[{"scopus_import":"1","article_processing_charge":"No","day":"06","page":"129-139","citation":{"chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In Annual ACM Symposium on Parallelism in Algorithms and Architectures, 129–39, 2021. https://doi.org/10.1145/3409964.3461785.","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–139.","mla":"Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token Dropping.” Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–39, doi:10.1145/3409964.3461785.","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2021). Efficient load-balancing through distributed token dropping. In Annual ACM Symposium on Parallelism in Algorithms and Architectures (pp. 129–139). Virtual Event, United States. https://doi.org/10.1145/3409964.3461785","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing through distributed token dropping,” in Annual ACM Symposium on Parallelism in Algorithms and Architectures, Virtual Event, United States, 2021, pp. 129–139.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures , 129–139.","ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing through distributed token dropping. In: Annual ACM Symposium on Parallelism in Algorithms and Architectures. ; 2021:129-139. doi:10.1145/3409964.3461785"},"publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","date_published":"2021-07-06T00:00:00Z","type":"conference","abstract":[{"text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.","lang":"eng"}],"status":"public","title":"Efficient load-balancing through distributed token dropping","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9678","oa_version":"Preprint","publication_identifier":{"isbn":["9781450380706"]},"month":"07","project":[{"call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.07761"}],"external_id":{"arxiv":["2005.07761"]},"language":[{"iso":"eng"}],"doi":"10.1145/3409964.3461785","conference":{"end_date":"2021-07-08","start_date":"2021-07-06","location":" Virtual Event, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures "},"ec_funded":1,"department":[{"_id":"DaAl"}],"publication_status":"published","acknowledgement":"We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.","year":"2021","date_updated":"2024-03-05T07:13:12Z","date_created":"2021-07-18T22:01:22Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"15074"}]},"author":[{"last_name":"Brandt","first_name":"Sebastian","full_name":"Brandt, Sebastian"},{"first_name":"Barbara","last_name":"Keller","full_name":"Keller, Barbara"},{"full_name":"Rybicki, Joel","first_name":"Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646"},{"last_name":"Suomela","first_name":"Jukka","full_name":"Suomela, Jukka"},{"full_name":"Uitto, Jara","last_name":"Uitto","first_name":"Jara"}]},{"type":"journal_article","abstract":[{"text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. ","lang":"eng"}],"title":"Dynamic averaging load balancing on cycles","status":"public","ddc":["000"],"_id":"8286","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_name":"2021_Algorithmica_Alistarh.pdf","access_level":"open_access","content_type":"application/pdf","file_size":525950,"creator":"cchlebak","relation":"main_file","file_id":"10577","date_updated":"2021-12-27T10:36:40Z","date_created":"2021-12-27T10:36:40Z","checksum":"21169b25b0c8e17b21e12af22bff9870","success":1}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"24","article_type":"original","citation":{"ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. Algorithmica. 2021. doi:10.1007/s00453-021-00905-9","ista":"Alistarh D-A, Nadiradze G, Sabour A. 2021. Dynamic averaging load balancing on cycles. Algorithmica.","apa":"Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2021). Dynamic averaging load balancing on cycles. Algorithmica. Virtual, Online; Germany: Springer Nature. https://doi.org/10.1007/s00453-021-00905-9","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” Algorithmica. Springer Nature, 2021.","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica, Springer Nature, 2021, doi:10.1007/s00453-021-00905-9.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021).","chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” Algorithmica. Springer Nature, 2021. https://doi.org/10.1007/s00453-021-00905-9."},"publication":"Algorithmica","date_published":"2021-12-24T00:00:00Z","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"file_date_updated":"2021-12-27T10:36:40Z","department":[{"_id":"DaAl"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments. Open access funding provided by Institute of Science and Technology (IST Austria). Funding was provided by European Research Council (Grant No. PR1042ERC01).","year":"2021","date_created":"2020-08-24T06:24:04Z","date_updated":"2024-03-05T07:35:53Z","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.4230/LIPIcs.ICALP.2020.7"}],"record":[{"relation":"earlier_version","status":"public","id":"15077"}]},"author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"first_name":"Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi"},{"id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba","last_name":"Sabour","full_name":"Sabour, Amirmojtaba"}],"publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"month":"12","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000734004600001"],"arxiv":["2003.09297"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00453-021-00905-9","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming ","end_date":"2020-07-11","location":"Virtual, Online; Germany","start_date":"2020-07-08"}},{"abstract":[{"lang":"eng","text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_size":1958710,"content_type":"application/pdf","creator":"dfelicia","file_name":"Thesis_FeliciangeliA.pdf","access_level":"open_access","date_updated":"2021-09-06T09:28:56Z","date_created":"2021-08-19T14:03:48Z","checksum":"e88bb8ca43948abe060eb2d2fa719881","relation":"main_file","file_id":"9944"},{"file_name":"thesis.7z","access_level":"closed","file_size":3771669,"content_type":"application/octet-stream","creator":"dfelicia","relation":"source_file","file_id":"9945","date_updated":"2022-03-10T12:13:57Z","date_created":"2021-08-19T14:06:35Z","checksum":"72810843abee83705853505b3f8348aa"}],"oa_version":"Published Version","_id":"9733","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["515","519","539"],"status":"public","title":"The polaron at strong coupling","article_processing_charge":"No","has_accepted_license":"1","day":"20","date_published":"2021-08-20T00:00:00Z","citation":{"ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733","apa":"Feliciangeli, D. (2021). The polaron at strong coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9733","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","mla":"Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9733.","chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733."},"page":"180","ec_funded":1,"file_date_updated":"2022-03-10T12:13:57Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9787"},{"status":"public","relation":"part_of_dissertation","id":"9792"},{"id":"9225","status":"public","relation":"part_of_dissertation"},{"id":"9781","relation":"part_of_dissertation","status":"public"},{"id":"9791","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli","first_name":"Dario"}],"date_created":"2021-07-27T15:48:30Z","date_updated":"2024-03-06T12:30:44Z","year":"2021","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"08","doi":"10.15479/at:ista:9733","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"},{"last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"}],"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9571","intvolume":" 22","ddc":["000"],"title":"NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization","status":"public","file":[{"success":1,"checksum":"6428aa8bcb67768b6949c99b55d5281d","date_created":"2021-06-23T07:09:41Z","date_updated":"2021-06-23T07:09:41Z","file_id":"9595","relation":"main_file","creator":"asandaue","file_size":11237154,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"114","abstract":[{"lang":"eng","text":"As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods."}],"citation":{"ista":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. 2021. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 22(114), 1−43.","ieee":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, and D. M. Roy, “NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization,” Journal of Machine Learning Research, vol. 22, no. 114. Journal of Machine Learning Research, p. 1−43, 2021.","apa":"Ramezani-Kebrya, A., Faghri, F., Markov, I., Aksenov, V., Alistarh, D.-A., & Roy, D. M. (2021). NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. Journal of Machine Learning Research.","ama":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 2021;22(114):1−43.","chicago":"Ramezani-Kebrya, Ali, Fartash Faghri, Ilya Markov, Vitalii Aksenov, Dan-Adrian Alistarh, and Daniel M. Roy. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research. Journal of Machine Learning Research, 2021.","mla":"Ramezani-Kebrya, Ali, et al. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” Journal of Machine Learning Research, vol. 22, no. 114, Journal of Machine Learning Research, 2021, p. 1−43.","short":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, D.M. Roy, Journal of Machine Learning Research 22 (2021) 1−43."},"publication":"Journal of Machine Learning Research","page":"1−43","article_type":"original","date_published":"2021-04-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","year":"2021","department":[{"_id":"DaAl"}],"publisher":"Journal of Machine Learning Research","publication_status":"published","author":[{"last_name":"Ramezani-Kebrya","first_name":"Ali","full_name":"Ramezani-Kebrya, Ali"},{"full_name":"Faghri, Fartash","last_name":"Faghri","first_name":"Fartash"},{"first_name":"Ilya","last_name":"Markov","full_name":"Markov, Ilya"},{"last_name":"Aksenov","first_name":"Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","full_name":"Aksenov, Vitalii"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"first_name":"Daniel M.","last_name":"Roy","full_name":"Roy, Daniel M."}],"volume":22,"date_created":"2021-06-20T22:01:33Z","date_updated":"2024-03-06T12:22:07Z","file_date_updated":"2021-06-23T07:09:41Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1908.06077"]},"main_file_link":[{"open_access":"1","url":"https://www.jmlr.org/papers/v22/20-255.html"}],"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15337928"],"issn":["15324435"]},"month":"04"},{"_id":"8544","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells","intvolume":" 109","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis.","lang":"eng"}],"issue":"4","publication":"Neuron","citation":{"ama":"Takeo YH, Shuster SA, Jiang L, et al. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 2021;109(4):P629-644.E8. doi:10.1016/j.neuron.2020.11.028","ieee":"Y. H. Takeo et al., “GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells,” Neuron, vol. 109, no. 4. Elsevier, p. P629–644.E8, 2021.","apa":"Takeo, Y. H., Shuster, S. A., Jiang, L., Hu, M., Luginbuhl, D. J., Rülicke, T., … Luo, L. (2021). GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.11.028","ista":"Takeo YH, Shuster SA, Jiang L, Hu M, Luginbuhl DJ, Rülicke T, Contreras X, Hippenmeyer S, Wagner MJ, Ganguli S, Luo L. 2021. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 109(4), P629–644.E8.","short":"Y.H. Takeo, S.A. Shuster, L. Jiang, M. Hu, D.J. Luginbuhl, T. Rülicke, X. Contreras, S. Hippenmeyer, M.J. Wagner, S. Ganguli, L. Luo, Neuron 109 (2021) P629–644.E8.","mla":"Takeo, Yukari H., et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron, vol. 109, no. 4, Elsevier, 2021, p. P629–644.E8, doi:10.1016/j.neuron.2020.11.028.","chicago":"Takeo, Yukari H., S. Andrew Shuster, Linnie Jiang, Miley Hu, David J. Luginbuhl, Thomas Rülicke, Ximena Contreras, et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron. Elsevier, 2021. https://doi.org/10.1016/j.neuron.2020.11.028."},"article_type":"original","page":"P629-644.E8","date_published":"2021-02-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"No","year":"2021","acknowledgement":"We thank M. Mishina for GluD2fl frozen embryos, T.C. Südhof and J.I. Morgan for Cbln1fl mice, L. Anderson for help in generating the MADM alleles, W. Joo for a previously unpublished construct, M. Yuzaki, K. Shen, J. Ding, and members of the Luo lab, including J.M. Kebschull, H. Li, J. Li, T. Li, C.M. McLaughlin, D. Pederick, J. Ren, D.C. Wang and C. Xu for discussions and critiques of the manuscript, and M. Yuzaki for supporting Y.H.T. during the final phase of this project. Y.H.T. was supported by a JSPS fellowship; S.A.S. was supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; L.J. is supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; M.J.W. is supported by a Burroughs Wellcome Fund CASI Award. This work was supported by an NIH grant (R01-NS050538) to L.L.; the European Research Council (ERC) under the European Union's Horizon 2020 research and innovations programme (No. 725780 LinPro) to S.H.; and Simons and James S. McDonnell Foundations and an NSF CAREER award to S.G.; L.L. is an HHMI investigator.","publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Elsevier","author":[{"last_name":"Takeo","first_name":"Yukari H.","full_name":"Takeo, Yukari H."},{"full_name":"Shuster, S. Andrew","first_name":"S. Andrew","last_name":"Shuster"},{"full_name":"Jiang, Linnie","last_name":"Jiang","first_name":"Linnie"},{"last_name":"Hu","first_name":"Miley","full_name":"Hu, Miley"},{"first_name":"David J.","last_name":"Luginbuhl","full_name":"Luginbuhl, David J."},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","first_name":"Ximena","full_name":"Contreras, Ximena"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"full_name":"Wagner, Mark J.","first_name":"Mark J.","last_name":"Wagner"},{"full_name":"Ganguli, Surya","first_name":"Surya","last_name":"Ganguli"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"}],"date_updated":"2024-03-06T12:12:48Z","date_created":"2020-09-21T11:59:47Z","volume":109,"ec_funded":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.06.14.151258"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"doi":"10.1016/j.neuron.2020.11.028","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["1097-4199"]}},{"author":[{"full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli","first_name":"Dario"},{"orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","last_name":"Rademacher","first_name":"Simone Anna Elvira","full_name":"Rademacher, Simone Anna Elvira"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"related_material":{"record":[{"id":"10755","status":"public","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"9733"}]},"date_updated":"2024-03-06T12:30:45Z","date_created":"2021-08-06T08:49:45Z","oa_version":"Preprint","acknowledgement":"We thank Herbert Spohn for helpful comments. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged..","_id":"9791","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","publication_status":"submitted","ddc":["510"],"title":"The effective mass problem for the Landau-Pekar equations","status":"public","department":[{"_id":"RoSe"}],"abstract":[{"text":"We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar.","lang":"eng"}],"ec_funded":1,"article_number":"2107.03720 ","type":"preprint","date_published":"2021-07-08T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","citation":{"apa":"Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (n.d.). The effective mass problem for the Landau-Pekar equations. arXiv.","ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” arXiv. .","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv, 2107.03720.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv.","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, n.d.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.).","mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, 2107.03720."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.03720"}],"oa":1,"external_id":{"arxiv":["2107.03720"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"month":"07","day":"08","article_processing_charge":"No"},{"publication_status":"published","publisher":"Cell Press","department":[{"_id":"GaTk"}],"year":"2021","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.","date_updated":"2024-03-06T14:22:51Z","date_created":"2020-02-28T11:00:12Z","volume":109,"author":[{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","first_name":"Thomas R","last_name":"Sokolowski"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"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","relation":"dissertation_contains","id":"15020"}]},"ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"oa":1,"external_id":{"isi":["000637809600006"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/848374"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2021.01.020","month":"04","status":"public","title":"Statistical analysis and optimality of neural systems","intvolume":" 109","_id":"7553","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"7","page":"1227-1241.e5","publication":"Neuron","citation":{"short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.","chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press, 2021. https://doi.org/10.1016/j.neuron.2021.01.020.","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020","apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5."},"date_published":"2021-04-07T00:00:00Z","scopus_import":"1","day":"07","article_processing_charge":"No"},{"date_published":"2021-04-01T00:00:00Z","page":"397-405","citation":{"short":"M. Mondelli, R. Venkataramanan, in:, A. Banerjee, K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2021, pp. 397–405.","mla":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, vol. 130, ML Research Press, 2021, pp. 397–405.","chicago":"Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with Spectral Initialization for Generalized Linear Models.” In Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, edited by Arindam Banerjee and Kenji Fukumizu, 130:397–405. ML Research Press, 2021.","ama":"Mondelli M, Venkataramanan R. Approximate message passing with spectral initialization for generalized linear models. In: Banerjee A, Fukumizu K, eds. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. Vol 130. ML Research Press; 2021:397-405.","apa":"Mondelli, M., & Venkataramanan, R. (2021). Approximate message passing with spectral initialization for generalized linear models. In A. Banerjee & K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial Intelligence and Statistics (Vol. 130, pp. 397–405). Virtual, San Diego, CA, United States: ML Research Press.","ieee":"M. Mondelli and R. Venkataramanan, “Approximate message passing with spectral initialization for generalized linear models,” in Proceedings of The 24th International Conference on Artificial Intelligence and Statistics, Virtual, San Diego, CA, United States, 2021, vol. 130, pp. 397–405.","ista":"Mondelli M, Venkataramanan R. 2021. Approximate message passing with spectral initialization for generalized linear models. Proceedings of The 24th International Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence and Statistics, Proceedings of Machine Learning Research, vol. 130, 397–405."},"publication":"Proceedings of The 24th International Conference on Artificial Intelligence and Statistics","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 130","title":"Approximate message passing with spectral initialization for generalized linear models","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10598","abstract":[{"text":" We consider the problem of estimating a signal from measurements obtained via a generalized linear model. We focus on estimators based on approximate message passing (AMP), a family of iterative algorithms with many appealing features: the performance of AMP in the high-dimensional limit can be succinctly characterized under suitable model assumptions; AMP can also be tailored to the empirical distribution of the signal entries, and for a wide class of estimation problems, AMP is conjectured to be optimal among all polynomial-time algorithms. However, a major issue of AMP is that in many models (such as phase retrieval), it requires an initialization correlated with the ground-truth signal and independent from the measurement matrix. Assuming that such an initialization is available is typically not realistic. In this paper, we solve this problem by proposing an AMP algorithm initialized with a spectral estimator. With such an initialization, the standard AMP analysis fails since the spectral estimator depends in a complicated way on the design matrix. Our main contribution is a rigorous characterization of the performance of AMP with spectral initialization in the high-dimensional limit. The key technical idea is to define and analyze a two-phase artificial AMP algorithm that first produces the spectral estimator, and then closely approximates the iterates of the true AMP. We also provide numerical results that demonstrate the validity of the proposed approach. ","lang":"eng"}],"alternative_title":["Proceedings of Machine Learning Research"],"type":"conference","language":[{"iso":"eng"}],"conference":{"end_date":"2021-04-15","start_date":"2021-04-13","location":"Virtual, San Diego, CA, United States","name":"AISTATS: Artificial Intelligence and Statistics"},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","external_id":{"arxiv":["2010.03460"]},"main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v130/mondelli21a.html"}],"oa":1,"publication_identifier":{"issn":["2640-3498"]},"month":"04","volume":130,"date_created":"2022-01-03T11:34:22Z","date_updated":"2024-03-07T10:36:53Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"12480"}]},"author":[{"full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"last_name":"Venkataramanan","first_name":"Ramji","full_name":"Venkataramanan, Ramji"}],"editor":[{"full_name":"Banerjee, Arindam","first_name":"Arindam","last_name":"Banerjee"},{"first_name":"Kenji","last_name":"Fukumizu","full_name":"Fukumizu, Kenji"}],"department":[{"_id":"MaMo"}],"publisher":"ML Research Press","publication_status":"published","acknowledgement":"The authors would like to thank Andrea Montanari for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.","year":"2021"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000559345400001"]},"quality_controlled":"1","isi":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s11081-020-09544-5","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["1573-2924"],"issn":["1389-4420"]},"year":"2021","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7—2007–2013) (Grant Agreement No. 616160). The authors are grateful to the anonymous referees and the handling Editor for their comments and suggestions which have improved the earlier version of the manuscript greatly.","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"VlKo"}],"author":[{"full_name":"Shehu, Yekini","last_name":"Shehu","first_name":"Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dong","first_name":"Qiao-Li","full_name":"Dong, Qiao-Li"},{"last_name":"Liu","first_name":"Lu-Lu","full_name":"Liu, Lu-Lu"},{"last_name":"Yao","first_name":"Jen-Chih","full_name":"Yao, Jen-Chih"}],"date_created":"2020-08-03T14:29:57Z","date_updated":"2024-03-07T14:39:29Z","volume":22,"file_date_updated":"2020-08-03T15:24:39Z","ec_funded":1,"publication":"Optimization and Engineering","citation":{"mla":"Shehu, Yekini, et al. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering, vol. 22, Springer Nature, 2021, pp. 2627–53, doi:10.1007/s11081-020-09544-5.","short":"Y. Shehu, Q.-L. Dong, L.-L. Liu, J.-C. Yao, Optimization and Engineering 22 (2021) 2627–2653.","chicago":"Shehu, Yekini, Qiao-Li Dong, Lu-Lu Liu, and Jen-Chih Yao. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering. Springer Nature, 2021. https://doi.org/10.1007/s11081-020-09544-5.","ama":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 2021;22:2627-2653. doi:10.1007/s11081-020-09544-5","ista":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. 2021. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 22, 2627–2653.","apa":"Shehu, Y., Dong, Q.-L., Liu, L.-L., & Yao, J.-C. (2021). New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. Springer Nature. https://doi.org/10.1007/s11081-020-09544-5","ieee":"Y. Shehu, Q.-L. Dong, L.-L. Liu, and J.-C. Yao, “New strong convergence method for the sum of two maximal monotone operators,” Optimization and Engineering, vol. 22. Springer Nature, pp. 2627–2653, 2021."},"article_type":"original","page":"2627-2653","date_published":"2021-02-25T00:00:00Z","scopus_import":"1","day":"25","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8196","ddc":["510"],"title":"New strong convergence method for the sum of two maximal monotone operators","status":"public","intvolume":" 22","file":[{"date_created":"2020-08-03T15:24:39Z","date_updated":"2020-08-03T15:24:39Z","success":1,"relation":"main_file","file_id":"8197","file_size":2137860,"content_type":"application/pdf","creator":"dernst","file_name":"2020_OptimizationEngineering_Shehu.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis.","lang":"eng"}]},{"article_type":"original","page":"926–943 ","publication":"Nature Reviews Materials","citation":{"chicago":"Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss, Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and Menno Veldhorst. “The Germanium Quantum Information Route.” Nature Reviews Materials. Springer Nature, 2021. https://doi.org/10.1038/s41578-020-00262-z.","short":"G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang, S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021) 926–943.","mla":"Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” Nature Reviews Materials, vol. 6, Springer Nature, 2021, pp. 926–943, doi:10.1038/s41578-020-00262-z.","apa":"Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang, J.-J., … Veldhorst, M. (2021). The germanium quantum information route. Nature Reviews Materials. Springer Nature. https://doi.org/10.1038/s41578-020-00262-z","ieee":"G. Scappucci et al., “The germanium quantum information route,” Nature Reviews Materials, vol. 6. Springer Nature, pp. 926–943, 2021.","ista":"Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature Reviews Materials. 6, 926–943.","ama":"Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information route. Nature Reviews Materials. 2021;6:926–943. doi:10.1038/s41578-020-00262-z"},"date_published":"2021-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"The germanium quantum information route","status":"public","intvolume":" 6","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8911","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects\r\ntoward scalable quantum information processing. "}],"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425"},{"grant_number":"Y00715","_id":"2552F888-B435-11E9-9278-68D0E5697425","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","call_identifier":"FWF"},{"name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.08133"}],"external_id":{"arxiv":["2004.08133"],"isi":["000600826100003"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41578-020-00262-z","month":"10","publication_identifier":{"eissn":["2058-8437"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GeKa"}],"year":"2021","acknowledgement":"G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under Grand Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497, FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge the Swiss National Science Foundation and NCCR QSIT.","date_updated":"2024-03-07T14:48:57Z","date_created":"2020-12-02T10:52:51Z","volume":6,"author":[{"first_name":"Giordano","last_name":"Scappucci","full_name":"Scappucci, Giordano"},{"first_name":"Christoph","last_name":"Kloeffel","full_name":"Kloeffel, Christoph"},{"full_name":"Zwanenburg, Floris A.","last_name":"Zwanenburg","first_name":"Floris A."},{"last_name":"Loss","first_name":"Daniel","full_name":"Loss, Daniel"},{"full_name":"Myronov, Maksym","last_name":"Myronov","first_name":"Maksym"},{"full_name":"Zhang, Jian-Jun","first_name":"Jian-Jun","last_name":"Zhang"},{"full_name":"Franceschi, Silvano De","first_name":"Silvano De","last_name":"Franceschi"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Veldhorst, Menno","first_name":"Menno","last_name":"Veldhorst"}],"ec_funded":1},{"acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”. W.K.S. was also supported by the Australian Research Council (DP1401000851). A.V.A. was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha).","year":"2021","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"full_name":"Bobenko, Alexander I.","last_name":"Bobenko","first_name":"Alexander I."},{"full_name":"Schief, Wolfgang K.","first_name":"Wolfgang K.","last_name":"Schief"},{"full_name":"Techter, Jan","last_name":"Techter","first_name":"Jan"}],"volume":66,"date_updated":"2024-03-07T14:51:11Z","date_created":"2020-09-06T22:01:13Z","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.00856"}],"oa":1,"external_id":{"arxiv":["1908.00856"],"isi":["000564488500002"]},"project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00454-020-00240-w","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8338","intvolume":" 66","status":"public","title":"On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Canonical parametrisations of classical confocal coordinate systems are introduced and exploited to construct non-planar analogues of incircular (IC) nets on individual quadrics and systems of confocal quadrics. Intimate connections with classical deformations of quadrics that are isometric along asymptotic lines and circular cross-sections of quadrics are revealed. The existence of octahedral webs of surfaces of Blaschke type generated by asymptotic and characteristic lines that are diagonally related to lines of curvature is proved theoretically and established constructively. Appropriate samplings (grids) of these webs lead to three-dimensional extensions of non-planar IC nets. Three-dimensional octahedral grids composed of planes and spatially extending (checkerboard) IC-nets are shown to arise in connection with systems of confocal quadrics in Minkowski space. In this context, the Laguerre geometric notion of conical octahedral grids of planes is introduced. The latter generalise the octahedral grids derived from systems of confocal quadrics in Minkowski space. An explicit construction of conical octahedral grids is presented. The results are accompanied by various illustrations which are based on the explicit formulae provided by the theory.","lang":"eng"}],"citation":{"chicago":"Akopyan, Arseniy, Alexander I. Bobenko, Wolfgang K. Schief, and Jan Techter. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00240-w.","mla":"Akopyan, Arseniy, et al. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 938–76, doi:10.1007/s00454-020-00240-w.","short":"A. Akopyan, A.I. Bobenko, W.K. Schief, J. Techter, Discrete and Computational Geometry 66 (2021) 938–976.","ista":"Akopyan A, Bobenko AI, Schief WK, Techter J. 2021. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 66, 938–976.","apa":"Akopyan, A., Bobenko, A. I., Schief, W. K., & Techter, J. (2021). On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00240-w","ieee":"A. Akopyan, A. I. Bobenko, W. K. Schief, and J. Techter, “On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 938–976, 2021.","ama":"Akopyan A, Bobenko AI, Schief WK, Techter J. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 2021;66:938-976. doi:10.1007/s00454-020-00240-w"},"publication":"Discrete and Computational Geometry","page":"938-976","article_type":"original","date_published":"2021-10-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). We thank Mohsen Ghaffari, Michael Elkin and Merav Parter for fruitful discussions. This project has received funding from the European Union’s Horizon 2020 Research And Innovation Program under Grant Agreement No. 755839.","year":"2021","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"publication_status":"published","related_material":{"record":[{"id":"6933","relation":"earlier_version","status":"public"}]},"author":[{"last_name":"Censor-Hillel","first_name":"Keren","full_name":"Censor-Hillel, Keren"},{"first_name":"Michal","last_name":"Dory","full_name":"Dory, Michal"},{"id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne","last_name":"Korhonen","full_name":"Korhonen, Janne"},{"full_name":"Leitersdorf, Dean","first_name":"Dean","last_name":"Leitersdorf"}],"volume":34,"date_updated":"2024-03-07T14:43:39Z","date_created":"2020-06-07T22:00:54Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00446-020-00380-5"}],"external_id":{"isi":["000556444600001"],"arxiv":["1903.05956"]},"oa":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00446-020-00380-5","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"month":"12","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"7939","intvolume":" 34","title":"Fast approximate shortest paths in the congested clique","status":"public","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include:\r\n A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds. "}],"citation":{"short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, Distributed Computing 34 (2021) 463–487.","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing, vol. 34, Springer Nature, 2021, pp. 463–87, doi:10.1007/s00446-020-00380-5.","chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing. Springer Nature, 2021. https://doi.org/10.1007/s00446-020-00380-5.","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. Distributed Computing. 2021;34:463-487. doi:10.1007/s00446-020-00380-5","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2021). Fast approximate shortest paths in the congested clique. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-020-00380-5","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” Distributed Computing, vol. 34. Springer Nature, pp. 463–487, 2021.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2021. Fast approximate shortest paths in the congested clique. Distributed Computing. 34, 463–487."},"publication":"Distributed Computing","page":"463-487","article_type":"original","date_published":"2021-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","day":"01"},{"ec_funded":1,"volume":66,"date_updated":"2024-03-07T14:54:59Z","date_created":"2020-08-11T07:11:51Z","author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"first_name":"Ramsay","last_name":"Dyer","full_name":"Dyer, Ramsay"},{"full_name":"Ghosh, Arijit","first_name":"Arijit","last_name":"Ghosh"},{"full_name":"Lieutier, Andre","last_name":"Lieutier","first_name":"Andre"},{"orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","first_name":"Mathijs","full_name":"Wintraecken, Mathijs"}],"department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria). Arijit Ghosh is supported by the Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India.\r\nThis work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India. The fifth author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/s00454-020-00233-9","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00233-9","open_access":"1"}],"external_id":{"isi":["000558119300001"]},"abstract":[{"lang":"eng","text":"We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 66","ddc":["510"],"status":"public","title":"Local conditions for triangulating submanifolds of Euclidean space","_id":"8248","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2021-09-01T00:00:00Z","page":"666-686","article_type":"original","citation":{"ista":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. 2021. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 66, 666–686.","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, and M. Wintraecken, “Local conditions for triangulating submanifolds of Euclidean space,” Discrete and Computational Geometry, vol. 66. Springer Nature, pp. 666–686, 2021.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., Lieutier, A., & Wintraecken, M. (2021). Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00233-9","ama":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 2021;66:666-686. doi:10.1007/s00454-020-00233-9","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, Andre Lieutier, and Mathijs Wintraecken. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00233-9.","mla":"Boissonnat, Jean-Daniel, et al. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” Discrete and Computational Geometry, vol. 66, Springer Nature, 2021, pp. 666–86, doi:10.1007/s00454-020-00233-9.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete and Computational Geometry 66 (2021) 666–686."},"publication":"Discrete and Computational Geometry"},{"_id":"7883","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Regulation of size and scale in vertebrate spinal cord development","file":[{"file_size":2527276,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","checksum":"f0a7745d48afa09ea7025e876a0145a8","success":1,"date_updated":"2020-11-24T13:11:39Z","date_created":"2020-11-24T13:11:39Z","relation":"main_file","file_id":"8800"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","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."}],"citation":{"ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021.","apa":"Kuzmicz-Kowalska, K., & Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. Wiley. https://doi.org/10.1002/wdev.383","ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology. 2021. doi:10.1002/wdev.383","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology. Wiley, 2021. https://doi.org/10.1002/wdev.383.","mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental Biology, e383, Wiley, 2021, doi:10.1002/wdev.383.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021)."},"publication":"Wiley Interdisciplinary Reviews: Developmental Biology","article_type":"original","date_published":"2021-04-15T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"15","pmid":1,"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","year":"2021","department":[{"_id":"AnKi"}],"publisher":"Wiley","publication_status":"published","related_material":{"record":[{"id":"14323","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","full_name":"Kuzmicz-Kowalska, Katarzyna"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna"}],"date_created":"2020-05-24T22:01:00Z","date_updated":"2024-03-07T15:03:00Z","article_number":"e383","ec_funded":1,"file_date_updated":"2020-11-24T13:11:39Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32391980"],"isi":["000531419400001"]},"oa":1,"project":[{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Morphogen control of growth and pattern in the spinal cord"}],"quality_controlled":"1","isi":1,"doi":"10.1002/wdev.383","language":[{"iso":"eng"}],"publication_identifier":{"issn":["17597684"],"eissn":["17597692"]},"month":"04"},{"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was partially supported by NSF IIS-1513616 and NSF ABI-1661375. The authors would like to thank the anonymous referees for their insightful comments.","year":"2021","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"author":[{"id":"70B7FDF6-608D-11E9-9333-8535E6697425","last_name":"Brown","first_name":"Adam","full_name":"Brown, Adam"},{"full_name":"Wang, Bei","last_name":"Wang","first_name":"Bei"}],"date_created":"2020-05-30T10:26:04Z","date_updated":"2024-03-07T15:01:58Z","volume":65,"file_date_updated":"2020-11-25T09:06:41Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1712.07734"],"isi":["000536324700001"]},"isi":1,"quality_controlled":"1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"doi":"10.1007/s00454-020-00206-y","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"_id":"7905","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"status":"public","title":"Sheaf-theoretic stratification learning from geometric and topological perspectives","intvolume":" 65","oa_version":"Published Version","file":[{"file_id":"8803","relation":"main_file","date_created":"2020-11-25T09:06:41Z","date_updated":"2020-11-25T09:06:41Z","success":1,"checksum":"487a84ea5841b75f04f66d7ebd71b67e","file_name":"2020_DiscreteCompGeometry_Brown.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1013730}],"type":"journal_article","abstract":[{"lang":"eng","text":"We investigate a sheaf-theoretic interpretation of stratification learning from geometric and topological perspectives. Our main result is the construction of stratification learning algorithms framed in terms of a sheaf on a partially ordered set with the Alexandroff topology. We prove that the resulting decomposition is the unique minimal stratification for which the strata are homogeneous and the given sheaf is constructible. In particular, when we choose to work with the local homology sheaf, our algorithm gives an alternative to the local homology transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2), 195–222, 2020). Additionally, we give examples of stratifications based on the geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018), illustrating how the sheaf-theoretic approach can be used to study stratifications from both topological and geometric perspectives. This approach also points toward future applications of sheaf theory in the study of topological data analysis by illustrating the utility of the language of sheaf theory in generalizing existing algorithms."}],"publication":"Discrete and Computational Geometry","citation":{"mla":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry, vol. 65, Springer Nature, 2021, pp. 1166–98, doi:10.1007/s00454-020-00206-y.","short":"A. Brown, B. Wang, Discrete and Computational Geometry 65 (2021) 1166–1198.","chicago":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00206-y.","ama":"Brown A, Wang B. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 2021;65:1166-1198. doi:10.1007/s00454-020-00206-y","ista":"Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198.","apa":"Brown, A., & Wang, B. (2021). Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00206-y","ieee":"A. Brown and B. Wang, “Sheaf-theoretic stratification learning from geometric and topological perspectives,” Discrete and Computational Geometry, vol. 65. Springer Nature, pp. 1166–1198, 2021."},"article_type":"original","page":"1166-1198","date_published":"2021-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"date_published":"2021-02-01T00:00:00Z","article_type":"original","publication":"Probability Theory and Related Fields","citation":{"ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian random matrices,” Probability Theory and Related Fields. Springer Nature, 2021.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-020-01003-7","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields.","ama":"Cipolloni G, Erdös L, Schröder DJ. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields. 2021. doi:10.1007/s00440-020-01003-7","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields. Springer Nature, 2021. https://doi.org/10.1007/s00440-020-01003-7.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2021).","mla":"Cipolloni, Giorgio, et al. “Edge Universality for Non-Hermitian Random Matrices.” Probability Theory and Related Fields, Springer Nature, 2021, doi:10.1007/s00440-020-01003-7."},"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2020_ProbTheory_Cipolloni.pdf","access_level":"open_access","content_type":"application/pdf","file_size":497032,"creator":"dernst","relation":"main_file","file_id":"8612","date_updated":"2020-10-05T14:53:40Z","date_created":"2020-10-05T14:53:40Z","checksum":"611ae28d6055e1e298d53a57beb05ef4","success":1}],"ddc":["510"],"title":"Edge universality for non-Hermitian random matrices","status":"public","_id":"8601","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider large non-Hermitian real or complex random matrices X with independent, identically distributed centred entries. We prove that their local eigenvalue statistics near the spectral edge, the unit circle, coincide with those of the Ginibre ensemble, i.e. when the matrix elements of X are Gaussian. This result is the non-Hermitian counterpart of the universality of the Tracy–Widom distribution at the spectral edges of the Wigner ensemble."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s00440-020-01003-7","isi":1,"quality_controlled":"1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"external_id":{"isi":["000572724600002"],"arxiv":["1908.00969"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"02","publication_identifier":{"issn":["01788051"],"eissn":["14322064"]},"date_created":"2020-10-04T22:01:37Z","date_updated":"2024-03-07T15:07:53Z","author":[{"last_name":"Cipolloni","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"LaEr"}],"year":"2021","file_date_updated":"2020-10-05T14:53:40Z","ec_funded":1},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","page":"2109-2126","article_type":"original","citation":{"ama":"Shehu Y, Gibali A. New inertial relaxed method for solving split feasibilities. Optimization Letters. 2021;15:2109-2126. doi:10.1007/s11590-020-01603-1","ieee":"Y. Shehu and A. Gibali, “New inertial relaxed method for solving split feasibilities,” Optimization Letters, vol. 15. Springer Nature, pp. 2109–2126, 2021.","apa":"Shehu, Y., & Gibali, A. (2021). New inertial relaxed method for solving split feasibilities. Optimization Letters. Springer Nature. https://doi.org/10.1007/s11590-020-01603-1","ista":"Shehu Y, Gibali A. 2021. New inertial relaxed method for solving split feasibilities. Optimization Letters. 15, 2109–2126.","short":"Y. Shehu, A. Gibali, Optimization Letters 15 (2021) 2109–2126.","mla":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters, vol. 15, Springer Nature, 2021, pp. 2109–26, doi:10.1007/s11590-020-01603-1.","chicago":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” Optimization Letters. Springer Nature, 2021. https://doi.org/10.1007/s11590-020-01603-1."},"publication":"Optimization Letters","date_published":"2021-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper, we introduce a relaxed CQ method with alternated inertial step for solving split feasibility problems. We give convergence of the sequence generated by our method under some suitable assumptions. Some numerical implementations from sparse signal and image deblurring are reported to show the efficiency of our method."}],"intvolume":" 15","ddc":["510"],"title":"New inertial relaxed method for solving split feasibilities","status":"public","_id":"7925","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"2021_OptimizationLetters_Shehu.pdf","access_level":"open_access","creator":"kschuh","file_size":2148882,"content_type":"application/pdf","file_id":"15089","relation":"main_file","date_updated":"2024-03-07T14:58:51Z","date_created":"2024-03-07T14:58:51Z","success":1,"checksum":"63c5f31cd04626152a19f97a2476281b"}],"publication_identifier":{"eissn":["1862-4480"],"issn":["1862-4472"]},"month":"09","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000537342300001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11590-020-01603-1","ec_funded":1,"file_date_updated":"2024-03-07T14:58:51Z","department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are grateful to the referees for their insightful comments which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","volume":15,"date_updated":"2024-03-07T15:00:43Z","date_created":"2020-06-04T11:28:33Z","author":[{"full_name":"Shehu, Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","first_name":"Yekini","last_name":"Shehu"},{"first_name":"Aviv","last_name":"Gibali","full_name":"Gibali, Aviv"}]},{"date_published":"2021-07-08T00:00:00Z","publication":"Cell","citation":{"mla":"Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” Cell, vol. 184, no. 14, Elsevier, 2021, pp. 3599–611, doi:10.1016/j.cell.2021.05.029.","short":"A.K. Michael, N.H. Thomä, Cell 184 (2021) 3599–3611.","chicago":"Michael, Alicia K., and Nicolas H. Thomä. “Reading the Chromatinized Genome.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.05.029.","ama":"Michael AK, Thomä NH. Reading the chromatinized genome. Cell. 2021;184(14):3599-3611. doi:10.1016/j.cell.2021.05.029","ista":"Michael AK, Thomä NH. 2021. Reading the chromatinized genome. Cell. 184(14), 3599–3611.","apa":"Michael, A. K., & Thomä, N. H. (2021). Reading the chromatinized genome. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.05.029","ieee":"A. K. Michael and N. H. Thomä, “Reading the chromatinized genome,” Cell, vol. 184, no. 14. Elsevier, pp. 3599–3611, 2021."},"article_type":"review","page":"3599-3611","day":"08","article_processing_charge":"No","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology"],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15151","title":"Reading the chromatinized genome","status":"public","intvolume":" 184","abstract":[{"text":"Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core, thereby rendering a large fraction of the DNA surface inaccessible to DNA-binding proteins. Nevertheless, first responders in DNA repair and sequence-specific transcription factors bind DNA target sites obstructed by chromatin. While early studies examined protein binding to histone-free DNA, it is only now beginning to emerge how DNA sequences are interrogated on nucleosomes. These readout strategies range from the release of nucleosomal DNA from histones, to rotational/translation register shifts of the DNA motif, and nucleosome-specific DNA binding modes that differ from those observed on naked DNA. Since DNA motif engagement on nucleosomes strongly depends on position and orientation, we argue that motif location and nucleosome positioning co-determine protein access to DNA in transcription and DNA repair.","lang":"eng"}],"issue":"14","type":"journal_article","doi":"10.1016/j.cell.2021.05.029","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2021.05.029","open_access":"1"}],"quality_controlled":"1","month":"07","publication_identifier":{"issn":["0092-8674"]},"author":[{"full_name":"Michael, Alicia","orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","first_name":"Alicia"},{"full_name":"Thomä, Nicolas H.","last_name":"Thomä","first_name":"Nicolas H."}],"date_updated":"2024-03-25T12:31:39Z","date_created":"2024-03-21T07:54:19Z","volume":184,"year":"2021","publication_status":"published","publisher":"Elsevier","extern":"1"},{"issue":"6","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."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"VandaeletalAuthorVersion2021.pdf","file_size":38574802,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","embargo":"2021-12-01","file_id":"9639","checksum":"7eb580abd8893cdb0b410cf41bc8c263","date_updated":"2021-12-02T23:30:05Z","date_created":"2021-07-08T12:27:55Z"}],"oa_version":"Submitted Version","_id":"9438","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 16","title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","ddc":["570"],"status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2021-06-01T00:00:00Z","citation":{"chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:10.1038/s41596-021-00526-0.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0"},"publication":"Nature Protocols","page":"2947–2967","article_type":"original","ec_funded":1,"file_date_updated":"2021-12-02T23:30:05Z","author":[{"last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094","first_name":"Yuji","last_name":"Okamoto","full_name":"Okamoto, Yuji"},{"last_name":"Borges Merjane","first_name":"Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina"},{"full_name":"Vargas Barroso, Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","last_name":"Vargas Barroso","first_name":"Victor M"},{"orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","last_name":"Suter","first_name":"Benjamin","full_name":"Suter, Benjamin"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"volume":16,"date_updated":"2023-08-10T22:30:51Z","date_created":"2021-05-30T22:01:24Z","pmid":1,"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.","year":"2021","publisher":"Springer Nature","department":[{"_id":"PeJo"}],"publication_status":"published","publication_identifier":{"issn":["17542189"],"eissn":["17502799"]},"month":"06","doi":"10.1038/s41596-021-00526-0","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"oa":1,"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Structural plasticity at mossy fiber-CA3 synapses","call_identifier":"FWF","grant_number":"V00739","_id":"2696E7FE-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"date_updated":"2023-09-07T13:38:33Z","date_created":"2021-09-09T07:37:20Z","related_material":{"record":[{"id":"6351","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6943"},{"status":"public","relation":"part_of_dissertation","id":"8002"}]},"author":[{"full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","year":"2021","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2021-09-15T22:30:26Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:9992","project":[{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["2663-337X"]},"month":"09","file":[{"file_size":25179004,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"lhoermaye","embargo_to":"open_access","file_name":"Thesis_vupload.docx","access_level":"closed","date_created":"2021-09-09T07:29:48Z","date_updated":"2021-09-15T22:30:26Z","checksum":"c763064adaa720e16066c1a4f9682bbb","relation":"source_file","file_id":"9993"},{"file_id":"9996","embargo":"2021-09-09","relation":"main_file","date_updated":"2021-09-15T22:30:26Z","date_created":"2021-09-09T14:25:08Z","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","file_name":"Thesis_vfinal_pdfa.pdf","access_level":"open_access","creator":"lhoermaye","file_size":6246900,"content_type":"application/pdf"}],"oa_version":"Published Version","title":"Wound healing in the Arabidopsis root meristem","status":"public","ddc":["575"],"_id":"9992","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-09-13T00:00:00Z","page":"168","citation":{"ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","apa":"Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","mla":"Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992."},"article_processing_charge":"No","has_accepted_license":"1","day":"13"},{"file_date_updated":"2022-06-18T22:30:03Z","ec_funded":1,"author":[{"full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán","first_name":"José"},{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"full_name":"Espinoza Martinez, Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","first_name":"Claudia ","last_name":"Espinoza Martinez"},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Xiaomin","full_name":"Zhang, Xiaomin"},{"first_name":"Benjamin","last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936","full_name":"Suter, Benjamin"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"related_material":{"record":[{"relation":"software","status":"public","id":"10110"}],"link":[{"url":"https://ista.ac.at/en/news/spot-the-difference/","relation":"press_release"}]},"date_created":"2022-03-04T08:32:36Z","date_updated":"2023-08-10T22:30:10Z","volume":1,"acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","year":"2021","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Springer Nature","month":"12","publication_identifier":{"issn":["2662-8457"]},"doi":"10.1038/s43588-021-00157-1","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/647800","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}],"abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"issue":"12","type":"journal_article","file":[{"relation":"main_file","file_id":"11430","embargo":"2022-06-17","checksum":"9fec5b667909ef52be96d502e4f8c2ae","date_created":"2022-06-02T12:51:07Z","date_updated":"2022-06-18T22:30:03Z","access_level":"open_access","file_name":"Guzmanetal2021.pdf","content_type":"application/pdf","file_size":1699466,"creator":"patrickd"},{"relation":"supplementary_material","file_id":"11431","title":"Supplementary Material","embargo":"2022-06-17","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","date_created":"2022-06-02T12:53:47Z","date_updated":"2022-06-18T22:30:03Z","access_level":"open_access","file_name":"Guzmanetal2021Suppl.pdf","content_type":"application/pdf","file_size":3005651,"creator":"patrickd"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10816","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","ddc":["610"],"status":"public","intvolume":" 1","day":"16","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["general medicine"],"date_published":"2021-12-16T00:00:00Z","publication":"Nature Computational Science","citation":{"short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:10.1038/s43588-021-00157-1.","chicago":"Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 2021;1(12):830-842. doi:10.1038/s43588-021-00157-1","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 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Jonas, (2021).","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., & Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. https://doi.org/10.15479/AT:ISTA:10110","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110"},"oa":1,"has_accepted_license":"1","month":"12","day":"16","related_material":{"record":[{"id":"10816","status":"public","relation":"used_for_analysis_in"}],"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/spot-the-difference/"}]},"author":[{"last_name":"Guzmán","first_name":"José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José"},{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois"},{"full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","first_name":"Claudia "},{"full_name":"Zhang, Xiaomin","first_name":"Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","last_name":"Suter","first_name":"Benjamin","full_name":"Suter, Benjamin"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"file":[{"file_name":"patternseparation-main (1).zip","access_level":"open_access","content_type":"application/x-zip-compressed","file_size":332990101,"creator":"cchlebak","relation":"main_file","file_id":"10114","date_created":"2021-10-08T08:46:04Z","date_updated":"2021-10-08T08:46:04Z","checksum":"f92f8931cad0aa7e411c1715337bf408","success":1}],"date_updated":"2024-03-27T23:30:11Z","date_created":"2021-10-08T06:44:22Z","_id":"10110","year":"2021","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publisher":"IST Austria","ddc":["005"],"status":"public","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","file_date_updated":"2021-10-08T08:46:04Z","abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"license":"https://opensource.org/licenses/GPL-3.0","type":"software"},{"article_processing_charge":"No","day":"29","month":"09","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602."},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602"}],"oa":1,"publication":"bioRxiv","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"}],"doi":"10.1101/2021.09.28.460602","date_published":"2021-09-29T00:00:00Z","language":[{"iso":"eng"}],"type":"preprint","ec_funded":1,"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."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10077","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.","year":"2021","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","publication_status":"submitted","status":"public","related_material":{"record":[{"id":"11932","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"}],"oa_version":"Preprint","date_updated":"2024-03-27T23:30:16Z","date_created":"2021-10-04T06:23:34Z"},{"doi":"10.1038/s41557-021-00643-z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa":1,"external_id":{"pmid":["33723377"],"isi":["000629296400001"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"month":"03","author":[{"last_name":"Petit","first_name":"Yann K.","full_name":"Petit, Yann K."},{"full_name":"Mourad, Eléonore","first_name":"Eléonore","last_name":"Mourad"},{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"full_name":"Leypold, Christian","last_name":"Leypold","first_name":"Christian"},{"first_name":"Andreas","last_name":"Windischbacher","full_name":"Windischbacher, Andreas"},{"last_name":"Mijailovic","first_name":"Daniel","full_name":"Mijailovic, Daniel"},{"last_name":"Slugovc","first_name":"Christian","full_name":"Slugovc, Christian"},{"full_name":"Borisov, Sergey M.","first_name":"Sergey M.","last_name":"Borisov"},{"last_name":"Zojer","first_name":"Egbert","full_name":"Zojer, Egbert"},{"last_name":"Brutti","first_name":"Sergio","full_name":"Brutti, Sergio"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander"}],"volume":13,"date_created":"2021-03-16T11:12:20Z","date_updated":"2023-09-05T15:34:44Z","pmid":1,"year":"2021","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","department":[{"_id":"StFr"}],"publication_status":"published","file_date_updated":"2021-09-16T22:30:03Z","date_published":"2021-03-15T00:00:00Z","citation":{"ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 2021;13(5):465-471. doi:10.1038/s41557-021-00643-z","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. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-021-00643-z","ieee":"Y. K. Petit et al., “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” Nature Chemistry, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature Chemistry, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:10.1038/s41557-021-00643-z.","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.","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.” Nature Chemistry. Springer Nature, 2021. https://doi.org/10.1038/s41557-021-00643-z."},"publication":"Nature Chemistry","page":"465-471","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1","keyword":["General Chemistry","General Chemical Engineering"],"oa_version":"Submitted Version","file":[{"date_created":"2021-03-22T11:46:00Z","date_updated":"2021-09-16T22:30:03Z","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","file_id":"9276","embargo":"2021-09-15","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1811448,"file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9250","intvolume":" 13","ddc":["540"],"title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","status":"public","issue":"5","abstract":[{"lang":"eng","text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate."}],"type":"journal_article"},{"article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-07-01T00:00:00Z","citation":{"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. https://doi.org/10.15479/at:ista:9623.","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.","mla":"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, doi:10.15479/at:ista:9623.","apa":"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. https://doi.org/10.15479/at:ista:9623","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.","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:10.15479/at:ista:9623"},"page":"111","abstract":[{"lang":"eng","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"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","file_id":"9624","checksum":"e039225a47ef32666d59bf35ddd30ecf","date_updated":"2022-07-02T22:30:06Z","date_created":"2021-07-01T14:48:54Z","access_level":"closed","embargo_to":"open_access","file_name":"PhDThesis_SCM.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":131946790,"creator":"scaballe"},{"creator":"scaballe","file_size":17094958,"content_type":"application/pdf","file_name":"PhDThesis_SCM.pdf","access_level":"open_access","date_created":"2021-07-01T14:46:25Z","date_updated":"2022-07-02T22:30:06Z","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","file_id":"9625","embargo":"2022-07-01","relation":"main_file"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9623","status":"public","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","ddc":["570"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-012-1"]},"month":"07","doi":"10.15479/at:ista:9623","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"file_date_updated":"2022-07-02T22:30:06Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9750"},{"id":"9006","status":"public","relation":"part_of_dissertation"}]},"author":[{"last_name":"Caballero Mancebo","first_name":"Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia"}],"date_updated":"2023-09-07T13:33:27Z","date_created":"2021-07-01T14:50:17Z","year":"2021","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published"},{"month":"01","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2020.12.002"}],"external_id":{"pmid":["33321104"],"isi":["000613273900009"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2020.12.002","publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Elsevier","acknowledgement":"We would like to thank Justine Renno for illustrations and Edouard Hannezo and members of the Heisenberg group for their comments on previous versions of the manuscript.","year":"2021","pmid":1,"date_updated":"2024-03-27T23:30:18Z","date_created":"2021-01-17T23:01:10Z","volume":56,"author":[{"first_name":"Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","first_name":"Silvia","full_name":"Caballero Mancebo, Silvia"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9623"}]},"scopus_import":"1","day":"25","article_processing_charge":"No","article_type":"original","page":"P213-226","publication":"Developmental Cell","citation":{"ama":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. Developmental Cell. 2021;56(2):P213-226. doi:10.1016/j.devcel.2020.12.002","ieee":"S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s got moves,” Developmental Cell, vol. 56, no. 2. Elsevier, pp. P213-226, 2021.","apa":"Shamipour, S., Caballero Mancebo, S., & Heisenberg, C.-P. J. (2021). Cytoplasm’s got moves. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.12.002","ista":"Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves. Developmental Cell. 56(2), P213-226.","short":"S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell 56 (2021) P213-226.","mla":"Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” Developmental Cell, vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:10.1016/j.devcel.2020.12.002.","chicago":"Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg. “Cytoplasm’s Got Moves.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2020.12.002."},"date_published":"2021-01-25T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Cytoplasm is a gel-like crowded environment composed of various macromolecules, organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm is highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules are restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm at the microscopic scale, large-scale reorganization of the cytoplasm is essential for important cellular functions, such as cell division and polarization. How such mesoscale reorganization of the cytoplasm is achieved, especially for large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, is only beginning to be understood. In this review, we will discuss recent advances in elucidating the molecular, cellular, and biophysical mechanisms by which the cytoskeleton drives cytoplasmic reorganization across different scales, structures, and species."}],"issue":"2","status":"public","title":"Cytoplasm's got moves","intvolume":" 56","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9006","oa_version":"Published Version"},{"article_number":"3058","ec_funded":1,"file_date_updated":"2021-05-28T12:39:43Z","publisher":"Springer Nature","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_status":"published","acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","year":"2021","volume":12,"date_created":"2021-05-28T11:49:46Z","date_updated":"2024-03-27T23:30:23Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7800"},{"id":"12401","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/","relation":"press_release"}]},"author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin"},{"full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Lena A"},{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","first_name":"Bernadette","last_name":"Basilico","full_name":"Basilico, Bernadette"},{"full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","last_name":"Tasciyan","first_name":"Saren"},{"full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161"},{"full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","last_name":"Nicolas"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M"},{"last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"full_name":"Dotter, Christoph","last_name":"Dotter","first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","last_name":"Knaus","full_name":"Knaus, Lisa"},{"first_name":"Zoe","last_name":"Dobler","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","full_name":"Dobler, Zoe"},{"full_name":"Cacci, Emanuele","first_name":"Emanuele","last_name":"Cacci"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"publication_identifier":{"eissn":["2041-1723"]},"month":"05","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Neural stem cells in autism and epilepsy"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000658769900010"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"}],"doi":"10.1038/s41467-021-23123-x","type":"journal_article","issue":"1","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."}],"intvolume":" 12","ddc":["572"],"title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9429","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9430","date_created":"2021-05-28T12:39:43Z","date_updated":"2021-05-28T12:39:43Z","checksum":"337e0f7959c35ec959984cacdcb472ba","success":1,"file_name":"2021_NatureCommunications_Morandell.pdf","access_level":"open_access","file_size":9358599,"content_type":"application/pdf","creator":"kschuh"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"has_accepted_license":"1","article_processing_charge":"No","day":"24","article_type":"original","citation":{"mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.","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).","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x","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.","ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23123-x"},"publication":"Nature Communications","date_published":"2021-05-24T00:00:00Z"},{"_id":"10058","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["621","539"],"title":"Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases","status":"public","file":[{"relation":"source_file","file_id":"10061","date_updated":"2022-12-20T23:30:07Z","date_created":"2021-09-30T14:29:14Z","checksum":"ad6bcb24083ed7c02baaf1885c9ea3d5","embargo_to":"open_access","file_name":"PHD_Thesis_Jirovec_Source.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":32397600,"creator":"djirovec"},{"relation":"main_file","embargo":"2022-10-06","file_id":"10087","date_created":"2021-10-05T07:56:49Z","date_updated":"2022-12-20T23:30:07Z","checksum":"5fbe08d4f66d1153e04c47971538fae8","file_name":"PHD_Thesis_pdfa2b_1.pdf","access_level":"open_access","content_type":"application/pdf","file_size":26910829,"creator":"djirovec"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments.","lang":"eng"}],"citation":{"chicago":"Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058.","short":"D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021.","mla":"Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.","ieee":"D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021.","apa":"Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058","ista":"Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria.","ama":"Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058"},"page":"151","date_published":"2021-10-05T00:00:00Z","keyword":["qubits","quantum computing","holes"],"day":"05","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation.","year":"2021","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Jirovec, Daniel","first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8831"},{"id":"10065","relation":"part_of_dissertation","status":"public"},{"id":"10066","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8909"},{"relation":"part_of_dissertation","status":"public","id":"5816"}]},"date_updated":"2023-09-08T11:41:08Z","date_created":"2021-09-30T07:53:49Z","file_date_updated":"2022-12-20T23:30:07Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:10058","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"supervisor":[{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["2663-337X"]}},{"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Nature Materials","citation":{"ama":"Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 2021;20(8):1106–1112. doi:10.1038/s41563-021-01022-2","ista":"Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M, Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin qubit in planar Ge. Nature Materials. 20(8), 1106–1112.","ieee":"D. Jirovec et al., “A singlet triplet hole spin qubit in planar Ge,” Nature Materials, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.","apa":"Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll, M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-021-01022-2","mla":"Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:10.1038/s41563-021-01022-2.","short":"D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll, A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez, M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials 20 (2021) 1106–1112.","chicago":"Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter, Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature Materials. Springer Nature, 2021. https://doi.org/10.1038/s41563-021-01022-2."},"article_type":"original","page":"1106–1112","date_published":"2021-08-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies."}],"issue":"8","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8909","title":"A singlet triplet hole spin qubit in planar Ge","status":"public","intvolume":" 20","oa_version":"Preprint","month":"08","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.13755"}],"external_id":{"isi":["000657596400001"],"arxiv":["2011.13755"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020","grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"doi":"10.1038/s41563-021-01022-2","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"ec_funded":1,"year":"2021","acknowledgement":"This research was supported by the Scientific Service Units of Institute of Science and Technology (IST) Austria through resources provided by the Miba Machine Shop and the nanofabrication facility, and was made possible with the support of the NOMIS Foundation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207 project. A.B. acknowledges support from the European Union Horizon 2020 FET project microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology (ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has been performed within the framework of the Universitat Autónoma de Barcelona Materials Science PhD programme. Part of the HAADF scanning transmission electron microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior Council of Scientific Research (CSIC) Research Platform on Quantum Technologies PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators (FI) PhD grant.","publication_status":"published","department":[{"_id":"GeKa"},{"_id":"NanoFab"},{"_id":"GradSch"}],"publisher":"Springer Nature","author":[{"first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"},{"full_name":"Hofmann, Andrea C","first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ballabio, Andrea","first_name":"Andrea","last_name":"Ballabio"},{"full_name":"Mutter, Philipp M.","last_name":"Mutter","first_name":"Philipp M."},{"first_name":"Giulio","last_name":"Tavani","full_name":"Tavani, Giulio"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"first_name":"Alessandro","last_name":"Crippa","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","orcid":"0000-0002-2968-611X","full_name":"Crippa, Alessandro"},{"full_name":"Kukucka, Josip","first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","last_name":"Sagi","full_name":"Sagi, Oliver"},{"full_name":"Martins, Frederico","last_name":"Martins","first_name":"Frederico","orcid":"0000-0003-2668-2401","id":"38F80F9A-1CB8-11EA-BC76-B49B3DDC885E"},{"last_name":"Saez Mollejo","first_name":"Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime"},{"full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","first_name":"Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Borovkov, Maksim","first_name":"Maksim","last_name":"Borovkov","id":"2ac7a0a2-3562-11eb-9256-fbd18ea55087"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"related_material":{"record":[{"id":"9323","status":"public","relation":"research_data"},{"id":"10058","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/quantum-computing-with-holes/"}]},"date_updated":"2024-03-27T23:30:26Z","date_created":"2020-12-02T10:50:47Z","volume":20},{"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","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","file_id":"9398","checksum":"7f98532f5324a0b2f3fa8de2967baa19","date_created":"2021-05-17T12:29:12Z","date_updated":"2022-05-21T22:30:04Z","access_level":"closed","embargo_to":"open_access","file_name":"KHuljev_Thesis_corrections.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":47799741,"creator":"khuljev"},{"content_type":"application/pdf","file_size":16542131,"creator":"khuljev","access_level":"open_access","file_name":"new_KHuljev_Thesis_corrections.pdf","checksum":"bf512f8a1e572a543778fc4b227c01ba","date_updated":"2022-05-21T22:30:04Z","date_created":"2021-05-18T14:50:28Z","relation":"main_file","file_id":"9401","embargo":"2022-05-20"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9397","title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","status":"public","ddc":["571"],"day":"18","article_processing_charge":"No","has_accepted_license":"1","date_published":"2021-05-18T00:00:00Z","citation":{"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. https://doi.org/10.15479/at:ista:9397.","mla":"Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.","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.","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.","apa":"Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397","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.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397"},"page":"101","file_date_updated":"2022-05-21T22:30:04Z","author":[{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla"}],"date_updated":"2023-09-07T13:32:32Z","date_created":"2021-05-17T12:31:30Z","year":"2021","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","month":"05","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:9397","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1},{"project":[{"grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells"}],"publication":"arXiv","external_id":{"arxiv":["2107.12975"]},"citation":{"mla":"Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, 2107.12975, doi:10.48550/arXiv.2107.12975.","short":"B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec, A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab, A.V. Kuhlmann, F.R. Braakman, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne, D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, ArXiv (n.d.).","chicago":"Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum Devices Using Machine Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2107.12975.","ama":"Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. doi:10.48550/arXiv.2107.12975","ista":"Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio A, Chrastina D, Isella G, Kruijf M de, Carballido MJ, Svab S, Kuhlmann AV, Braakman FR, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl DM, Briggs GAD, Ares N. Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv, 2107.12975.","ieee":"B. Severin et al., “Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning,” arXiv. .","apa":"Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec, D., … Ares, N. (n.d.). Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning. arXiv. https://doi.org/10.48550/arXiv.2107.12975"},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2107.12975","open_access":"1"}],"oa":1,"acknowledged_ssus":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2107.12975","date_published":"2021-07-27T00:00:00Z","day":"27","month":"07","article_processing_charge":"No","title":"Cross-architecture tuning of silicon and SiGe-based quantum devices using machine learning","status":"public","publication_status":"submitted","department":[{"_id":"GeKa"}],"year":"2021","_id":"10066","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven) for the fabrication of the Ge/Si nanowire. This work was supported by the Royal Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform Grant\r\n(EP/R029229/1), the European Research Council (Grant agreement 948932), the Swiss Nanoscience Institute, the\r\nNCCR SPIN, the EU H2020 European Microkelvin Platform EMP grant No. 824109, the Scientific Service Units\r\nof IST Austria through resources provided by the nanofabrication facility and, the FWF-P30207 project. This publication was also made possible through support from Templeton World Charity Foundation and John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the Templeton Foundations.","date_created":"2021-10-01T12:40:22Z","date_updated":"2024-03-27T23:30:26Z","oa_version":"Preprint","author":[{"full_name":"Severin, B.","last_name":"Severin","first_name":"B."},{"full_name":"Lennon, D. T.","first_name":"D. T.","last_name":"Lennon"},{"full_name":"Camenzind, L. C.","first_name":"L. C.","last_name":"Camenzind"},{"full_name":"Vigneau, F.","last_name":"Vigneau","first_name":"F."},{"first_name":"F.","last_name":"Fedele","full_name":"Fedele, F."},{"full_name":"Jirovec, Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","last_name":"Jirovec","first_name":"Daniel"},{"full_name":"Ballabio, A.","first_name":"A.","last_name":"Ballabio"},{"last_name":"Chrastina","first_name":"D.","full_name":"Chrastina, D."},{"full_name":"Isella, G.","first_name":"G.","last_name":"Isella"},{"last_name":"Kruijf","first_name":"M. de","full_name":"Kruijf, M. de"},{"full_name":"Carballido, M. J.","last_name":"Carballido","first_name":"M. J."},{"first_name":"S.","last_name":"Svab","full_name":"Svab, S."},{"full_name":"Kuhlmann, A. V.","last_name":"Kuhlmann","first_name":"A. V."},{"first_name":"F. R.","last_name":"Braakman","full_name":"Braakman, F. R."},{"full_name":"Geyer, S.","last_name":"Geyer","first_name":"S."},{"full_name":"Froning, F. N. M.","first_name":"F. N. M.","last_name":"Froning"},{"full_name":"Moon, H.","first_name":"H.","last_name":"Moon"},{"full_name":"Osborne, M. A.","last_name":"Osborne","first_name":"M. A."},{"full_name":"Sejdinovic, D.","last_name":"Sejdinovic","first_name":"D."},{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"},{"last_name":"Zumbühl","first_name":"D. M.","full_name":"Zumbühl, D. M."},{"full_name":"Briggs, G. A. D.","last_name":"Briggs","first_name":"G. A. D."},{"full_name":"Ares, N.","first_name":"N.","last_name":"Ares"}],"related_material":{"record":[{"id":"10058","relation":"dissertation_contains","status":"public"}]},"article_number":"2107.12975","type":"preprint","abstract":[{"lang":"eng","text":"The potential of Si and SiGe-based devices for the scaling of quantum circuits is tainted by device variability. Each device needs to be tuned to operation conditions. We give a key step towards tackling this variability with an algorithm that, without modification, is capable of tuning a 4-gate Si FinFET, a 5-gate GeSi nanowire and a 7-gate SiGe heterostructure double quantum dot device from scratch. We achieve tuning times of 30, 10, and 92 minutes, respectively. The algorithm also provides insight into the parameter space landscape for each of these devices. These results show that overarching solutions for the tuning of quantum devices are enabled by machine learning."}]},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"29","citation":{"ista":"Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D, Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B, Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.","apa":"Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst, D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. ELife. eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274","ieee":"P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals,” eLife, vol. 10. eLife Sciences Publications, 2021.","ama":"Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife. 2021;10. doi:10.7554/ELIFE.68274","chicago":"Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274.","mla":"Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife Sciences Publications, 2021, doi:10.7554/ELIFE.68274.","short":"P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst, H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B. Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021)."},"publication":"eLife","article_type":"original","date_published":"2021-04-29T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation."}],"_id":"9437","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 10","title":"GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals","ddc":["570"],"status":"public","file":[{"relation":"main_file","file_id":"9440","checksum":"6ebcb79999f889766f7cd79ee134ad28","success":1,"date_created":"2021-05-31T09:43:09Z","date_updated":"2021-05-31T09:43:09Z","access_level":"open_access","file_name":"2021_eLife_Bhandari.pdf","file_size":8174719,"content_type":"application/pdf","creator":"cziletti"}],"oa_version":"Published Version","publication_identifier":{"eissn":["2050-084X"]},"month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000651761700001"]},"oa":1,"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"isi":1,"quality_controlled":"1","doi":"10.7554/ELIFE.68274","language":[{"iso":"eng"}],"article_number":"e68274","ec_funded":1,"file_date_updated":"2021-05-31T09:43:09Z","acknowledgement":"We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided by Tsutomu Tanabe. This project has received funding from the European Research Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020 research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto, no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385 to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.","year":"2021","department":[{"_id":"RySh"},{"_id":"PeJo"}],"publisher":"eLife Sciences Publications","publication_status":"published","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.04.16.045112"}],"record":[{"id":"9562","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Bhandari","first_name":"Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep"},{"full_name":"Vandael, David H","last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fernández-Fernández","first_name":"Diego","full_name":"Fernández-Fernández, Diego"},{"full_name":"Fritzius, Thorsten","last_name":"Fritzius","first_name":"Thorsten"},{"full_name":"Kleindienst, David","first_name":"David","last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Önal","first_name":"Hüseyin C","orcid":"0000-0002-2771-2011","id":"4659D740-F248-11E8-B48F-1D18A9856A87","full_name":"Önal, Hüseyin C"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"first_name":"Martin","last_name":"Gassmann","full_name":"Gassmann, Martin"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"last_name":"Kulik","first_name":"Akos","full_name":"Kulik, Akos"},{"last_name":"Bettler","first_name":"Bernhard","full_name":"Bettler, Bernhard"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","first_name":"Peter","last_name":"Koppensteiner"}],"volume":10,"date_updated":"2024-03-27T23:30:30Z","date_created":"2021-05-30T22:01:23Z"},{"date_updated":"2023-09-11T12:55:53Z","date_created":"2021-06-17T14:10:47Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9756"},{"status":"public","relation":"part_of_dissertation","id":"9437"},{"relation":"part_of_dissertation","status":"public","id":"8532"},{"status":"public","relation":"part_of_dissertation","id":"612"}]},"author":[{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","last_name":"Kleindienst","first_name":"David"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","file_date_updated":"2022-07-02T22:30:04Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.15479/at:ista:9562","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"06","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Thesis.pdf","file_size":77299142,"content_type":"application/pdf","creator":"dkleindienst","relation":"main_file","embargo":"2022-07-01","file_id":"9563","checksum":"659df5518db495f679cb1df9e9bd1d94","date_updated":"2022-07-02T22:30:04Z","date_created":"2021-06-17T14:03:14Z"},{"access_level":"closed","file_name":"Thesis_source.zip","embargo_to":"open_access","creator":"dkleindienst","file_size":369804895,"content_type":"application/zip","file_id":"9564","relation":"source_file","checksum":"3bcf63a2b19e5b6663be051bea332748","date_created":"2021-06-17T14:04:30Z","date_updated":"2022-07-02T22:30:04Z"}],"status":"public","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9562","abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2021-06-01T00:00:00Z","page":"124","citation":{"short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","mla":"Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562","ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","apa":"Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria."},"article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.","lang":"eng"}],"_id":"8934","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Parameterized and algebro-geometric advances in static program analysis","ddc":["005"],"file":[{"content_type":"application/pdf","file_size":5251507,"creator":"akafshda","access_level":"open_access","file_name":"Thesis-pdfa.pdf","checksum":"d1b9db3725aed34dadd81274aeb9426c","date_updated":"2021-12-23T23:30:04Z","date_created":"2020-12-22T20:08:44Z","relation":"main_file","embargo":"2021-12-22","file_id":"8969"},{"creator":"akafshda","file_size":10636756,"content_type":"application/zip","access_level":"closed","file_name":"source.zip","embargo_to":"open_access","checksum":"1661df7b393e6866d2460eba3c905130","date_updated":"2021-03-04T23:30:04Z","date_created":"2020-12-22T20:08:50Z","file_id":"8970","relation":"source_file"}],"oa_version":"Published Version","day":"01","has_accepted_license":"1","article_processing_charge":"No","citation":{"mla":"Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934.","short":"A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021.","chicago":"Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934.","ama":"Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934","ista":"Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria.","ieee":"A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021.","apa":"Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934"},"page":"278","date_published":"2021-01-01T00:00:00Z","file_date_updated":"2021-12-23T23:30:04Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","acknowledgement":"The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).","year":"2021","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"}],"related_material":{"record":[{"id":"1386","relation":"part_of_dissertation","status":"public"},{"id":"1437","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"311"},{"id":"6056","relation":"part_of_dissertation","status":"public"},{"id":"6380","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"639"},{"id":"66","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6780"},{"relation":"part_of_dissertation","status":"public","id":"6918"},{"status":"public","relation":"part_of_dissertation","id":"7810"},{"relation":"part_of_dissertation","status":"public","id":"6175"},{"status":"public","relation":"part_of_dissertation","id":"6378"},{"id":"6490","status":"public","relation":"part_of_dissertation"},{"id":"7014","status":"public","relation":"part_of_dissertation"},{"id":"8089","status":"public","relation":"part_of_dissertation"},{"id":"8728","relation":"part_of_dissertation","status":"public"},{"id":"7158","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"5977"},{"id":"6009","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6340"},{"id":"949","relation":"part_of_dissertation","status":"public"}]},"date_created":"2020-12-10T12:17:07Z","date_updated":"2023-09-22T10:03:21Z","month":"01","publication_identifier":{"issn":["2663-337X"]},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:8934","degree_awarded":"PhD","supervisor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"language":[{"iso":"eng"}]},{"citation":{"short":"K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021.","mla":"Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.","chicago":"Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.","ama":"Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307","ieee":"K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021.","apa":"Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307","ista":"Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria."},"page":"73","date_published":"2021-11-18T00:00:00Z","day":"18","article_processing_charge":"No","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10307","status":"public","title":"Pathogenic Escherichia coli hijack the host immune response","ddc":["570"],"oa_version":"Published Version","file":[{"file_name":"ThesisTomasekKathrin.pdf","access_level":"open_access","content_type":"application/pdf","file_size":13266088,"creator":"ktomasek","relation":"main_file","file_id":"10308","embargo":"2022-11-18","date_created":"2021-11-18T15:07:31Z","date_updated":"2022-12-20T23:30:05Z","checksum":"b39c9e0ef18d0484d537a67551effd02"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":7539509,"creator":"ktomasek","access_level":"closed","embargo_to":"open_access","file_name":"ThesisTomasekKathrin.docx","checksum":"c0c440ee9e5ef1102a518a4f9f023e7c","date_updated":"2022-12-20T23:30:05Z","date_created":"2021-11-18T15:07:46Z","relation":"source_file","file_id":"10309"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response."}],"oa":1,"doi":"10.15479/at:ista:10307","degree_awarded":"PhD","supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["2663-337X"]},"year":"2021","publication_status":"published","department":[{"_id":"MiSi"},{"_id":"CaGu"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10316"}]},"date_created":"2021-11-18T15:05:06Z","date_updated":"2023-09-07T13:34:38Z","file_date_updated":"2022-12-20T23:30:05Z"},{"date_published":"2021-10-18T00:00:00Z","doi":"10.1101/2021.10.18.464770","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"publication":"bioRxiv","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1"}],"oa":1,"citation":{"ista":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv, 10.1101/2021.10.18.464770.","apa":"Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., & Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.10.18.464770","ieee":"K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M. K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14,” bioRxiv. Cold Spring Harbor Laboratory.","ama":"Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. bioRxiv. doi:10.1101/2021.10.18.464770","chicago":"Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch, Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770.","mla":"Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.10.18.464770.","short":"K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt, BioRxiv (n.d.)."},"project":[{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"},{"_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","call_identifier":"FWF"}],"month":"10","day":"18","article_processing_charge":"No","author":[{"first_name":"Kathrin","last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin"},{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","first_name":"Alexander F","last_name":"Leithner"},{"full_name":"Glatzová, Ivana","id":"727b3c7d-4939-11ec-89b3-b9b0750ab74d","first_name":"Ivana","last_name":"Glatzová"},{"last_name":"Lukesch","first_name":"Michael S.","full_name":"Lukesch, Michael S."},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"11843","status":"public","relation":"later_version"},{"id":"10307","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-27T23:30:35Z","date_created":"2021-11-19T12:24:16Z","oa_version":"Preprint","_id":"10316","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2021","acknowledgement":"We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis. We thank the IST Austria Scientific Service Units, especially the Bioimaging facility, the Preclinical facility and the Electron microscopy facility for technical support, Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions and Daria Siekhaus for critically reading the manuscript. This work was supported by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G., the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911) to M.S.","title":"Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14","publication_status":"submitted","status":"public","department":[{"_id":"CaGu"},{"_id":"MiSi"}],"publisher":"Cold Spring Harbor Laboratory","abstract":[{"lang":"eng","text":"A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on dendritic cells as a previously undescribed binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced dendritic cell migration and blunted expression of co-stimulatory molecules, both rate-limiting factors of T cell activation. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease."}],"ec_funded":1,"type":"preprint"},{"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2021-02-01T00:00:00Z","publication":"EMBO Journal","citation":{"ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3). doi:10.15252/embj.2020106862","ieee":"K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo Press, 2021.","apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862, Embo Press, 2021, doi:10.15252/embj.2020106862.","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2020106862."},"article_type":"original","abstract":[{"text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.","lang":"eng"}],"issue":"3","type":"journal_article","file":[{"file_name":"2021_Embo_Otvos.pdf","access_level":"open_access","file_size":2358617,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"9110","date_created":"2021-02-11T12:28:29Z","date_updated":"2021-02-11T12:28:29Z","checksum":"dc55c900f3b061d6c2790b8813d759a3","success":1}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9010","title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","ddc":["580"],"status":"public","intvolume":" 40","month":"02","publication_identifier":{"eissn":["14602075"],"issn":["02614189"]},"doi":"10.15252/embj.2020106862","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000604645600001"],"pmid":[" 33399250"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"},{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"file_date_updated":"2021-02-11T12:28:29Z","article_number":"e106862","author":[{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","last_name":"Ötvös","first_name":"Krisztina"},{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"last_name":"Vega","first_name":"Andrea","full_name":"Vega, Andrea"},{"full_name":"O’Brien, Jose","first_name":"Jose","last_name":"O’Brien"},{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"full_name":"Abualia, Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","first_name":"Rashed","last_name":"Abualia"},{"full_name":"Antonielli, Livio","first_name":"Livio","last_name":"Antonielli"},{"full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","first_name":"Juan C","last_name":"Montesinos López"},{"full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","last_name":"Zhang"},{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan"},{"full_name":"Cuesta, Candela","last_name":"Cuesta","first_name":"Candela","orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner","first_name":"Christina","full_name":"Artner, Christina"},{"last_name":"Bouguyon","first_name":"Eleonore","full_name":"Bouguyon, Eleonore"},{"full_name":"Gojon, Alain","last_name":"Gojon","first_name":"Alain"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"last_name":"Gutiérrez","first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A."},{"full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/"}]},"date_created":"2021-01-17T23:01:12Z","date_updated":"2024-03-27T23:30:39Z","volume":40,"year":"2021","acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Embo Press"},{"author":[{"full_name":"Vega, Andrea","first_name":"Andrea","last_name":"Vega"},{"full_name":"Fredes, Isabel","first_name":"Isabel","last_name":"Fredes"},{"full_name":"O’Brien, José","first_name":"José","last_name":"O’Brien"},{"last_name":"Shen","first_name":"Zhouxin","full_name":"Shen, Zhouxin"},{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","last_name":"Ötvös","first_name":"Krisztina"},{"full_name":"Abualia, Rashed","first_name":"Rashed","last_name":"Abualia","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"last_name":"Briggs","first_name":"Steven P.","full_name":"Briggs, Steven P."},{"full_name":"Gutiérrez, Rodrigo A.","first_name":"Rodrigo A.","last_name":"Gutiérrez"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10303"}]},"date_updated":"2024-03-27T23:30:39Z","date_created":"2021-08-15T22:01:30Z","volume":22,"acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","year":"2021","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"file_date_updated":"2021-10-05T13:36:42Z","article_number":"e51813","doi":"10.15252/embr.202051813","language":[{"iso":"eng"}],"external_id":{"pmid":["34357701 "],"isi":["000681754200001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","month":"09","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"oa_version":"Published Version","file":[{"file_id":"10090","relation":"main_file","date_created":"2021-10-05T13:36:42Z","date_updated":"2021-10-05T13:36:42Z","success":1,"checksum":"750de03dc3b715c37090126c1548ba13","file_name":"2021_EmboR_Vega.pdf","access_level":"open_access","creator":"cchlebak","file_size":3144854,"content_type":"application/pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9913","status":"public","title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","ddc":["580"],"intvolume":" 22","abstract":[{"text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.","lang":"eng"}],"issue":"9","type":"journal_article","date_published":"2021-09-06T00:00:00Z","publication":"EMBO Reports","citation":{"ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 2021;22(9). doi:10.15252/embr.202051813","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813","ieee":"A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” EMBO Reports, vol. 22, no. 9. Wiley, 2021.","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22, no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813.","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).","chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813."},"article_type":"original","day":"06","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1"},{"abstract":[{"lang":"eng","text":"Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"date_updated":"2022-12-20T23:30:06Z","date_created":"2021-11-22T14:48:21Z","checksum":"dea38b98aa4da1cea03dcd0f10862818","file_id":"10331","embargo":"2022-11-23","relation":"main_file","creator":"rabualia","file_size":28005730,"content_type":"application/pdf","file_name":"AbualiaPhDthesisfinalv3.pdf","access_level":"open_access"},{"relation":"source_file","file_id":"10332","checksum":"4cd62da5ec5ba4c32e61f0f6d9e61920","date_updated":"2022-12-20T23:30:06Z","date_created":"2021-11-22T14:48:34Z","access_level":"closed","embargo_to":"open_access","file_name":"AbualiaPhDthesisfinalv3.docx","file_size":62841883,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"rabualia"}],"title":"Role of hormones in nitrate regulated growth","status":"public","ddc":["580","581"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10303","day":"22","has_accepted_license":"1","article_processing_charge":"No","date_published":"2021-11-22T00:00:00Z","page":"139","citation":{"ieee":"R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021.","apa":"Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303","ista":"Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria.","ama":"Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303","chicago":"Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.","short":"R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021.","mla":"Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303."},"file_date_updated":"2022-12-20T23:30:06Z","date_updated":"2023-09-19T14:42:45Z","date_created":"2021-11-18T11:20:59Z","author":[{"full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","first_name":"Rashed"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9010"},{"status":"public","relation":"part_of_dissertation","id":"9913"},{"relation":"part_of_dissertation","status":"public","id":"47"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"publisher":"Institute of Science and Technology Austria","year":"2021","month":"11","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10303","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"file_date_updated":"2022-09-03T22:30:04Z","date_created":"2021-08-29T12:36:50Z","date_updated":"2023-09-22T09:58:30Z","related_material":{"record":[{"id":"8569","relation":"part_of_dissertation","status":"public"},{"id":"960","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","publication_identifier":{"issn":["2663-337X"]},"month":"09","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"doi":"10.15479/at:ista:9962","project":[{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"source_file","file_id":"9971","date_updated":"2022-09-03T22:30:04Z","date_created":"2021-08-30T09:17:39Z","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","embargo_to":"open_access","file_name":"Thesis_Hansen.docx","access_level":"closed","file_size":10629190,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"ahansen"},{"file_id":"9972","embargo":"2022-09-02","relation":"main_file","date_created":"2021-08-30T09:29:44Z","date_updated":"2022-09-03T22:30:04Z","checksum":"204fa40321a1c6289b68c473634c4bf3","file_name":"Thesis_Hansen_PDFA-1a.pdf","access_level":"open_access","creator":"ahansen","content_type":"application/pdf","file_size":13457469}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9962","has_accepted_license":"1","article_processing_charge":"No","day":"02","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"date_published":"2021-09-02T00:00:00Z","page":"182","citation":{"mla":"Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962.","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","apa":"Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962","ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021."}},{"date_created":"2021-05-28T09:03:50Z","date_updated":"2023-10-18T08:20:59Z","volume":17,"author":[{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"publication_status":"published","publisher":"Nature Research","department":[{"_id":"MaSe"}],"year":"2021","acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","file_date_updated":"2021-12-02T23:30:03Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41567-021-01230-2","isi":1,"quality_controlled":"1","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"oa":1,"external_id":{"isi":["000655563800002"],"arxiv":["2011.09486"]},"month":"06","publication_identifier":{"eissn":["1745-2481"]},"oa_version":"Preprint","file":[{"access_level":"open_access","file_name":"RevisedQMBSreview.pdf","creator":"patrickd","file_size":10028836,"content_type":"application/pdf","file_id":"10026","embargo":"2021-12-01","relation":"main_file","checksum":"316ed42ea1b42b0f1a3025bb476266fc","date_updated":"2021-12-02T23:30:03Z","date_created":"2021-09-20T09:27:43Z"}],"status":"public","title":"Quantum many-body scars and weak breaking of ergodicity","ddc":["539"],"intvolume":" 17","_id":"9428","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology."}],"issue":"6","type":"journal_article","date_published":"2021-06-01T00:00:00Z","article_type":"review","page":"675–685","publication":"Nature Physics","citation":{"ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","apa":"Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research, 2021. https://doi.org/10.1038/s41567-021-01230-2."},"day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"oa_version":"Published Version","file":[{"checksum":"a7f2562bdca62d67dfa88e271b62a629","success":1,"date_created":"2021-02-04T07:49:25Z","date_updated":"2021-02-04T07:49:25Z","relation":"main_file","file_id":"9083","file_size":12563728,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2021_PlantScience_Gelova.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8931","status":"public","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","ddc":["580"],"intvolume":" 303","abstract":[{"lang":"eng","text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy."}],"type":"journal_article","date_published":"2021-02-01T00:00:00Z","publication":"Plant Science","citation":{"ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 2021;303. doi:10.1016/j.plantsci.2020.110750","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110750","ieee":"Z. Gelová et al., “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” Plant Science, vol. 303. Elsevier, 2021.","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science, vol. 303, 110750, Elsevier, 2021, doi:10.1016/j.plantsci.2020.110750.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” Plant Science. Elsevier, 2021. https://doi.org/10.1016/j.plantsci.2020.110750."},"article_type":"original","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"author":[{"orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","first_name":"Zuzana","full_name":"Gelová, Zuzana"},{"last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"full_name":"Brunoud, Géraldine","last_name":"Brunoud","first_name":"Géraldine"},{"orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","first_name":"Xixi","full_name":"Zhang, Xixi"},{"full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin"},{"full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","first_name":"Jaroslav","last_name":"Michalko"},{"full_name":"Pavlovicova, Zlata","first_name":"Zlata","last_name":"Pavlovicova"},{"first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hajny, Jakub","last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych"},{"full_name":"Xu, Tongda","first_name":"Tongda","last_name":"Xu"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"10083"}]},"date_updated":"2024-03-27T23:30:43Z","date_created":"2020-12-09T14:48:28Z","volume":303,"year":"2021","acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publisher":"Elsevier","file_date_updated":"2021-02-04T07:49:25Z","ec_funded":1,"article_number":"110750","doi":"10.1016/j.plantsci.2020.110750","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"month":"02","publication_identifier":{"issn":["0168-9452"]}},{"abstract":[{"text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. ","lang":"eng"}],"issue":"2","type":"journal_article","file":[{"checksum":"532bb9469d3b665907f06df8c383eade","success":1,"date_created":"2021-11-11T15:07:51Z","date_updated":"2021-11-11T15:07:51Z","relation":"main_file","file_id":"10273","file_size":2289127,"content_type":"application/pdf","creator":"cziletti","access_level":"open_access","file_name":"2021_PlantPhysio_Narasimhan.pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9287","status":"public","title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","ddc":["580"],"intvolume":" 186","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","date_published":"2021-06-01T00:00:00Z","publication":"Plant Physiology","citation":{"ieee":"M. Narasimhan et al., “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” Plant Physiology, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. Oxford University Press. https://doi.org/10.1093/plphys/kiab134","ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 2021;186(2):1122–1142. doi:10.1093/plphys/kiab134","chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology. Oxford University Press, 2021. https://doi.org/10.1093/plphys/kiab134.","short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” Plant Physiology, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:10.1093/plphys/kiab134."},"article_type":"original","page":"1122–1142","file_date_updated":"2021-11-11T15:07:51Z","ec_funded":1,"author":[{"full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C"},{"last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li"},{"full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Han, Huibin","first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Himschoot, E","last_name":"Himschoot","first_name":"E"},{"full_name":"Wang, R","last_name":"Wang","first_name":"R"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"last_name":"Sánchez-Simarro","first_name":"J","full_name":"Sánchez-Simarro, J"},{"full_name":"Aniento, F","last_name":"Aniento","first_name":"F"},{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek","full_name":"Adamowski, Maciek"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"related_material":{"link":[{"relation":"erratum","url":"10.1093/plphys/kiab380"}],"record":[{"relation":"dissertation_contains","status":"public","id":"11626"},{"id":"10083","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-27T23:30:43Z","date_created":"2021-03-26T12:08:38Z","volume":186,"acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","month":"06","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"doi":"10.1093/plphys/kiab134","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33734402"],"isi":["000671555900031"]},"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}]},{"file_date_updated":"2022-12-20T23:30:03Z","ec_funded":1,"year":"2021","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"author":[{"last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"442"},{"id":"8931","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9287"},{"relation":"part_of_dissertation","status":"public","id":"8283"},{"status":"public","relation":"part_of_dissertation","id":"8986"},{"id":"6627","status":"public","relation":"part_of_dissertation"},{"id":"10095","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10015"}]},"date_updated":"2023-10-31T19:30:02Z","date_created":"2021-10-04T13:33:10Z","month":"10","publication_identifier":{"issn":["2663-337X"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351"}],"doi":"10.15479/at:ista:10083","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. "}],"_id":"10083","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Rapid cell growth regulation in Arabidopsis","ddc":["575"],"oa_version":"Published Version","file":[{"date_created":"2021-10-14T08:00:07Z","date_updated":"2022-12-20T23:30:03Z","checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","file_id":"10138","embargo":"2022-10-14","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":8616142,"file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","access_level":"open_access"},{"relation":"source_file","file_id":"10139","checksum":"f23ed258ca894f6aabf58b0c128bf242","date_created":"2021-10-14T08:00:13Z","date_updated":"2022-12-20T23:30:03Z","access_level":"closed","embargo_to":"open_access","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","file_size":15058499,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak"}],"day":"06","has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083.","mla":"Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria.","apa":"Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083"},"date_published":"2021-10-06T00:00:00Z"},{"keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"day":"02","has_accepted_license":"1","article_processing_charge":"Yes","article_type":"original","publication":"Cells","citation":{"chicago":"Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071665.","mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” Cells, vol. 10, 1665, MDPI, 2021, doi:10.3390/cells10071665.","short":"N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L. Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg, P. Morris, Z. Ding, I. De Smet, Cells 10 (2021).","ista":"Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z, De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 10, 1665.","ieee":"N. Nikonorova et al., “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” Cells, vol. 10. MDPI, 2021.","apa":"Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B., Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. MDPI. https://doi.org/10.3390/cells10071665","ama":"Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 2021;10. doi:10.3390/cells10071665"},"date_published":"2021-07-02T00:00:00Z","alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"type":"journal_article","abstract":[{"text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip.","lang":"eng"}],"ddc":["575"],"title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","status":"public","intvolume":" 10","_id":"10015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":2667848,"file_name":"2021_Cells_Nikonorova.pdf","access_level":"open_access","date_updated":"2021-09-16T09:07:06Z","date_created":"2021-09-16T09:07:06Z","success":1,"checksum":"2a9f534b9c2200e72e2cde95afaf4eed","file_id":"10021","relation":"main_file"}],"month":"07","publication_identifier":{"issn":["2073-4409"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34359847"],"isi":["000676604700001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/cells10071665","article_number":"1665 ","file_date_updated":"2021-09-16T09:07:06Z","ec_funded":1,"publication_status":"published","publisher":"MDPI","department":[{"_id":"JiFr"}],"year":"2021","acknowledgement":"We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF).","pmid":1,"date_updated":"2024-03-27T23:30:43Z","date_created":"2021-09-14T11:36:20Z","volume":10,"author":[{"full_name":"Nikonorova, N","first_name":"N","last_name":"Nikonorova"},{"first_name":"E","last_name":"Murphy","full_name":"Murphy, E"},{"first_name":"CF","last_name":"Fonseca de Lima","full_name":"Fonseca de Lima, CF"},{"last_name":"Zhu","first_name":"S","full_name":"Zhu, S"},{"last_name":"van de Cotte","first_name":"B","full_name":"van de Cotte, B"},{"full_name":"Vu, LD","last_name":"Vu","first_name":"LD"},{"last_name":"Balcerowicz","first_name":"D","full_name":"Balcerowicz, D"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li"},{"last_name":"Kong","first_name":"X","full_name":"Kong, X"},{"full_name":"De Rop, G","last_name":"De Rop","first_name":"G"},{"last_name":"Beeckman","first_name":"T","full_name":"Beeckman, T"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"last_name":"Vissenberg","first_name":"K","full_name":"Vissenberg, K"},{"full_name":"Morris, PC","last_name":"Morris","first_name":"PC"},{"full_name":"Ding, Z","first_name":"Z","last_name":"Ding"},{"full_name":"De Smet, I","last_name":"De Smet","first_name":"I"}],"related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]}},{"date_updated":"2024-03-27T23:30:43Z","date_created":"2021-10-06T08:56:22Z","author":[{"last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge","full_name":"Verstraeten, Inge"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","first_name":"Lesia","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chen, Jian","last_name":"Chen","first_name":"Jian"},{"last_name":"Shabala","first_name":"Lana","full_name":"Shabala, Lana"},{"last_name":"Smet","first_name":"Wouter","full_name":"Smet, Wouter"},{"last_name":"Ren","first_name":"Hong","full_name":"Ren, Hong"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"full_name":"Gray, William M.","last_name":"Gray","first_name":"William M."},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"related_material":{"record":[{"id":"10223","relation":"later_version","status":"public"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"publication_status":"accepted","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","year":"2021","ec_funded":1,"article_number":"266395","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.21203/rs.3.rs-266395/v3","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"month":"09","publication_identifier":{"issn":["2693-5015"]},"oa_version":"Preprint","status":"public","title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","_id":"10095","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment."}],"type":"preprint","date_published":"2021-09-09T00:00:00Z","publication":"Research Square","citation":{"chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, n.d. https://doi.org/10.21203/rs.3.rs-266395/v3.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” Research Square, 266395, doi:10.21203/rs.3.rs-266395/v3.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” Research Square. .","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. https://doi.org/10.21203/rs.3.rs-266395/v3","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square. doi:10.21203/rs.3.rs-266395/v3"},"day":"09","article_processing_charge":"No"},{"day":"17","has_accepted_license":"1","article_processing_charge":"No","page":"171","citation":{"ista":"Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria.","ieee":"L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021.","apa":"Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293","ama":"Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293","chicago":"Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293.","mla":"Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293.","short":"L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021."},"date_published":"2021-11-17T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient.","lang":"eng"}],"status":"public","title":"Evolution of cooperation via (in)direct reciprocity under imperfect information","ddc":["519","576"],"_id":"10293","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"submission_new.zip","embargo_to":"open_access","access_level":"closed","creator":"lschmid","content_type":"application/zip","file_size":29703124,"file_id":"10305","relation":"source_file","date_updated":"2022-12-20T23:30:08Z","date_created":"2021-11-18T12:41:46Z","checksum":"86a05b430756ca12ae8107b6e6f3c1e5"},{"date_created":"2021-11-18T12:59:15Z","date_updated":"2022-12-20T23:30:08Z","checksum":"d940af042e94660c6b6a7b4f0b184d47","embargo":"2022-10-18","file_id":"10306","relation":"main_file","creator":"lschmid","content_type":"application/pdf","file_size":8320985,"file_name":"thesis_new_upload.pdf","access_level":"open_access"}],"oa_version":"Published Version","month":"11","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"oa":1,"supervisor":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:10293","file_date_updated":"2022-12-20T23:30:08Z","ec_funded":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","year":"2021","date_updated":"2023-11-07T08:28:29Z","date_created":"2021-11-15T17:12:57Z","author":[{"first_name":"Laura","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9997"},{"status":"public","relation":"part_of_dissertation","id":"2"},{"status":"public","relation":"part_of_dissertation","id":"9402"}]}},{"article_number":"17443","file_date_updated":"2021-09-13T10:31:21Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"year":"2021","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).","pmid":1,"date_created":"2021-09-11T16:22:02Z","date_updated":"2024-03-27T23:30:44Z","volume":11,"author":[{"orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","first_name":"Laura","full_name":"Schmid, Laura"},{"last_name":"Shati","first_name":"Pouya","full_name":"Shati, Pouya"},{"first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"related_material":{"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}]},"month":"08","publication_identifier":{"eissn":["2045-2322"]},"isi":1,"quality_controlled":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["34465830"],"isi":["000692406400018"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-021-96932-1","type":"journal_article","abstract":[{"lang":"eng","text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms."}],"issue":"1","status":"public","ddc":["003"],"title":"The evolution of indirect reciprocity under action and assessment generosity","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9997","file":[{"file_name":"2021_ScientificReports_Schmid.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":2424943,"file_id":"10006","relation":"main_file","date_created":"2021-09-13T10:31:21Z","date_updated":"2021-09-13T10:31:21Z","success":1,"checksum":"19df8816cf958b272b85841565c73182"}],"oa_version":"Published Version","keyword":["Multidisciplinary"],"day":"31","article_processing_charge":"Yes","has_accepted_license":"1","article_type":"original","publication":"Scientific Reports","citation":{"chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports. Springer Nature, 2021. https://doi.org/10.1038/s41598-021-96932-1.","mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” Scientific Reports, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:10.1038/s41598-021-96932-1.","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","ista":"Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443.","apa":"Schmid, L., Shati, P., Hilbe, C., & Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-96932-1","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.","ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-96932-1"},"date_published":"2021-08-31T00:00:00Z"},{"related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-emergence-of-cooperation/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"10293"}]},"author":[{"full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","first_name":"Laura","last_name":"Schmid"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"volume":5,"date_updated":"2024-03-27T23:30:44Z","date_created":"2021-05-18T16:56:57Z","pmid":1,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Start Grant 279307: Graph Games (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","year":"2021","publisher":"Springer Nature","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-11-07T08:27:23Z","doi":"10.1038/s41562-021-01114-8","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["33986519"],"isi":["000650304000002"]},"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2397-3374"]},"month":"05","oa_version":"Submitted Version","file":[{"creator":"dernst","file_size":5232761,"content_type":"application/pdf","file_name":"2021_NatureHumanBehaviour_Schmid_accepted.pdf","access_level":"open_access","date_created":"2023-11-07T08:27:23Z","date_updated":"2023-11-07T08:27:23Z","success":1,"checksum":"34f55e173f90dc1dab731063458ac780","file_id":"14496","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9402","intvolume":" 5","status":"public","ddc":["000"],"title":"A unified framework of direct and indirect reciprocity","issue":"10","abstract":[{"text":"Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability.","lang":"eng"}],"type":"journal_article","date_published":"2021-05-13T00:00:00Z","citation":{"short":"L. Schmid, K. Chatterjee, C. Hilbe, M.A. Nowak, Nature Human Behaviour 5 (2021) 1292–1302.","mla":"Schmid, Laura, et al. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour, vol. 5, no. 10, Springer Nature, 2021, pp. 1292–1302, doi:10.1038/s41562-021-01114-8.","chicago":"Schmid, Laura, Krishnendu Chatterjee, Christian Hilbe, and Martin A. Nowak. “A Unified Framework of Direct and Indirect Reciprocity.” Nature Human Behaviour. Springer Nature, 2021. https://doi.org/10.1038/s41562-021-01114-8.","ama":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 2021;5(10):1292–1302. doi:10.1038/s41562-021-01114-8","apa":"Schmid, L., Chatterjee, K., Hilbe, C., & Nowak, M. A. (2021). A unified framework of direct and indirect reciprocity. Nature Human Behaviour. Springer Nature. https://doi.org/10.1038/s41562-021-01114-8","ieee":"L. Schmid, K. Chatterjee, C. Hilbe, and M. A. Nowak, “A unified framework of direct and indirect reciprocity,” Nature Human Behaviour, vol. 5, no. 10. Springer Nature, pp. 1292–1302, 2021.","ista":"Schmid L, Chatterjee K, Hilbe C, Nowak MA. 2021. A unified framework of direct and indirect reciprocity. Nature Human Behaviour. 5(10), 1292–1302."},"publication":"Nature Human Behaviour","page":"1292–1302","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"13","scopus_import":"1"},{"_id":"9817","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 40","status":"public","title":"The design space of plane elastic curves","ddc":["516"],"oa_version":"Published Version","file":[{"creator":"chafner","file_size":17064290,"content_type":"application/pdf","file_name":"elastic-curves-paper.pdf","access_level":"open_access","date_created":"2021-10-18T10:42:15Z","date_updated":"2021-10-18T10:42:15Z","success":1,"checksum":"7e5d08ce46b0451b3102eacd3d00f85f","file_id":"10150","relation":"main_file"},{"access_level":"open_access","file_name":"elastic-curves-supp.pdf","creator":"chafner","content_type":"application/pdf","file_size":547156,"file_id":"10151","relation":"supplementary_material","checksum":"0088643478be7c01a703b5b10767348f","date_updated":"2021-10-18T10:42:22Z","date_created":"2021-10-18T10:42:22Z"}],"type":"journal_article","issue":"4","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."}],"citation":{"short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459800.","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459800.","ama":"Hafner C, Bickel B. The design space of plane elastic curves. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459800","apa":"Hafner, C., & Bickel, B. (2021). The design space of plane elastic curves. ACM Transactions on Graphics. Virtual: Association for Computing Machinery. https://doi.org/10.1145/3450626.3459800","ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126."},"publication":"ACM Transactions on Graphics","article_type":"original","date_published":"2021-07-19T00:00:00Z","scopus_import":"1","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"article_processing_charge":"No","has_accepted_license":"1","day":"19","year":"2021","acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","publication_status":"published","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","relation":"dissertation_contains","id":"12897"}]},"author":[{"last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"}],"volume":40,"date_created":"2021-08-08T22:01:26Z","date_updated":"2024-03-27T23:30:45Z","article_number":"126","ec_funded":1,"file_date_updated":"2021-10-18T10:42:22Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000674930900091"]},"project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1145/3450626.3459800","conference":{"location":"Virtual","start_date":"2021-08-09","end_date":"2021-08-13","name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"month":"07"}]