[{"_id":"6184","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Correlated random matrices: Band rigidity and edge universality","status":"public","intvolume":" 48","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models.","lang":"eng"}],"issue":"2","publication":"Annals of Probability","citation":{"ama":"Alt J, Erdös L, Krüger TH, Schröder DJ. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 2020;48(2):963-1001. doi:10.1214/19-AOP1379","ieee":"J. Alt, L. Erdös, T. H. Krüger, and D. J. Schröder, “Correlated random matrices: Band rigidity and edge universality,” Annals of Probability, vol. 48, no. 2. Institute of Mathematical Statistics, pp. 963–1001, 2020.","apa":"Alt, J., Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Correlated random matrices: Band rigidity and edge universality. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/19-AOP1379","ista":"Alt J, Erdös L, Krüger TH, Schröder DJ. 2020. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 48(2), 963–1001.","short":"J. Alt, L. Erdös, T.H. Krüger, D.J. Schröder, Annals of Probability 48 (2020) 963–1001.","mla":"Alt, Johannes, et al. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability, vol. 48, no. 2, Institute of Mathematical Statistics, 2020, pp. 963–1001, doi:10.1214/19-AOP1379.","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Dominik J Schröder. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/19-AOP1379."},"article_type":"original","page":"963-1001","date_published":"2020-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2020","publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"author":[{"full_name":"Alt, Johannes","first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297"},{"last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}],"related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"6179"}]},"date_updated":"2024-02-22T14:34:33Z","date_created":"2019-03-28T09:20:08Z","volume":48,"ec_funded":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.07744","open_access":"1"}],"external_id":{"isi":["000528269100013"],"arxiv":["1804.07744"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"doi":"10.1214/19-AOP1379","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0091-1798"]}},{"keyword":["Plant Science","Molecular Biology"],"has_accepted_license":"1","article_processing_charge":"No","day":"04","citation":{"mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012.","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012","ieee":"J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” Molecular Plant, vol. 13, no. 5. Elsevier, pp. 717–731, 2020."},"publication":"Molecular Plant","page":"717-731","article_type":"original","date_published":"2020-05-04T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15037","intvolume":" 13","ddc":["580"],"status":"public","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","file":[{"content_type":"application/pdf","file_size":3089212,"creator":"dernst","access_level":"open_access","file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","checksum":"c538a5008f7827f62d17d40a3bfabe65","success":1,"date_created":"2024-02-28T12:39:56Z","date_updated":"2024-02-28T12:39:56Z","relation":"main_file","file_id":"15038"}],"oa_version":"Published Version","publication_identifier":{"issn":["1674-2052"]},"month":"05","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":["32087370"]},"quality_controlled":"1","doi":"10.1016/j.molp.2020.02.012","language":[{"iso":"eng"}],"file_date_updated":"2024-02-28T12:39:56Z","pmid":1,"year":"2020","department":[{"_id":"EvBe"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Moulinier-Anzola, Jeanette","first_name":"Jeanette","last_name":"Moulinier-Anzola"},{"full_name":"Schwihla, Maximilian","last_name":"Schwihla","first_name":"Maximilian"},{"full_name":"De-Araújo, Lucinda","first_name":"Lucinda","last_name":"De-Araújo"},{"first_name":"Christina","last_name":"Artner","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina"},{"last_name":"Jörg","first_name":"Lisa","full_name":"Jörg, Lisa"},{"first_name":"Nataliia","last_name":"Konstantinova","full_name":"Konstantinova, Nataliia"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"},{"last_name":"Korbei","first_name":"Barbara","full_name":"Korbei, Barbara"}],"volume":13,"date_updated":"2024-02-28T12:41:52Z","date_created":"2024-02-28T08:55:56Z"},{"oa_version":"Published Version","title":"Molecular recognition at septin interfaces: The switches hold the key","status":"public","intvolume":" 432","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15036","abstract":[{"lang":"eng","text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed."}],"issue":"21","type":"journal_article","date_published":"2020-10-02T00:00:00Z","article_type":"original","page":"5784-5801","publication":"Journal of Molecular Biology","citation":{"mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801. doi:10.1016/j.jmb.2020.09.001","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","ieee":"H. V. D. Rosa et al., “Molecular recognition at septin interfaces: The switches hold the key,” Journal of Molecular Biology, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2020.09.001"},"day":"02","article_processing_charge":"No","keyword":["Molecular Biology","Structural Biology"],"date_created":"2024-02-28T08:50:34Z","date_updated":"2024-02-28T12:37:54Z","volume":432,"author":[{"full_name":"Rosa, Higor Vinícius Dias","last_name":"Rosa","first_name":"Higor Vinícius Dias"},{"last_name":"Leonardo","first_name":"Diego Antonio","full_name":"Leonardo, Diego Antonio"},{"full_name":"Brognara, Gabriel","last_name":"Brognara","first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"first_name":"José","last_name":"Brandão-Neto","full_name":"Brandão-Neto, José"},{"full_name":"D'Muniz Pereira, Humberto","last_name":"D'Muniz Pereira","first_name":"Humberto"},{"first_name":"Ana Paula Ulian","last_name":"Araújo","full_name":"Araújo, Ana Paula Ulian"},{"last_name":"Garratt","first_name":"Richard Charles","full_name":"Garratt, Richard Charles"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"MaLo"}],"year":"2020","pmid":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jmb.2020.09.001","quality_controlled":"1","external_id":{"pmid":["32910969"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.jmb.2020.09.001","open_access":"1"}],"oa":1,"month":"10","publication_identifier":{"issn":["0022-2836"]}},{"volume":39,"date_updated":"2024-02-28T12:57:31Z","date_created":"2020-09-13T22:01:18Z","author":[{"first_name":"Sadashige","last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","full_name":"Ishida, Sadashige"},{"last_name":"Synak","first_name":"Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87","full_name":"Synak, Peter"},{"last_name":"Narita","first_name":"Fumiya","full_name":"Narita, Fumiya"},{"full_name":"Hachisuka, Toshiya","last_name":"Hachisuka","first_name":"Toshiya"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"department":[{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","publication_status":"published","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","year":"2020","ec_funded":1,"file_date_updated":"2020-11-23T09:03:19Z","article_number":"31","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1145/3386569.3392405","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392405","open_access":"1"}],"external_id":{"isi":["000583700300004"]},"publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"month":"07","oa_version":"Submitted Version","file":[{"file_size":14935529,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_soapfilm_submitted.pdf","checksum":"813831ca91319d794d9748c276b24578","success":1,"date_created":"2020-11-23T09:03:19Z","date_updated":"2020-11-23T09:03:19Z","relation":"main_file","file_id":"8795"}],"intvolume":" 39","title":"A model for soap film dynamics with evolving thickness","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8384","issue":"4","abstract":[{"text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film.","lang":"eng"}],"type":"journal_article","date_published":"2020-07-08T00:00:00Z","article_type":"original","citation":{"mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392405.","short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392405.","ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392405","ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., & Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392405","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020."},"publication":"ACM Transactions on Graphics","has_accepted_license":"1","article_processing_charge":"No","day":"08","scopus_import":"1"},{"month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.05390"}],"external_id":{"arxiv":["1912.05390"],"isi":["000744436200015"]},"oa":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"doi":"10.1145/3350755.3400282","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","end_date":"2020-07-17","location":"Virtual Event, United States","start_date":"2020-07-15"},"language":[{"iso":"eng"}],"ec_funded":1,"year":"2020","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","publication_status":"published","related_material":{"record":[{"id":"9541","status":"public","relation":"later_version"}]},"author":[{"orcid":"0000-0002-5646-9524","first_name":"Artur","last_name":"Czumaj","full_name":"Czumaj, Artur"},{"full_name":"Davies, Peter","last_name":"Davies","first_name":"Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425"},{"first_name":"Merav","last_name":"Parter","full_name":"Parter, Merav"}],"date_created":"2020-05-06T08:53:34Z","date_updated":"2024-02-28T12:53:09Z","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” in Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Virtual Event, United States, 2020, no. 7, pp. 175–185.","apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for derandomizing massively parallel computation with low space. In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020) (pp. 175–185). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400282","ista":"Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing massively parallel computation with low space. Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on Parallelism in Algorithms and Architectures, 175–185.","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. In: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). Association for Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing Machinery, 2020, pp. 175–185.","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282."},"publication":"Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)","page":"175-185","date_published":"2020-07-01T00:00:00Z","type":"conference","issue":"7","abstract":[{"text":"The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space.\r\n\t\r\nRecent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \\emph{significant} global progress, i.e., progress towards solving the problem for the original input graph.\r\n\t\r\nUsing this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel et al. [DISC'17].","lang":"eng"}],"_id":"7802","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Graph sparsification for derandomizing massively parallel computation with low space","status":"public","oa_version":"Preprint"},{"type":"conference","abstract":[{"text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures.","lang":"eng"}],"status":"public","title":"Non-blocking interpolation search trees with doubly-logarithmic running time","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7636","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"19","page":"276-291","citation":{"ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:276-291. doi:10.1145/3332466.3374542","apa":"Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 276–291.","ista":"Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice of Parallel Programming, 276–291.","short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91, doi:10.1145/3332466.3374542.","chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542."},"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","date_published":"2020-02-19T00:00:00Z","ec_funded":1,"publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program, grant agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). ","year":"2020","date_updated":"2024-02-28T12:55:14Z","date_created":"2020-04-05T22:00:49Z","author":[{"last_name":"Brown","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"},{"last_name":"Prokopec","first_name":"Aleksandar","full_name":"Prokopec, Aleksandar"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"publication_identifier":{"isbn":["9781450368186"]},"month":"02","project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000564476500020"]},"main_file_link":[{"url":"https://doi.org/10.1145/3332466.3374542","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3332466.3374542","conference":{"name":"PPOPP: Principles and Practice of Parallel Programming","end_date":"2020-02-26","location":"San Diego, CA, United States","start_date":"2020-02-22"}},{"volume":39,"date_created":"2020-09-13T22:01:18Z","date_updated":"2024-02-28T12:57:47Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12358"}]},"author":[{"full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl","first_name":"Georg"},{"first_name":"Rahul","last_name":"Narain","full_name":"Narain, Rahul"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"publication_status":"published","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring discussions and help with Mathematica code generation. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","year":"2020","ec_funded":1,"file_date_updated":"2020-11-23T09:01:22Z","article_number":"48","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1145/3386569.3392412","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392412"}],"oa":1,"external_id":{"isi":["000583700300021"]},"publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"month":"07","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2020_hylc_submitted.pdf","creator":"dernst","file_size":38922662,"content_type":"application/pdf","file_id":"8794","relation":"main_file","success":1,"checksum":"cf4c1d361c3196c4bd424520a5588205","date_updated":"2020-11-23T09:01:22Z","date_created":"2020-11-23T09:01:22Z"}],"intvolume":" 39","title":"Homogenized yarn-level cloth","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8385","issue":"4","abstract":[{"lang":"eng","text":"We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver."}],"type":"journal_article","date_published":"2020-07-08T00:00:00Z","article_type":"original","citation":{"chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392412.","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","mla":"Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392412.","apa":"Sperl, G., Narain, R., & Wojtan, C. (2020). Homogenized yarn-level cloth. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392412","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48.","ama":"Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392412"},"publication":"ACM Transactions on Graphics","has_accepted_license":"1","article_processing_charge":"No","day":"08","scopus_import":"1"},{"ec_funded":1,"article_number":"204905","related_material":{"record":[{"id":"10759","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Pȩkalski, J.","first_name":"J.","last_name":"Pȩkalski"},{"first_name":"Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech"},{"full_name":"Panagiotopoulos, A. Z.","first_name":"A. Z.","last_name":"Panagiotopoulos"}],"volume":152,"date_created":"2020-06-14T22:00:49Z","date_updated":"2024-02-28T13:00:28Z","year":"2020","department":[{"_id":"MiLe"}],"publisher":"AIP Publishing","publication_status":"published","publication_identifier":{"eissn":["10897690"]},"month":"05","doi":"10.1063/5.0005194","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1063/5.0005194","open_access":"1"}],"external_id":{"isi":["000537900300001"],"arxiv":["2002.07294"]},"oa":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"issue":"20","abstract":[{"text":"When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7956","intvolume":" 152","title":"Shear-induced ordering in systems with competing interactions: A machine learning study","status":"public","article_processing_charge":"No","day":"29","scopus_import":"1","date_published":"2020-05-29T00:00:00Z","citation":{"chicago":"Pȩkalski, J., Wojciech Rzadkowski, and A. Z. Panagiotopoulos. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005194.","short":"J. Pȩkalski, W. Rzadkowski, A.Z. Panagiotopoulos, The Journal of Chemical Physics 152 (2020).","mla":"Pȩkalski, J., et al. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics, vol. 152, no. 20, 204905, AIP Publishing, 2020, doi:10.1063/5.0005194.","apa":"Pȩkalski, J., Rzadkowski, W., & Panagiotopoulos, A. Z. (2020). Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0005194","ieee":"J. Pȩkalski, W. Rzadkowski, and A. Z. Panagiotopoulos, “Shear-induced ordering in systems with competing interactions: A machine learning study,” The Journal of chemical physics, vol. 152, no. 20. AIP Publishing, 2020.","ista":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. 2020. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 152(20), 204905.","ama":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 2020;152(20). doi:10.1063/5.0005194"},"publication":"The Journal of chemical physics","article_type":"original"},{"abstract":[{"lang":"eng","text":"We present the first deterministic wait-free long-lived snapshot algorithm, using only read and write operations, that guarantees polylogarithmic amortized step complexity in all executions. This is the first non-blocking snapshot algorithm, using reads and writes only, that has sub-linear amortized step complexity in executions of arbitrary length. The key to our construction is a novel implementation of a 2-component max array object which may be of independent interest."}],"type":"conference","date_updated":"2024-02-28T12:54:30Z","date_created":"2020-09-13T22:01:17Z","oa_version":"Preprint","author":[{"last_name":"Baig","first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","full_name":"Baig, Mirza Ahad"},{"full_name":"Hendler, Danny","last_name":"Hendler","first_name":"Danny"},{"full_name":"Milani, Alessia","first_name":"Alessia","last_name":"Milani"},{"last_name":"Travers","first_name":"Corentin","full_name":"Travers, Corentin"}],"status":"public","title":"Long-lived snapshots with polylogarithmic amortized step complexity","publication_status":"published","publisher":"Association for Computing Machinery","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8382","year":"2020","day":"31","month":"07","article_processing_charge":"No","publication_identifier":{"isbn":["9781450375825"]},"scopus_import":"1","language":[{"iso":"eng"}],"conference":{"location":"Virtual, Italy","start_date":"2020-08-03","end_date":"2020-08-07","name":"PODC: Principles of Distributed Computing"},"doi":"10.1145/3382734.3406005","date_published":"2020-07-31T00:00:00Z","quality_controlled":"1","page":"31-40","publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","oa":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-02860087/document","open_access":"1"}],"citation":{"mla":"Baig, Mirza Ahad, et al. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40, doi:10.1145/3382734.3406005.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” In Proceedings of the 39th Symposium on Principles of Distributed Computing, 31–40. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3406005.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived snapshots with polylogarithmic amortized step complexity. In: Proceedings of the 39th Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:31-40. doi:10.1145/3382734.3406005","ista":"Baig MA, Hendler D, Milani A, Travers C. 2020. Long-lived snapshots with polylogarithmic amortized step complexity. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 31–40.","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived snapshots with polylogarithmic amortized step complexity,” in Proceedings of the 39th Symposium on Principles of Distributed Computing, Virtual, Italy, 2020, pp. 31–40.","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2020). Long-lived snapshots with polylogarithmic amortized step complexity. In Proceedings of the 39th Symposium on Principles of Distributed Computing (pp. 31–40). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3406005"}},{"month":"01","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.101.020504","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1907.02077","open_access":"1"}],"external_id":{"arxiv":["1907.02077"],"isi":["000506843500001"]},"oa":1,"article_number":"020504","date_updated":"2024-02-28T13:11:13Z","date_created":"2020-02-02T23:01:01Z","volume":101,"author":[{"full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"full_name":"Lopes, P. L.S.","last_name":"Lopes","first_name":"P. L.S."},{"first_name":"Pavan","last_name":"Hosur","full_name":"Hosur, Pavan"},{"first_name":"Matthew J.","last_name":"Gilbert","full_name":"Gilbert, Matthew J."},{"last_name":"Ghaemi","first_name":"Pouyan","full_name":"Ghaemi, Pouyan"}],"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2020","day":"13","article_processing_charge":"No","scopus_import":"1","date_published":"2020-01-13T00:00:00Z","article_type":"original","publication":"Physical Review B","citation":{"mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:10.1103/PhysRevB.101.020504.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020).","chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.020504.","ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 2020;101(2). doi:10.1103/PhysRevB.101.020504","ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” Physical Review B, vol. 101, no. 2. American Physical Society, 2020.","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., & Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.020504"},"abstract":[{"text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Preprint","status":"public","title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","intvolume":" 101","_id":"7428","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"07","publication_identifier":{"eissn":["24699934"],"issn":["24699926"]},"doi":"10.1103/PhysRevA.102.012224","language":[{"iso":"eng"}],"external_id":{"arxiv":["1912.08334"],"isi":["000555104200011"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1912.08334","open_access":"1"}],"quality_controlled":"1","isi":1,"article_number":"012224","author":[{"full_name":"Wu, Yunfan","first_name":"Yunfan","last_name":"Wu"},{"full_name":"Krishnakumar, Rajiv","last_name":"Krishnakumar","first_name":"Rajiv"},{"last_name":"Martínez-Rincón","first_name":"Julián","full_name":"Martínez-Rincón, Julián"},{"last_name":"Malia","first_name":"Benjamin K.","full_name":"Malia, Benjamin K."},{"orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","first_name":"Onur","full_name":"Hosten, Onur"},{"full_name":"Kasevich, Mark A.","last_name":"Kasevich","first_name":"Mark A."}],"date_updated":"2024-02-28T13:11:28Z","date_created":"2020-08-30T22:01:10Z","volume":102,"acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","year":"2020","publication_status":"published","department":[{"_id":"OnHo"}],"publisher":"American Physical Society","day":"30","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-30T00:00:00Z","publication":"Physical Review A","citation":{"chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224.","mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224.","short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224.","ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020.","apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224","ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224"},"article_type":"original","abstract":[{"lang":"eng","text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated."}],"issue":"1","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8319","title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","status":"public","intvolume":" 102"},{"author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Petr","last_name":"Novotný","full_name":"Novotný, Petr"},{"full_name":"Vahala, Jiří","first_name":"Jiří","last_name":"Vahala"}],"volume":34,"date_created":"2024-03-04T08:07:22Z","date_updated":"2024-03-04T08:30:16Z","year":"2020","acknowledgement":"Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala are supported by the Czech Science Foundation grant No. GJ19-15134Y.","department":[{"_id":"KrCh"}],"publisher":"Association for the Advancement of Artificial Intelligence","publication_status":"published","publication_identifier":{"issn":["2374-3468"]},"month":"04","doi":"10.1609/aaai.v34i06.6531","conference":{"end_date":"2020-02-12","location":"New York, NY, United States","start_date":"2020-02-07","name":"AAAI: Conference on Artificial Intelligence"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2002.12086"}],"oa":1,"external_id":{"arxiv":["2002.12086"]},"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"}],"quality_controlled":"1","issue":"06","abstract":[{"text":"Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15055","intvolume":" 34","status":"public","title":"Reinforcement learning of risk-constrained policies in Markov decision processes","article_processing_charge":"No","day":"03","keyword":["General Medicine"],"date_published":"2020-04-03T00:00:00Z","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i06.6531.","short":"T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.","mla":"Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06, Association for the Advancement of Artificial Intelligence, 2020, pp. 9794–801, doi:10.1609/aaai.v34i06.6531.","ieee":"T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning of risk-constrained policies in Markov decision processes,” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06. Association for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020.","apa":"Brázdil, T., Chatterjee, K., Novotný, P., & Vahala, J. (2020). Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i06.6531","ista":"Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.","ama":"Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 2020;34(06):9794-9801. doi:10.1609/aaai.v34i06.6531"},"publication":"Proceedings of the 34th AAAI Conference on Artificial Intelligence","page":"9794-9801","article_type":"original"},{"month":"07","publication_identifier":{"eissn":["2375-2548"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"quality_controlled":"1","doi":"10.1126/sciadv.aaw7824","language":[{"iso":"eng"}],"article_number":"aaw7824","file_date_updated":"2024-03-04T09:46:41Z","acknowledgement":"This research was supported by grants NRF-2019R1A3B2067745 and NRF-2017R1A5A1015366 funded by the Korean Government (MSIT) through the National Research Foundation (NRF) of Korea to S.-J.V.L. and by grant Basic Science Research Program (No. 2019R1A2C2009440) funded by the Korean Government (MSIT) through the NRF of Korea to K.-T.K. ","year":"2020","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"MaDe"}],"author":[{"full_name":"Park, Sangsoon","last_name":"Park","first_name":"Sangsoon"},{"full_name":"Artan, Murat","last_name":"Artan","first_name":"Murat","orcid":"0000-0001-8945-6992","id":"C407B586-6052-11E9-B3AE-7006E6697425"},{"last_name":"Han","first_name":"Seung Hyun","full_name":"Han, Seung Hyun"},{"full_name":"Park, Hae-Eun H.","first_name":"Hae-Eun H.","last_name":"Park"},{"full_name":"Jung, Yoonji","last_name":"Jung","first_name":"Yoonji"},{"last_name":"Hwang","first_name":"Ara B.","full_name":"Hwang, Ara B."},{"full_name":"Shin, Won Sik","last_name":"Shin","first_name":"Won Sik"},{"full_name":"Kim, Kyong-Tai","last_name":"Kim","first_name":"Kyong-Tai"},{"first_name":"Seung-Jae V.","last_name":"Lee","full_name":"Lee, Seung-Jae V."}],"date_updated":"2024-03-04T09:52:09Z","date_created":"2024-03-04T09:41:57Z","volume":6,"day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Science Advances","citation":{"mla":"Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances, vol. 6, no. 27, aaw7824, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.aaw7824.","short":"S. Park, M. Artan, S.H. Han, H.-E.H. Park, Y. Jung, A.B. Hwang, W.S. Shin, K.-T. Kim, S.-J.V. Lee, Science Advances 6 (2020).","chicago":"Park, Sangsoon, Murat Artan, Seung Hyun Han, Hae-Eun H. Park, Yoonji Jung, Ara B. Hwang, Won Sik Shin, Kyong-Tai Kim, and Seung-Jae V. Lee. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.aaw7824.","ama":"Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 2020;6(27). doi:10.1126/sciadv.aaw7824","ista":"Park S, Artan M, Han SH, Park H-EH, Jung Y, Hwang AB, Shin WS, Kim K-T, Lee S-JV. 2020. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 6(27), aaw7824.","ieee":"S. Park et al., “VRK-1 extends life span by activation of AMPK via phosphorylation,” Science Advances, vol. 6, no. 27. American Association for the Advancement of Science, 2020.","apa":"Park, S., Artan, M., Han, S. H., Park, H.-E. H., Jung, Y., Hwang, A. B., … Lee, S.-J. V. (2020). VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw7824"},"article_type":"original","date_published":"2020-07-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans."}],"issue":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15057","ddc":["570"],"status":"public","title":"VRK-1 extends life span by activation of AMPK via phosphorylation","intvolume":" 6","file":[{"file_size":1864415,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_ScienceAdvances_Park.pdf","checksum":"a37157cd0de709dce5fe03f4a31cd0b6","success":1,"date_updated":"2024-03-04T09:46:41Z","date_created":"2024-03-04T09:46:41Z","relation":"main_file","file_id":"15058"}],"oa_version":"Published Version"},{"volume":117,"date_created":"2024-03-04T10:03:52Z","date_updated":"2024-03-04T10:14:44Z","author":[{"last_name":"Pinotsis","first_name":"Nikos","full_name":"Pinotsis, Nikos"},{"first_name":"Karolina","last_name":"Zielinska","full_name":"Zielinska, Karolina"},{"full_name":"Babuta, Mrigya","first_name":"Mrigya","last_name":"Babuta"},{"full_name":"Arolas, Joan L.","last_name":"Arolas","first_name":"Joan L."},{"last_name":"Kostan","first_name":"Julius","full_name":"Kostan, Julius"},{"full_name":"Khan, Muhammad Bashir","first_name":"Muhammad Bashir","last_name":"Khan"},{"full_name":"Schreiner, Claudia","last_name":"Schreiner","first_name":"Claudia"},{"full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P","last_name":"Testa Salmazo"},{"full_name":"Ciccarelli, Luciano","first_name":"Luciano","last_name":"Ciccarelli"},{"last_name":"Puchinger","first_name":"Martin","full_name":"Puchinger, Martin"},{"full_name":"Gkougkoulia, Eirini A.","first_name":"Eirini A.","last_name":"Gkougkoulia"},{"full_name":"Ribeiro, Euripedes de Almeida","last_name":"Ribeiro","first_name":"Euripedes de Almeida"},{"full_name":"Marlovits, Thomas C.","first_name":"Thomas C.","last_name":"Marlovits"},{"last_name":"Bhattacharya","first_name":"Alok","full_name":"Bhattacharya, Alok"},{"full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina","last_name":"Djinovic-Carugo"}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"CaBe"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"We thank the staff of the macromolecular crystallography (MX) and SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss Light Source for excellent support, and the Life Sciences Facility of the Institute of Science and Technology Austria for usage of the rheometer. We thank Life Sciences editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423), Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF) Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R. ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I 2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological Macromolecules. M.B. acknowledges the University Grant Commission, India, for a senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science Engineering Research Council. ","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"09","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.1073/pnas.1917269117","quality_controlled":"1","external_id":{"pmid":["32848067"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.191726911"}],"issue":"36","abstract":[{"lang":"eng","text":"The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 117","title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","status":"public","_id":"15061","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"08","date_published":"2020-09-08T00:00:00Z","page":"22101-22112","article_type":"original","citation":{"ieee":"N. Pinotsis et al., “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020.","apa":"Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M. B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1917269117","ista":"Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A, Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 117(36), 22101–22112.","ama":"Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117","chicago":"Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117.","short":"N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan, C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia, E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings of the National Academy of Sciences 117 (2020) 22101–22112.","mla":"Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117."},"publication":"Proceedings of the National Academy of Sciences"},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2020-12-01T00:00:00Z","citation":{"ama":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 2020;4(4):455-480. doi:10.1007/s41468-020-00058-8","ieee":"U. Bauer, H. Edelsbrunner, G. Jablonski, and M. Mrozek, “Čech-Delaunay gradient flow and homology inference for self-maps,” Journal of Applied and Computational Topology, vol. 4, no. 4. Springer Nature, pp. 455–480, 2020.","apa":"Bauer, U., Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2020). Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00058-8","ista":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. 2020. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 4(4), 455–480.","short":"U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and Computational Topology 4 (2020) 455–480.","mla":"Bauer, U., et al. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology, vol. 4, no. 4, Springer Nature, 2020, pp. 455–80, doi:10.1007/s41468-020-00058-8.","chicago":"Bauer, U., Herbert Edelsbrunner, Grzegorz Jablonski, and M. Mrozek. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology. Springer Nature, 2020. https://doi.org/10.1007/s41468-020-00058-8."},"publication":"Journal of Applied and Computational Topology","page":"455-480","article_type":"original","issue":"4","abstract":[{"text":"We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspaces of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for Čech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive Čech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":851190,"creator":"dernst","access_level":"open_access","file_name":"2020_JourApplCompTopology_Bauer.pdf","checksum":"eed1168b6e66cd55272c19bb7fca8a1c","success":1,"date_updated":"2024-03-04T10:52:42Z","date_created":"2024-03-04T10:52:42Z","relation":"main_file","file_id":"15065"}],"_id":"15064","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 4","status":"public","ddc":["500"],"title":"Čech-Delaunay gradient flow and homology inference for self-maps","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"month":"12","doi":"10.1007/s41468-020-00058-8","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"},"oa":1,"quality_controlled":"1","file_date_updated":"2024-03-04T10:52:42Z","author":[{"full_name":"Bauer, U.","first_name":"U.","last_name":"Bauer"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"last_name":"Jablonski","first_name":"Grzegorz","orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz"},{"full_name":"Mrozek, M.","last_name":"Mrozek","first_name":"M."}],"volume":4,"date_created":"2024-03-04T10:47:49Z","date_updated":"2024-03-04T10:54:04Z","year":"2020","acknowledgement":"This research has been supported by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”, by Polish MNiSzW Grant No. 2621/7.PR/12/2013/2, by the Polish National Science Center under Maestro Grant No. 2014/14/A/ST1/00453 and Grant No. DEC-2013/09/N/ST6/02995. Open Access funding provided by Projekt DEAL.","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published"},{"publication_identifier":{"issn":["2690-1005","2690-0998"]},"month":"11","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1908.01653","open_access":"1"}],"external_id":{"arxiv":["1908.01653"]},"oa":1,"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.2140/pmp.2020.1.101","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"Partially supported by ERC Advanced Grant No. 338804. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 66538","year":"2020","department":[{"_id":"LaEr"}],"publisher":"Mathematical Sciences Publishers","publication_status":"published","author":[{"full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","first_name":"Giorgio","last_name":"Cipolloni"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder"}],"volume":1,"date_created":"2024-03-04T10:27:57Z","date_updated":"2024-03-04T10:33:15Z","scopus_import":"1","keyword":["General Medicine"],"article_processing_charge":"No","day":"16","citation":{"mla":"Cipolloni, Giorgio, et al. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics, vol. 1, no. 1, Mathematical Sciences Publishers, 2020, pp. 101–46, doi:10.2140/pmp.2020.1.101.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability and Mathematical Physics 1 (2020) 101–146.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Lower Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/pmp.2020.1.101.","ama":"Cipolloni G, Erdös L, Schröder DJ. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 2020;1(1):101-146. doi:10.2140/pmp.2020.1.101","ista":"Cipolloni G, Erdös L, Schröder DJ. 2020. Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. 1(1), 101–146.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2020). Optimal lower bound on the least singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2020.1.101","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal lower bound on the least singular value of the shifted Ginibre ensemble,” Probability and Mathematical Physics, vol. 1, no. 1. Mathematical Sciences Publishers, pp. 101–146, 2020."},"publication":"Probability and Mathematical Physics","page":"101-146","article_type":"original","date_published":"2020-11-16T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"We consider the least singular value of a large random matrix with real or complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal lower tail estimate on this singular value in the critical regime where z is around the spectral edge, thus improving the classical bound of Sankar, Spielman and Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395).","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15063","intvolume":" 1","title":"Optimal lower bound on the least singular value of the shifted Ginibre ensemble","status":"public","oa_version":"Preprint"},{"month":"10","conference":{"start_date":"2020-10-12","location":"Virtual","end_date":"2020-10-16","name":"DISC: Symposium on Distributed Computing"},"doi":"10.4230/LIPIcs.DISC.2020.40","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2005.07761"]},"oa":1,"quality_controlled":"1","file_date_updated":"2024-03-05T07:08:27Z","license":"https://creativecommons.org/licenses/by/3.0/","article_number":"40","author":[{"full_name":"Brandt, Sebastian","first_name":"Sebastian","last_name":"Brandt"},{"last_name":"Keller","first_name":"Barbara","full_name":"Keller, Barbara"},{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"},{"last_name":"Uitto","first_name":"Jara","full_name":"Uitto, Jara"}],"related_material":{"record":[{"id":"9678","status":"public","relation":"later_version"}]},"date_updated":"2024-03-05T07:13:13Z","date_created":"2024-03-05T07:09:12Z","volume":179,"year":"2020","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"07","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-10-07T00:00:00Z","publication":"34th International Symposium on Distributed Computing","citation":{"chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” In 34th International Symposium on Distributed Computing, Vol. 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.DISC.2020.40.","mla":"Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” 34th International Symposium on Distributed Computing, vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.DISC.2020.40.","short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, 34th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2020. Brief announcement: Efficient load-balancing through distributed token dropping. 34th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 179, 40.","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement: Efficient load-balancing through distributed token dropping,” in 34th International Symposium on Distributed Computing, Virtual, 2020, vol. 179.","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2020). Brief announcement: Efficient load-balancing through distributed token dropping. In 34th International Symposium on Distributed Computing (Vol. 179). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2020.40","ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Brief announcement: Efficient load-balancing through distributed token dropping. In: 34th International Symposium on Distributed Computing. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.DISC.2020.40"},"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 the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":303529,"file_name":"2020_LIPIcs_Brandt.pdf","access_level":"open_access","date_created":"2024-03-05T07:08:27Z","date_updated":"2024-03-05T07:08:27Z","success":1,"checksum":"23e2d9321aef53092dc1e24a8ab82d72","file_id":"15075","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15074","ddc":["000"],"status":"public","title":"Brief announcement: Efficient load-balancing through distributed token dropping","intvolume":" 179"},{"citation":{"ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. In: 47th International Colloquium on Automata, Languages, and Programming. Vol 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ICALP.2020.7","ista":"Alistarh D-A, Nadiradze G, Sabour A. 2020. Dynamic averaging load balancing on cycles. 47th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 168, 7.","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” in 47th International Colloquium on Automata, Languages, and Programming, Saarbrücken, Germany, Virtual, 2020, vol. 168.","apa":"Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2020). Dynamic averaging load balancing on cycles. In 47th International Colloquium on Automata, Languages, and Programming (Vol. 168). Saarbrücken, Germany, Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2020.7","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” 47th International Colloquium on Automata, Languages, and Programming, vol. 168, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ICALP.2020.7.","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, in:, 47th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” In 47th International Colloquium on Automata, Languages, and Programming, Vol. 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ICALP.2020.7."},"publication":"47th International Colloquium on Automata, Languages, and Programming","date_published":"2020-06-29T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"29","_id":"15077","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 168","title":"Dynamic averaging load balancing on cycles","status":"public","ddc":["000"],"file":[{"access_level":"open_access","file_name":"2020_LIPIcs_Alistarh.pdf","file_size":782987,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"15078","checksum":"e5eb16199f4ccfd77a321977eb3f026f","success":1,"date_updated":"2024-03-05T07:25:15Z","date_created":"2024-03-05T07:25:15Z"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"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"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2003.09297"]},"oa":1,"project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.ICALP.2020.7","conference":{"end_date":"2020-07-11","start_date":"2020-07-08","location":"Saarbrücken, Germany, Virtual","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"language":[{"iso":"eng"}],"month":"06","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\r\nversions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments.\r\nFunding: European Research Council funding award PR1042ERC01","year":"2020","department":[{"_id":"DaAl"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","related_material":{"record":[{"status":"public","relation":"later_version","id":"8286"}]},"author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi","orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sabour","first_name":"Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","full_name":"Sabour, Amirmojtaba"}],"volume":168,"date_created":"2024-03-05T07:25:37Z","date_updated":"2024-03-05T07:35:53Z","article_number":"7","ec_funded":1,"file_date_updated":"2024-03-05T07:25:15Z"},{"language":[{"iso":"eng"}],"date_published":"2020-04-01T00:00:00Z","conference":{"name":"EuroCG: European Workshop on Computational Geometry","end_date":"2020-03-18","location":"Würzburg, Germany, Virtual","start_date":"2020-03-16"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www1.pub.informatik.uni-wuerzburg.de/eurocg2020/data/uploads/papers/eurocg20_paper_56.pdf"}],"oa":1,"citation":{"chicago":"Aichholzer, Oswin, Julia Obmann, Pavel Patak, Daniel Perz, and Josef Tkadlec. “Disjoint Tree-Compatible Plane Perfect Matchings.” In 36th European Workshop on Computational Geometry, 2020.","mla":"Aichholzer, Oswin, et al. “Disjoint Tree-Compatible Plane Perfect Matchings.” 36th European Workshop on Computational Geometry, 56, 2020.","short":"O. Aichholzer, J. Obmann, P. Patak, D. Perz, J. Tkadlec, in:, 36th European Workshop on Computational Geometry, 2020.","ista":"Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. 2020. Disjoint tree-compatible plane perfect matchings. 36th European Workshop on Computational Geometry. EuroCG: European Workshop on Computational Geometry, 56.","ieee":"O. Aichholzer, J. Obmann, P. Patak, D. Perz, and J. Tkadlec, “Disjoint tree-compatible plane perfect matchings,” in 36th European Workshop on Computational Geometry, Würzburg, Germany, Virtual, 2020.","apa":"Aichholzer, O., Obmann, J., Patak, P., Perz, D., & Tkadlec, J. (2020). Disjoint tree-compatible plane perfect matchings. In 36th European Workshop on Computational Geometry. Würzburg, Germany, Virtual.","ama":"Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. Disjoint tree-compatible plane perfect matchings. In: 36th European Workshop on Computational Geometry. ; 2020."},"publication":"36th European Workshop on Computational Geometry","article_processing_charge":"No","month":"04","day":"01","oa_version":"Published Version","date_created":"2024-03-05T08:57:17Z","date_updated":"2024-03-05T09:00:07Z","author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"full_name":"Obmann, Julia","first_name":"Julia","last_name":"Obmann"},{"full_name":"Patak, Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83","last_name":"Patak","first_name":"Pavel"},{"last_name":"Perz","first_name":"Daniel","full_name":"Perz, Daniel"},{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"}],"department":[{"_id":"KrCh"},{"_id":"UlWa"}],"title":"Disjoint tree-compatible plane perfect matchings","status":"public","publication_status":"published","_id":"15082","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Research on this work was initiated at the 6th Austrian-Japanese-Mexican-Spanish Workshop on Discrete Geometry and continued during the 16th European Geometric Graph-Week, both held near Strobl, Austria. We are grateful to the participants for the inspiring atmosphere. We especially thank Alexander Pilz for bringing this class of problems to our attention and Birgit Vogtenhuber for inspiring discussions. D.P. is partially supported by the FWF grant I 3340-N35 (Collaborative DACH project Arrangements and Drawings). The research stay of P.P. at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement of internationalization in the field of research and development at Charles University, through the support of quality projects MSCA-IF. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 734922.","abstract":[{"text":"Two plane drawings of geometric graphs on the same set of points are called disjoint compatible if their union is plane and they do not have an edge in common. For a given set S of 2n points two plane drawings of perfect matchings M1 and M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible if there exists a plane drawing of a spanning tree T on S which is disjoint compatible to both M1 and M2.\r\nWe show that the graph of all disjoint tree-compatible perfect geometric matchings on 2n points in convex position is connected if and only if 2n ≥ 10. Moreover, in that case the diameter\r\nof this graph is either 4 or 5, independent of n.","lang":"eng"}],"type":"conference","article_number":"56"},{"publication_identifier":{"issn":["1932-6157"],"eissn":["1941-7330"]},"month":"12","isi":1,"quality_controlled":"1","external_id":{"arxiv":["1901.01375"],"isi":["000598369200021"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.01375"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/20-AOS1945","publisher":"Institute of Mathematical Statistics","department":[{"_id":"MaMo"}],"publication_status":"published","year":"2020","volume":48,"date_updated":"2024-03-06T08:28:50Z","date_created":"2019-07-31T09:39:42Z","author":[{"full_name":"Javanmard, Adel","last_name":"Javanmard","first_name":"Adel"},{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli"},{"first_name":"Andrea","last_name":"Montanari","full_name":"Montanari, Andrea"}],"article_processing_charge":"No","day":"11","page":"3619-3642","article_type":"original","citation":{"mla":"Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” Annals of Statistics, vol. 48, no. 6, Institute of Mathematical Statistics, 2020, pp. 3619–42, doi:10.1214/20-AOS1945.","short":"A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.","chicago":"Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” Annals of Statistics. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-AOS1945.","ama":"Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 2020;48(6):3619-3642. doi:10.1214/20-AOS1945","ista":"Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 48(6), 3619–3642.","apa":"Javanmard, A., Mondelli, M., & Montanari, A. (2020). Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/20-AOS1945","ieee":"A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural network via displacement convexity,” Annals of Statistics, vol. 48, no. 6. Institute of Mathematical Statistics, pp. 3619–3642, 2020."},"publication":"Annals of Statistics","date_published":"2020-12-11T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.\r\nHere we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge.","lang":"eng"}],"intvolume":" 48","status":"public","title":"Analysis of a two-layer neural network via displacement convexity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6748","oa_version":"Preprint"},{"date_published":"2020-06-01T00:00:00Z","citation":{"ama":"Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 2020;7(6). doi:10.1098/rsos.200599","apa":"Klose, A. K., Karle, V., Winkelmann, R., & Donges, J. F. (2020). Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.200599","ieee":"A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements,” Royal Society Open Science, vol. 7, no. 6. The Royal Society, 2020.","ista":"Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 7(6), 200599.","short":"A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science 7 (2020).","mla":"Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science, vol. 7, no. 6, 200599, The Royal Society, 2020, doi:10.1098/rsos.200599.","chicago":"Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F. Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science. The Royal Society, 2020. https://doi.org/10.1098/rsos.200599."},"publication":"Royal Society Open Science","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"8748","relation":"main_file","date_created":"2020-11-09T09:07:11Z","date_updated":"2020-11-09T09:07:11Z","success":1,"checksum":"5505c445de373bfd836eb4d3b48b1f37","file_name":"2020_RoyalSocOpenScience_Klose.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1611485}],"_id":"8741","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","ddc":["530","550"],"title":"Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements","status":"public","issue":"6","abstract":[{"lang":"eng","text":"In ecology, climate and other fields, (sub)systems have been identified that can transition into a qualitatively different state when a critical threshold or tipping point in a driving process is crossed. An understanding of those tipping elements is of great interest given the increasing influence of humans on the biophysical Earth system. Complex interactions exist between tipping elements, e.g. physical mechanisms connect subsystems of the climate system. Based on earlier work on such coupled nonlinear systems, we systematically assessed the qualitative long-term behaviour of interacting tipping elements. We developed an understanding of the consequences of interactions\r\non the tipping behaviour allowing for tipping cascades to emerge under certain conditions. The (narrative) application of\r\nthese qualitative results to real-world examples of interacting tipping elements indicates that tipping cascades with profound consequences may occur: the interacting Greenland ice sheet and thermohaline ocean circulation might tip before the tipping points of the isolated subsystems are crossed. The eutrophication of the first lake in a lake chain might propagate through the following lakes without a crossing of their individual critical nutrient input levels. The possibility of emerging cascading tipping dynamics calls for the development of a unified theory of interacting tipping elements and the quantitative analysis of interacting real-world tipping elements."}],"type":"journal_article","doi":"10.1098/rsos.200599","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":{"arxiv":["1910.12042"],"isi":["000545625200001"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["20545703"]},"month":"06","author":[{"first_name":"Ann Kristin","last_name":"Klose","full_name":"Klose, Ann Kristin"},{"first_name":"Volker","last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","orcid":"0000-0002-6963-0129","full_name":"Karle, Volker"},{"full_name":"Winkelmann, Ricarda","last_name":"Winkelmann","first_name":"Ricarda"},{"full_name":"Donges, Jonathan F.","last_name":"Donges","first_name":"Jonathan F."}],"volume":7,"date_created":"2020-11-08T23:01:25Z","date_updated":"2024-03-12T12:31:30Z","year":"2020","acknowledgement":"V.K. thanks the German National Academic Foundation (Studienstiftung des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork (PB.net), the Earth League’s EarthDoc program and the European Research Council Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements. This work has been performed in the context of the copan collaboration and the FutureLab on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments by N. Wunderling, J. Heitzig and M. Wiedermann.","department":[{"_id":"MiLe"}],"publisher":"The Royal Society","publication_status":"published","file_date_updated":"2020-11-09T09:07:11Z","article_number":"200599"},{"year":"2020","publication_status":"published","department":[{"_id":"E-Lib"}],"publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","author":[{"full_name":"Ernst, Doris","last_name":"Ernst","first_name":"Doris","orcid":"0000-0002-2354-0195","id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novotny","first_name":"Gertraud","full_name":"Novotny, Gertraud"},{"full_name":"Schönher, Eva Maria","last_name":"Schönher","first_name":"Eva Maria"}],"date_created":"2020-04-28T08:37:38Z","date_updated":"2024-03-12T10:12:33Z","volume":73,"file_date_updated":"2024-03-12T10:12:33Z","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,"doi":"10.31263/voebm.v73i1.3491","language":[{"iso":"ger"}],"month":"04","publication_identifier":{"issn":["1022-2588"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7687","ddc":["020"],"status":"public","title":"(Core Trust) Seal your repository!","intvolume":" 73","popular_science":"1","file":[{"access_level":"open_access","file_name":"2020_VOEB_Ernst.pdf","file_size":579291,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7970","checksum":"fee784f15a489deb7def6ccf8c5bf8c3","date_updated":"2024-03-12T10:12:33Z","date_created":"2020-06-17T10:50:13Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested.","lang":"eng"},{"text":" Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen (RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür wurden jenen Organisationen, die in Österreich bereits mit CTS zertifiziert sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die Entwicklung einer DINI-Zertifizierung in Österreich.","lang":"ger"}],"issue":"1","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","citation":{"short":"D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 46–59.","mla":"Ernst, Doris, et al. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 46–59, doi:10.31263/voebm.v73i1.3491.","chicago":"Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal your repository!” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. https://doi.org/10.31263/voebm.v73i1.3491.","ama":"Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2020;73(1):46-59. doi:10.31263/voebm.v73i1.3491","ieee":"D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 46–59, 2020.","apa":"Ernst, D., Novotny, G., & Schönher, E. M. (2020). (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v73i1.3491","ista":"Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59."},"article_type":"original","page":"46-59","date_published":"2020-04-28T00:00:00Z","scopus_import":"1","day":"28","article_processing_charge":"No","has_accepted_license":"1"},{"citation":{"chicago":"Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In Proceedings of 1st International Electronic Conference on Microbiology. MDPI, 2020. https://doi.org/10.3390/ecm2020-07116.","short":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V. Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020.","mla":"Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020, doi:10.3390/ecm2020-07116.","apa":"Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O., & Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In Proceedings of 1st International Electronic Conference on Microbiology. Virtual: MDPI. https://doi.org/10.3390/ecm2020-07116","ieee":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T,” in Proceedings of 1st International Electronic Conference on Microbiology, Virtual, 2020.","ista":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology. ECM: Electronic Conference on Microbiology.","ama":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In: Proceedings of 1st International Electronic Conference on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116"},"publication":"Proceedings of 1st International Electronic Conference on Microbiology","date_published":"2020-11-02T00:00:00Z","has_accepted_license":"1","article_processing_charge":"Yes","day":"02","_id":"15071","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T","status":"public","file":[{"file_id":"15127","relation":"main_file","date_created":"2024-03-20T08:05:46Z","date_updated":"2024-03-20T08:05:46Z","success":1,"checksum":"d1914af7811a21a4b2744eb51b5834e3","file_name":"2020_ECM_Oshurkova.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":595543}],"oa_version":"Published Version","type":"conference","abstract":[{"lang":"eng","text":"A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic [1]. After long-term extensive cultivation at 15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and grew on methanol, acetate and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive. Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M.mazei was 98.5%, which is higher than the values recommended for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation of JL01 with S. associata GLS2T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative genes involved in methanochondroithin catabolism."}],"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"},"quality_controlled":"1","doi":"10.3390/ecm2020-07116","conference":{"name":"ECM: Electronic Conference on Microbiology","location":"Virtual","start_date":"2020-11-02","end_date":"2020-11-30"},"language":[{"iso":"eng"}],"month":"11","acknowledgement":"The work was supported by of Russian Foundation of Basic Research: grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334 for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST, Austria) for their help in obtaining the genomic sequence of strain JL01. ","year":"2020","publisher":"MDPI","department":[{"_id":"FyKo"}],"publication_status":"published","author":[{"full_name":"Oshurkova, Viktoriia","last_name":"Oshurkova","first_name":"Viktoriia"},{"full_name":"Troshina, Olga","last_name":"Troshina","first_name":"Olga"},{"first_name":"Vladimir","last_name":"Trubitsyn","full_name":"Trubitsyn, Vladimir"},{"last_name":"Ryzhmanova","first_name":"Yana","full_name":"Ryzhmanova, Yana"},{"orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga","full_name":"Bochkareva, Olga"},{"full_name":"Shcherbakova, Viktoria","last_name":"Shcherbakova","first_name":"Viktoria"}],"date_updated":"2024-03-20T08:06:22Z","date_created":"2024-03-04T11:41:31Z","file_date_updated":"2024-03-20T08:05:46Z"},{"date_published":"2020-02-26T00:00:00Z","article_type":"original","citation":{"chicago":"Fribourgh, Jennifer L, Ashutosh Srivastava, Colby R Sandate, Alicia K. Michael, Peter L Hsu, Christin Rakers, Leslee T Nguyen, et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55275.","mla":"Fribourgh, Jennifer L., et al. “Dynamics at the Serine Loop Underlie Differential Affinity of Cryptochromes for CLOCK:BMAL1 to Control Circadian Timing.” ELife, vol. 9, 55275, eLife Sciences Publications, 2020, doi:10.7554/elife.55275.","short":"J.L. Fribourgh, A. Srivastava, C.R. Sandate, A.K. Michael, P.L. Hsu, C. Rakers, L.T. Nguyen, M.R. Torgrimson, G.C.G. Parico, S. Tripathi, N. Zheng, G.C. Lander, T. Hirota, F. Tama, C.L. Partch, ELife 9 (2020).","ista":"Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL. 2020. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 9, 55275.","ieee":"J. L. Fribourgh et al., “Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Fribourgh, J. L., Srivastava, A., Sandate, C. R., Michael, A. K., Hsu, P. L., Rakers, C., … Partch, C. L. (2020). Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55275","ama":"Fribourgh JL, Srivastava A, Sandate CR, et al. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. eLife. 2020;9. doi:10.7554/elife.55275"},"publication":"eLife","article_processing_charge":"No","day":"26","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"scopus_import":"1","oa_version":"Published Version","intvolume":" 9","title":"Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15153","abstract":[{"text":"Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.7554/elife.55275","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.55275"}],"publication_identifier":{"issn":["2050-084X"]},"month":"02","volume":9,"date_updated":"2024-03-25T12:25:02Z","date_created":"2024-03-21T07:55:12Z","author":[{"last_name":"Fribourgh","first_name":"Jennifer L","full_name":"Fribourgh, Jennifer L"},{"full_name":"Srivastava, Ashutosh","last_name":"Srivastava","first_name":"Ashutosh"},{"full_name":"Sandate, Colby R","first_name":"Colby R","last_name":"Sandate"},{"last_name":"Michael","first_name":"Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia Kathleen"},{"full_name":"Hsu, Peter L","last_name":"Hsu","first_name":"Peter L"},{"full_name":"Rakers, Christin","first_name":"Christin","last_name":"Rakers"},{"last_name":"Nguyen","first_name":"Leslee T","full_name":"Nguyen, Leslee T"},{"last_name":"Torgrimson","first_name":"Megan R","full_name":"Torgrimson, Megan R"},{"full_name":"Parico, Gian Carlo G","last_name":"Parico","first_name":"Gian Carlo G"},{"full_name":"Tripathi, Sarvind","last_name":"Tripathi","first_name":"Sarvind"},{"full_name":"Zheng, Ning","last_name":"Zheng","first_name":"Ning"},{"full_name":"Lander, Gabriel C","first_name":"Gabriel C","last_name":"Lander"},{"full_name":"Hirota, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Hirota"},{"first_name":"Florence","last_name":"Tama","full_name":"Tama, Florence"},{"first_name":"Carrie L","last_name":"Partch","full_name":"Partch, Carrie L"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2020","extern":"1","article_number":"55275"},{"author":[{"full_name":"Bhandari, Pradeep","first_name":"Pradeep","last_name":"Bhandari","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481"}],"date_updated":"2023-09-07T13:20:03Z","date_created":"2020-02-26T10:56:37Z","year":"2020","department":[{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2021-03-01T23:30:04Z","doi":"10.15479/AT:ISTA:7525","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"02","oa_version":"Published Version","file":[{"relation":"main_file","embargo":"2021-02-28","file_id":"7538","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","date_updated":"2021-03-01T23:30:04Z","date_created":"2020-02-28T08:37:53Z","checksum":"4589234fdb12b4ad72273b311723a7b4","file_name":"Pradeep Bhandari Thesis.pdf","access_level":"open_access","content_type":"application/pdf","file_size":9646346,"creator":"pbhandari"},{"access_level":"closed","embargo_to":"open_access","file_name":"Pradeep Bhandari Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":35252164,"creator":"pbhandari","relation":"source_file","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file_id":"7539","checksum":"aa79490553ca0a5c9b6fbcd152e93928","date_updated":"2021-03-01T23:30:04Z","date_created":"2020-02-28T08:47:14Z"}],"_id":"7525","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","ddc":["570"],"status":"public","abstract":[{"text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-02-28T00:00:00Z","citation":{"short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020.","mla":"Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7525.","chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525.","ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525","apa":"Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7525","ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020.","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria."},"page":"79","article_processing_charge":"No","has_accepted_license":"1","day":"28","keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"]},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"date_published":"2020-12-01T00:00:00Z","citation":{"ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633.","apa":"Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633","ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020.","ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633","chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier, 2020. https://doi.org/10.1016/j.jsb.2020.107633.","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020)."},"publication":"Journal of Structural Biology","article_type":"original","issue":"3","abstract":[{"lang":"eng","text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications."}],"type":"journal_article","file":[{"success":1,"checksum":"c48cbf594e84fc2f91966ffaafc0918c","date_created":"2020-12-10T14:01:10Z","date_updated":"2020-12-10T14:01:10Z","file_id":"8937","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":7076870,"access_level":"open_access","file_name":"2020_JourStrucBiology_Faessler.pdf"}],"oa_version":"Published Version","_id":"8586","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 212","ddc":["570"],"status":"public","title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","publication_identifier":{"issn":["1047-8477"]},"month":"12","doi":"10.1016/j.jsb.2020.107633","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"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":["000600997800008"]},"oa":1,"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","isi":1,"file_date_updated":"2020-12-10T14:01:10Z","article_number":"107633","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14592"},{"relation":"dissertation_contains","status":"public","id":"12491"}]},"author":[{"full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler"},{"orcid":"0000-0002-9561-1239","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","first_name":"Bettina","full_name":"Zens, Bettina"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"volume":212,"date_updated":"2024-03-28T23:30:05Z","date_created":"2020-09-29T13:24:06Z","year":"2020","acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","publisher":"Elsevier","department":[{"_id":"FlSc"}],"publication_status":"published"},{"oa_version":"Published Version","file":[{"file_name":"kavcicB_thesis202009.pdf","access_level":"open_access","content_type":"application/pdf","file_size":52636162,"creator":"bkavcic","relation":"main_file","embargo":"2021-10-06","file_id":"8663","date_created":"2020-10-15T06:41:20Z","date_updated":"2021-10-07T22:30:03Z","checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb"},{"date_created":"2020-10-15T06:41:53Z","date_updated":"2021-10-07T22:30:03Z","checksum":"bb35f2352a04db19164da609f00501f3","file_id":"8664","relation":"source_file","creator":"bkavcic","file_size":321681247,"content_type":"application/zip","file_name":"2020b.zip","embargo_to":"open_access","access_level":"closed"}],"_id":"8657","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","status":"public","ddc":["571","530","570"],"abstract":[{"lang":"eng","text":"Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-10-14T00:00:00Z","citation":{"ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657","ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria.","apa":"Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657","ieee":"B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.","mla":"Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.","chicago":"Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657."},"page":"271","day":"14","article_processing_charge":"No","has_accepted_license":"1","author":[{"full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic"}],"related_material":{"record":[{"id":"7673","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8250"}]},"date_updated":"2023-09-07T13:20:48Z","date_created":"2020-10-13T16:46:14Z","year":"2020","acknowledgement":"I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop.","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"file_date_updated":"2021-10-07T22:30:03Z","doi":"10.15479/AT:ISTA:8657","supervisor":[{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"oa":1,"month":"10","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-011-4"]}},{"month":"03","publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2019.12.022","language":[{"iso":"eng"}],"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"},"external_id":{"isi":["000520854700008"],"pmid":["31928842"]},"oa":1,"quality_controlled":"1","isi":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":"708497","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","call_identifier":"H2020"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Zellkommunikation in Gesundheit und Krankheit","grant_number":"W01205","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-11-20T08:58:53Z","ec_funded":1,"author":[{"full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","first_name":"Carolina","last_name":"Borges Merjane"},{"full_name":"Kim, Olena","first_name":"Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"11196","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/","relation":"press_release","description":"News on IST Homepage"}]},"date_created":"2020-02-10T15:59:45Z","date_updated":"2024-03-28T23:30:07Z","volume":105,"acknowledgement":"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. 692692 and Marie Sklodowska-Curie 708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27 Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa Zheden for extensive EM training, advice, and experimental assistance; Benjamin Suter for substantial help with light stimulation, ImageJ plugins for analysis, and manuscript editing; Florian Marr and Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger (Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing the Prox1-CreERT2 mouse line.","year":"2020","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"PeJo"}],"day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-03-18T00:00:00Z","publication":"Neuron","citation":{"short":"C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.","mla":"Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron, vol. 105, Elsevier, 2020, pp. 992–1006, doi:10.1016/j.neuron.2019.12.022.","chicago":"Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2019.12.022.","ama":"Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 2020;105:992-1006. doi:10.1016/j.neuron.2019.12.022","ieee":"C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy (‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” Neuron, vol. 105. Elsevier, pp. 992–1006, 2020.","apa":"Borges Merjane, C., Kim, O., & Jonas, P. M. (2020). Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.12.022","ista":"Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105, 992–1006."},"article_type":"original","page":"992-1006","abstract":[{"text":"How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2020_Neuron_BorgesMerjane.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":9712957,"file_id":"8778","relation":"main_file","date_updated":"2020-11-20T08:58:53Z","date_created":"2020-11-20T08:58:53Z","success":1,"checksum":"3582664addf26859e86ac5bec3e01416"}],"_id":"7473","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices","status":"public","intvolume":" 105"},{"abstract":[{"lang":"eng","text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2020_NatureComm_Kavcic.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1965672,"creator":"dernst","relation":"main_file","file_id":"8275","date_updated":"2020-08-17T07:36:57Z","date_created":"2020-08-17T07:36:57Z","checksum":"986bebb308850a55850028d3d2b5b664","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8250","intvolume":" 11","ddc":["570"],"title":"Mechanisms of drug interactions between translation-inhibiting antibiotics","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"11","date_published":"2020-08-11T00:00:00Z","citation":{"short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).","mla":"Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020, doi:10.1038/s41467-020-17734-z.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z.","ama":"Kavcic B, Tkačik G, Bollenbach MT. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions between translation-inhibiting antibiotics,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17734-z","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between translation-inhibiting antibiotics. Nature Communications. 11, 4013."},"publication":"Nature Communications","article_type":"original","file_date_updated":"2020-08-17T07:36:57Z","article_number":"4013","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8657"}]},"author":[{"full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}],"volume":11,"date_updated":"2024-03-28T23:30:08Z","date_created":"2020-08-12T09:13:50Z","year":"2020","acknowledgement":"We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K. Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support, which rendered this\r\nwork possible. B.K. thanks all members of Guet group for many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work. We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A. Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310 (to T.B.). Open access funding provided by\r\nProjekt DEAL.","department":[{"_id":"GaTk"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"month":"08","doi":"10.1038/s41467-020-17734-z","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"},"oa":1,"external_id":{"isi":["000562769300008"]},"project":[{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"quality_controlled":"1","isi":1},{"type":"preprint","abstract":[{"text":"Combining drugs can improve the efficacy of treatments. However, predicting the effect of drug combinations is still challenging. The combined potency of drugs determines the drug interaction, which is classified as synergistic, additive, antagonistic, or suppressive. While probabilistic, non-mechanistic models exist, there is currently no biophysical model that can predict antibiotic interactions. Here, we present a physiologically relevant model of the combined action of antibiotics that inhibit protein synthesis by targeting the ribosome. This model captures the kinetics of antibiotic binding and transport, and uses bacterial growth laws to predict growth in the presence of antibiotic combinations. We find that this biophysical model can produce all drug interaction types except suppression. We show analytically that antibiotics which cannot bind to the ribosome simultaneously generally act as substitutes for one another, leading to additive drug interactions. Previously proposed null expectations for higher-order drug interactions follow as a limiting case of our model. We further extend the model to include the effects of direct physical or allosteric interactions between individual drugs on the ribosome. Notably, such direct interactions profoundly change the combined drug effect, depending on the kinetic parameters of the drugs used. The model makes additional predictions for the effects of resistance genes on drug interactions and for interactions between ribosome-targeting antibiotics and antibiotics with other targets. These findings enhance our understanding of the interplay between drug action and cell physiology and are a key step toward a general framework for predicting drug interactions.","lang":"eng"}],"title":"A minimal biophysical model of combined antibiotic action","status":"public","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Cold Spring Harbor Laboratory","_id":"7673","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-22T08:27:56Z","date_updated":"2024-03-28T23:30:08Z","oa_version":"Preprint","author":[{"last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias"}],"related_material":{"record":[{"id":"8997","relation":"later_version","status":"public"},{"id":"8657","relation":"dissertation_contains","status":"public"}]},"month":"04","day":"18","article_processing_charge":"No","project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"publication":"bioRxiv","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.18.047886 "}],"citation":{"short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).","mla":"Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.18.047886.","ama":"Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.18.047886","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, 10.1101/2020.04.18.047886."},"language":[{"iso":"eng"}],"doi":"10.1101/2020.04.18.047886","date_published":"2020-04-18T00:00:00Z"},{"month":"06","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"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,"external_id":{"isi":["000565729700033"],"pmid":["32541049"]},"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF"}],"doi":"10.1073/pnas.2003346117","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"article_number":"202003346","file_date_updated":"2020-07-14T12:48:07Z","ec_funded":1,"year":"2020","pmid":1,"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"author":[{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas"},{"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":"Marhavá, Petra","last_name":"Marhavá","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"full_name":"Yoshida, Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/"}],"record":[{"id":"9992","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:10Z","date_created":"2020-06-22T13:33:52Z","volume":117,"scopus_import":"1","day":"30","has_accepted_license":"1","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2003346117.","short":"L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J. Friml, Proceedings of the National Academy of Sciences 117 (2020).","mla":"Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings of the National Academy of Sciences, vol. 117, no. 26, 202003346, Proceedings of the National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.","apa":"Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S., & Friml, J. (2020). Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2003346117","ieee":"L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots,” Proceedings of the National Academy of Sciences, vol. 117, no. 26. Proceedings of the National Academy of Sciences, 2020.","ista":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. 2020. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 117(26), 202003346.","ama":"Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J. Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots. Proceedings of the National Academy of Sciences. 2020;117(26). doi:10.1073/pnas.2003346117"},"article_type":"original","date_published":"2020-06-30T00:00:00Z","type":"journal_article","abstract":[{"text":"Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity.","lang":"eng"}],"issue":"26","_id":"8002","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots","status":"public","ddc":["580"],"intvolume":" 117","file":[{"date_created":"2020-06-23T11:30:53Z","date_updated":"2020-07-14T12:48:07Z","checksum":"908b09437680181de9990915f2113aca","file_id":"8009","relation":"main_file","creator":"dernst","file_size":2407102,"content_type":"application/pdf","file_name":"2020_PNAS_Hoermayer.pdf","access_level":"open_access"}],"oa_version":"None"},{"date_created":"2020-04-24T16:00:51Z","date_updated":"2023-09-22T09:20:10Z","author":[{"last_name":"Kainrath","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie"}],"related_material":{"record":[{"id":"1028","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"year":"2020","file_date_updated":"2021-10-31T23:30:05Z","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7680","oa":1,"month":"04","publication_identifier":{"eissn":["2663-337X"]},"file":[{"relation":"main_file","embargo":"2021-10-30","file_id":"7692","date_updated":"2021-10-31T23:30:05Z","date_created":"2020-04-28T11:19:21Z","checksum":"fb9a4468eb27be92690728e35c823796","file_name":"Thesis_without-signatures_PDFA.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3268017,"creator":"stgingl"},{"file_id":"7693","relation":"source_file","date_created":"2020-04-28T11:19:24Z","date_updated":"2021-10-31T23:30:05Z","checksum":"f6c80ca97104a631a328cb79a2c53493","file_name":"Thesis_without signatures.docx","embargo_to":"open_access","access_level":"closed","creator":"stgingl","file_size":5167703,"content_type":"application/octet-stream"}],"oa_version":"None","ddc":["570"],"title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","status":"public","_id":"7680","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2020-04-24T00:00:00Z","page":"98","citation":{"ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","apa":"Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:10.15479/AT:ISTA:7680","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7680.","short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","mla":"Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680."},"day":"24","has_accepted_license":"1","article_processing_charge":"No"},{"status":"public","ddc":["610"],"title":"Illuminating the role of Cul3 in autism spectrum disorder pathogenesis","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8620","file":[{"relation":"main_file","file_id":"8621","embargo":"2021-10-15","checksum":"7ee83e42de3e5ce2fedb44dff472f75f","date_created":"2020-10-07T14:41:49Z","date_updated":"2021-10-16T22:30:04Z","access_level":"open_access","file_name":"Jasmin_Morandell_Thesis-2020_final.pdf","content_type":"application/pdf","file_size":16155786,"creator":"jmorande"},{"checksum":"5e0464af453734210ce7aab7b4a92e3a","date_updated":"2021-10-16T22:30:04Z","date_created":"2020-10-07T14:45:07Z","relation":"source_file","file_id":"8622","file_size":24344152,"content_type":"application/x-zip-compressed","creator":"jmorande","access_level":"closed","embargo_to":"open_access","file_name":"Jasmin_Morandell_Thesis-2020_final.zip"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"The development of the human brain occurs through a tightly regulated series of dynamic and adaptive processes during prenatal and postnatal life. A disruption of this strictly orchestrated series of events can lead to a number of neurodevelopmental conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common, etiologically and phenotypically heterogeneous group of disorders sharing the core symptoms of social interaction and communication deficits and restrictive and repetitive interests and behaviors. They are estimated to affect one in 59 individuals in the U.S. and, over the last three decades, mutations in more than a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet, for the vast majority of these ASD-risk genes their role during brain development and precise molecular function still remain elusive.\r\nDe novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In the study described here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display cortical lamination abnormalities due to defective migration of post-mitotic excitatory neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal cortical organization, Cul3 heterozygous deletion is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neural cells results in atypical organization of the actin mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult mice does not induce the majority of the behavioral defects observed in constitutive Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn conclusion, our data indicate that Cul3 plays a critical role in the regulation of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral abnormalities are primarily due to dosage sensitive Cul3 functions at early brain developmental stages."}],"page":"138","citation":{"ama":"Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. 2020. doi:10.15479/AT:ISTA:8620","apa":"Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620","ieee":"J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020.","ista":"Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria.","short":"J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis, Institute of Science and Technology Austria, 2020.","mla":"Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620.","chicago":"Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620."},"date_published":"2020-10-12T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"12","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaNo"}],"publication_status":"published","year":"2020","acknowledgement":"I would like to especially thank Armel Nicolas from the Proteomics and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka, Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line maintenance and their great support.","date_created":"2020-10-07T14:53:13Z","date_updated":"2023-09-07T13:22:14Z","related_material":{"record":[{"id":"7800","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8131"}]},"author":[{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Morandell","full_name":"Morandell, Jasmin"}],"file_date_updated":"2021-10-16T22:30:04Z","project":[{"grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets"},{"name":"Neural stem cells in autism and epilepsy","grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"}],"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"doi":"10.15479/AT:ISTA:8620","publication_identifier":{"issn":["2663-337X"]},"month":"10"},{"file_date_updated":"2021-09-11T22:30:04Z","ec_funded":1,"date_updated":"2023-09-07T13:26:17Z","date_created":"2020-09-07T18:42:23Z","author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen","last_name":"Kampjut"}],"related_material":{"record":[{"id":"6848","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"LeSa"}],"year":"2020","acknowledgement":"I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","month":"09","publication_identifier":{"isbn":["978-3-99078-008-4"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8340","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"oa":1,"abstract":[{"lang":"eng","text":"Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"None","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":166146359,"creator":"dkampjut","embargo_to":"open_access","file_name":"ThesisFull20200908.docx","access_level":"closed","date_updated":"2021-09-11T22:30:04Z","date_created":"2020-09-08T13:32:06Z","checksum":"dd270baf82121eb4472ad19d77bf227c","relation":"source_file","file_id":"8345"},{"file_id":"8393","embargo":"2021-09-10","relation":"main_file","date_created":"2020-09-14T15:02:20Z","date_updated":"2021-09-11T22:30:04Z","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c","file_name":"2020_Thesis_Kampjut.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":13873769}],"title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","ddc":["572"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8340","day":"09","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-09-09T00:00:00Z","page":"242","citation":{"chicago":"Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340.","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","mla":"Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340.","apa":"Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020.","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:10.15479/AT:ISTA:8340"}},{"file":[{"access_level":"open_access","file_name":"2020.01.10.902064v1.full.pdf","content_type":"application/pdf","file_size":2931370,"creator":"rsix","relation":"main_file","file_id":"7801","checksum":"c6799ab5daba80efe8e2ed63c15f8c81","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-05T14:31:19Z"}],"oa_version":"Preprint","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7800","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization, Cul3 haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development, Cul3 deficiency appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutive Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due to Cul3 functions at early developmental stages.","lang":"eng"}],"type":"preprint","date_published":"2020-01-11T00:00:00Z","citation":{"ieee":"J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer, C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.01.10.902064 ","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv, 10.1101/2020.01.10.902064 .","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. bioRxiv. doi:10.1101/2020.01.10.902064 ","chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.01.10.902064 .","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer, C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv (n.d.).","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.01.10.902064 ."},"publication":"bioRxiv","has_accepted_license":"1","article_processing_charge":"No","day":"11","date_updated":"2024-03-28T23:30:14Z","date_created":"2020-05-05T14:31:33Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"9429"},{"id":"8620","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin","full_name":"Morandell, Jasmin"},{"full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Lena A"},{"full_name":"Basilico, Bernadette","first_name":"Bernadette","last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173"},{"first_name":"Saren","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren"},{"full_name":"Nicolas, Armel","first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline"},{"full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","first_name":"Lisa"},{"full_name":"Dobler, Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","last_name":"Dobler","first_name":"Zoe"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"JoDa"},{"_id":"GaNo"},{"_id":"LifeSc"}],"publication_status":"submitted","year":"2020","file_date_updated":"2020-07-14T12:48:03Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"}],"doi":"10.1101/2020.01.10.902064 ","project":[{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF"}],"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"},"month":"01"},{"date_published":"2020-12-01T00:00:00Z","publication":"Current Opinion in Genetics and Development","citation":{"ista":"Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137.","ieee":"B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted ASD treatments,” Current Opinion in Genetics and Development, vol. 65, no. 12. Elsevier, pp. 126–137, 2020.","apa":"Basilico, B., Morandell, J., & Novarino, G. (2020). Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2020.06.004","ama":"Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 2020;65(12):126-137. doi:10.1016/j.gde.2020.06.004","chicago":"Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms for Targeted ASD Treatments.” Current Opinion in Genetics and Development. Elsevier, 2020. https://doi.org/10.1016/j.gde.2020.06.004.","mla":"Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.” Current Opinion in Genetics and Development, vol. 65, no. 12, Elsevier, 2020, pp. 126–37, doi:10.1016/j.gde.2020.06.004.","short":"B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics and Development 65 (2020) 126–137."},"article_type":"original","page":"126-137","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_CurrentOpGenetics_Basilico.pdf","creator":"dernst","content_type":"application/pdf","file_size":1381545,"file_id":"8146","relation":"main_file","success":1,"date_created":"2020-07-22T06:47:45Z","date_updated":"2020-07-22T06:47:45Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8131","title":"Molecular mechanisms for targeted ASD treatments","status":"public","ddc":["570"],"intvolume":" 65","abstract":[{"lang":"eng","text":"The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes."}],"issue":"12","type":"journal_article","doi":"10.1016/j.gde.2020.06.004","language":[{"iso":"eng"}],"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"},"external_id":{"pmid":["32659636"],"isi":["000598918900019"]},"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"name":"Neural stem cells in autism and epilepsy","grant_number":"F07807","_id":"05A0D778-7A3F-11EA-A408-12923DDC885E"}],"month":"12","publication_identifier":{"issn":["0959437X"],"eissn":["18790380"]},"author":[{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","first_name":"Bernadette","last_name":"Basilico","full_name":"Basilico, Bernadette"},{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin","full_name":"Morandell, Jasmin"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8620"}]},"date_updated":"2024-03-28T23:30:14Z","date_created":"2020-07-19T22:00:58Z","volume":65,"year":"2020","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-22T06:47:45Z","ec_funded":1},{"keyword":["Cell Biology"],"article_processing_charge":"No","has_accepted_license":"1","day":"09","article_type":"original","citation":{"ieee":"G. A. Dimchev et al., “Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation,” Journal of Cell Science, vol. 133, no. 7. The Company of Biologists, 2020.","apa":"Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal, T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.239020","ista":"Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 133(7), jcs239020.","ama":"Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science. 2020;133(7). doi:10.1242/jcs.239020","chicago":"Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks, Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.239020.","short":"G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal, J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133 (2020).","mla":"Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal of Cell Science, vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:10.1242/jcs.239020."},"publication":"Journal of Cell Science","date_published":"2020-04-09T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"text":"Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. ","lang":"eng"}],"intvolume":" 133","status":"public","title":"Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation","ddc":["570"],"_id":"8434","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"checksum":"ba917e551acc4ece2884b751434df9ae","date_created":"2020-09-17T14:07:51Z","date_updated":"2020-10-11T22:30:02Z","file_id":"8435","embargo":"2020-10-10","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":13493302,"access_level":"open_access","file_name":"2020_JournalCellScience_Dimchev.pdf"}],"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"month":"04","project":[{"name":"Protein structure and function in filopodia across scales","call_identifier":"FWF","grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":[" 32094266"],"isi":["000534387800005"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1242/jcs.239020","article_number":"jcs239020","file_date_updated":"2020-10-11T22:30:02Z","publisher":"The Company of Biologists","department":[{"_id":"FlSc"}],"publication_status":"published","pmid":1,"acknowledgement":"This work was supported in part by Deutsche Forschungsgemeinschaft (DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.). G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program [M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives its core funding from Cancer Research UK [FC001209], theMedical Research Council [FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1]. Deposited in PMC for release after 6months.","year":"2020","volume":133,"date_created":"2020-09-17T14:00:33Z","date_updated":"2023-09-05T15:41:48Z","author":[{"full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161"},{"first_name":"Behnam","last_name":"Amiri","full_name":"Amiri, Behnam"},{"first_name":"Ashley C.","last_name":"Humphries","full_name":"Humphries, Ashley C."},{"first_name":"Matthias","last_name":"Schaks","full_name":"Schaks, Matthias"},{"full_name":"Dimchev, Vanessa","last_name":"Dimchev","first_name":"Vanessa"},{"last_name":"Stradal","first_name":"Theresia E. B.","full_name":"Stradal, Theresia E. B."},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"},{"full_name":"Krause, Matthias","first_name":"Matthias","last_name":"Krause"},{"first_name":"Michael","last_name":"Way","full_name":"Way, Michael"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"}]},{"day":"27","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-04-27T00:00:00Z","publication":"Nature Biotechnology","citation":{"chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology. Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9.","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946.","mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9.","ieee":"T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,” Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020.","apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9","ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9"},"article_type":"original","page":"944-946","abstract":[{"text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","creator":"dernst","content_type":"application/pdf","file_size":1180086,"file_id":"8316","embargo":"2021-03-01","relation":"main_file","checksum":"1b30467500ec6277229a875b06e196d0","date_created":"2020-08-28T08:57:07Z","date_updated":"2021-03-02T23:30:03Z"}],"_id":"7889","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Plants with genetically encoded autoluminescence","status":"public","ddc":["570"],"intvolume":" 38","month":"04","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"doi":"10.1038/s41587-020-0500-9","language":[{"iso":"eng"}],"external_id":{"pmid":["32341562"],"isi":["000529298800003"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2021-03-02T23:30:03Z","ec_funded":1,"author":[{"full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana","last_name":"Mitiouchkina"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"last_name":"Gonzalez Somermeyer","first_name":"Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa"},{"full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M.","last_name":"Markina"},{"first_name":"Tatiana V.","last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V."},{"first_name":"Elena B.","last_name":"Guglya","full_name":"Guglya, Elena B."},{"first_name":"Tatiana A.","last_name":"Karataeva","full_name":"Karataeva, Tatiana A."},{"full_name":"Palkina, Kseniia A.","first_name":"Kseniia A.","last_name":"Palkina"},{"full_name":"Shakhova, Ekaterina S.","last_name":"Shakhova","first_name":"Ekaterina S."},{"full_name":"Fakhranurova, Liliia I.","first_name":"Liliia I.","last_name":"Fakhranurova"},{"last_name":"Chekova","first_name":"Sofia V.","full_name":"Chekova, Sofia V."},{"full_name":"Tsarkova, Aleksandra S.","last_name":"Tsarkova","first_name":"Aleksandra S."},{"last_name":"Golubev","first_name":"Yaroslav V.","full_name":"Golubev, Yaroslav V."},{"full_name":"Negrebetsky, Vadim V.","first_name":"Vadim V.","last_name":"Negrebetsky"},{"full_name":"Dolgushin, Sergey A.","first_name":"Sergey A.","last_name":"Dolgushin"},{"first_name":"Pavel V.","last_name":"Shalaev","full_name":"Shalaev, Pavel V."},{"last_name":"Shlykov","first_name":"Dmitry","full_name":"Shlykov, Dmitry"},{"last_name":"Melnik","first_name":"Olesya A.","full_name":"Melnik, Olesya A."},{"full_name":"Shipunova, Victoria O.","first_name":"Victoria O.","last_name":"Shipunova"},{"last_name":"Deyev","first_name":"Sergey M.","full_name":"Deyev, Sergey M."},{"full_name":"Bubyrev, Andrey I.","last_name":"Bubyrev","first_name":"Andrey I."},{"first_name":"Alexander S.","last_name":"Pushin","full_name":"Pushin, Alexander S."},{"last_name":"Choob","first_name":"Vladimir V.","full_name":"Choob, Vladimir V."},{"first_name":"Sergey V.","last_name":"Dolgov","full_name":"Dolgov, Sergey V."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"last_name":"Yampolsky","first_name":"Ilia V.","full_name":"Yampolsky, Ilia V."},{"full_name":"Sarkisyan, Karen S.","last_name":"Sarkisyan","first_name":"Karen S."}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41587-020-0578-0"}]},"date_updated":"2023-09-05T15:30:34Z","date_created":"2020-05-25T15:02:00Z","volume":38,"year":"2020","acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","pmid":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature"},{"article_processing_charge":"No","day":"20","month":"11","date_published":"2020-11-20T00:00:00Z","doi":"10.1101/2020.11.20.391284","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"SSU"}],"citation":{"chicago":"Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.11.20.391284.","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.11.20.391284.","short":"J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K. Huljev, C.-P.J. Heisenberg, BioRxiv (2020).","ista":"Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K, Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv, 10.1101/2020.11.20.391284.","apa":"Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W., Huljev, K., & Heisenberg, C.-P. J. (2020). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.20.391284","ieee":"J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","ama":"Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion. bioRxiv. 2020. doi:10.1101/2020.11.20.391284"},"main_file_link":[{"url":"https://doi.org/10.1101/2020.11.20.391284","open_access":"1"}],"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":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013","_id":"2521E28E-B435-11E9-9278-68D0E5697425"}],"page":"41","ec_funded":1,"abstract":[{"lang":"eng","text":"Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact."}],"type":"preprint","related_material":{"record":[{"id":"10766","status":"public","relation":"later_version"},{"id":"9623","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","last_name":"Slovakova","first_name":"Jana","full_name":"Slovakova, Jana"},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora"},{"full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346"},{"last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Huljev, Karla","first_name":"Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"oa_version":"Preprint","date_updated":"2024-03-28T23:30:19Z","date_created":"2021-07-29T11:29:50Z","_id":"9750","acknowledgement":"We would like to thank Edouard Hannezo for discussions, Shayan Shami Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript. We also thank Jack Merrin for preparing the microwells, and the Scientific Service Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC) to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie COFUND No. P_IST_EU01 to J.S.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2020","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"status":"public","title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion","publication_status":"published"},{"date_published":"2020-05-01T00:00:00Z","publication":"Nonlinear Analysis: Hybrid Systems","citation":{"ama":"Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 2020;36(5). doi:10.1016/j.nahs.2020.100856","ieee":"M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5. Elsevier, 2020.","apa":"Garcia Soto, M., & Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2020.100856","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems, vol. 36, no. 5, 100856, Elsevier, 2020, doi:10.1016/j.nahs.2020.100856.","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2020. https://doi.org/10.1016/j.nahs.2020.100856."},"article_type":"original","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"checksum":"560abfddb53f9fe921b6744f59f2cfaa","date_created":"2020-10-21T13:16:45Z","date_updated":"2022-05-16T22:30:04Z","embargo":"2022-05-15","file_id":"8688","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":818774,"access_level":"open_access","file_name":"2020_NAHS_GarciaSoto.pdf"}],"oa_version":"Submitted Version","_id":"7426","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["000"],"title":"Abstraction based verification of stability of polyhedral switched systems","status":"public","intvolume":" 36","abstract":[{"lang":"eng","text":"This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method."}],"issue":"5","type":"journal_article","doi":"10.1016/j.nahs.2020.100856","language":[{"iso":"eng"}],"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,"external_id":{"isi":["000528828600003"]},"quality_controlled":"1","isi":1,"project":[{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"month":"05","publication_identifier":{"issn":["1751-570X"]},"author":[{"last_name":"Garcia Soto","first_name":"Miriam","orcid":"0000−0003−2936−5719","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Soto, Miriam"},{"first_name":"Pavithra","last_name":"Prabhakar","full_name":"Prabhakar, Pavithra"}],"date_updated":"2023-08-17T14:32:54Z","date_created":"2020-02-02T23:00:59Z","volume":36,"year":"2020","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Elsevier","file_date_updated":"2022-05-16T22:30:04Z","article_number":"100856"},{"status":"public","title":"Metabolic regulation of Drosophila macrophage tissue invasion","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8983","file":[{"checksum":"ec2797ab7a6f253b35df0572b36d1b43","date_created":"2020-12-30T15:34:01Z","date_updated":"2021-12-31T23:30:04Z","file_id":"8984","embargo":"2021-12-30","relation":"main_file","creator":"semtenan","file_size":10848175,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf"},{"content_type":"application/pdf","file_size":10073648,"creator":"semtenan","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","checksum":"cc30e6608a9815414024cf548dff3b3a","date_updated":"2021-12-31T23:30:04Z","date_created":"2020-12-30T15:37:36Z","relation":"source_file","file_id":"8985"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers.","lang":"eng"}],"page":"141","citation":{"ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","apa":"Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983","ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:10.15479/AT:ISTA:8983","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983.","mla":"Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983.","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020."},"date_published":"2020-12-30T00:00:00Z","day":"30","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","year":"2020","date_updated":"2023-09-07T13:24:17Z","date_created":"2020-12-30T15:41:26Z","author":[{"first_name":"Shamsi","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi"}],"related_material":{"record":[{"id":"8557","status":"public","relation":"part_of_dissertation"},{"id":"6187","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2021-12-31T23:30:04Z","oa":1,"supervisor":[{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8983","month":"12","publication_identifier":{"issn":["2663-337X"]}},{"doi":"10.1101/2020.09.18.301481","date_published":"2020-09-18T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"publication":"bioRxiv","main_file_link":[{"url":"https://doi.org/10.1101/2020.09.18.301481","open_access":"1"}],"citation":{"ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. doi:10.1101/2020.09.18.301481","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, 10.1101/2020.09.18.301481.","apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. https://doi.org/10.1101/2020.09.18.301481","ieee":"V. Belyaeva et al., “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” bioRxiv. .","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, doi:10.1101/2020.09.18.301481.","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, n.d. https://doi.org/10.1101/2020.09.18.301481."},"oa":1,"project":[{"grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7"},{"grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425","name":"Tissue barrier penetration is crucial for immunity and metastasis"}],"day":"18","month":"09","article_processing_charge":"No","author":[{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","last_name":"Belyaeva","first_name":"Vera","full_name":"Belyaeva, Vera"},{"first_name":"Stephanie","last_name":"Wachner","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","full_name":"Wachner, Stephanie"},{"last_name":"Gridchyn","first_name":"Igor","orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","full_name":"Gridchyn, Igor"},{"last_name":"Linder","first_name":"Markus","full_name":"Linder, Markus"},{"first_name":"Shamsi","last_name":"Emtenani","id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","first_name":"Attila","last_name":"György","full_name":"György, Attila"},{"full_name":"Sibilia, Maria","first_name":"Maria","last_name":"Sibilia"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10614"},{"id":"8983","relation":"dissertation_contains","status":"public"}]},"date_created":"2020-09-23T09:36:47Z","date_updated":"2024-03-28T23:30:25Z","oa_version":"Preprint","year":"2020","_id":"8557","acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","publication_status":"submitted","status":"public","department":[{"_id":"DaSi"},{"_id":"JoCs"}],"abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues."}],"ec_funded":1,"type":"preprint"},{"article_number":"2012.00322","ec_funded":1,"file_date_updated":"2020-12-02T10:42:31Z","acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. GS and MV acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO).","year":"2020","department":[{"_id":"GeKa"}],"publication_status":"submitted","related_material":{"record":[{"id":"10559","status":"public","relation":"later_version"},{"status":"public","relation":"research_data","id":"8834"},{"status":"public","relation":"dissertation_contains","id":"10058"}]},"author":[{"full_name":"Aggarwal, Kushagra","orcid":"0000-0001-9985-9293","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","last_name":"Aggarwal","first_name":"Kushagra"},{"full_name":"Hofmann, Andrea C","last_name":"Hofmann","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jirovec, Daniel","last_name":"Jirovec","first_name":"Daniel","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prieto Gonzalez","first_name":"Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan"},{"full_name":"Sammak, Amir","last_name":"Sammak","first_name":"Amir"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"full_name":"Marti-Sanchez, Sara","last_name":"Marti-Sanchez","first_name":"Sara"},{"full_name":"Veldhorst, Menno","last_name":"Veldhorst","first_name":"Menno"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"full_name":"Scappucci, Giordano","first_name":"Giordano","last_name":"Scappucci"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-28T23:30:27Z","date_created":"2020-12-02T10:42:53Z","month":"12","external_id":{"arxiv":["2012.00322"]},"oa":1,"project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020","grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"type":"preprint","abstract":[{"lang":"eng","text":"Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8831","title":"Enhancement of proximity induced superconductivity in planar Germanium","ddc":["530"],"status":"public","file":[{"checksum":"22a612e206232fa94b138b2c2f957582","date_created":"2020-12-02T10:42:31Z","date_updated":"2020-12-02T10:42:31Z","relation":"main_file","file_id":"8832","file_size":1697939,"content_type":"application/pdf","creator":"gkatsaro","access_level":"open_access","file_name":"Superconducting_2D_Ge.pdf"}],"oa_version":"Submitted Version","article_processing_charge":"No","has_accepted_license":"1","day":"02","citation":{"ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. arXiv, 2012.00322.","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity in planar Germanium. arXiv.","ieee":"K. Aggarwal et al., “Enhancement of proximity induced superconductivity in planar Germanium,” arXiv. .","ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced superconductivity in planar Germanium. arXiv.","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, n.d.","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, 2012.00322.","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros, ArXiv (n.d.)."},"publication":"arXiv","date_published":"2020-12-02T00:00:00Z"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"14","citation":{"ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 2020;21(18). doi:10.3390/ijms21186737","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., & Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21186737","ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” International Journal of Molecular Sciences, vol. 21, no. 18. MDPI, 2020.","mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences, vol. 21, no. 18, 6737, MDPI, 2020, doi:10.3390/ijms21186737.","short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21186737."},"publication":"International Journal of Molecular Sciences","article_type":"original","date_published":"2020-09-14T00:00:00Z","type":"journal_article","issue":"18","abstract":[{"lang":"eng","text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8532","intvolume":" 21","ddc":["570"],"status":"public","title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","oa_version":"Published Version","file":[{"success":1,"checksum":"2e4f62f3cfe945b7391fc3070e5a289f","date_updated":"2020-09-21T14:08:58Z","date_created":"2020-09-21T14:08:58Z","file_id":"8551","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":5748456,"access_level":"open_access","file_name":"2020_JournMolecSciences_Kleindienst.pdf"}],"publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"month":"09","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":["000579945300001"]},"project":[{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"},{"_id":"25D32BC0-B435-11E9-9278-68D0E5697425","name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus"},{"_id":"26436750-B435-11E9-9278-68D0E5697425","grant_number":"785907","call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)"}],"quality_controlled":"1","isi":1,"doi":"10.3390/ijms21186737","language":[{"iso":"eng"}],"article_number":"6737","ec_funded":1,"file_date_updated":"2020-09-21T14:08:58Z","year":"2020","acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","publisher":"MDPI","department":[{"_id":"RySh"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9562"}]},"author":[{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst","full_name":"Kleindienst, David"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber"},{"full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481","first_name":"Pradeep","last_name":"Bhandari"},{"first_name":"Matthew J","last_name":"Case","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Case, Matthew J"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"volume":21,"date_updated":"2024-03-28T23:30:31Z","date_created":"2020-09-20T22:01:35Z"},{"month":"04","publication_identifier":{"eissn":["16113349"],"isbn":["9783030449131"],"issn":["03029743"]},"external_id":{"isi":["000681656800005"]},"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","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"conference":{"end_date":"2020-04-30","start_date":"2020-04-25","location":"Dublin, Ireland","name":"ESOP: Programming Languages and Systems"},"doi":"10.1007/978-3-030-44914-8_5","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:03Z","year":"2020","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"date_updated":"2024-03-28T23:30:34Z","date_created":"2020-05-10T22:00:50Z","volume":12075,"scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","publication":"European Symposium on Programming","citation":{"short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European Symposium on Programming, Springer Nature, 2020, pp. 112–140.","mla":"Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” European Symposium on Programming, vol. 12075, Springer Nature, 2020, pp. 112–40, doi:10.1007/978-3-030-44914-8_5.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” In European Symposium on Programming, 12075:112–40. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-44914-8_5.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In: European Symposium on Programming. Vol 12075. Springer Nature; 2020:112-140. doi:10.1007/978-3-030-44914-8_5","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A. (2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In European Symposium on Programming (Vol. 12075, pp. 112–140). Dublin, Ireland: Springer Nature. https://doi.org/10.1007/978-3-030-44914-8_5","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal and perfectly parallel algorithms for on-demand data-flow analysis,” in European Symposium on Programming, Dublin, Ireland, 2020, vol. 12075, pp. 112–140.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140."},"page":"112-140","date_published":"2020-04-18T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries.\r\nIn this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7810","title":"Optimal and perfectly parallel algorithms for on-demand data-flow analysis","status":"public","ddc":["000"],"intvolume":" 12075","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-26T13:34:48Z","checksum":"8618b80f4cf7b39a60e61a6445ad9807","file_id":"7895","relation":"main_file","creator":"dernst","file_size":651250,"content_type":"application/pdf","file_name":"2020_LNCS_Chatterjee.pdf","access_level":"open_access"}]},{"abstract":[{"lang":"eng","text":"Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improvements. In this work, we show that treewidth can also be used to obtain faster algorithms for the quantitative problems. For an MC with n states and m transitions, we show that each of the classical quantitative objectives can be computed in O((n+m)⋅t2) time, given a tree decomposition of the MC with width t. Our results also imply a bound of O(κ⋅(n+m)⋅t2) for each objective on MDPs, where κ is the number of strategy-iteration refinements required for the given input and objective. Finally, we make an experimental evaluation of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms outperform existing well-established methods by one or more orders of magnitude."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2020_LNCS_ATVA_Asadi_accepted.pdf","creator":"dernst","file_size":726648,"content_type":"application/pdf","file_id":"8729","relation":"main_file","success":1,"checksum":"ae83f27e5b189d5abc2e7514f1b7e1b5","date_updated":"2020-11-06T07:41:03Z","date_created":"2020-11-06T07:41:03Z"}],"_id":"8728","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth","ddc":["000"],"intvolume":" 12302","day":"12","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-10-12T00:00:00Z","publication":"Automated Technology for Verification and Analysis","citation":{"ama":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In: Automated Technology for Verification and Analysis. Vol 12302. Springer Nature; 2020:253-270. doi:10.1007/978-3-030-59152-6_14","ista":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. 2020. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 12302, 253–270.","ieee":"A. Asadi, K. Chatterjee, A. K. Goharshady, K. Mohammadi, and A. Pavlogiannis, “Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth,” in Automated Technology for Verification and Analysis, Hanoi, Vietnam, 2020, vol. 12302, pp. 253–270.","apa":"Asadi, A., Chatterjee, K., Goharshady, A. K., Mohammadi, K., & Pavlogiannis, A. (2020). Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In Automated Technology for Verification and Analysis (Vol. 12302, pp. 253–270). Hanoi, Vietnam: Springer Nature. https://doi.org/10.1007/978-3-030-59152-6_14","mla":"Asadi, Ali, et al. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” Automated Technology for Verification and Analysis, vol. 12302, Springer Nature, 2020, pp. 253–70, doi:10.1007/978-3-030-59152-6_14.","short":"A. Asadi, K. Chatterjee, A.K. Goharshady, K. Mohammadi, A. Pavlogiannis, in:, Automated Technology for Verification and Analysis, Springer Nature, 2020, pp. 253–270.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Kiarash Mohammadi, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” In Automated Technology for Verification and Analysis, 12302:253–70. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-59152-6_14."},"page":"253-270","file_date_updated":"2020-11-06T07:41:03Z","author":[{"full_name":"Asadi, Ali","last_name":"Asadi","first_name":"Ali"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Mohammadi, Kiarash","first_name":"Kiarash","last_name":"Mohammadi"},{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"date_updated":"2024-03-28T23:30:34Z","date_created":"2020-11-06T07:30:05Z","volume":12302,"year":"2020","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","month":"10","publication_identifier":{"eisbn":["9783030591526"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030591519"]},"conference":{"location":"Hanoi, Vietnam","start_date":"2020-10-19","end_date":"2020-10-23","name":"ATVA: Automated Technology for Verification and Analysis"},"doi":"10.1007/978-3-030-59152-6_14","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000723555700014"]},"isi":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}]},{"page":"672-687","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","citation":{"ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial invariant generation for non-deterministic recursive programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 672–687.","apa":"Chatterjee, K., Fu, H., Goharshady, A. K., & Goharshady, E. K. (2020). Polynomial invariant generation for non-deterministic recursive programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 672–687). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385969","ista":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant generation for non-deterministic recursive programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 672–687.","ama":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation for non-deterministic recursive programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:672-687. doi:10.1145/3385412.3385969","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 672–87. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385969.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–687.","mla":"Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–87, doi:10.1145/3385412.3385969."},"date_published":"2020-06-11T00:00:00Z","scopus_import":"1","day":"11","article_processing_charge":"No","title":"Polynomial invariant generation for non-deterministic recursive programs","status":"public","_id":"8089","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"conference","abstract":[{"text":"We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example.","lang":"eng"}],"isi":1,"quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1902.04373","open_access":"1"}],"external_id":{"isi":["000614622300045"],"arxiv":["1902.04373"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2020-06-20","location":"London, United Kingdom","start_date":"2020-06-15","name":"PLDI: Programming Language Design and Implementation"},"doi":"10.1145/3385412.3385969","month":"06","publication_identifier":{"isbn":["9781450376136"]},"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"year":"2020","date_created":"2020-07-05T22:00:45Z","date_updated":"2024-03-28T23:30:34Z","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Fu","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","full_name":"Fu, Hongfei"},{"orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar"},{"first_name":"Ehsan Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar"}],"related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]}},{"publication_identifier":{"issn":["09518320"]},"month":"01","project":[{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.09692"}],"oa":1,"external_id":{"isi":["000501641400050"],"arxiv":["1712.09692"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.ress.2019.106665","article_number":"106665","department":[{"_id":"KrCh"}],"publisher":"Elsevier","publication_status":"published","acknowledgement":"We are grateful to the anonymous reviewers for their comments, which significantly improved the present work. The research was partially supported by the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian Academy of Sciences (ÖAW).","year":"2020","volume":193,"date_created":"2019-09-29T22:00:44Z","date_updated":"2024-03-28T23:30:34Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"author":[{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Mohammadi, Fatemeh","first_name":"Fatemeh","last_name":"Mohammadi"}],"scopus_import":"1","article_processing_charge":"No","day":"01","article_type":"original","citation":{"ama":"Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 2020;193. doi:10.1016/j.ress.2019.106665","apa":"Goharshady, A. K., & Mohammadi, F. (2020). An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. Elsevier. https://doi.org/10.1016/j.ress.2019.106665","ieee":"A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network reliability in small treewidth,” Reliability Engineering and System Safety, vol. 193. Elsevier, 2020.","ista":"Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665.","short":"A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (2020).","mla":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety, vol. 193, 106665, Elsevier, 2020, doi:10.1016/j.ress.2019.106665.","chicago":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety. Elsevier, 2020. https://doi.org/10.1016/j.ress.2019.106665."},"publication":"Reliability Engineering and System Safety","date_published":"2020-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem."}],"intvolume":" 193","title":"An efficient algorithm for computing network reliability in small treewidth","status":"public","_id":"6918","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint"},{"publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Springer Nature","acknowledgement":"We are grateful to the anonymous referees and editor whose insightful comments helped to considerably improve an earlier version of this paper. The research of the first author is supported by an ERC Grant from the Institute of Science and Technology (IST).","year":"2020","date_updated":"2023-09-06T11:27:15Z","date_created":"2019-12-09T21:33:44Z","volume":184,"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"},{"full_name":"Sagratella, Simone","last_name":"Sagratella","first_name":"Simone"}],"file_date_updated":"2021-03-16T23:30:04Z","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"external_id":{"isi":["000511805200009"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s10957-019-01616-6","month":"03","publication_identifier":{"eissn":["1573-2878"],"issn":["0022-3239"]},"ddc":["518","510","515"],"status":"public","title":"Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces","intvolume":" 184","_id":"7161","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"9f6dc6c6bf2b48cb3a2091a9ed5feaf2","date_created":"2020-10-12T10:40:27Z","date_updated":"2021-03-16T23:30:04Z","relation":"main_file","embargo":"2021-03-15","file_id":"8647","file_size":332641,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_JourOptimizationTheoryApplic_Shehu.pdf"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"In this paper, we introduce an inertial projection-type method with different updating strategies for solving quasi-variational inequalities with strongly monotone and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions, we establish different strong convergence results for the proposed algorithm. Primary numerical experiments demonstrate the potential applicability of our scheme compared with some related methods in the literature.","lang":"eng"}],"article_type":"original","page":"877–894","publication":"Journal of Optimization Theory and Applications","citation":{"ama":"Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6","ieee":"Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces,” Journal of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894, 2020.","apa":"Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6","ista":"Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 184, 877–894.","short":"Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications 184 (2020) 877–894.","mla":"Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications, vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6.","chicago":"Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6."},"date_published":"2020-03-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"8640","checksum":"ef3bbf42023e30b2c24a6278025d2040","success":1,"date_created":"2020-10-09T09:56:01Z","date_updated":"2020-10-09T09:56:01Z","access_level":"open_access","file_name":"2020_NatureEcolEvo_Tomanek.pdf","content_type":"application/pdf","file_size":745242,"creator":"dernst"}],"intvolume":" 4","title":"Gene amplification as a form of population-level gene expression regulation","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7652","issue":"4","abstract":[{"text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature.","lang":"eng"}],"type":"journal_article","date_published":"2020-04-01T00:00:00Z","page":"612-625","article_type":"original","citation":{"chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7.","short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.","mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.","apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7","ieee":"I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.","ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 4(4), 612–625.","ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7"},"publication":"Nature Ecology & Evolution","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","volume":4,"date_updated":"2024-03-28T23:30:37Z","date_created":"2020-04-08T15:20:53Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"relation":"dissertation_contains","status":"public","id":"8155"},{"relation":"research_data","status":"public","id":"7383"},{"id":"7016","status":"public","relation":"research_data"},{"id":"8653","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87","last_name":"Tomanek","first_name":"Isabella"},{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","first_name":"Rok","last_name":"Grah","full_name":"Grah, Rok"},{"full_name":"Lagator, M.","last_name":"Lagator","first_name":"M."},{"first_name":"A. M. C.","last_name":"Andersson","full_name":"Andersson, A. M. C."},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"}],"publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"publication_status":"published","year":"2020","acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.","file_date_updated":"2020-10-09T09:56:01Z","language":[{"iso":"eng"}],"doi":"10.1038/s41559-020-1132-7","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000519008300005"]},"oa":1,"publication_identifier":{"issn":["2397-334X"]},"month":"04"}]