[{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","intvolume":"       153","quality_controlled":"1","department":[{"_id":"KrCh"}],"publication":"Proceedings of the 23rd International Conference on Principles of Distributed Systems","date_created":"2020-01-21T16:00:26Z","month":"02","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"ddc":["000"],"doi":"10.4230/LIPIcs.OPODIS.2019.21","language":[{"iso":"eng"}],"conference":{"name":"OPODIS: International Conference on Principles of Distributed Systems","start_date":"2019-12-17","end_date":"2019-12-19","location":"Neuchâtel, Switzerland"},"title":"The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game","citation":{"chicago":"Schmid, Laura, Krishnendu Chatterjee, and Stefan Schmid. “The Evolutionary Price of Anarchy: Locally Bounded Agents in a Dynamic Virus Game.” In <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>, Vol. 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.21</a>.","ista":"Schmid L, Chatterjee K, Schmid S. 2020. The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. Proceedings of the 23rd International Conference on Principles of Distributed Systems. OPODIS: International Conference on Principles of Distributed Systems, LIPIcs, vol. 153, 21.","ieee":"L. Schmid, K. Chatterjee, and S. Schmid, “The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game,” in <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>, Neuchâtel, Switzerland, 2020, vol. 153.","mla":"Schmid, Laura, et al. “The Evolutionary Price of Anarchy: Locally Bounded Agents in a Dynamic Virus Game.” <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>, vol. 153, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">10.4230/LIPIcs.OPODIS.2019.21</a>.","short":"L. Schmid, K. Chatterjee, S. Schmid, in:, Proceedings of the 23rd International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ama":"Schmid L, Chatterjee K, Schmid S. The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. In: <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>. Vol 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">10.4230/LIPIcs.OPODIS.2019.21</a>","apa":"Schmid, L., Chatterjee, K., &#38; Schmid, S. (2020). The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. In <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i> (Vol. 153). Neuchâtel, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.21</a>"},"alternative_title":["LIPIcs"],"author":[{"orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","first_name":"Laura","full_name":"Schmid, Laura"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"type":"conference","day":"10","oa":1,"publication_status":"published","volume":153,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:47:56Z","article_processing_charge":"No","arxiv":1,"_id":"7346","date_published":"2020-02-10T00:00:00Z","abstract":[{"lang":"eng","text":"The Price of Anarchy (PoA) is a well-established game-theoretic concept to shed light on coordination issues arising in open distributed systems. Leaving agents to selfishly optimize comes with the risk of ending up in sub-optimal states (in terms of performance and/or costs), compared to a centralized system design. However, the PoA relies on strong assumptions about agents' rationality (e.g., resources and information) and interactions, whereas in many distributed systems agents interact locally with bounded resources. They do so repeatedly over time (in contrast to \"one-shot games\"), and their strategies may evolve. Using a more realistic evolutionary game model, this paper introduces a realized evolutionary Price of Anarchy (ePoA). The ePoA allows an exploration of equilibrium selection in dynamic distributed systems with multiple equilibria, based on local interactions of simple memoryless agents. Considering a fundamental game related to virus propagation on networks, we present analytical bounds on the ePoA in basic network topologies and for different strategy update dynamics. In particular, deriving stationary distributions of the stochastic evolutionary process, we find that the Nash equilibria are not always the most abundant states, and that different processes can feature significant off-equilibrium behavior, leading to a significantly higher ePoA compared to the PoA studied traditionally in the literature. "}],"file":[{"checksum":"9a91916ac2c21ab42458fcda39ef0b8d","date_updated":"2020-07-14T12:47:56Z","access_level":"open_access","file_name":"2019_LIPIcS_Schmid.pdf","file_size":630752,"creator":"dernst","date_created":"2020-03-23T09:14:06Z","content_type":"application/pdf","file_id":"7608","relation":"main_file"}],"article_number":"21","date_updated":"2023-02-23T13:05:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","external_id":{"arxiv":["1906.00110"]},"oa_version":"Preprint","year":"2020","has_accepted_license":"1"},{"oa_version":"Published Version","year":"2020","has_accepted_license":"1","publication_identifier":{"isbn":["9783959771320"],"issn":["1868-8969"]},"date_updated":"2021-01-12T08:13:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1910.06097"]},"scopus_import":1,"article_processing_charge":"No","arxiv":1,"abstract":[{"text":"The monitoring of event frequencies can be used to recognize behavioral anomalies, to identify trends, and to deduce or discard hypotheses about the underlying system. For example, the performance of a web server may be monitored based on the ratio of the total count of requests from the least and most active clients. Exact frequency monitoring, however, can be prohibitively expensive; in the above example it would require as many counters as there are clients. In this paper, we propose the efficient probabilistic monitoring of common frequency properties, including the mode (i.e., the most common event) and the median of an event sequence. We define a logic to express composite frequency properties as a combination of atomic frequency properties. Our main contribution is an algorithm that, under suitable probabilistic assumptions, can be used to monitor these important frequency properties with four counters, independent of the number of different events. Our algorithm samples longer and longer subwords of an infinite event sequence. We prove the almost-sure convergence of our algorithm by generalizing ergodic theory from increasing-length prefixes to increasing-length subwords of an infinite sequence. A similar algorithm could be used to learn a connected Markov chain of a given structure from observing its outputs, to arbitrary precision, for a given confidence. ","lang":"eng"}],"_id":"7348","date_published":"2020-01-15T00:00:00Z","article_number":"20","file":[{"file_name":"main.pdf","creator":"bkragl","file_size":617206,"date_updated":"2020-07-14T12:47:56Z","access_level":"open_access","checksum":"b9a691d658d075c6369d3304d17fb818","content_type":"application/pdf","file_id":"7349","relation":"main_file","date_created":"2020-01-21T11:21:04Z"}],"oa":1,"publication_status":"published","volume":152,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:47:56Z","conference":{"location":"Barcelona, Spain","name":"CSL: Computer Science Logic","start_date":"2020-01-13","end_date":"2020-01-16"},"title":"Monitoring event frequencies","citation":{"chicago":"Ferrere, Thomas, Thomas A Henzinger, and Bernhard Kragl. “Monitoring Event Frequencies.” In <i>28th EACSL Annual Conference on Computer Science Logic</i>, Vol. 152. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">https://doi.org/10.4230/LIPIcs.CSL.2020.20</a>.","ieee":"T. Ferrere, T. A. Henzinger, and B. Kragl, “Monitoring event frequencies,” in <i>28th EACSL Annual Conference on Computer Science Logic</i>, Barcelona, Spain, 2020, vol. 152.","ista":"Ferrere T, Henzinger TA, Kragl B. 2020. Monitoring event frequencies. 28th EACSL Annual Conference on Computer Science Logic. CSL: Computer Science Logic, LIPIcs, vol. 152, 20.","mla":"Ferrere, Thomas, et al. “Monitoring Event Frequencies.” <i>28th EACSL Annual Conference on Computer Science Logic</i>, vol. 152, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">10.4230/LIPIcs.CSL.2020.20</a>.","short":"T. Ferrere, T.A. Henzinger, B. Kragl, in:, 28th EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ama":"Ferrere T, Henzinger TA, Kragl B. Monitoring event frequencies. In: <i>28th EACSL Annual Conference on Computer Science Logic</i>. Vol 152. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">10.4230/LIPIcs.CSL.2020.20</a>","apa":"Ferrere, T., Henzinger, T. A., &#38; Kragl, B. (2020). Monitoring event frequencies. In <i>28th EACSL Annual Conference on Computer Science Logic</i> (Vol. 152). Barcelona, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">https://doi.org/10.4230/LIPIcs.CSL.2020.20</a>"},"alternative_title":["LIPIcs"],"author":[{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ferrere, Thomas","last_name":"Ferrere"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Kragl","full_name":"Kragl, Bernhard","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117"}],"type":"conference","day":"15","project":[{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S11402-N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"doi":"10.4230/LIPIcs.CSL.2020.20","ddc":["000"],"language":[{"iso":"eng"}],"date_created":"2020-01-21T11:22:21Z","month":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","intvolume":"       152","quality_controlled":"1","department":[{"_id":"ToHe"}],"publication":"28th EACSL Annual Conference on Computer Science Logic"},{"publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:56Z","volume":10,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","article_number":"1680","file":[{"file_id":"7366","relation":"main_file","content_type":"application/pdf","date_created":"2020-01-27T09:07:02Z","creator":"dernst","file_size":1951438,"file_name":"2020_FrontiersPlantScience_Nibau.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:56Z","checksum":"d1f92e60a713fbd15097ce895e5c7ccb"}],"date_published":"2020-01-22T00:00:00Z","_id":"7350","abstract":[{"lang":"eng","text":"The ability to sense environmental temperature and to coordinate growth and development accordingly, is critical to the reproductive success of plants. Flowering time is regulated at the level of gene expression by a complex network of factors that integrate environmental and developmental cues. One of the main players, involved in modulating flowering time in response to changes in ambient temperature is FLOWERING LOCUS M (FLM). FLM transcripts can undergo extensive alternative splicing producing multiple variants, of which FLM-β and FLM-δ are the most representative. While FLM-β codes for the flowering repressor FLM protein, translation of FLM-δ has the opposite effect on flowering. Here we show that the cyclin-dependent kinase G2 (CDKG2), together with its cognate cyclin, CYCLYN L1 (CYCL1) affects the alternative splicing of FLM, balancing the levels of FLM-β and FLM-δ across the ambient temperature range. In the absence of the CDKG2/CYCL1 complex, FLM-β expression is reduced while FLM-δ is increased in a temperature dependent manner and these changes are associated with an early flowering phenotype in the cdkg2 mutant lines. In addition, we found that transcript variants retaining the full FLM intron 1 are sequestered in the cell nucleus. Strikingly, FLM intron 1 splicing is also regulated by CDKG2/CYCL1. Our results provide evidence that temperature and CDKs regulate the alternative splicing of FLM, contributing to flowering time definition."}],"date_updated":"2023-08-17T14:21:45Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000511376000001"]},"scopus_import":"1","publication_identifier":{"issn":["1664-462X"]},"article_type":"original","has_accepted_license":"1","year":"2020","oa_version":"Published Version","publisher":"Frontiers Media","isi":1,"department":[{"_id":"EvBe"}],"quality_controlled":"1","publication":"Frontiers in Plant Science","intvolume":"        10","status":"public","month":"01","date_created":"2020-01-22T15:23:57Z","language":[{"iso":"eng"}],"ddc":["580"],"doi":"10.3389/fpls.2019.01680","citation":{"apa":"Nibau, C., Gallemi, M., Dadarou, D., Doonan, J. H., &#38; Cavallari, N. (2020). Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. <i>Frontiers in Plant Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fpls.2019.01680\">https://doi.org/10.3389/fpls.2019.01680</a>","ama":"Nibau C, Gallemi M, Dadarou D, Doonan JH, Cavallari N. Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. <i>Frontiers in Plant Science</i>. 2020;10. doi:<a href=\"https://doi.org/10.3389/fpls.2019.01680\">10.3389/fpls.2019.01680</a>","short":"C. Nibau, M. Gallemi, D. Dadarou, J.H. Doonan, N. Cavallari, Frontiers in Plant Science 10 (2020).","mla":"Nibau, Candida, et al. “Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2.” <i>Frontiers in Plant Science</i>, vol. 10, 1680, Frontiers Media, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2019.01680\">10.3389/fpls.2019.01680</a>.","ista":"Nibau C, Gallemi M, Dadarou D, Doonan JH, Cavallari N. 2020. Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. Frontiers in Plant Science. 10, 1680.","ieee":"C. Nibau, M. Gallemi, D. Dadarou, J. H. Doonan, and N. Cavallari, “Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2,” <i>Frontiers in Plant Science</i>, vol. 10. Frontiers Media, 2020.","chicago":"Nibau, Candida, Marçal Gallemi, Despoina Dadarou, John H. Doonan, and Nicola Cavallari. “Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2.” <i>Frontiers in Plant Science</i>. Frontiers Media, 2020. <a href=\"https://doi.org/10.3389/fpls.2019.01680\">https://doi.org/10.3389/fpls.2019.01680</a>."},"title":"Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2","day":"22","author":[{"first_name":"Candida","full_name":"Nibau, Candida","last_name":"Nibau"},{"first_name":"Marçal","full_name":"Gallemi, Marçal","last_name":"Gallemi","id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893"},{"last_name":"Dadarou","first_name":"Despoina","full_name":"Dadarou, Despoina"},{"last_name":"Doonan","full_name":"Doonan, John H.","first_name":"John H."},{"last_name":"Cavallari","full_name":"Cavallari, Nicola","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article"},{"title":"nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow","citation":{"ama":"Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. <i>SoftwareX</i>. 2020;11. doi:<a href=\"https://doi.org/10.1016/j.softx.2019.100395\">10.1016/j.softx.2019.100395</a>","apa":"Lopez Alonso, J. M., Feldmann, D., Rampp, M., Vela-Martín, A., Shi, L., &#38; Avila, M. (2020). nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. <i>SoftwareX</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.softx.2019.100395\">https://doi.org/10.1016/j.softx.2019.100395</a>","short":"J.M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, M. Avila, SoftwareX 11 (2020).","mla":"Lopez Alonso, Jose M., et al. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” <i>SoftwareX</i>, vol. 11, 100395, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.softx.2019.100395\">10.1016/j.softx.2019.100395</a>.","chicago":"Lopez Alonso, Jose M, Daniel Feldmann, Markus Rampp, Alberto Vela-Martín, Liang Shi, and Marc Avila. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” <i>SoftwareX</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.softx.2019.100395\">https://doi.org/10.1016/j.softx.2019.100395</a>.","ista":"Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. 2020. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. SoftwareX. 11, 100395.","ieee":"J. M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, and M. Avila, “nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow,” <i>SoftwareX</i>, vol. 11. Elsevier, 2020."},"author":[{"id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso","first_name":"Jose M","full_name":"Lopez Alonso, Jose M"},{"last_name":"Feldmann","first_name":"Daniel","full_name":"Feldmann, Daniel"},{"last_name":"Rampp","first_name":"Markus","full_name":"Rampp, Markus"},{"full_name":"Vela-Martín, Alberto","first_name":"Alberto","last_name":"Vela-Martín"},{"id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang","full_name":"Shi, Liang","last_name":"Shi"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"}],"type":"journal_article","day":"17","doi":"10.1016/j.softx.2019.100395","ddc":["000"],"language":[{"iso":"eng"}],"date_created":"2020-01-26T23:00:35Z","month":"01","isi":1,"publisher":"Elsevier","intvolume":"        11","status":"public","publication":"SoftwareX","quality_controlled":"1","department":[{"_id":"BjHo"}],"oa_version":"Published Version","year":"2020","has_accepted_license":"1","article_type":"original","publication_identifier":{"eissn":["23527110"]},"scopus_import":"1","external_id":{"isi":["000552271200011"],"arxiv":["1908.00587"]},"date_updated":"2023-08-17T14:29:59Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","arxiv":1,"date_published":"2020-01-17T00:00:00Z","_id":"7364","abstract":[{"text":"We present nsCouette, a highly scalable software tool to solve the Navier–Stokes equations for incompressible fluid flow between differentially heated and independently rotating, concentric cylinders. It is based on a pseudospectral spatial discretization and dynamic time-stepping. It is implemented in modern Fortran with a hybrid MPI-OpenMP parallelization scheme and thus designed to compute turbulent flows at high Reynolds and Rayleigh numbers. An additional GPU implementation (C-CUDA) for intermediate problem sizes and a version for pipe flow (nsPipe) are also provided.","lang":"eng"}],"file":[{"date_created":"2020-01-27T07:32:46Z","file_id":"7365","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:56Z","checksum":"2af1a1a3cc33557b345145276f221668","file_size":679707,"creator":"dernst","file_name":"2020_SoftwareX_Lopez.pdf"}],"article_number":"100395","oa":1,"publication_status":"published","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":11,"file_date_updated":"2020-07-14T12:47:56Z"},{"day":"01","type":"journal_article","author":[{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","last_name":"Cubero","full_name":"Cubero, Ryan J","first_name":"Ryan J"},{"last_name":"Marsili","first_name":"Matteo","full_name":"Marsili, Matteo"},{"first_name":"Yasser","full_name":"Roudi, Yasser","last_name":"Roudi"}],"citation":{"short":"R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience 48 (2020) 85–102.","ama":"Cubero RJ, Marsili M, Roudi Y. Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. 2020;48:85-102. doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>","apa":"Cubero, R. J., Marsili, M., &#38; Roudi, Y. (2020). Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>","chicago":"Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>.","ista":"Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 48, 85–102.","ieee":"R. J. Cubero, M. Marsili, and Y. Roudi, “Multiscale relevance and informative encoding in neuronal spike trains,” <i>Journal of Computational Neuroscience</i>, vol. 48. Springer Nature, pp. 85–102, 2020.","mla":"Cubero, Ryan J., et al. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>, vol. 48, Springer Nature, 2020, pp. 85–102, doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>."},"ec_funded":1,"title":"Multiscale relevance and informative encoding in neuronal spike trains","keyword":["Time series analysis","Multiple time scale analysis","Spike train data","Information theory","Bayesian decoding"],"language":[{"iso":"eng"}],"doi":"10.1007/s10827-020-00740-x","ddc":["004","519","570"],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"acknowledgement":"This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation). RJC is currently receiving funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","month":"02","date_created":"2020-01-28T10:34:00Z","page":"85-102","publication":"Journal of Computational Neuroscience","quality_controlled":"1","department":[{"_id":"SaSi"}],"status":"public","intvolume":"        48","publisher":"Springer Nature","isi":1,"article_type":"original","has_accepted_license":"1","oa_version":"Published Version","year":"2020","external_id":{"isi":["000515321800006"]},"scopus_import":"1","date_updated":"2023-08-17T14:35:22Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1573-6873"],"issn":["0929-5313"]},"file":[{"date_created":"2020-01-28T09:31:09Z","relation":"supplementary_material","file_id":"7380","content_type":"application/pdf","checksum":"036e9451d6cd0c190ad25791bf82393b","access_level":"open_access","date_updated":"2020-07-14T12:47:56Z","creator":"rcubero","file_size":1941355,"file_name":"10827_2020_740_MOESM1_ESM.pdf"},{"date_created":"2020-01-28T09:31:09Z","content_type":"application/pdf","relation":"main_file","file_id":"7381","date_updated":"2020-07-14T12:47:56Z","access_level":"open_access","checksum":"4dd8b1fd4b54486f79d82ac7b2a412b2","file_name":"Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf","file_size":3257880,"creator":"rcubero"}],"_id":"7369","date_published":"2020-02-01T00:00:00Z","abstract":[{"lang":"eng","text":"Neuronal responses to complex stimuli and tasks can encompass a wide range of time scales. Understanding these responses requires measures that characterize how the information on these response patterns are represented across multiple temporal resolutions. In this paper we propose a metric – which we call multiscale relevance (MSR) – to capture the dynamical variability of the activity of single neurons across different time scales. The MSR is a non-parametric, fully featureless indicator in that it uses only the time stamps of the firing activity without resorting to any a priori covariate or invoking any specific structure in the tuning curve for neural activity. When applied to neural data from the mEC and from the ADn and PoS regions of freely-behaving rodents, we found that neurons having low MSR tend to have low mutual information and low firing sparsity across the correlates that are believed to be encoded by the region of the brain where the recordings were made. In addition, neurons with high MSR contain significant information on spatial navigation and allow to decode spatial position or head direction as efficiently as those neurons whose firing activity has high mutual information with the covariate to be decoded and significantly better than the set of neurons with high local variations in their interspike intervals. Given these results, we propose that the MSR can be used as a measure to rank and select neurons for their information content without the need to appeal to any a priori covariate."}],"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2020-07-14T12:47:56Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":48,"publication_status":"published","oa":1},{"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:57Z","status":"public","publisher":"Institute of Science and Technology Austria","oa":1,"month":"01","file":[{"file_name":"Scripts.zip","file_size":73363365,"creator":"rgrah","date_updated":"2020-07-14T12:47:57Z","access_level":"open_access","checksum":"9d292cf5207b3829225f44c044cdb3fd","content_type":"application/zip","relation":"main_file","file_id":"7384","date_created":"2020-01-28T10:39:40Z"},{"checksum":"4076ceab32ef588cc233802bab24c1ab","access_level":"open_access","date_updated":"2020-07-14T12:47:57Z","file_size":962,"creator":"rgrah","file_name":"READ_ME_MAIN.txt","date_created":"2020-01-28T10:39:30Z","file_id":"7385","relation":"main_file","content_type":"text/plain"}],"date_created":"2020-01-28T10:41:49Z","_id":"7383","date_published":"2020-01-28T00:00:00Z","abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where 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 expression of any gene, without leaving any genomic signature.","lang":"eng"}],"article_processing_charge":"No","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:42:31Z","doi":"10.15479/AT:ISTA:7383","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7652"}]},"contributor":[{"first_name":"Calin C","last_name":"Guet","contributor_type":"project_leader","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"day":"28","type":"research_data","author":[{"last_name":"Grah","full_name":"Grah, Rok","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"}],"year":"2020","has_accepted_license":"1","oa_version":"Published Version","citation":{"mla":"Grah, Rok. <i>Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>.","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>.","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>.","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>","short":"R. Grah, (2020)."},"title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation"},{"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","related_material":{"record":[{"status":"public","id":"14280","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","relation":"press_release"}]},"pmid":1,"project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41564-019-0657-5","ec_funded":1,"citation":{"ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. 2020;5:407-417. doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>, vol. 5, Springer Nature, 2020, pp. 407–17, doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>.","ieee":"N. S. Baranova <i>et al.</i>, “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” <i>Nature Microbiology</i>, vol. 5. Springer Nature, pp. 407–417, 2020.","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417."},"title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","day":"20","author":[{"id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","first_name":"Natalia S.","full_name":"Baranova, Natalia S.","last_name":"Baranova"},{"first_name":"Philipp","full_name":"Radler, Philipp","last_name":"Radler","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hernández-Rocamora, Víctor M.","first_name":"Víctor M.","last_name":"Hernández-Rocamora"},{"first_name":"Carlos","full_name":"Alfonso, Carlos","last_name":"Alfonso"},{"full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rivas","full_name":"Rivas, Germán","first_name":"Germán"},{"last_name":"Vollmer","first_name":"Waldemar","full_name":"Vollmer, Waldemar"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose"}],"type":"journal_article","publisher":"Springer Nature","isi":1,"department":[{"_id":"MaLo"}],"quality_controlled":"1","publication":"Nature Microbiology","intvolume":"         5","status":"public","page":"407-417","month":"01","date_created":"2020-01-28T16:14:41Z","date_updated":"2023-10-06T12:22:38Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000508584700007"],"pmid":["31959972"]},"publication_identifier":{"issn":["2058-5276"]},"article_type":"letter_note","year":"2020","oa_version":"Submitted Version","publication_status":"published","oa":1,"main_file_link":[{"url":"http://europepmc.org/article/PMC/7048620","open_access":"1"}],"volume":5,"article_processing_charge":"No","date_published":"2020-01-20T00:00:00Z","_id":"7387","abstract":[{"text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site.","lang":"eng"}]},{"publisher":"Elsevier","isi":1,"publication":"Annales de l'Institut Henri Poincaré C, Analyse non linéaire","department":[{"_id":"JaMa"}],"quality_controlled":"1","intvolume":"        37","status":"public","page":"663-682","month":"05","date_created":"2020-01-29T09:39:41Z","language":[{"iso":"eng"}],"doi":"10.1016/j.anihpc.2020.01.003","citation":{"apa":"Gerencser, M. (2020). Nondivergence form quasilinear heat equations driven by space-time white noise. <i>Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">https://doi.org/10.1016/j.anihpc.2020.01.003</a>","ama":"Gerencser M. Nondivergence form quasilinear heat equations driven by space-time white noise. <i>Annales de l’Institut Henri Poincaré C, Analyse non linéaire</i>. 2020;37(3):663-682. doi:<a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">10.1016/j.anihpc.2020.01.003</a>","short":"M. Gerencser, Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire 37 (2020) 663–682.","mla":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” <i>Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire</i>, vol. 37, no. 3, Elsevier, 2020, pp. 663–82, doi:<a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">10.1016/j.anihpc.2020.01.003</a>.","ista":"Gerencser M. 2020. Nondivergence form quasilinear heat equations driven by space-time white noise. Annales de l’Institut Henri Poincaré C, Analyse non linéaire. 37(3), 663–682.","ieee":"M. Gerencser, “Nondivergence form quasilinear heat equations driven by space-time white noise,” <i>Annales de l’Institut Henri Poincaré C, Analyse non linéaire</i>, vol. 37, no. 3. Elsevier, pp. 663–682, 2020.","chicago":"Gerencser, Mate. “Nondivergence Form Quasilinear Heat Equations Driven by Space-Time White Noise.” <i>Annales de l’Institut Henri Poincaré C, Analyse Non Linéaire</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.anihpc.2020.01.003\">https://doi.org/10.1016/j.anihpc.2020.01.003</a>."},"title":"Nondivergence form quasilinear heat equations driven by space-time white noise","day":"01","type":"journal_article","author":[{"first_name":"Mate","full_name":"Gerencser, Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1902.07635","open_access":"1"}],"volume":37,"arxiv":1,"article_processing_charge":"No","issue":"3","_id":"7388","date_published":"2020-05-01T00:00:00Z","abstract":[{"text":"We give a Wong-Zakai type characterisation of the solutions of quasilinear heat equations driven by space-time white noise in 1 + 1 dimensions. In order to show that the renormalisation counterterms are local in the solution, a careful arrangement of a few hundred terms is required. The main tool in this computation is a general ‘integration by parts’ formula that provides a number of linear identities for the renormalisation constants.","lang":"eng"}],"external_id":{"isi":["000531049800007"],"arxiv":["1902.07635"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-17T14:35:46Z","publication_identifier":{"issn":["0294-1449"]},"article_type":"original","oa_version":"Preprint","year":"2020"},{"date_updated":"2023-08-17T14:31:03Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000551418100018"],"arxiv":["2002.00859"]},"publication_identifier":{"eissn":["10886850"],"issn":["00029947"]},"article_type":"original","year":"2020","oa_version":"Preprint","volume":373,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.00859"}],"oa":1,"date_published":"2020-08-01T00:00:00Z","_id":"7389","abstract":[{"text":"Recently Kloeckner described the structure of the isometry group of the quadratic Wasserstein space W_2(R^n). It turned out that the case of the real line is exceptional in the sense that there exists an exotic isometry flow. Following this line of investigation, we compute Isom(W_p(R)), the isometry group of the Wasserstein space\r\nW_p(R) for all p \\in [1,\\infty) \\setminus {2}. We show that W_2(R) is also exceptional regarding the\r\nparameter p: W_p(R) is isometrically rigid if and only if p is not equal to 2. Regarding the underlying\r\nspace, we prove that the exceptionality of p = 2 disappears if we replace R by the compact\r\ninterval [0,1]. Surprisingly, in that case, W_p([0,1]) is isometrically rigid if and only if\r\np is not equal to 1. Moreover, W_1([0,1]) admits isometries that split mass, and Isom(W_1([0,1]))\r\ncannot be embedded into Isom(W_1(R)).","lang":"eng"}],"arxiv":1,"issue":"8","article_processing_charge":"No","language":[{"iso":"eng"}],"keyword":["Wasserstein space","isometric embeddings","isometric rigidity","exotic isometry flow"],"ddc":["515"],"doi":"10.1090/tran/8113","project":[{"_id":"26A455A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Geometric study of Wasserstein spaces and free probability","grant_number":"846294"}],"day":"01","type":"journal_article","author":[{"full_name":"Geher, Gyorgy Pal","first_name":"Gyorgy Pal","last_name":"Geher"},{"last_name":"Titkos","first_name":"Tamas","full_name":"Titkos, Tamas"},{"first_name":"Daniel","full_name":"Virosztek, Daniel","last_name":"Virosztek","orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"citation":{"mla":"Geher, Gyorgy Pal, et al. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8, American Mathematical Society, 2020, pp. 5855–83, doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>.","ista":"Geher GP, Titkos T, Virosztek D. 2020. Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. 373(8), 5855–5883.","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Isometric study of Wasserstein spaces - the real line,” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8. American Mathematical Society, pp. 5855–5883, 2020.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2020. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>.","apa":"Geher, G. P., Titkos, T., &#38; Virosztek, D. (2020). Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>","ama":"Geher GP, Titkos T, Virosztek D. Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. 2020;373(8):5855-5883. doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>","short":"G.P. Geher, T. Titkos, D. Virosztek, Transactions of the American Mathematical Society 373 (2020) 5855–5883."},"title":"Isometric study of Wasserstein spaces - the real line","quality_controlled":"1","department":[{"_id":"LaEr"}],"publication":"Transactions of the American Mathematical Society","status":"public","intvolume":"       373","publisher":"American Mathematical Society","isi":1,"month":"08","date_created":"2020-01-29T10:20:46Z","page":"5855-5883"},{"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-36020-7_1","citation":{"chicago":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” In <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, 2256:1–27. LNM. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>.","ieee":"A. Akopyan and R. Karasev, “Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures,” in <i>Geometric Aspects of Functional Analysis</i>, vol. 2256, B. Klartag and E. Milman, Eds. Springer Nature, 2020, pp. 1–27.","ista":"Akopyan A, Karasev R. 2020.Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Geometric Aspects of Functional Analysis. vol. 2256, 1–27.","mla":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, vol. 2256, Springer Nature, 2020, pp. 1–27, doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>.","short":"A. Akopyan, R. Karasev, in:, B. Klartag, E. Milman (Eds.), Geometric Aspects of Functional Analysis, Springer Nature, 2020, pp. 1–27.","ama":"Akopyan A, Karasev R. Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Klartag B, Milman E, eds. <i>Geometric Aspects of Functional Analysis</i>. Vol 2256. LNM. Springer Nature; 2020:1-27. doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>","apa":"Akopyan, A., &#38; Karasev, R. (2020). Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In B. Klartag &#38; E. Milman (Eds.), <i>Geometric Aspects of Functional Analysis</i> (Vol. 2256, pp. 1–27). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>"},"ec_funded":1,"title":"Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures","day":"21","type":"book_chapter","author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"first_name":"Roman","full_name":"Karasev, Roman","last_name":"Karasev"}],"publisher":"Springer Nature","isi":1,"publication":"Geometric Aspects of Functional Analysis","quality_controlled":"1","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"intvolume":"      2256","status":"public","page":"1-27","month":"06","series_title":"LNM","date_created":"2018-12-11T11:44:29Z","external_id":{"arxiv":["1808.07350"],"isi":["000557689300003"]},"scopus_import":"1","date_updated":"2023-08-17T13:48:31Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["16179692"],"isbn":["9783030360191"],"issn":["00758434"],"eisbn":["9783030360207"]},"editor":[{"last_name":"Klartag","full_name":"Klartag, Bo'az","first_name":"Bo'az"},{"last_name":"Milman","first_name":"Emanuel","full_name":"Milman, Emanuel"}],"year":"2020","oa_version":"Preprint","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1808.07350","open_access":"1"}],"oa":1,"volume":2256,"arxiv":1,"article_processing_charge":"No","_id":"74","abstract":[{"lang":"eng","text":"We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean  space,  motivated  by  the  famous  theorem  of  Gromov  about  the  waist  of  radially symmetric Gaussian measures.  In particular, it turns our possible to extend Gromov’s original result  to  the  case  of  not  necessarily  radially  symmetric  Gaussian  measure.   We  also  provide examples of measures having no t-neighborhood waist property, including a rather wide class\r\nof compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2.\r\nWe  use  a  simpler  form  of  Gromov’s  pancake  argument  to  produce  some  estimates  of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for reader’s convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian\r\nmeasures."}],"date_published":"2020-06-21T00:00:00Z"},{"title":"Mechanisms of zebrafish epiboly: A current view","citation":{"apa":"Bruce, A. E. E., &#38; Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish epiboly: A current view. In L. Solnica-Krezel (Ed.), <i>Gastrulation: From Embryonic Pattern to Form</i> (Vol. 136, pp. 319–341). Elsevier. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>","ama":"Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view. In: Solnica-Krezel L, ed. <i>Gastrulation: From Embryonic Pattern to Form</i>. Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>","short":"A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.","mla":"Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>.","ista":"Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.","ieee":"A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly: A current view,” in <i>Gastrulation: From Embryonic Pattern to Form</i>, vol. 136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341.","chicago":"Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” In <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, 136:319–41. Current Topics in Developmental Biology. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>."},"author":[{"full_name":"Bruce, Ashley E.E.","first_name":"Ashley E.E.","last_name":"Bruce"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"type":"book_chapter","day":"01","doi":"10.1016/bs.ctdb.2019.07.001","language":[{"iso":"eng"}],"page":"319-341","series_title":"Current Topics in Developmental Biology","date_created":"2020-01-30T09:24:06Z","month":"01","isi":1,"publisher":"Elsevier","intvolume":"       136","status":"public","quality_controlled":"1","department":[{"_id":"CaHe"}],"publication":"Gastrulation: From Embryonic Pattern to Form","editor":[{"full_name":"Solnica-Krezel, Lilianna ","first_name":"Lilianna ","last_name":"Solnica-Krezel"}],"oa_version":"None","year":"2020","publication_identifier":{"issn":["0070-2153"],"isbn":["9780128127988"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-22T13:23:09Z","external_id":{"isi":["000611830600012"]},"scopus_import":"1","article_processing_charge":"No","abstract":[{"text":"Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed.","lang":"eng"}],"_id":"7410","date_published":"2020-01-01T00:00:00Z","publication_status":"published","volume":136},{"year":"2020","oa_version":"Submitted Version","article_type":"original","publication_identifier":{"issn":["1559-2324"]},"date_updated":"2023-10-17T09:01:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000494909300001"],"pmid":["31696764"]},"scopus_import":"1","date_published":"2020-01-01T00:00:00Z","_id":"7416","abstract":[{"text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements.","lang":"eng"}],"article_number":"1687175","issue":"1","article_processing_charge":"No","volume":15,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054","open_access":"1"}],"oa":1,"publication_status":"published","author":[{"last_name":"Sinclair","full_name":"Sinclair, Scott A","first_name":"Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krämer, U.","first_name":"U.","last_name":"Krämer"}],"type":"journal_article","day":"01","title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","citation":{"ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Taylor &#38; Francis, 2020.","ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling &#38; Behavior. 15(1), 1687175.","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>.","mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, 1687175, Taylor &#38; Francis, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>.","short":"S.A. Sinclair, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","apa":"Sinclair, S. A., &#38; Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>"},"doi":"10.1080/15592324.2019.1687175","language":[{"iso":"eng"}],"pmid":1,"date_created":"2020-01-30T10:12:04Z","month":"01","intvolume":"        15","status":"public","department":[{"_id":"JiFr"}],"quality_controlled":"1","publication":"Plant Signaling & Behavior","isi":1,"publisher":"Taylor & Francis"},{"article_type":"original","oa_version":"Submitted Version","year":"2020","scopus_import":"1","external_id":{"isi":["000494907500001"],"pmid":["31696770"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-06T15:23:04Z","publication_identifier":{"issn":["1559-2324"]},"article_processing_charge":"No","issue":"1","article_number":"e1687185","date_published":"2020-01-01T00:00:00Z","_id":"7417","abstract":[{"text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development.","lang":"eng"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154"}],"oa":1,"volume":15,"citation":{"short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>","apa":"Sinclair, S. A., Gille, S., Pauly, M., &#38; Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>","chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling &#38; Behavior. 15(1), e1687185.","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Informa UK Limited, 2020.","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>."},"title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","day":"01","type":"journal_article","author":[{"orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A","full_name":"Sinclair, Scott A","last_name":"Sinclair"},{"last_name":"Gille","full_name":"Gille, S.","first_name":"S."},{"last_name":"Pauly","full_name":"Pauly, M.","first_name":"M."},{"first_name":"U.","full_name":"Krämer, U.","last_name":"Krämer"}],"pmid":1,"language":[{"iso":"eng"}],"doi":"10.1080/15592324.2019.1687185","month":"01","date_created":"2020-01-30T10:14:14Z","publisher":"Informa UK Limited","isi":1,"publication":"Plant Signaling & Behavior","department":[{"_id":"JiFr"}],"quality_controlled":"1","intvolume":"        15","status":"public"},{"_id":"7426","abstract":[{"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.","lang":"eng"}],"date_published":"2020-05-01T00:00:00Z","file":[{"file_name":"2020_NAHS_GarciaSoto.pdf","creator":"dernst","file_size":818774,"embargo":"2022-05-15","checksum":"560abfddb53f9fe921b6744f59f2cfaa","date_updated":"2022-05-16T22:30:04Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"8688","date_created":"2020-10-21T13:16:45Z"}],"article_number":"100856","article_processing_charge":"No","issue":"5","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":36,"file_date_updated":"2022-05-16T22:30:04Z","oa":1,"publication_status":"published","has_accepted_license":"1","year":"2020","oa_version":"Submitted Version","article_type":"original","publication_identifier":{"issn":["1751-570X"]},"scopus_import":"1","external_id":{"isi":["000528828600003"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-17T14:32:54Z","date_created":"2020-02-02T23:00:59Z","month":"05","intvolume":"        36","status":"public","publication":"Nonlinear Analysis: Hybrid Systems","department":[{"_id":"ToHe"}],"quality_controlled":"1","isi":1,"publisher":"Elsevier","type":"journal_article","author":[{"id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0003−2936−5719","first_name":"Miriam","full_name":"Garcia Soto, Miriam","last_name":"Garcia Soto"},{"last_name":"Prabhakar","full_name":"Prabhakar, Pavithra","first_name":"Pavithra"}],"day":"01","title":"Abstraction based verification of stability of polyhedral switched systems","citation":{"mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 36, no. 5, 100856, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">10.1016/j.nahs.2020.100856</a>.","ieee":"M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability of polyhedral switched systems,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 36, no. 5. Elsevier, 2020.","ista":"Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification of Stability of Polyhedral Switched Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">https://doi.org/10.1016/j.nahs.2020.100856</a>.","apa":"Garcia Soto, M., &#38; Prabhakar, P. (2020). Abstraction based verification of stability of polyhedral switched systems. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">https://doi.org/10.1016/j.nahs.2020.100856</a>","ama":"Garcia Soto M, Prabhakar P. Abstraction based verification of stability of polyhedral switched systems. <i>Nonlinear Analysis: Hybrid Systems</i>. 2020;36(5). doi:<a href=\"https://doi.org/10.1016/j.nahs.2020.100856\">10.1016/j.nahs.2020.100856</a>","short":"M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020)."},"doi":"10.1016/j.nahs.2020.100856","ddc":["000"],"language":[{"iso":"eng"}],"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"page":"381-395.e8","month":"02","date_created":"2020-02-02T23:01:00Z","publisher":"Cell Press","isi":1,"quality_controlled":"1","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication":"Current Biology","intvolume":"        30","status":"public","ec_funded":1,"citation":{"apa":"Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">https://doi.org/10.1016/j.cub.2019.11.058</a>","ama":"Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. <i>Current Biology</i>. 2020;30(3):381-395.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">10.1016/j.cub.2019.11.058</a>","short":"S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8.","mla":"Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” <i>Current Biology</i>, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">10.1016/j.cub.2019.11.058</a>.","ista":"Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8.","ieee":"S. Tan <i>et al.</i>, “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” <i>Current Biology</i>, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020.","chicago":"Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” <i>Current Biology</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.cub.2019.11.058\">https://doi.org/10.1016/j.cub.2019.11.058</a>."},"title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","day":"03","type":"journal_article","author":[{"last_name":"Tan","full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285"},{"last_name":"Abas","first_name":"Melinda F","full_name":"Abas, Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Inge","full_name":"Verstraeten, Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328"},{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","full_name":"Glanc, Matous","last_name":"Glanc"},{"full_name":"Molnar, Gergely","first_name":"Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195"},{"last_name":"Lasák","first_name":"Pavel","full_name":"Lasák, Pavel"},{"first_name":"Ivan","full_name":"Petřík, Ivan","last_name":"Petřík"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"last_name":"Pospíšil","full_name":"Pospíšil, Jiří","first_name":"Jiří"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"acknowledgement":"We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). ","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship","grant_number":"723-2015"}],"related_material":{"record":[{"status":"public","id":"8822","relation":"dissertation_contains"}]},"pmid":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2019.11.058","ddc":["580"],"issue":"3","article_processing_charge":"No","file":[{"relation":"main_file","file_id":"8555","content_type":"application/pdf","date_created":"2020-09-22T09:51:28Z","success":1,"file_size":5360135,"creator":"dernst","file_name":"2020_CurrentBiology_Tan.pdf","checksum":"16f7d51fe28f91c21e4896a2028df40b","access_level":"open_access","date_updated":"2020-09-22T09:51:28Z"}],"date_published":"2020-02-03T00:00:00Z","_id":"7427","abstract":[{"lang":"eng","text":"Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense."}],"publication_status":"published","oa":1,"file_date_updated":"2020-09-22T09:51:28Z","volume":30,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_type":"original","has_accepted_license":"1","year":"2020","oa_version":"Published Version","date_updated":"2024-03-25T23:30:20Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000511287900018"],"pmid":["31956021"]},"publication_identifier":{"issn":["09609822"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}]},{"external_id":{"arxiv":["1907.02077"],"isi":["000506843500001"]},"scopus_import":"1","date_updated":"2024-02-28T13:11:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"article_type":"original","oa_version":"Preprint","year":"2020","publication_status":"published","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.02077","open_access":"1"}],"volume":101,"arxiv":1,"article_processing_charge":"No","issue":"2","article_number":"020504","_id":"7428","date_published":"2020-01-13T00:00:00Z","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.101.020504","citation":{"mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” <i>Physical Review B</i>, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>.","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.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>.","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,” <i>Physical Review B</i>, vol. 101, no. 2. American Physical Society, 2020.","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.","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. <i>Physical Review B</i>. 2020;101(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., &#38; Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020)."},"title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","day":"13","type":"journal_article","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg"},{"last_name":"Lopes","first_name":"P. L.S.","full_name":"Lopes, P. L.S."},{"full_name":"Hosur, Pavan","first_name":"Pavan","last_name":"Hosur"},{"full_name":"Gilbert, Matthew J.","first_name":"Matthew J.","last_name":"Gilbert"},{"full_name":"Ghaemi, Pouyan","first_name":"Pouyan","last_name":"Ghaemi"}],"publisher":"American Physical Society","isi":1,"publication":"Physical Review B","quality_controlled":"1","department":[{"_id":"MiLe"}],"intvolume":"       101","status":"public","month":"01","date_created":"2020-02-02T23:01:01Z"},{"article_type":"original","oa_version":"Preprint","year":"2020","date_updated":"2023-08-17T14:31:28Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"pmid":["31964273"],"isi":["000538369800002"],"arxiv":["1903.10693"]},"publication_identifier":{"eissn":["17425662"]},"arxiv":1,"issue":"162","article_processing_charge":"No","article_number":"0623","_id":"7431","date_published":"2020-01-29T00:00:00Z","abstract":[{"text":"In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.","lang":"eng"}],"publication_status":"published","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1903.10693","open_access":"1"}],"volume":17,"citation":{"chicago":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>.","ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623.","ieee":"A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation,” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162. The Royal Society, 2020.","mla":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” <i>Journal of the Royal Society Interface</i>, vol. 17, no. 162, 0623, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>.","short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","ama":"Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. 2020;17(162). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0623\">10.1098/rsif.2019.0623</a>","apa":"Kolchinsky, A., &#38; Corominas-Murtra, B. (2020). Decomposing information into copying versus transformation. <i>Journal of the Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0623\">https://doi.org/10.1098/rsif.2019.0623</a>"},"title":"Decomposing information into copying versus transformation","day":"29","type":"journal_article","author":[{"last_name":"Kolchinsky","full_name":"Kolchinsky, Artemy","first_name":"Artemy"},{"last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643"}],"acknowledgement":"AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation, and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions, as well as the anonymous\r\nreviewers for their insightful suggestions. ","pmid":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2019.0623","month":"01","date_created":"2020-02-02T23:01:03Z","publisher":"The Royal Society","isi":1,"department":[{"_id":"EdHa"}],"quality_controlled":"1","publication":"Journal of the Royal Society Interface","intvolume":"        17","status":"public"},{"date_updated":"2023-09-07T13:15:30Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","oa_version":"Published Version","year":"2020","file_date_updated":"2020-07-14T12:47:58Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa":1,"file":[{"date_created":"2020-02-06T14:43:54Z","content_type":"application/pdf","relation":"main_file","file_id":"7461","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","date_updated":"2020-07-14T12:47:58Z","access_level":"open_access","file_name":"thesis_ist-final_noack.pdf","creator":"koelsboe","file_size":76195184},{"access_level":"closed","date_updated":"2020-07-14T12:47:58Z","checksum":"7a52383c812b0be64d3826546509e5a4","description":"latex source files, figures","file_size":122103715,"creator":"koelsboe","file_name":"latex-files.zip","date_created":"2020-02-06T14:52:45Z","file_id":"7462","relation":"source_file","content_type":"application/x-zip-compressed"}],"_id":"7460","abstract":[{"text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries.","lang":"eng"}],"date_published":"2020-02-10T00:00:00Z","article_processing_charge":"No","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7460","ddc":["514"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"6608","status":"public"}]},"day":"10","type":"dissertation","author":[{"last_name":"Ölsböck","first_name":"Katharina","full_name":"Ölsböck, Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4672-8297"}],"alternative_title":["ISTA Thesis"],"citation":{"mla":"Ölsböck, Katharina. <i>The Hole System of Triangulated Shapes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>.","apa":"Ölsböck, K. (2020). <i>The hole system of triangulated shapes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020."},"title":"The hole system of triangulated shapes","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"status":"public","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","month":"02","supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner"}],"date_created":"2020-02-06T14:56:53Z","page":"155"},{"oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":16,"file_date_updated":"2020-07-14T12:47:59Z","article_processing_charge":"No","issue":"1","_id":"7464","abstract":[{"lang":"eng","text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly."}],"date_published":"2020-01-27T00:00:00Z","file":[{"file_size":4551246,"creator":"dernst","file_name":"2020_PLOSPatho_Dick.pdf","checksum":"a297f54d1fef0efe4789ca00f37f241e","access_level":"open_access","date_updated":"2020-07-14T12:47:59Z","file_id":"7484","relation":"main_file","content_type":"application/pdf","date_created":"2020-02-11T10:07:28Z"}],"article_number":"e1008277","publication_identifier":{"issn":["1553-7374"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"scopus_import":"1","date_updated":"2023-10-17T12:29:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","year":"2020","has_accepted_license":"1","article_type":"original","isi":1,"publisher":"Public Library of Science","status":"public","intvolume":"        16","publication":"PLOS Pathogens","department":[{"_id":"FlSc"}],"quality_controlled":"1","date_created":"2020-02-06T18:47:17Z","month":"01","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"deleted","relation":"research_data","id":"9723"}]},"pmid":1,"doi":"10.1371/journal.ppat.1008277","ddc":["570"],"language":[{"iso":"eng"}],"title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","citation":{"short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. 2020;16(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","ieee":"R. A. Dick <i>et al.</i>, “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” <i>PLOS Pathogens</i>, vol. 16, no. 1. Public Library of Science, 2020.","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>.","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>."},"type":"journal_article","author":[{"first_name":"Robert A.","full_name":"Dick, Robert A.","last_name":"Dick"},{"first_name":"Chaoyi","full_name":"Xu, Chaoyi","last_name":"Xu"},{"last_name":"Morado","first_name":"Dustin R.","full_name":"Morado, Dustin R."},{"full_name":"Kravchuk, Vladyslav","first_name":"Vladyslav","last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9523-9089"},{"full_name":"Ricana, Clifton L.","first_name":"Clifton L.","last_name":"Ricana"},{"full_name":"Lyddon, Terri D.","first_name":"Terri D.","last_name":"Lyddon"},{"last_name":"Broad","full_name":"Broad, Arianna M.","first_name":"Arianna M."},{"last_name":"Feathers","first_name":"J. Ryan","full_name":"Feathers, J. Ryan"},{"first_name":"Marc C.","full_name":"Johnson, Marc C.","last_name":"Johnson"},{"first_name":"Volker M.","full_name":"Vogt, Volker M.","last_name":"Vogt"},{"full_name":"Perilla, Juan R.","first_name":"Juan R.","last_name":"Perilla"},{"first_name":"John A. G.","full_name":"Briggs, John A. G.","last_name":"Briggs"},{"last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"day":"27"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":293,"file_date_updated":"2020-07-14T12:47:59Z","oa":1,"publication_status":"published","_id":"7465","abstract":[{"text":"The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization.","lang":"eng"}],"date_published":"2020-04-01T00:00:00Z","file":[{"date_created":"2020-02-10T08:59:36Z","content_type":"application/pdf","file_id":"7471","relation":"main_file","checksum":"f7f27c6a8fea985ceb9279be2204461c","date_updated":"2020-07-14T12:47:59Z","access_level":"open_access","file_name":"2020_PlantScience_Mazur.pdf","creator":"dernst","file_size":3499069}],"article_number":"110414","article_processing_charge":"No","issue":"4","publication_identifier":{"issn":["01689452"],"eissn":["18732259"]},"scopus_import":"1","external_id":{"isi":["000520609800009"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-17T14:37:32Z","oa_version":"Published Version","has_accepted_license":"1","year":"2020","article_type":"original","status":"public","intvolume":"       293","publication":"Plant Science","quality_controlled":"1","department":[{"_id":"JiFr"}],"isi":1,"publisher":"Elsevier","date_created":"2020-02-09T23:00:50Z","month":"04","ddc":["580"],"doi":"10.1016/j.plantsci.2020.110414","language":[{"iso":"eng"}],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"}]},"author":[{"first_name":"Ewa","full_name":"Mazur, Ewa","last_name":"Mazur"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C","full_name":"Gallei, Michelle C"},{"last_name":"Adamowski","full_name":"Adamowski, Maciek","first_name":"Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Robert","first_name":"Hélène S.","full_name":"Robert, Hélène S."},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"01","title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","citation":{"chicago":"Mazur, Ewa, Michelle C Gallei, Maciek Adamowski, Huibin Han, Hélène S. Robert, and Jiří Friml. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>.","ieee":"E. Mazur, M. C. Gallei, M. Adamowski, H. Han, H. S. Robert, and J. Friml, “Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis,” <i>Plant Science</i>, vol. 293, no. 4. Elsevier, 2020.","ista":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. 2020. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 293(4), 110414.","mla":"Mazur, Ewa, et al. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>, vol. 293, no. 4, 110414, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>.","short":"E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020).","ama":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. 2020;293(4). doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>","apa":"Mazur, E., Gallei, M. C., Adamowski, M., Han, H., Robert, H. S., &#38; Friml, J. (2020). Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>"},"ec_funded":1}]