Z","success":1,"file_name":"2021_NatureCommunications_Morandell.pdf","relation":"main_file","creator":"kschuh","file_size":9358599,"file_id":"9430","checksum":"337e0f7959c35ec959984cacdcb472ba"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508"},{"grant_number":"W1232","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","grant_number":"F7807","name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and epilepsy"},{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"}],"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."}],"volume":12,"type":"journal_article","fulldoi":"https://doi.org/10.1038/s41467-021-23123-x","month":"05","keyword":["General Biochemistry","Genetics and Molecular Biology"],"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","publication_identifier":{"eissn":["2041-1723"]},"related_material":{"link":[{"url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/","relation":"press_release"}],"record":[{"relation":"earlier_version","status":"public","id":"7800"},{"relation":"dissertation_contains","status":"public","id":"12401"},{"status":"public","id":"19557","relation":"dissertation_contains"}]},"ddc":["572"],"corr_author":"1","external_id":{"isi":["000658769900010"]},"issue":"1","publication_status":"published","isi":1,"doi":"10.1038/s41467-021-23123-x","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).","publisher":"Springer Nature","date_created":"2021-05-28T11:49:46Z","author":[{"last_name":"Morandell","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin"},{"full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","last_name":"Schwarz"},{"first_name":"Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico"},{"last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X"},{"first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","last_name":"Dimchev"},{"last_name":"Nicolas","full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"last_name":"Dotter","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","full_name":"Knaus, Lisa","last_name":"Knaus"},{"last_name":"Dobler","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","first_name":"Zoe","full_name":"Dobler, Zoe"},{"first_name":"Emanuele","full_name":"Cacci, Emanuele","last_name":"Cacci"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"intvolume":"        12","date_updated":"2026-11-11T23:30:14Z"},{"project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits"},{"call_identifier":"FWF","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","name":"Structural plasticity at mossy fiber-CA3 synapses","grant_number":"V00739"}],"file":[{"creator":"cziletti","checksum":"7eb580abd8893cdb0b410cf41bc8c263","file_id":"9639","file_size":38574802,"date_created":"2021-07-08T12:27:55Z","embargo":"2021-12-01","date_updated":"2021-12-02T23:30:05Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"VandaeletalAuthorVersion2021.pdf"}],"fulldoi":"https://doi.org/10.1038/s41596-021-00526-0","type":"journal_article","volume":16,"abstract":[{"lang":"eng","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."}],"publication_identifier":{"issn":["1754-2189"],"eissn":["1750-2799"]},"title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","month":"06","ddc":["570"],"issue":"6","corr_author":"1","external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"isi":1,"publication_status":"published","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.","doi":"10.1038/s41596-021-00526-0","date_updated":"2025-04-22T22:30:43Z","department":[{"_id":"PeJo"}],"intvolume":"        16","author":[{"last_name":"Vandael","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H"},{"orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji","first_name":"Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","last_name":"Okamoto"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina","full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane"},{"full_name":"Vargas Barroso, Victor M","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","last_name":"Vargas Barroso"},{"full_name":"Suter, Benjamin","orcid":"0000-0002-9885-6936","first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","last_name":"Suter"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"date_created":"2021-05-30T22:01:24Z","publisher":"Springer Nature","page":"2947–2967","status":"public","quality_controlled":"1","citation":{"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.","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>","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>","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>.","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.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967."},"_id":"9438","scopus_import":"1","article_type":"original","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Nature Protocols","has_accepted_license":"1","ec_funded":1,"file_date_updated":"2021-12-02T23:30:05Z","acknowledged_ssus":[{"_id":"M-Shop"}],"article_processing_charge":"No","oa_version":"Submitted Version","oa":1,"pmid":1,"language":[{"iso":"eng"}],"date_published":"2021-06-01T00:00:00Z","year":"2021"},{"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","doi":"10.1002/wdev.383","author":[{"last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","first_name":"Katarzyna"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"date_created":"2020-05-24T22:01:00Z","OA_type":"hybrid","date_updated":"2026-11-11T23:30:17Z","department":[{"_id":"AnKi"}],"publisher":"Wiley","external_id":{"isi":["000531419400001"],"pmid":["32391980"]},"corr_author":"1","isi":1,"OA_place":"publisher","publication_status":"published","publication_identifier":{"eissn":["1759-7692"],"issn":["1759-7684"]},"related_material":{"record":[{"status":"public","id":"14323","relation":"dissertation_contains"}]},"month":"04","title":"Regulation of size and scale in vertebrate spinal cord development","ddc":["570"],"file":[{"date_updated":"2020-11-24T13:11:39Z","content_type":"application/pdf","success":1,"date_created":"2020-11-24T13:11:39Z","access_level":"open_access","relation":"main_file","file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","creator":"dernst","checksum":"f0a7745d48afa09ea7025e876a0145a8","file_size":2527276,"file_id":"8800"}],"project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"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"}],"type":"journal_article","fulldoi":"https://doi.org/10.1002/wdev.383","oa":1,"date_published":"2021-04-15T00:00:00Z","year":"2021","pmid":1,"language":[{"iso":"eng"}],"file_date_updated":"2020-11-24T13:11:39Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","article_type":"original","publication":"Wiley Interdisciplinary Reviews: Developmental Biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","ec_funded":1,"article_number":"e383","has_accepted_license":"1","quality_controlled":"1","status":"public","_id":"7883","citation":{"ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","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>","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>.","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>.","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.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021)."},"scopus_import":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"ddc":["570"],"publication_identifier":{"eissn":["1478-3975"]},"related_material":{"record":[{"relation":"dissertation_contains","id":"13081","status":"public"}]},"month":"04","title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","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"}],"volume":18,"type":"journal_article","fulldoi":"https://doi.org/10.1088/1478-3975/abd0db","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"file":[{"date_created":"2021-04-27T08:38:35Z","success":1,"date_updated":"2021-04-27T08:38:35Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2021_PhysBio_Lenne.pdf","creator":"cziletti","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","file_size":6296324,"file_id":"9355"}],"author":[{"last_name":"Lenne","first_name":"Pierre François","full_name":"Lenne, Pierre François"},{"last_name":"Munro","first_name":"Edwin","full_name":"Munro, Edwin"},{"last_name":"Heemskerk","first_name":"Idse","full_name":"Heemskerk, Idse"},{"full_name":"Warmflash, Aryeh","first_name":"Aryeh","last_name":"Warmflash"},{"id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Bocanegra, Laura","last_name":"Bocanegra"},{"last_name":"Kishi","orcid":"0000-0001-6060-4795","full_name":"Kishi, Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi"},{"last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"},{"full_name":"Long, Yuchen","first_name":"Yuchen","last_name":"Long"},{"last_name":"Fruleux","first_name":"Antoine","full_name":"Fruleux, Antoine"},{"full_name":"Boudaoud, Arezki","first_name":"Arezki","last_name":"Boudaoud"},{"full_name":"Saunders, Timothy E.","first_name":"Timothy E.","last_name":"Saunders"},{"first_name":"Paolo","full_name":"Caldarelli, Paolo","last_name":"Caldarelli"},{"last_name":"Michaut","first_name":"Arthur","full_name":"Michaut, Arthur"},{"last_name":"Gros","first_name":"Jerome","full_name":"Gros, Jerome"},{"last_name":"Maroudas-Sacks","full_name":"Maroudas-Sacks, Yonit","first_name":"Yonit"},{"full_name":"Keren, Kinneret","first_name":"Kinneret","last_name":"Keren"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"first_name":"Zev J.","full_name":"Gartner, Zev J.","last_name":"Gartner"},{"first_name":"Benjamin","full_name":"Stormo, Benjamin","last_name":"Stormo"},{"last_name":"Gladfelter","full_name":"Gladfelter, Amy","first_name":"Amy"},{"first_name":"Alan","full_name":"Rodrigues, Alan","last_name":"Rodrigues"},{"full_name":"Shyer, Amy","first_name":"Amy","last_name":"Shyer"},{"first_name":"Nicolas","full_name":"Minc, Nicolas","last_name":"Minc"},{"full_name":"Maître, Jean Léon","first_name":"Jean Léon","last_name":"Maître"},{"first_name":"Stefano","full_name":"Di Talia, Stefano","last_name":"Di Talia"},{"last_name":"Khamaisi","first_name":"Bassma","full_name":"Khamaisi, Bassma"},{"last_name":"Sprinzak","full_name":"Sprinzak, David","first_name":"David"},{"first_name":"Sham","full_name":"Tlili, Sham","last_name":"Tlili"}],"date_created":"2021-04-25T22:01:29Z","date_updated":"2026-11-11T23:30:19Z","department":[{"_id":"AnKi"},{"_id":"EdHa"}],"intvolume":"        18","publisher":"IOP Publishing","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).","doi":"10.1088/1478-3975/abd0db","isi":1,"publication_status":"published","external_id":{"pmid":["33276350"],"isi":["000640396400001"]},"issue":"4","ec_funded":1,"article_number":"041501","has_accepted_license":"1","article_type":"original","day":"14","publication":"Physical biology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","status":"public","_id":"9349","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>","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>","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.","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>.","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>.","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.","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)."},"year":"2021","date_published":"2021-04-14T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2021-04-27T08:38:35Z"},{"oa":1,"pmid":1,"language":[{"iso":"eng"}],"year":"2021","date_published":"2021-03-15T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"}],"file_date_updated":"2021-09-16T22:30:03Z","article_processing_charge":"No","oa_version":"Submitted Version","article_type":"original","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"15","publication":"Nature Chemistry","has_accepted_license":"1","citation":{"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.","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.","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>.","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>.","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.","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>"},"_id":"9250","status":"public","quality_controlled":"1","scopus_import":"1","doi":"10.1038/s41557-021-00643-z","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.","publisher":"Springer Nature","page":"465-471","intvolume":"        13","department":[{"_id":"StFr"}],"date_updated":"2024-10-09T21:00:28Z","author":[{"last_name":"Petit","first_name":"Yann K.","full_name":"Petit, Yann K."},{"last_name":"Mourad","first_name":"Eléonore","full_name":"Mourad, Eléonore"},{"last_name":"Prehal","full_name":"Prehal, Christian","first_name":"Christian"},{"first_name":"Christian","full_name":"Leypold, Christian","last_name":"Leypold"},{"last_name":"Windischbacher","first_name":"Andreas","full_name":"Windischbacher, Andreas"},{"last_name":"Mijailovic","full_name":"Mijailovic, Daniel","first_name":"Daniel"},{"last_name":"Slugovc","first_name":"Christian","full_name":"Slugovc, Christian"},{"last_name":"Borisov","full_name":"Borisov, Sergey M.","first_name":"Sergey M."},{"full_name":"Zojer, Egbert","first_name":"Egbert","last_name":"Zojer"},{"last_name":"Brutti","first_name":"Sergio","full_name":"Brutti, Sergio"},{"last_name":"Fontaine","first_name":"Olivier","full_name":"Fontaine, Olivier"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger"}],"date_created":"2021-03-16T11:12:20Z","issue":"5","external_id":{"pmid":["33723377"],"isi":["000629296400001"]},"corr_author":"1","publication_status":"published","isi":1,"title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","keyword":["General Chemistry","General Chemical Engineering"],"month":"03","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"ddc":["540"],"file":[{"checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","file_size":1811448,"file_id":"9276","creator":"dernst","relation":"main_file","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","embargo":"2021-09-15","date_created":"2021-03-22T11:46:00Z","date_updated":"2021-09-16T22:30:03Z","content_type":"application/pdf","access_level":"open_access"}],"type":"journal_article","fulldoi":"https://doi.org/10.1038/s41557-021-00643-z","abstract":[{"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.","lang":"eng"}],"volume":13},{"type":"journal_article","fulldoi":"https://doi.org/10.1038/s41567-021-01230-2","volume":17,"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"}],"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"file":[{"checksum":"316ed42ea1b42b0f1a3025bb476266fc","file_size":10028836,"file_id":"10026","creator":"patrickd","relation":"main_file","file_name":"RevisedQMBSreview.pdf","date_created":"2021-09-20T09:27:43Z","embargo":"2021-12-01","content_type":"application/pdf","date_updated":"2021-12-02T23:30:03Z","access_level":"open_access"}],"arxiv":1,"ddc":["539"],"publication_identifier":{"eissn":["1745-2481"]},"title":"Quantum many-body scars and weak breaking of ergodicity","month":"06","isi":1,"publication_status":"published","issue":"6","external_id":{"arxiv":["2011.09486"],"isi":["000655563800002"]},"date_updated":"2025-04-14T07:52:09Z","intvolume":"        17","department":[{"_id":"MaSe"}],"date_created":"2021-05-28T09:03:50Z","author":[{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"publisher":"Nature Research","page":"675–685","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.","doi":"10.1038/s41567-021-01230-2","scopus_import":"1","status":"public","quality_controlled":"1","citation":{"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>.","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>","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","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>","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” <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>."},"_id":"9428","has_accepted_license":"1","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publication":"Nature Physics","article_type":"review","article_processing_charge":"No","oa_version":"Preprint","file_date_updated":"2021-12-02T23:30:03Z","language":[{"iso":"eng"}],"date_published":"2021-06-01T00:00:00Z","year":"2021","oa":1},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"18","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","_id":"9397","citation":{"short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>.","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>.","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>","ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>"},"status":"public","oa":1,"degree_awarded":"PhD","date_published":"2021-05-18T00:00:00Z","year":"2021","language":[{"iso":"eng"}],"file_date_updated":"2022-05-21T22:30:04Z","oa_version":"Published Version","article_processing_charge":"No","month":"05","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","publication_identifier":{"issn":["2663-337X"]},"ddc":["571"],"file":[{"relation":"source_file","file_name":"KHuljev_Thesis_corrections.docx","date_created":"2021-05-17T12:29:12Z","date_updated":"2022-05-21T22:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","embargo_to":"open_access","checksum":"7f98532f5324a0b2f3fa8de2967baa19","file_id":"9398","file_size":47799741,"creator":"khuljev"},{"file_size":16542131,"file_id":"9401","checksum":"bf512f8a1e572a543778fc4b227c01ba","creator":"khuljev","file_name":"new_KHuljev_Thesis_corrections.pdf","relation":"main_file","access_level":"open_access","embargo":"2022-05-20","date_created":"2021-05-18T14:50:28Z","date_updated":"2022-05-21T22:30:04Z","content_type":"application/pdf"}],"abstract":[{"text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.","lang":"eng"}],"type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:9397","doi":"10.15479/at:ista:9397","page":"101","publisher":"Institute of Science and Technology Austria","date_created":"2021-05-17T12:31:30Z","author":[{"last_name":"Huljev","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","full_name":"Huljev, Karla"}],"date_updated":"2026-04-08T07:12:51Z","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"corr_author":"1","publication_status":"published","OA_place":"publisher","supervisor":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}]},{"doi":"10.15479/at:ista:9992","page":"168","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926"}],"date_created":"2021-09-09T07:37:20Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"date_updated":"2026-04-08T07:11:47Z","corr_author":"1","publication_status":"published","OA_place":"publisher","supervisor":[{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"month":"09","title":"Wound healing in the Arabidopsis root meristem","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"6943","status":"public"},{"status":"public","id":"8002","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6351","status":"public"}]},"ddc":["575"],"project":[{"call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file":[{"file_size":25179004,"file_id":"9993","checksum":"c763064adaa720e16066c1a4f9682bbb","creator":"lhoermaye","file_name":"Thesis_vupload.docx","relation":"source_file","embargo_to":"open_access","access_level":"closed","date_updated":"2021-09-15T22:30:26Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2021-09-09T07:29:48Z"},{"creator":"lhoermaye","file_id":"9996","file_size":6246900,"checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","access_level":"open_access","date_created":"2021-09-09T14:25:08Z","embargo":"2021-09-09","content_type":"application/pdf","date_updated":"2021-09-15T22:30:26Z","file_name":"Thesis_vfinal_pdfa.pdf","relation":"main_file"}],"abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"fulldoi":"https://doi.org/10.15479/at:ista:9992","type":"dissertation","oa":1,"degree_awarded":"PhD","year":"2021","date_published":"2021-09-13T00:00:00Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2021-09-15T22:30:26Z","oa_version":"Published Version","article_processing_charge":"No","day":"13","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"ec_funded":1,"has_accepted_license":"1","_id":"9992","citation":{"ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021."},"status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"}},{"acknowledged_ssus":[{"_id":"M-Shop"}],"file_date_updated":"2022-07-29T22:30:05Z","article_processing_charge":"No","oa_version":"Published Version","oa":1,"degree_awarded":"PhD","language":[{"iso":"eng"}],"year":"2021","date_published":"2021-07-29T00:00:00Z","citation":{"mla":"Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>","apa":"Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden pipe flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>.","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021."},"_id":"9728","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"29","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","corr_author":"1","publication_status":"published","supervisor":[{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"OA_place":"publisher","doi":"10.15479/at:ista:9728","publisher":"Institute of Science and Technology Austria","page":"118","date_updated":"2026-04-16T08:43:20Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"date_created":"2021-07-27T13:40:30Z","author":[{"last_name":"Agrawal","full_name":"Agrawal, Nishchal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"}],"file":[{"embargo_to":"open_access","access_level":"closed","date_updated":"2022-07-29T22:30:05Z","content_type":"application/x-zip-compressed","date_created":"2021-07-28T13:32:02Z","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","relation":"source_file","creator":"nagrawal","file_size":22859658,"file_id":"9744","checksum":"77436be3563a90435024307b1b5ee7e8"},{"file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","relation":"main_file","access_level":"open_access","embargo":"2022-07-28","date_created":"2021-07-28T13:32:05Z","content_type":"application/pdf","date_updated":"2022-07-29T22:30:05Z","file_id":"9745","file_size":18658048,"checksum":"72a891d7daba85445c29b868c22575ed","creator":"nagrawal"}],"type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:9728","abstract":[{"lang":"eng","text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work."}],"keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"title":"Transition to turbulence and drag reduction in particle-laden pipe flows","month":"07","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6189"}]},"publication_identifier":{"issn":["2663-337X"]},"ddc":["532"]},{"date_updated":"2026-11-11T23:30:27Z","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Savin, Cristina","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin"}],"year":"2021","date_created":"2021-10-04T06:23:34Z","date_published":"2021-09-29T00:00:00Z","doi":"10.1101/2021.09.28.460602","oa":1,"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.","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602"}],"publication_status":"draft","article_processing_charge":"No","oa_version":"Preprint","das_tickbox":"1","ec_funded":1,"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","day":"29","month":"09","publication":"bioRxiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11932"},{"relation":"later_version","id":"14656","status":"public"}]},"type":"preprint","fulldoi":"https://doi.org/10.1101/2021.09.28.460602","abstract":[{"lang":"eng","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."}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"citation":{"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>. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>","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>.","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>, doi:<a href=\"https://doi.org/10.1101/2021.09.28.460602\">10.1101/2021.09.28.460602</a>.","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>. .","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>, n.d. <a href=\"https://doi.org/10.1101/2021.09.28.460602\">https://doi.org/10.1101/2021.09.28.460602</a>.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.)."},"_id":"10077","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"}],"status":"public"},{"abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"type":"dissertation","fulldoi":"https://doi.org/10.15479/at:ista:9623","file":[{"date_created":"2021-07-01T14:48:54Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2022-07-02T22:30:06Z","access_level":"closed","embargo_to":"open_access","relation":"source_file","file_name":"PhDThesis_SCM.docx","creator":"scaballe","checksum":"e039225a47ef32666d59bf35ddd30ecf","file_id":"9624","file_size":131946790},{"creator":"scaballe","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","file_size":17094958,"file_id":"9625","date_updated":"2022-07-02T22:30:06Z","content_type":"application/pdf","embargo":"2022-07-01","date_created":"2021-07-01T14:46:25Z","access_level":"open_access","relation":"main_file","file_name":"PhDThesis_SCM.pdf"}],"ddc":["570"],"publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"9006","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"9750"}]},"month":"07","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","OA_place":"publisher","supervisor":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"publication_status":"published","corr_author":"1","author":[{"last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia"}],"date_created":"2021-07-01T14:50:17Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"date_updated":"2026-07-06T12:45:39Z","page":"111","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:9623","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","_id":"9623","citation":{"short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021.","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>.","mla":"Caballero Mancebo, Silvia. <i>Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>.","apa":"Caballero Mancebo, S. (2021). <i>Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>"},"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2022-07-02T22:30:06Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_published":"2021-07-01T00:00:00Z","year":"2021","language":[{"iso":"eng"}],"oa":1,"degree_awarded":"PhD"}]
